MagnetoWiki - User contributions [en]

Pica

2025-11-25T12:31:32Z

Chuck: Updated perm redirect

Multiple uses of the word Pica or Pika

=Pika=

rock rabbit

a lagomorph (relative of rabbits) in the mountains of the western United States

=Pica=

eating clay or other nonnutirive subantances to detoxify ingested toxins. Named after the behavior of magpies.

Can be [https://newsfeed.time.com/2013/01/30/japanese-restaurant-serves-meal-of-dirt-for-110/ pricey.]

=Pica Pica=

The European Magpie

=Hyrax=

[https://en.wikipedia.org/wiki/Hyrax Not] a pica. Also not a rodent; related to elephants.

=Puca=

A creature of Celtic folklore, Though the púca enjoys confusing and often terrifying humans, it is considered to be benevolent.

=Pooka=

https://en.wikipedia.org/wiki/Harvey_(film)

=Pica=

A typographic unit of measure corresponding to 1/72nd of its respective foot, and therefore to 1/6th of an inch. .

=Pica, Chile=

[https://en.wikipedia.org/wiki/Pica,_Chile Pica] in the north of Chile is famous for its "small and unusually acidic lemons." Coincidentally, it is also the site of substantial [https://www.mining.com/mammoth-energy-group-continues-to-acquire-chilean-lithium-assets/ lithium concessions] acquired by Mammoth Energy Group's Compania Lithium Investments Limitada, from the dry lake bed of Laguna Lagunilla.

=Pika=

[https://www.pika.dev/about Pika] is a “project to move the JavaScript ecosystem forward.” Allows searching for ES module syntax packages, and integrates ESM packages with npm.

Has an icon of a pika for a mascot.

=Piku=

How I love a verse
Contrived to unhusk dryly
One image nutshell

(count the letters)

=Pika Pika=

[https://nakamotoforestry.com/products/shou-sugi-ban/ Pika Pika] ( ぴかぴか ) is variant of charred cedar boards (焼杉板 or “yakisugi-ita”) used for siding in Japanese building. The charing helps preserve the boards. Pika Pika boards are scrapped with a wire brush that increases contrast by removing soot from softer grain in the wood.

=PikaPython=

[https://github.com/pikasTech/PikaPython PikaPython] is a cross platform ultra lightweight embedded Python engine.

=PICA=

Paillier-based InChain Aggregation PMID 39275535

=PICA=

Physics-Integrated Clothed Avatar PMID 41004371
[[Category:Taste Aversion]]

Bruker MRI

2025-05-06T12:57:36Z

Chuck: Archive UBC link

==File Formats==

Description of [https://imaging.mrc-cbu.cam.ac.uk/imaging/FormatBruker Bruker MRI data file formats].

Additional description taken from [https://web.archive.org/web/20240522201702/https://mriresearch.med.ubc.ca/facilities/7t-mri/researchers-guide/naming-conventions/ https://mriresearch.med.ubc.ca/facilities/7t-mri/researchers-guide/naming-conventions/]

Each Experiment directory contains another subdirectory called pdata as well as several data files:
:'''fid''': the raw unreconstructed data file (i.e. the “k-space” time-domain data)

:'''method''': text file containing the high-level acquisition parameters (e.g. number of pixels, measurement method, field of view, echo time, repetition time, number of averages, etc.)

:'''acqp''': text file containing the base-level acquisition parameters (the method parameters are derived from these acqp parameters, which are a bit like the “machine-code” variables of the pulse sequence that was used)

:'''pulseprogram''': text file containing the MRI sequence

:'''pdata folder''': only exists for image data. It contains subdirectories corresponding to the different Processed Datasets of the current Experiment – each directory is named after the<ProcNo>(e.g.1,2,etc.). For the majority of cases,the“1”directory contains the processed image data. Files in “1” include the following:

::'''2dseq''': the processed image data, expressed in a raw binary format without header. If there are multiple slices in the dataset, they are usually stored contiguously. The default binary word type is 16 bit signed integer, little endian.

::'''Reco''': text file including all reconstruction parameters

PET-1

2025-03-18T14:15:00Z

Chuck: Add link to TESS shutdown notice

=PET-1 Promoter=

According to TESS (reference below)

There are the following potential RAR sites in the mouse PET-1 promoter:

''(Note: substract from 2000 to get upstream position)''

:RAR-alpha at 1061-1069 (La/Len = 1.53)
:RAR-beta at 599-604 (1.69)
:RAR-beta at 1596-1604 (1.71)
:RAR-beta at 1926-1931 (1.71)

:RXR-alpha/RXR-beta at 1595-1601 (2.0)
:RXR-alpha/RXR-beta at 1926-1931 (2.0)

Hi probability of ER-alpha binding (all La/Len = 1.9 - 2.0) at:
:599-603
:1065-1069
:1597-1601
:1867-1871
:1926-1030

ER/SP-1 binding (all La/Len = 2.0) at:
:990-994
:1243-1247

Found transcription factor binding sites using TESS:

BLAST of mus FEV mRNA ( NM_153111) leads to 100% homology with mus chromosome 1 (AC104542.10) bases 38140 to 40385

So took 2000 bases upstream of transcription start AC104542.10: 36140 – 38149

<tt>
1 ggggaagggg aaggggaagg ggaaggggaa ggggagagga ggagttagtg agtgaataac 
61 actgggcctg ggtggttcat aggcgatctg ggaaaggatg ctcacccaca ctcactccaa 
121 actctaacta cccaggcttc caccttcatt tctccattct gccaaggaca cggaaatctc 
181 ctgcttgcct gacagaggac caagatatca aggcattctc ccacaaatga ctttgttctg 
241 gaaataccta caactatcct cctgaaagtt ttcttttttt tttctttttt tttttaaaga 
301 tttatttatt atatgtaagt acactgtagc tgtcttcaga cactccagaa gagggagtca 
361 gatctcgtta cggatggttg tgagccacca tgtggttgct gggatttgaa ctctggacct 
421 tcggaagagc agtcgggtgc tcttacccac tgagccatct caccagcccc tgaaagtttt 
481 cttatgaggg gagacatcta aggtcgcttc ccagacagca ggtttttaga aaagaaaaca 
541 gagataagga ttacaagtgc ctctgaatgg tgagccctga cgcctcagaa agatcacttg 
601 acccacttcc cagacctcac aaggctggat tcaggatgaa aggtctgggt ccctcctttt 
661 acccctcact ctgaagcgca aaggaaatgt ggaggcaacc cggccctggt ccttttgtct 
721 tagtaggtaa agcacctaat ggccttccat caaatcttcc ctagatttag ccatagaccg 
781 gcctatcctc tctcggacca gcagagggcg cgcaccacta gcgggaaaag agtggaccag 
841 tcgccaaacg cagtccgaga aagcctttaa agagcagagg catctatcta acagggagga 
901 tcagagccat agctactggg agccagcagg agatttgtga aggaaagtga gaggtggtct 
961 tgggagaatg gcacgaagca gggagtggag gcggggaaaa gtattaaatt aggataaaat 
1021 ggagagtggc tgatgcaaga agtttcggat ggaatggagg aaaaggtcac gggttgttgg 
1081 atgcgatgct gcgaggagat ggcagaatgg cgagatggag gaaggcgagt acttgttgga 
1141 ttgaaagttg gagtgaaatg ggatggggtg a'''gggtga'''gag aggca'''ccctc tc'''aggatctc 
1201 acccactggg tcctcctcac tccaggccac cccacgcttg cttgccctca cacttggagg 
1261 ccttttgctc tgcctgcctg agcctttaac cttctactct ccctgaaggg gccctggtgc 
1321 agcaatgaac ggacagagga ggcagtaggg cgcttgggag ctttaatggg gctgaaaggg 
1381 atatatacag gctggggtcc ttgggccaga gtgtgatatg ggagaaaggg aagccagagt 
1441 gttgatatag ggatggggaa cggcagagat gtttatcgag gcttctcata tcccgaggaa 
1501 ataggggagt gcgagaagcc ttgaggtact accttttgga gtgggttgtg ggagagagtc 
1561 agaaaatgag gaccaagaaa atcccagaaa aataggggtc ataacgaggt gcaggggtgc 
1621 aagtgagaaa agaaaaagac acgggagttc cagaatctgg agacttggaa gagaaaaatt 
1681 aaagtgggag cccatgcacc cttcctgggg cgaagataac ggggcctgga agcctgatgt 
1741 tcaaggaaga cctcgggggt ttcccatcct ttcttccctg ggctgggcgc ggctgctgca 
1801 atgaaatctg tgttaaagga acgtcgggga aagcttcggg gctcctccga ggatgaggat 
1861 gggattggtc actgggccat gtgagagagg ccccgctgta cccggccgtc cccgtctagt 
1921 gataatgacc ccccaagtgc gaagctgccg ccactgcgcc gaagggcccg ggagggggct 
1981 gcaagcccgg ggtggggtag 
</tt>

Searched using TESS: Combined search query and defaults, on September 30, 2007

Schug, Jonathan, Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence, Wiley’s Current Protocols in Bioinformatics, ed. Baxevanis, A. D. J. Wiley & sons, 2003. Chapter 5

TESS: Transcription Element Search Software on the WWW,
Jonathan Schug and G. Christian Overton,
Technical Report CBIL-TR-1997-1001-v0.0
Computational Biology and Informatics Laboratory
School of Medicine
University of Pennsylvania, 1997

URL: [https://cstoeckert.github.io/past-projects/TESS.html http://www.cbil.upenn.edu/tess/] ([https://cstoeckert.github.io/past-projects/TESS.html now discontinued])

[[Category:Depression]]
[[Category:Ingestive Behavior]]

Sweeteners

2025-01-14T14:22:04Z

Chuck: Fix USDA Data link in anticipation of perm-redirect

{| class="wikitable sortable" border = "1" cellspacing="0" cellpadding = "3"
|+'''Sweeteners'''
|-bgcolor="silver"
! width="125" | Chemical Name !! width="150" | Tradename !! Wiki !! width="75" | MW !! width="125" | Formula !! width="100" | CAS !! width="75" | Calories !! width="100" | Sweetness
|-
| [[Saccharin]] || [https://www.sweetnlow.com Sweet n Lo] || [https://en.wikipedia.org/wiki/Saccharin Wiki] || align="center"| 183.18 ||align="center"| C7H5NO3S || align="center"|81-07-2 || calories || rs
|-
| [[Sucrose]] || [https://www.sucrose.com/ Sugar] || [https://en.wikipedia.org/wiki/Sucrose Wiki] || align="center"| 342.29 || align="center"|C12H22O11 || align="center"|57-50-1 || calories || rs
|-
| [[ Fructose]] || [https://corn.org/products/sweeteners/ HFCS] || [https://en.wikipedia.org/wiki/Fructose Wiki] || align="center"| 180.16 || align="center"|C6H12O6 || align="center"|57-48-7 || calories || rs
|-
| [[Xylitol]] || Xylitol || [https://en.wikipedia.org/wiki/Xylitol Wiki] || align="center"| 152.15 || align="center"|C5H12O5 || align="center"|87-99-0 || calories || rs
|-
| [[Aspartame]] || [https://web.archive.org/web/20180721024410/http://www.nutrasweet.com:80/ NutraSweet] || [https://en.wikipedia.org/wiki/Aspartame Wiki] || align="center"| 294.3 || align="center"|C14H18N2O5 || align="center"|22839-47-0 || calories || rs
|-
| [[Steviol glycoside]] || [https://www.truvia.com Truvia] || [https://en.wikipedia.org/wiki/Steviol_glycoside Wiki] || align="center"| 318.45|| align="center"|C20H30O3 || align="center"|471-80-7 || calories || rs
|-
| [[ Sucralose]] || [https://www.splenda.com Splenda] || [https://en.wikipedia.org/wiki/Sucralose Wiki] || align="center"| 397.64 || align="center"| C12H19Cl3O8 || align="center"|56038-13-2 || calories || rs
|-
| [[ Acesulfame K]]||[https://www.celanese.com/food-ingredients/products/sunett.aspx Sunett], [http://www.sweetone.com/ Sweet One]|| [https://en.wikipedia.org/wiki/Acesulfame_K Wiki] || align="center"| 201.24 || align="center"| C4H4KNO4S || align="center"|55589-62-3 || calories || rs
|-
| [[ Dulcin]] || sucrol, valzin|| [https://en.wikipedia.org/wiki/Dulcin Wiki] || align="center"| 180.20 || align="center"|C9H12N2O2 || align="center"|150-69-6|| calories || rs
|-
| [[ Perillartine]] || (Japanese name: ペリラルチン, available from [https://highchem.co.jp/chem/details.php?cas=30950-27-7 HighChem] and others) japanese product page?|| [https://en.wikipedia.org/wiki/Perillartine Wiki] || align="center"| 165.23 || align="center"| C10H15NO || align="center"|30950-27-7 || calories || rs
|}

Notes:

'''Tradename''' links to manufacturer's website

'''Calories''' (kcal/g) is available calories to humans following ingestion

'''Sweetness''' (g/g sucrose) is reported (maximal?) sweetness to humans relative to sucrose (at a particular concentration)?

= USDA Sugar and Sweeteners Data=

[https://www.ers.usda.gov/data-products/sugar-and-sweeteners-yearbook-tables Recommended Data]

[https://www.ers.usda.gov/topics/crops/sugar-and-sweeteners/readings Recommended Readings]

[https://usda.library.cornell.edu/concern/publications/pv63g024f?locale=en Sugar and Sweeteners Outlook] (PDF file)
(January, May, and September) provides an update of current market and policy developments and their impacts on the sugar and corn sweetener industries.

[[Category:Taste Aversion]]
[[Category:Ingestive Behavior]]

Sweeteners

2025-01-14T13:48:26Z

Chuck: Follow perm redirect

{| class="wikitable sortable" border = "1" cellspacing="0" cellpadding = "3"
|+'''Sweeteners'''
|-bgcolor="silver"
! width="125" | Chemical Name !! width="150" | Tradename !! Wiki !! width="75" | MW !! width="125" | Formula !! width="100" | CAS !! width="75" | Calories !! width="100" | Sweetness
|-
| [[Saccharin]] || [https://www.sweetnlow.com Sweet n Lo] || [https://en.wikipedia.org/wiki/Saccharin Wiki] || align="center"| 183.18 ||align="center"| C7H5NO3S || align="center"|81-07-2 || calories || rs
|-
| [[Sucrose]] || [https://www.sucrose.com/ Sugar] || [https://en.wikipedia.org/wiki/Sucrose Wiki] || align="center"| 342.29 || align="center"|C12H22O11 || align="center"|57-50-1 || calories || rs
|-
| [[ Fructose]] || [https://corn.org/products/sweeteners/ HFCS] || [https://en.wikipedia.org/wiki/Fructose Wiki] || align="center"| 180.16 || align="center"|C6H12O6 || align="center"|57-48-7 || calories || rs
|-
| [[Xylitol]] || Xylitol || [https://en.wikipedia.org/wiki/Xylitol Wiki] || align="center"| 152.15 || align="center"|C5H12O5 || align="center"|87-99-0 || calories || rs
|-
| [[Aspartame]] || [https://web.archive.org/web/20180721024410/http://www.nutrasweet.com:80/ NutraSweet] || [https://en.wikipedia.org/wiki/Aspartame Wiki] || align="center"| 294.3 || align="center"|C14H18N2O5 || align="center"|22839-47-0 || calories || rs
|-
| [[Steviol glycoside]] || [https://www.truvia.com Truvia] || [https://en.wikipedia.org/wiki/Steviol_glycoside Wiki] || align="center"| 318.45|| align="center"|C20H30O3 || align="center"|471-80-7 || calories || rs
|-
| [[ Sucralose]] || [https://www.splenda.com Splenda] || [https://en.wikipedia.org/wiki/Sucralose Wiki] || align="center"| 397.64 || align="center"| C12H19Cl3O8 || align="center"|56038-13-2 || calories || rs
|-
| [[ Acesulfame K]]||[https://www.celanese.com/food-ingredients/products/sunett.aspx Sunett], [http://www.sweetone.com/ Sweet One]|| [https://en.wikipedia.org/wiki/Acesulfame_K Wiki] || align="center"| 201.24 || align="center"| C4H4KNO4S || align="center"|55589-62-3 || calories || rs
|-
| [[ Dulcin]] || sucrol, valzin|| [https://en.wikipedia.org/wiki/Dulcin Wiki] || align="center"| 180.20 || align="center"|C9H12N2O2 || align="center"|150-69-6|| calories || rs
|-
| [[ Perillartine]] || (Japanese name: ペリラルチン, available from [https://highchem.co.jp/chem/details.php?cas=30950-27-7 HighChem] and others) japanese product page?|| [https://en.wikipedia.org/wiki/Perillartine Wiki] || align="center"| 165.23 || align="center"| C10H15NO || align="center"|30950-27-7 || calories || rs
|}

Notes:

'''Tradename''' links to manufacturer's website

'''Calories''' (kcal/g) is available calories to humans following ingestion

'''Sweetness''' (g/g sucrose) is reported (maximal?) sweetness to humans relative to sucrose (at a particular concentration)?

= USDA Sugar and Sweeteners Data=

[https://www.ers.usda.gov/data-products/sugar-and-sweeteners-yearbook-tables.aspx Recommended Data]

[https://www.ers.usda.gov/topics/crops/sugar-and-sweeteners/readings Recommended Readings]

[https://usda.library.cornell.edu/concern/publications/pv63g024f?locale=en Sugar and Sweeteners Outlook] (PDF file)
(January, May, and September) provides an update of current market and policy developments and their impacts on the sugar and corn sweetener industries.

[[Category:Taste Aversion]]
[[Category:Ingestive Behavior]]

Laser Capture Microscopy (LCM)

2024-12-17T14:21:10Z

Chuck: Updated CryoJane manual link

==Overview==

[https://houptlab.org/talks/LCM_of_VTA-SN.pptx.zip Example Powerpoint] with videos and calibration images.

==Supplies for LCM==

===CapSure Caps===

[https://www.thermofisher.com/us/en/home/life-science/gene-expression-analysis-genotyping/laser-capture-microdissection/laser-capture-microdissection-lcm-slides-accessories/laser-capture-microdissection-lcm-caps.html ThermoFisher LCM site]

* [https://www.thermofisher.com/order/catalog/product/LCM0213 LCM0213 caps] and alignment tray and incubation block (dont know if we need all that)

* [https://www.thermofisher.com/order/catalog/product/LCM0213 LCM0214 32 caps] $560

* [https://www.thermofisher.com/order/catalog/product/LCM0215 LCM0215 160 caps] $2400

===Cryo-Jane System for Adhesive Slides===

<del>[https://web.archive.org/web/*/http://www.instrumedics.com/ Instrumedics Inc.]
5918 Evergreen Blvd.
St. Louis, Mo 63134
Phone: 314-522-8671
Fax: 314-522-6360
email: sales@instrumedics.com</del> 
Now part of [https://shop.leicabiosystems.com/us/histology-consumables/ancillaries/pid-tape-transfer-system Leica Biosystems]

(prices updated 2022)

Adhesive-Coated Slides CFSA 1X Slides White (125/box) item # 39475208 $375

Adhesive Tape Windows 1x3 Slides (RL200per) item #39475214 $114

see also [https://www.emsdiasum.com/cryojane-the-cryostat-frozen-sectioning-aid-system Electron Microscopy Sciences page]

[https://www.emsdiasum.com/docs/technical/manuals/62800.pdf CryoJane Manual]

video: [https://youtu.be/nkzGdc0IAEY Univ Vermont]

==Protocol for Amygdala Regions ==

Reference Kwon et al, 2008, PMID 18374904

The frozen brains were sectioned between -2.30 and -3.14 mm from bregma (Paxinos and Watson, 1986) at 5 µm thickness and mounted on slides in a –20 ºC cryostat using the CryoJane system (Instrumedics, Hackensack, NJ). The frozen brain sections were defrosted at room temperature for 30 sec, then stained and dehydrated by the following procedure: 75% ethanol for 30 sec, DEPC-treated deionized H2O (DEPC-dH2O) for 30 sec, Histogene Staining solution (Arcturus, Mountain View, CA) for 3 min, DEPC-dH2O for 30 sec, 75% ethanol for 30 sec, 95% ethanol for 30 sec, 100% ethanol for 30 sec, xylene for 5 min, air dried in a fume hood for 15 min, and then desiccated with Drierite (W.A. Hammond Drierite, Xenia, OH) for 1 h.
LCM parameters were 15 or 30 µm diameter laser spot, a 10 ms laser pulse duration, and a 65 mW laser power. Multiple laser shots (150-200) were required to transfer each amygdala region. Following dissection, tissue sections were stained with methyl green (Vector Laboratories, Burlingame, CA) and coverslipped to verify the specificity of the dissection.

Total RNA was extracted from individual LCM samples with the Total RNA Microprep Kit (Stratagene, La Jolla, CA) according to the manufacturer’s protocols. RT-PCR was performed by using the OneStep RT-PCR Kit (Qiagen, Valencia, CA).

==Protocol for X-Gal Stained Cells ==

Reference Kwon and Houpt 2010 PMID 19925827

In order to confirm mRNA expression and preservation in β-Gal-positive cells, we performed RT-PCR after LCM of single cells. Transgenic mice were injected with LiCl (0.15 M, 40 ml/kg, i.p.). One hour later, they were anesthetized with sodium pentobarbitol, decapitated, and the brains were dissected. The brains were emmersed in M-1 Embedding Matrix (Shandon, Pittsburgh, PA), immediately frozen with dry ice, and stored at –80 ºC freezer until used. The frozen brains were sectioned at 8 µm and mounted on slides in a –20ºC cryostat using the CryoJane tape transfer system (Instrumedics, Hackensack, NJ). The sections were defrosted at room temperature for 30 s and then briefly washed with DEPC-dH2O. The brain sections were fixed in 70% ethanol at room temperature for 5 min and then washed with DEPC-dH2O for 5 min. Brain sections were then stained as above in X-Gal reaction buffer containing 1 mg/ml of X-Gal in DEPC-dH2O. The reaction was performed for 16 h at 37ºC in darkness.

Subsequent to X-Gal staining, the sections were washed in DEPC-dH2O for 5 min and dehydrated by the following procedure: 70% ethanol for 30 s, 95% ethanol for 30 s, 100% ethanol for 30 s, xylene for 5 min, air dried in a fume hood for 15 min, and then desiccated with Drierite (W.A. Hammond Drierite, Xenia, OH) for 1 h. X-Gal stained cells in the CeA, cortex and hippocampus were microdissected using the PixCell II LCM system (Arcturus, Mountain view, CA). A 7 um diameter laser spot, a 10 ms laser pulse duration, and a 85 mW laser power were used for the microdissection. Cells from cortex and hippocampus were included as positive controls, because those areas have previously been reported to have high levels of c-Fos and lacZ expression (Smeyne et al., 1992b and 1993). Total RNA was extracted from the LCM samples with the Total RNA Microprep Kit (Stratagene, La Jolla, CA) according to the manufacturer’s protocols. RT-PCR using primer pairs for c-Fos and β-actin was performed by using the OneStep RT-PCR Kit (Qiagen, Valencia, CA) as described above. The total RNA extract from each LCM sample of single cells was used in each RT-PCR reaction (15-20 single cells for β-actin and 30-40 single cells for c-Fos).

==Houpt Lab LCM Operating Procedure==

===Startup===

1. Turn on power for Samsung monitor, VGA up-converter,and MTI camera

2. Turn on power for PixCell II Microscope

3. turn on power for Controller (very stiff switch!)

===Dissection===

1. Place slide on stage, covering up the "I" shaped vacuum port

2. Engage vacuum on Controller, to secure slide to stage

3. Use "Prep strip" on slide to clean up surface of section

3. Pick up CapSure cap in swing arm, and swing over to place cap on top of slide (by grabbing the "beer can")

4. Turn laser "interlock" key clockwise from noon to 3 o'clock: this unlocks the laser

5. Press "Laser Enable" to get targeting laser. If you decrease microscope lamp illumination, you should see the red dot of the targeting laser. (It will be more less diffuse until the laser is focused).

6. Adjust size and focus of the laser spot with the controls on the left side of the laser mounted on the Microscope

7. Adjust the duration and power parameter of the laser pulse on the Controller.

* use the upper up-and-down arrows to select pulse parameter
* use the lower up-and-down arrows to set the parameter value
* Spotsize is set with the controls on the laser in previous step
* Temperature is read-only

8. Use microscope joystick to maneuver red dot over target region on the slide

9. Press the laser button to fire the laser. Can fire repeatedly to ensure collection.

10. Use microscope joystick to maneuver to an adjacent (or distant) spot to collect more samples.

11. Move cap over to "cap holder" on right of microscope.

[[Category:Protocols]]

Computers

2024-10-08T13:26:13Z

Chuck: Updated DNSUpdate link to point at archived source code

=Computers in the Houpt Lab=

king subnet mask: 255.255.252.0
IP Gateway: 128.186.177.1

{| border = "1"
|+
! Computer !! Location !! IP address !! MAC address !! URL
|-
| Principia || 3009 || 128.186.177.169 || 00:03:93:7c:43:02 (en0) || kin3010-mac1-bio.fsu.edu
|-
| Voyages || laptop || DHCP || c8:bc:c8:8f:2f:55 (en0), 78:ca:39:ba:71:cd (wifi) ||

|-
| Tesla || 3029 || 128.186.177.166 || 00:1f:5b:35:2c:2d (en1) || kin3029-mac2-bio.fsu.edu
|-
| Micrographia || 3029A || 128.186.177.165 || || kin3029-mac1.bio.fsu.edu
|-
| Vaio || 3029 || || ||
|-
| Brother HL-6180DW || 3029 || 128.186.177.168 || 30:05:5c:86:10
|-
| MacMini || 3013 || || 00:1f:f3:45:6d:18 (en0), 00:23:6c:7a:23:b3 (wifi) ||
|-
| BRF iMac || 115 || DHCP
|-
|}

=Setup of sftp server for EvoCam=

Make sure sftp is selected.

The url for storing the image is (e.g. for an image named "magnet.jpg"): 
<blockquote>
<tt> sftp://www.magnet.neuro.fsu.edu//Library/FTPServer/FTPRoot/WebPages/Webcams/magnet.jpg</tt> 
</blockquote>
Note that two slashes are required between the root url ( sftp://www.magnet.neuro.fsu.edu) and the start of the working directory (//Library/...). EvoCam first connects to the root url, and then attempts to put the image file into the directory. If the directory is not a subdirectory of the user's login directory, then an initial slash is required. Two slashes makes EvoCam parse the directory with an initial slash.

=Computer Hints=

1. '''Acid Search''' from [http://www.pozytron.com pozytron.com ]
<blockquote>
Add a search channel for PubMed: 
:<tt><nowiki>http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?DB=pubmed&term=</nowiki></tt> 
Add a search channel for Wikipedia: 
:<tt><nowiki>http://en.wikipedia.org/wiki/Special:Search?search=</nowiki></tt> 
Add a search channel for YouTube: 
:<tt><nowiki>http://www.youtube.com/results?search_query=</nowiki></tt> 
</blockquote>

2. '''Add Debug/Develop menu to Safari''':

: Safari > Preferences... > Advanced > Show Develop menu in menu bar

3. '''to make Safari pass PDFs to Preview''' instead of opening itself:
<blockquote>
<tt>defaults write com.apple.Safari WebKitOmitPDFSupport -bool YES</tt> 

(also remove Adobe PDF viewer from /Library/Internet Plug-Ins) 

(could also try using Safari Enhancer (Discontinued))
</blockquote>

4. '''To change the __MyCompanyName__''' in Xcode (from MacOSXGuru.Net):
<blockquote>
Open the ProjectBuilder preferences file (~/Library/Preferences/com.apple.ProjectBuilder.plist) or the Xcode one (~/Library/Preferences/com.apple.Xcode.plist) and edit the dictionary associated with the key PBXCustomTemplateMacroDefinitions (create one if it does not exist, as child of the root node), edit or add the key ORGANIZATIONNAME, the associated string value will be used when PB creates new source files. 

You could also do it via Terminal.app: 

:<tt>defaults write com.apple.ProjectBuilder PBXCustomTemplateMacroDefinitions '{ "ORGANIZATIONNAME" = "Behavioral Cybernetics";}' </tt> 

or 

:<tt>defaults write com.apple.Xcode PBXCustomTemplateMacroDefinitions '{ "ORGANIZATIONNAME" = "Behavioral Cybernetics";}' </tt> 

</blockquote>

5. '''download [https://my.smithmicro.com/index.html stuffit expander]'''

6. ''' make iChat autoconnect '''
<blockquote>
<tt>defaults write com.apple.ichat AutoAcceptVCInvitations -1 </tt>
</blockquote>

7. '''Making bootable backups''':
<blockquote>
<tt>sudo rsync -xrlptgoEv --progress --delete / /Volumes/Backup </tt> 

or just use [https://bombich.com Carbon Copy Cloner]
</blockquote>

8. '''Replace file extension of all files within a directory tree'''
<blockquote>
<tt>find ~/MyDirectory -name '*.txt' -exec bash -c 'mv "{}" "`dirname "{}"`/`basename "{}" txt`xls"' \;</tt> 

The first arg is the parent directory of the data. Find will recurse thru all sub-dirs. This command replaces ".txt" with ".xls"
</blockquote>

9. '''DNS Servers for use outside FSU's Network'''
<blockquote>
To avoid evil ISP DNS servers (comast 68.87.74.162), one can use any of the following DNS servers: 

[https://nationalmaglab.org/ FSU Magnet Lab]: 146.201.250.2 (addc1.ad.magnet.fsu.edu) 

<s>[https://easydns.com/blog/2008/07/24/easydns-soft-launches-dnsresolvers-com/ EasyDNS DNSresovlers]: 205.210.42.205, 66.207.199.44 (cache1-2.dnsresolvers.com)</s> [https://easydns.com/blog/2013/06/27/dnsresolvers-open-resolvers-will-be-shut-down/ DNSResolver shut down in 2013] 

DO NOT USE FSU's DNS SERVERS: Outside of FSU's network, the DNS servers are in cache-only mode, so only commonly accessed names can be resolved. 
</blockquote>

10. '''Epson C82 Blank Ouput Problem and Fix'''
<blockquote>
When an Epson C82 unexpectedly starts outputing blank pages, it is likely that the [https://web.archive.org/web/20160704210356/http://inkjetprinterhelp.us/duraink.html ink purge tube has become disconnected].
</blockquote>

11. '''Command-Line Downloading/Uploading a file from an offline WebDAV Volume'''

Sometime it is useful to send/receive files from a WebDAV server, without having to login and mount the Volume in the Finder.

Download "IGNATUS-SMALL.png" to current directory:
<pre>
curl -O http://www.magnet.neuro.fsu.edu/LabDisk/CEHoupt/IGNATUS-SMALL.png
</pre>

Upload "test.mov" in current directory to LabDisk:
<pre>
curl -u user:password -T test.mov http://www.magnet.neuro.fsu.edu/LabDisk/test.mov
</pre>

=DNS for home website=

Install [https://github.com/jonasf73/DNSUpdate DNSUpdate] to make sure the webserver's current IP address is sent to [https://easydns.com EasyDNS]

Give the webserver a dedicated IP address within the Airports sub-net (typically 10.0.1.X), but outside the DHCP range (typically 10.0.1.1-200) to avoid conflicts.

Tell the Airport to map public port 80 onto the web server's private address on port 80

=Notes on Micrographia Graphics Problems=

2008-03-24

Micrographia has been exhibiting graphic display problems for some time. windows, menus, and icons are displayed chopped up, usually with a diagonal dividing line down the drawing rectangle. The only immediate way to eliminate the problem was to set the displays color depth to 256.

Although we were initially suspicious of a hardware problem, performing a safe boot (boot with shift-key down) eliminates the problem. Further investigations revealed that the problem only occurs when Quartz Extreme is enabled (via System Profiler). Quartz Debug (/Developer/Applications/Performance Tools) can be used to manually enable/disable Quartz Extreme.

One possible work-around is to use the [https://web.archive.org/web/20161021001648/http://hints.macworld.com/article.php?story=20040724190553112 Disable Quartz Extreme Hack].

=Notes on repairing crashed Mediawiki Search Index=

https://web.archive.org/web/20191203132820/http://www.weblaminar.com/index.php/weblaminar-tools/wlt-howto#Index_Corruption

http://www.mediawiki.org/wiki/Project:Support_desk/Archives/Database/001#.28OUTDATED.29_Searchindex_always_crashing

As root run:

myisamchk -r /usr/local/mysql-5.1.30-osx10.4-powerpc/data/magnetowikidb/mw_searchindex

[[Category:Laboratory]]

Selenium

2024-09-03T13:21:40Z

Chuck: Archive Daily Show links, because of https://www.hollywoodreporter.com/tv/tv-news/daily-show-alumni-clip-archive-loss-1235934107/

Selenium is an essential micronutrient. Recently, a specific selenium salt, sodium selenate, was discovered to be a specific enhancer of the enzyme protein phosphatase 2A (PP2A). PP2A removes phosphate groups from target proteins, including tau, a protein implicated in Alzheimer’s disease Corcoran 2010a PMID 20537899, van Eersel 2010 PMID 20643941, and many other proteins implicated in the control of cancer (Corcoran 2010b PMID 20648008).

Because phosphatases like PP2A remove phosphate groups that activate other proteins, PP2A can be considered a “brake” on the activity of cells, including neurons involved in learning and memory. We have previously shown that inhibiting phosphatase PP2A with the non-specific blocker okadaic acid increased the strength of learned conditioned taste aversions in rats. In other words, blocking PP2A “cut the brakes” on the learning mechanism, causing the rats to acquire a stronger memory of a toxic fluid (saccharin paired with lithium chloride).

Because sodium selenate can act as an enhancer of PP2A, we hypothesize that administering sodium selenate before a conditioning trial will decrease the strength of conditioned taste aversion learning (i.e., the “brakes” will be enhanced, thus diminishing the learning.)

==Sodium Selenate==

[https://www.sigmaaldrich.com/US/en/product/sigma/s8295 Sigma-Aldrich S8295-10G] $56

CAS Number: 13410-01-0

Linear Formula: Na2SeO4

Molecular Weight: 188.94

EC Number: 236-501-8

MDL number: MFCD00003490

PubChem Substance ID: [https://pubchem.ncbi.nlm.nih.gov/substance/24899787 24899787]

'''Tonicity of Systemic Injection'''

Osmolarity of Na2Se04 at 12 mg/ml (63 mM) = 189 mOsm

So Na2Se04 at 12 mg/ml (63 mM), NaCl at 3.2 mg/ml (55mM) = 300 mOsm

'''Calculation of suggested i.c.v. injection concentration.'''

Assuming a 500 g rat, then systemic dose is 0.25 mg ( 250 µg). A central dose might be 1/100th of the system dose -> 2.5 µg.

Volume of i.c.v injection would be 5 µl; site specific injection 0.5 µl

So central dose would be 2.5 µg / 5 µl = 0.5 µg/ 1 µl = 0.5 g / L.

MW of sodium selenate is 188.94, so 0.5 g = 2.65 mmole

so central injection dose is 5 µl at 2.65 mM.

(Osmolarity is sufficiently low that can be diluted with saline).

==Toxicity of Selenate==

Selenium is an essential micronutrient and is naturally found a wide variety of food stuffs. As an antioxidant, it is frequently used to treat, e.g., heavy metal toxicosis or liver disease. The recommended dietary intake for adults is 55 micrograms/day, and selenium supplements of 200-300 micrograms/day have been recommended for prevention of several types of cancer. High doses of 1.5 to 5 mg/ day are associated with adverse effects (Brozmanova 2010, Reid 2004). The chemical form of selenium also contributes to toxicity. The form we will use, sodium selenate (Na2Se04), is well-tolerated in human trials (Corcoran 2010b).

Corcoran (2010a) administered sodium selenate to mice acutely at 12 mg/kg, and chronically at ~192 mg/kg per day in drinking water, and did not report any aversive or toxic effects on the mice. van Eersel (2010) administered sodium selenate to mice chrionically at ~ 1.9 mg/kg per day in drinking water, and also did not report any aversive or toxic effects.

Abdo (1994) reported on the effects of administering sodium selenate in the drinking water for 13 weeks. It was estimated that the "no-observed adverse level" in rat was 0.4 mg/kg per day of sodium selenate for 13 weeks. Doses of 0.6 mg/kg or 1.1 mg/kg per day for 13 weeks caused changes in mortality, body weight depression, decreased water consumption, and renal papillary lesions. However, these were chronic studies so that rats received a total dose of 54.6 mg/kg or 100.1 mg/kg sodium selenate over 13 weeks.

Aasif Mandvi ran a [https://web.archive.org/web/20240423122448/https://www.cc.com/video/jucn2a/the-daily-show-with-jon-stewart-a-simple-plot story] on selenium pollution of Idaho rivers as a consequence of phosphate mining.

==Selenium Ingestion and Aversions==

Selenium is an essential micronutrient. The mammalian selenoproteome consists of some 2 dozen selenocysteine-containing proteins (24 in rodents, 25 in human) including the glutathione peroxidase, thioredoxin reductase and iodothyronine deiodinase enzymes [PMID 12775843]. However, at doses not much higher than the dietary requirement, selenium is also toxic [PMID 3527390]. Selenium toxicity is due to the generation of superoxide and other reactive oxygen species, the oxidation of thiols, and by substituting for sulfur in methionine to form selenomethione which then may be incorporated into many sulfur containing proteins [PMID 11879936].

Reduced intake and avoidance of toxic diets containing selenium compounds has been demonstrated in many species. Because selenium is concentrated by certain species of plants in selenium-rich geographies, selenosis is a potential hazard for livestock and native herbivores. Waste from mining or agricultural run-off can also introduce selenium into the environment and hence into the food-chain. It has therefore been of interest to determine whether species can avoid selenium-rich food sources due to an aversive taste or odor of selenium compounds, or acute toxic effects, or learned food aversions. Aphids [PMID 17831208, JSTOR 1514562], crickets and grasshoppers [PMID 17635224], southern armyworms [PMID 10467057] mallard ducks [Heinz 1990], owls [Wiemeyer 1996], prairie dogs [PMID 21628258], sheep [Pfister 2010, PMID 3527390], and cattle [PMID 3527390] have been shown to reduce intake of selenium-containing foods, or show reduced preference for selenium-containing foods over control diets.

In laboratory studies, rats show a preference for control or low selenium-diets over high selenium diets [PMID 17788901][Franke and Potter 1935]. Consistent with the effects of other selenium compounds, selenate adulteration also causes a reduction of food [Franke and Moxon 1937] [Smith Stohlman Lillie 1937] or water intake [PMID 6053743, PMID 1255264] Acute injection of selenate can also reduce food intake and body weight gain [PMID 2609019]

Only a few of these studies (e.g. [Pfister 2010, PMID 3527390, Heinz & Sanderson 1990] ) have determined if animals were responding to an acute perception of selenium compounds, or if the animals used food-associated cues, to avoid consumption, after acquiring a selenium-induced conditioned food aversion. Selenium absorbing plants may themselves have salient taste or odor: for example, Provenza et al. have demonstrated that the odor of Astragalus bisulcatus, a sulfur-containing selenium-absorbing plant, can serve as a CS that reduced preference for CS+barley-straw after pairing with oral-intubation of LiCl. [Oikos 88(2000)424-432.] Selenium compounds may also present distinctive cues, e.g., the volatile dimethyldiselenide, a major metabolite of selenite and selenate, has a pungent garlic odor to humans, that may be innately aversive or serve as an indicative CS in learned selenium aversions.

==Government Documents on Selenium Safety==

National Toxicology Program / NIEHS: [https://ntp.niehs.nih.gov/sites/default/files/ntp/htdocs/st_rpts/tox038.pdf NTP Technical Report on Toxicity Studies of Sodium Selenate and Sodium Selenite] (1994)

CDC/NIOSH: [https://www.cdc.gov/niosh/idlh/7782492.html Selenium compounds (as Se)] from NIOSH Documentation for immediately dangerous to life or health concentrations (IDLHs)

WHO: [https://inchem.org/documents/ehc/ehc/ehc58.htm Environmental Health Criteria 58: Selenium] (1987) from International Programme on Chemical Safety

HHS: [https://www.atsdr.cdc.gov/ToxProfiles/tp92.pdf Toxicological Profile for Selenium] (2003)

Agency for Toxic Substances and Disease Registry: [https://wwwn.cdc.gov/TSP/ToxFAQs/ToxFAQsDetails.aspx?faqid=152&toxid=28 ToxFAQs for Selenium] (2003)

Agency for Toxic Substances and Disease Registry: [https://www.atsdr.cdc.gov/toxguides/toxguide-92.pdf ToxGuide for Selenium]

Division 9 of NRDC: [https://web.archive.org/web/20220504131238/https://apps.dtic.mil/sti/pdfs/AD0234270.pdf Chemical Warfare Agents and Related Chemical Problems, Parts I-II, Chapter 11] (1946)

==References==

Abdo, K.M. 1994. NTP Technical Report on Toxicity Studies of Sodium Selenate and Sodium Selenite (CAS Nos. 13410-01-0 and 10102-18-8) Administered in Drinking Water to F344/N Rats and B6C3F1 Mice. NIH Publication 9a4-3387. National Toxicology Program. Toxicity Report Series Number 38.

Brozmanova et al., 2010. Selenium: a double-edged sword for defense and offence in cancer, Arch. Toxicol. 84:919–938. PMID 20871980.

Corcoran NM, et al., 2010a. Sodium selenate specifically activates PP2A phosphatase, dephosphorylates tau and reverses memory deficits in an Alzheimer's disease model. J Clin Neurosci. 8:1025-33. PMID 20537899

Corcoran NM et al. 2010b. Open-label, phase I dose-escalation study of sodium selenate, a novel activator of PP2A, in patients with castration-resistant prostate cancer. Br J Cancer. 103:462-8. PMID 20648008

Mandvi, A. A Simple Plot. The Daily Show with Jon Stewart, aired June 14, 2012. https://web.archive.org/web/20240423122448/https://www.cc.com/video/jucn2a/the-daily-show-with-jon-stewart-a-simple-plot

Reid ME et al. 2004 A report of high-dose selenium supplementation: response and toxicities. J Trace Elem Med Biol 18:69–74 PMID 15487766

van Eersel J et al. 2010. Sodium selenate mitigates tau pathology, neurodegeneration, and functional deficits in Alzheimer's disease models. PNAS 107:13888-93. PMID 20643941

14-3-3

2024-08-29T19:53:12Z

Chuck: Follow redirect from diginole

==14-3-3==

https://medlineplus.gov/genetics/gene/ywhae/

Ywhae gene = 14-3-3 epsilon = tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (Ywhae)

Mus musculus tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (Ywhae), mRNA
NCBI Reference Sequence: NM_009536.4

==Dr. Yi Zhou's 14-3-3 FKO (Thy1-YFP-DIfopein) Transgenic Mice==

See SFN abstracts (2010) 53.1/M17 and (2011) 790.09/FF16

From Kourtney Graham's Honor's Thesis:

<blockquote>
In order to study the role of 14-3-3 proteins in the nervous system_ in
vivo_, we have successfully created lines of neuronal-specific
transgenic mice that may inhibit 14-3-3 dependent cellular processes.
These transgenic mice express a YFP-fused peptide (R18) which binds to
endogenous 14-3-3, and thus blocking its capability to interact with its
binding partners; and are therefore considered to be a functional
knockout. The transgenes are expressed under the control of the Thy-1
promoter which is neuronal-specific and produces variation of transgene
expression in different brain regions, which is great among founder
lines but minimal among descendants of a single founder (Feng et al.
2000). To minimize strain-dependent genetic variation, we have
backcrossed the founder lines with wild-type C57BL/6 mice for at least 8
generations.
</blockquote>

From Sun et al PMID 23861400 :
Glutamatergic kainate receptors (KAR) KAR-EPSCs at mossy fiber-CA3 synapses decay significantly faster in the 14-3-3 functional knock-out mice (but no difference in NMDA-R or AMPA-R EPSC in same synapses)

==R18 peptide ==

PMID 11577088

R18 is a synthetic 21 amino acid unphosphorylated peptide (MW 2309.6) which binds to the same amphipathic groove on the surface of 14-3-3 as phosphorylated peptides, with high affinity for all 7 mammalian isoforms of 14-3-3 PMID 10493820. Commercial source of peptide [https://www.enzo.com/product/r18-peptide/ Enzo #BML-P214-0001].

Difopein is a construct with two R18 monomers in a single 62 amino acid peptide PMID 11577088. Commercial source of peptide: [https://www.tocris.com/products/difopein_2145 Tocris #1245]

R18 Sequence:

Pro-His-Cys-Val-Pro-Arg-Asp-Leu-Ser-Trp-Leu-Asp-Leu-Glu-Ala- Asn-Met-Cys-Leu-Pro-OH

PHCVPRDLSWLDLEANMCLP

Difopein sequence (with individual R18 monomers in parentheses):

SADGA (PHCVP RDLSW LDLEA NMCLP) GAAGL DSADG A(PHCV PRDLS WLDLE ANMCL P) GAAG LE

C54 (consisting of the carboyl-terminal 54-amino acid region of theHMG-box binding protein Ste11p ) is another 14-3-3 inhibitor that is structurally unrelated to R18/difopein. The C54 region permits sequestration of Ste11p in the cytoplasm to inhibit nuclear localization PMID 12697825.

==Thy-1 Promoter==

PMID 11086982

==YFP==

YFP is 239 amino acids long (717 bp) according to plasmid map of Invitrogen [https://www.thermofisher.com/order/catalog/product/V35820 Vivid ColorsTM pcDNATM/6.2 N-terminal EmGFP/YFP-DEST vectors] see p, 28 of the manual. Difopein is 62 amino acids long (186 bp), so total YFP-difopein fusion protein should be ~ 301 amino acids (903 bp).

== 14-3-3 FKO papers==
Vogt, Peggy, [https://repository.lib.fsu.edu/islandora/object/fsu:204445 "Exploring the Function of 14-3-3 Proteins in Neurodegenerative Disease"] (2011). Honors Theses. Paper 42.

C. Sun, H. Qiao, Q. Zhou, Y. Wang, Y. Wu, Y. Zhou, et al., Modulation of GluK2a Subunit-containing Kainate Receptors by 14-3-3 Proteins, J Biol Chem. 288 (2013) 24676–24690. PMID 23861400

Qiao H, Foote M, Graham K, Wu Y, Zhou Y. 14-3-3 proteins are required for hippocampal long-term potentiation and associative learning and memory. J Neurosci. 34(2014):4801-8. PMID 24695700

==Antisera for IP Experiments==
anti-pan-14-3-3 (K-19) , rabbit polyclonal, Santa Cruz #sc-629, 200 ug/1 ml, $279 [https://www.scbt.com/p/pan-14-3-3-antibody-k-19 datasheet]

anti-HDAC4 (H-92), rabbit polyclonal, Santa Cruz #sc-11418, 200 ug/1 ml, $279 [https://www.scbt.com/p/hdac4-antibody-h-92 datasheet]

anti-Torc1 (C71D11), rabbit mAb, Cell Signaling #2587 $225 [https://www.cellsignal.com/products/primary-antibodies/torc1-crtc1-c71d11-rabbit-mab/2587 datasheet]

Anorexia anx/anx mutant mice

2024-06-11T10:24:36Z

Chuck: Fix product info fragment IDs due to neb.com site change

''Anorexia'' anx/anx mice [https://www.jax.org/strain/000624 Jackson Lab strain 000624].

Mutation mapped to a 0.2 cM interval residing between the markers D2Mit133 and Jojo5 chromosome 2 (Chr 2: bp 118, 889, 896–120, 175, 1081) (Lindfors et al., 2011).

== Possible genes affected ==

Lindfors 2011 PMID 22025706: NADH dehydrogenase (ubiquinone) 1a-subcomplex (Ndufaf1)

Kim 2017 PMID 28093506: tyrosine kinase receptor Tyro3 which they conclude is not the anx-mutation but a strain specific modifier of anx-phenotypes

== Abnormalities Table ==

== Tyro3 Genotyping ==

TYRO3 protein tyrosine kinase 3 (Tyro3) mutation (C19T-Tyro3 mutation) in anx/anx eliminates a NlaIV restriction site.

* primers forward 5′-GATGGCGCTGAGGCGGAGCATG and reverse 5′-CGCGGCCGGAGGTCTGGCAG ; annealing temperature 72C

* predicted PCR product size: 280bp equal to [https://www.ncbi.nlm.nih.gov/nucleotide/1877089967?from=119630270&to=119630549&report=gbwithparts Mus musculus strain C57BL/6J chromosome 2, GRCm39], where forward primer is 119630270-119630291 and reverse primer is 119630549-119630530

* subsequent digestion with NlaIV

* wildtype -> 175 bp fragment, anx/anx -> 250 bp product (eyeballing from Kim 2017)

[[File:anx_pcr_kim_2017.png|800px|border]]

== Genotyping 1998 mice ==

* 2024-1-17 Tyro3 primers ordered from FSU BIO Core

* 2024-1-18 [https://www.neb.com/en-us/products/r0126-nlaiv#Product-Information NlaIV] ordered from NEBiolabs, along with [https://www.neb.com/en-us/products/n0556-quickload-purple-50-bp-dna-ladder#Product-Information 50bp ladder]

* 2024-6-6 [https://www.promega.com/products/pcr/taq-polymerase/gotaq-master-mixes/?catNum=M7132 Promega GoTaq colorless master mix] ordered from Fisher (suspect green master mix interferes with digest)

===DNA extraction from tails/spleens===

[https://omegabiotek.com/product-category/genomic-dna/cultured-cells-and-tissue/ E.Z.N.A. Tissue DNA Kit] yields 200 ul in elution buffer.

===PCR===

PCR master-mix: [https://www.promega.com/products/pcr/taq-polymerase/gotaq-master-mixes/?catNum=M7132 Promega Gotaq colorless master mix].

For 50 ul reaction:

PCR: 95C for 1min, then 30 cycles of: 95C for 1min, 72C for 2min. (note annealing and extension steps combined into 2 min at 72C).

===PCR clean-up===

[https://omegabiotek.com/product/pcr-clean-up-kit-e-z-n-a-cycle-pure/ E.Z.N.A. Cycle Pure Kit (V-spin)] yields 30 ul in dH20

===Digestion===

===Gel===

1% agarose in TAE (1 g agarose in 100 ml TAE, microwave 2 min at 50 power; add 10 ul of SYBR safe 10000x)

load 10 ul of 50bp ladder, 10-20 ul of pre-digest and digest

Cassowary

2024-06-11T10:19:37Z

Chuck: Follow CAS perm redirect

Cassowary is a large, flightless, highly territorial, [https://www.apereo.org/programs/software/cas CAS] client.

<html>
<style>
.splash { width: 800px; overflow: hidden; }
.splash > img { width: 800px; animation-name: the-stare; animation-duration: 100s; animation-fill-mode: forwards; }
@keyframes the-stare { from {} to { transform: translate(-650px,190px) scale(4.5); }}
</style>
<div class="splash"><img src="/images/a/ab/Casuarius.jpg"></div>
</html>

Source Code: https://github.com/HouptLab/Cassowary

[[Category:Software]]

14-3-3

2024-06-04T10:25:42Z

Chuck: Follow Enzo R18 perm redirect

==14-3-3==

https://medlineplus.gov/genetics/gene/ywhae/

Ywhae gene = 14-3-3 epsilon = tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (Ywhae)

Mus musculus tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (Ywhae), mRNA
NCBI Reference Sequence: NM_009536.4

==Dr. Yi Zhou's 14-3-3 FKO (Thy1-YFP-DIfopein) Transgenic Mice==

See SFN abstracts (2010) 53.1/M17 and (2011) 790.09/FF16

From Kourtney Graham's Honor's Thesis:

<blockquote>
In order to study the role of 14-3-3 proteins in the nervous system_ in
vivo_, we have successfully created lines of neuronal-specific
transgenic mice that may inhibit 14-3-3 dependent cellular processes.
These transgenic mice express a YFP-fused peptide (R18) which binds to
endogenous 14-3-3, and thus blocking its capability to interact with its
binding partners; and are therefore considered to be a functional
knockout. The transgenes are expressed under the control of the Thy-1
promoter which is neuronal-specific and produces variation of transgene
expression in different brain regions, which is great among founder
lines but minimal among descendants of a single founder (Feng et al.
2000). To minimize strain-dependent genetic variation, we have
backcrossed the founder lines with wild-type C57BL/6 mice for at least 8
generations.
</blockquote>

From Sun et al PMID 23861400 :
Glutamatergic kainate receptors (KAR) KAR-EPSCs at mossy fiber-CA3 synapses decay significantly faster in the 14-3-3 functional knock-out mice (but no difference in NMDA-R or AMPA-R EPSC in same synapses)

==R18 peptide ==

PMID 11577088

R18 is a synthetic 21 amino acid unphosphorylated peptide (MW 2309.6) which binds to the same amphipathic groove on the surface of 14-3-3 as phosphorylated peptides, with high affinity for all 7 mammalian isoforms of 14-3-3 PMID 10493820. Commercial source of peptide [https://www.enzo.com/product/r18-peptide/ Enzo #BML-P214-0001].

Difopein is a construct with two R18 monomers in a single 62 amino acid peptide PMID 11577088. Commercial source of peptide: [https://www.tocris.com/products/difopein_2145 Tocris #1245]

R18 Sequence:

Pro-His-Cys-Val-Pro-Arg-Asp-Leu-Ser-Trp-Leu-Asp-Leu-Glu-Ala- Asn-Met-Cys-Leu-Pro-OH

PHCVPRDLSWLDLEANMCLP

Difopein sequence (with individual R18 monomers in parentheses):

SADGA (PHCVP RDLSW LDLEA NMCLP) GAAGL DSADG A(PHCV PRDLS WLDLE ANMCL P) GAAG LE

C54 (consisting of the carboyl-terminal 54-amino acid region of theHMG-box binding protein Ste11p ) is another 14-3-3 inhibitor that is structurally unrelated to R18/difopein. The C54 region permits sequestration of Ste11p in the cytoplasm to inhibit nuclear localization PMID 12697825.

==Thy-1 Promoter==

PMID 11086982

==YFP==

YFP is 239 amino acids long (717 bp) according to plasmid map of Invitrogen [https://www.thermofisher.com/order/catalog/product/V35820 Vivid ColorsTM pcDNATM/6.2 N-terminal EmGFP/YFP-DEST vectors] see p, 28 of the manual. Difopein is 62 amino acids long (186 bp), so total YFP-difopein fusion protein should be ~ 301 amino acids (903 bp).

== 14-3-3 FKO papers==
Vogt, Peggy, [https://diginole.lib.fsu.edu/islandora/object/fsu:204445 "Exploring the Function of 14-3-3 Proteins in Neurodegenerative Disease"] (2011). Honors Theses. Paper 42.

C. Sun, H. Qiao, Q. Zhou, Y. Wang, Y. Wu, Y. Zhou, et al., Modulation of GluK2a Subunit-containing Kainate Receptors by 14-3-3 Proteins, J Biol Chem. 288 (2013) 24676–24690. PMID 23861400

Qiao H, Foote M, Graham K, Wu Y, Zhou Y. 14-3-3 proteins are required for hippocampal long-term potentiation and associative learning and memory. J Neurosci. 34(2014):4801-8. PMID 24695700

==Antisera for IP Experiments==
anti-pan-14-3-3 (K-19) , rabbit polyclonal, Santa Cruz #sc-629, 200 ug/1 ml, $279 [https://www.scbt.com/p/pan-14-3-3-antibody-k-19 datasheet]

anti-HDAC4 (H-92), rabbit polyclonal, Santa Cruz #sc-11418, 200 ug/1 ml, $279 [https://www.scbt.com/p/hdac4-antibody-h-92 datasheet]

anti-Torc1 (C71D11), rabbit mAb, Cell Signaling #2587 $225 [https://www.cellsignal.com/products/primary-antibodies/torc1-crtc1-c71d11-rabbit-mab/2587 datasheet]

Water Maze

2024-04-10T17:19:01Z

Chuck: Fix perm redirect for Bioseb

Reference site: https://web.archive.org/web/20180317100212/http://watermaze.com/

==FSU setup for Mice==

===Currently have:===

Wading pool (approximate 2m diameter x 20 cm deep, dark blue)

Tripod and stand for video camera (could replace with ladder, or with ceiling mount)

Sony Digitial8 Camcorder

Heat lamps

Pump to empty pool

===Need to Get===
Platform for mice

White tempora or latex for making water opaque

geometric shapes or posters on walls to serve as visual cues

Heater for water

insulation to cover pool to prevent heat loss

drainage system (e.g. a spigot on side)

===Nice to get in future===

Ceiling mount for video camera or mount mirror on ceiling

Realtime tracking software

Table to get water maze off the floor.

==Sources of Water Mazes and Equipment==

[https://www.any-maze.com/mazes/water-maze/ ANY-maze] $1195 for 6-foot diameter, metal, with wheels and side drain

[https://sandiegoinstruments.com/product/water-maze/ SD Instruments] 6ft x 30" deep, polyethylene blue or white, drain kit

[https://hvsimage.com/information/3rd_party_pools.htm List of suppliers] HVS Image has a list of places that sell galvanized or polyethylene tanks

[https://bioseb.com/en/learningmemory-attention-addiction/1323-circular-pool.html Bioseb] French company

[https://www.tse-systems.com/products/behavior/maze-systems/water-maze.htm TSE Systems]

[https://muromachi.com/en/ Muromachi] Japanese company, I think they sell their own water maze pool.

==Aquaculture Tanks==

[http://www.solar-components.com/aqua.htm Solar Components] Transparent fiberglass tanks

[https://dolphinfiberglass.com Dolphin Fiberglass Products] located in Homestead, FL . They list 6' by 2' round tanks [https://www.aquaculturetanks.com/pricelist2.gif here]. Note that you can get feet put on the tanks. (see their picture catalog].

[https://web.archive.org/web/20090118141101/http://aquaticeco.com:80/categories/Tanks--Liners/97/0 Aquatic Eco-Systems] (now [https://pentairaes.com Pentair]) Located in Apopka, FL. Large selection.

[https://www.plastic-mart.com/water-tanks/plastic-stock-tanks-water-troughs/ Plastic-Mart] Livestock watering tubs.

==Tracking Software==

[https://web.archive.org/web/20180317100212/http://watermaze.com/ Watermaze Software (Edinburgh)] also sold by [https://web.archive.org/web/20220810202835/https://www.coulbourn.com/category_s/291.htm Coulbourn Instruments]

[https://actimetrics.com Actimetrics]

[https://hvsimage.com/ HVS Image]

[http://www.biobserve.com/products/viewer/plugins/watermaze.html?gclid=CLDQwIDU144CFRVBgAodVgbo6A Biobserve]

[https://www.viewpoint.fr/product/rodent/rodents-behavior-monitoring/videotrack Viewpoint]

[https://muromachi.com/archives/item/191 DV-Track] from Muromachi

[[Tracker]] from the [https://houptlab.org/ Houpt Lab]

[[Category:Magnetic_Fields]]
[[Category:Laboratory]]

In Situ Hybridization

2024-03-05T12:34:10Z

Chuck: Follow redirect from Perkin to new Revvity

In situ hybridization visualizes mRNA expression in intact tissue sections thus providing anatomical localization. Because it employs DNA or RNA probes complimentary to specific mRNA sequences, in situ hybridization visualizes only the product of the target gene and not related gene products; it thus can provide greater specificity than immunohistochemistry, which may visualize proteins that have a common epitope but are otherwise unrelated to the target protein.

A significant advantage of doing in situ hybridization on free-floating tissue sections (as opposed to slide-mounted sections) is that sections from different rats may be hybridized at the same time within the same vial, and thus under identical conditions. Tissue sections from different rats are distinguished by labeling the sections during cutting with notches or punctures, so that they may be sorted by individual after hybridization. Because rats from control and experimental groups are processed under identical conditions, quantitative comparisons are more reliable.

==Protocol==

==Reagents==

''prices as of 2011-11''

AG 501-X8 Resin (Mixed bed resin for deionizing formamide), 100g, BioRad #143-7424, $323

[https://www.revvity.com/product/datp-a-thio-35s-neg034h250uc dATP-alphaS35], (250 uCi vial = 20 ul) [https://www.perkinelmer.com/corporate/contactus Perkin Elmer] #NEG034H250UC $172
:made first Tuesday of every month

Denhardt's Solution 50x, 100 ml, Invitrogen # 750018 $122
:(made from PVP (polyvinyl pyrrolidone) 40 & Ficoll Type 400)

DEPC (diethylpyrocarbonate), Sigma #D-5758-50 ml $203

Dextran Sulfate sodium salt, Sigma #D-8906-50 g, $143

DTT (dithiothreitol) (aka Cleland's reagent) Ultrapure, 5 g, Invitrogen #15508013 $102.00

Formamide Ultrapure, 500g bottle, Invitrogen #15515026 $97

'''For cDNA ISH:''' High Prime DNA Labeling Kit, 50 reactions, Roche Applied Science, #11585584001 $333

'''For Oligo ISH:''' Terminal Transferase Tail-Labeling Kit,

ProbeQuant G-50 micro spin columns, 50 pack, GE Healthcare, # 28-9034-08 $199

Salmon Sperm DNA 10 mg/ml, 10 x 1 ml tubes, Invitrogen #AM9680 $198

SSC Buffer 20x Ultrapure, 1L bottle, Invitrogen #15557-044 $34

== Solutions==
'''DEPC-Treated Water'''
*1 ml of DEPC per 1 L ddH2O
*Squirt DEPC forcefully into water.
*Cover and shake vigorously.
*(Some protocols recommend sitting overnight.)
*Autoclave.

'''20x SSC'''
''(We now purchase this from Invitrogen).
*400 ml DEPC-H2O
*87.65 g NaCl
*441 g Citric Acid
*Bring to pH 7.0
*Bring volume to 500 ml with DEPC-H2O
*Autoclave. (make sure volume back to 500 ml)

Hybridization of DNA or RNA probes to target RNA is dependent on salt concentration (Na+ neutralizes the PO3- charges on the DNA/RNA backbones.) SSC is an old-time decoagulant that was a common buffer in early biochemical labs. The hybridization conditions are optimized for 2x SSC.

'''Deionized Formamide:'''
*Mix 50 ml formamide and 5 g of mixed bed ion exchange resion (Bio-Rad AG 501-X8, 20-50 mesh).
*Stir 30 min at room temperature.
*Filter twice thru Whatman #1 filter paper
*Store at -20C in 15 ml tubes covered with aluminum foil.

Formamide denatures nucleic acids (lowers effective Tm). Because the breakdown products of formamide degrade nucleic acids, for sensitive applications formamide should be deionized by treatment with a mixed-bed ion-exchange resin.

'''5x TED'''
*250 mM Tris, pH 7.4, 25 mM EDTA, 50% Dextran Sulphate
*Weigh 3.05 g Trizma Base
*Weigh 0.93 g EDTA
*Add ~35-40 ml DEPC-H2O
*Bring to pH 7.4 with HCL
*Add 50 g Deteran Sulfate slowly, while heating slowly to boil
*Bring volume to 100 ml with DEPC-H2O
*Store at 4C in 15 ml tubes covered with aluminum foil

Dextran is corn starch; serves as a thickener to increase effective concentration of all the other reagents.

'''50x Denhardt's Solution'''
''(We now purchase this from Invitrogen).
*1% Ficoll, 1% PVP, 1% BSA
*1 g Ficoll, 1 g PVP, 1 g BSA in 100 ml DEPC-H2O.
*Filter.
*Store in 1 ml tubes at -20C.

Denhardt's is a mixture of high molecular weight polymers that blocks non-specific binding sites

'''Herring/Salmon Sperm DNA'''
''(We now purchase this from Invitrogen).
*Dissolve 10 mg salmon or herring sperm DNA per 1 ml DEPC-H2O
*Extraction with phenol and phenol-chloroform optional.
*Sonicate for a few minutes until solution is no longer viscous (~3 min)
*An OD260 to determine exact concentration of DNA is also optional.
*Boil solution for 10 min
*Cool on ice
*Aliquot at 800 ul and store at -20C

Random DNA serves as blocker of nonspecific DNA binding

'''DTT (dithiothreitol)'''
Aka Cleland's reagent; prevents oxidation of thiol groups and breaks down disulfide bonds.

==Buffer Amounts==

* Denature salmon sperm by boiling for 10 minutes.
* Put DTT in foil-covered scintillation vial.
* Add SSC, formamide, TED, salmon sperm, & Denharts solution.
* Vortex. Keep heated at 55° C on heater block until use.

<tab class="wikitable" sep="tab" border = "1" cellspacing="3" cellpadding = "3" head = top>
10 ml - - - 8 ml - - - 5 ml - - - 4 ml - - - 3 ml - - - 2 ml - -
150 mg DTT 120 mg DTT 75 mg DTT 60 mg DTT 45 mg DTT 30 mg DTT
1.0 ml SSC 20x 800 ml SSC 20x 500 µl SSC 20x 400 µl SSC 20x 300 µl SSC 20x 200 µl SSC 20x
6.0 ml Formamide 4.8 ml Formamide 3.0 ml Formamide 2.4 ml Formamide 1.8 ml Formamide 1.2 ml Formamide
2.0 ml TED 5x 1.6 ml TED 5x 1 ml TED 5x 800 µl TED 5x 600 µl TED 5x 400 µl TED 5x
1.6 ml Salmon Sperm 1.28 ml Salmon Sperm 800 µl Salmon Sperm 640 µl Salmon Sperm 480 µl Salmon Sperm 320 µl Salmon Sperm
800 µl Denharts 50x 640 µl Denharts 50x 400 µl Denharts 50x 320 µl Denharts 50x 240 µl Denharts 50x 160 µl Denharts 50x
</tab>

==Methods Section==

===cDNA ISH===

Reference: From Rivera et al, 2009, PMID 19168037

Prepare cDNA probes by [[cDNA Random Priming]].

Free-floating tissue sections were collected into 20 ml glass scintillation vials containing ice-cold 2 X SSC (0.3M NaCl, 0.03M sodium citrate) for in situ hybridization. The SSC in each vial was pipetted off, and sections were then suspended in 1 ml of warm prehybridization buffer (50% formamide, 10% dextran sulfate, 2 X SSC, 1X Denhardt’s solution, 50mM dithiothreitol, 0.5 mg/mL denatured salmon sperm DNA) and placed in a 48°C water bath. Two h later, 35S-dCTP-labeled cDNA probes (10 x 10^6 CPM/vial) were added to the vials and hybridized overnight at 48°C. After overnight hybridization, the sections were washed at 15-min intervals in decreasing concentrations of SSC (2X, 2X, 1X, 0.5X, 0.25X, 0.125X, 0.125X) at 48°C. After washes, the tissue sections were stored in 0.1M phosphate buffer at 4°C and then mounted on gelatin-subbed slides, air-dried, and apposed to Kodak Biomax autoradiographic film (Eastman Kodak Co., NY,

===Riboprobe ISH===

Reference: Kwon, B.S., M. Goltz, and T.A. Houpt. Expression of AP-1 family transcription factors in the amygdala during conditioned taste aversion learning: role for Fra-2. Brain Res. 1207 (2008) 128-41. PMID 18374904. PMCID PMC2756721.

For in situ hybridization, antisense RNA probes of [c-fos, fra-2, c-jun, and junD] cDNAs were made by in vitro transcription. Amplified cDNAs from RT-PCR were inserted into pCRII-TOPO cloning vectors (Invitrogen, Carlsbad, CA). The cloning vectors containing each cDNA were linearized by restriction enzymes. The linearized plasmids were purified by QIAquick spin column (Qiagen, Valencia, CA), and the MAXIscript kit (Ambion, Austin, TX) was used for in vitro transcription. The linearized plasmid template (1 µg), 2µl of 10X transcription buffer, 1µlof ATP, CTP, and GTP (each 10 mM), 5µl of 35S-labeled UTP (20 mci/ml) (Amersham, UK) 2µl of T7 or SP6 RNA polymerase, and RNase-free H20 were mixed in a total reaction volume of 20 µl. The mixture was incubated at 37 ºC; after 30 min, DNase I (1 µl) was added and the incubation continued for another 15 min. After stopping the reaction by the addition of EDTA (1 µl, 500 mM), the probe solution was purified through ProbeQuantTM G-50 spin columns (Amersham, Piscataway, NJ).

Forty micron free floating sections were cut on a freezing, sliding microtome and transferred into 20-ml glass scintillation vials containing 0.15 M NaCl, 0.015 M sodium citrate (2xSSC) buffer. Sections were prehybridization at 55ºC for 2-3 h in 1 ml per vial of hyrbidization buffer (50% formamide, 2xSSC, 10% dextran sulfate, 0.7% Ficoll, 0.7% polyvinylpyrrolidone, 0.7% bovine serum albumin (BSA), 85 mM dithiothreitol (DTT) and 1.4 mg/ml of yeast transfer RNA). Sections were hybridized at 55ºC for 18 h with heat-denatured 35S-labeled or biotinylated antisense RNA probes. Sections were then washed sequentially in 2xSSC, 2xSSC, 1xSSC, 0.5xSSC, 0.25xSSC, 0.125xSSC, 0.125xSSC at 55ºC for 15 min each. To reduce background, tissue sections were incubated with RNase A (30 ug/ml) both before and after mounting on gelatin coated slides. Finally, slides were washed sequentially in 2xSSC/50% formamide/0.1% β-mercaptoethanol at 53ºC for 15 min, 0.1xSSC/1% β-mercaptoethanol at 53ºC for 30 min, 50% ethanol/0.3 M NH4OAC at RT for 3 min, 85% ethanol/0.3 M NH4OAC at RT for 3 min, 100% ethanol at RT for 3 min.
Radiolabeled tissue sections on slides were apposed to Biomax MR film. Biotin-labeled slides were processed for immunohistochemistry with anti-biotin antiserum (Roche) and fluorescently-tagged secondary antibodies (Vector) for visualization by fluorescent microscopy.

===Oligo ISH===

Reference: Swart, I., J.M. Overton, and T.A. Houpt. Hypothalamic NPY, AGRP and POMC mRNA responses to leptin and refeeding in mice. Am. J. Physiol. 283 (2002) R1020-R1026. PMID 12376393.

Prepare probes by [[Oligo Tail Labeling]].

Coronal 40 micron sections were cut on a sliding freezing microtome through the rostral caudal extent of the hypothalamus. Alternate sections were placed into ice-cold 2x SSC (SSC = 0.15M NaCl/0.015M Na Citrate). Free floating tissue sections were prehybridized in glass vials in 1ml of 60% formamide, 0.02 M Tris pH7.4, 1mM EDTA, 10% dextran sulfate, 0.8% Ficoll, 0.8% PVP, 0.8% BSA, 2x SSC, 0.1M dithiothreitol, and 1.6 mg/mL herring sperm DNA for 2h at 37°C. After 2h prehybridization, radiolabeled probe was added (~1.0 x 107 cpm/vial) and incubated for 16-20h at 37°C. Hybridization was performed with either tail labeled prepro NPY (ppNPY) antisense oligonucleotide (bases 59-88), agouti-related protein (AGRP) antisense oligonucleotide (bases 1-45) or proopiomelanocortin (POMC) antisense oligonucleotide (bases 482-517). The oligonucleotides were tail-labeled to approximately equal specific activities (~10^7 cpm/100ng) with 35S-dATP by terminal transferase reaction (Roche), Sections were then sequentially rinsed in 2x SSC, 1x SSC and 0.5x SSC for 10 minutes at 37°C. The tissue sections were mounted from 0.05M sodium phosphate onto gelatin- coated slides, air dried, and exposed to autoradiographic film (β-max, Amersham) for 2-3 days. Tissue sections from different groups were hybridized in parallel and exposed to film together to ensure that in situ hybridization was carried out on representative members of each experimental group at the same time under identical conditions, allowing direct comparison of mRNA expression.

===Quantification of ISH===

Reference:

For ISH results, pixel density is quantitated from the autoradiographic films using a custom software program (MindsEye, T. Houpt). Films were digitized through a Zeiss Stemi2000C dissecting scope with a Fostec flat fiberoptic light source; light levels are adjusted to standardize gray levels of film background across ISH experiments. Images werw captured in a 10 mm x 7.5 mm frame using a scientific-grade CCD camera (Dage MTI DC330E) [UPDATE CAMERA] and frame-capture board (Scion CG-7). The region of interest (i.e. the arcuate nucleus) is delineated automatically by an algorithm that finds clusters of 10 or more contiguous pixels with an intensity 2 standard deviations above the average tissue background (mRNA-positive pixels). This algorithm works particularly well on structures with relatively discrete patterns of gene expression. Arbitrary units of mRNA expression are then derived by summing the intensities of all the mRNA-positive pixels, and subtracting the average tissue background value. For each rat and probe, average pixel densities were obtained from 3-5 brain sections. Individual mean values for each region were then averaged across rats within experimental groups.

==Interpretation of ISH results==

'''Changes in area vs. density of autoradiographic in situ hybridization signal'''

In autoradiographic ISH, hybridization is measured as the optical density of film exposed to tissue hybridized with a radioactive probe. Both area and density (i.e. darkness of the exposed film) of the hybridization signal are presumed to reflect mRNA levels in the tissue.

Autoradiographic ISH assumes that there is a threshold of detection for measuring a hybridization signal above background. (Typically, we chose 2 standard deviations above the average background optical density of the film and nonhybridizated tissue as an objective threshold.). Thus, a tissue must express a certain minimum amount of mRNA in order for a hybridization signal to be visible on the film. Furthermore, if above the detection threshold, the signal is assumed to be roughly linear with increasing amounts of mRNA above threshold.

Given these assumptions, we interpret the variables as follows: "Area" represents the tissue area (i.e. number of cells) that express mRNA above the threshold of detection, within the specificed region. “Density” represents the amount of mRNA per unit area (i.e. mRNA per cell) within the specificed region. The total amount of RNA expressed within the specified region is the product of the two values (area X density).

Changes in either area or density represent changes in mRNA levels. Differential results for area and density are a consequence of ISH methodology. An increase in signal area after treatment would imply that some cells in the specified area express the mRNA below the threshold for detection in the control condition, and that the treatment increased mRNA levels in those cells above the detection threshold. A concomittant increase in signal density would imply a higher level of mRNA expression throughout the region, including those cells that were already above threshold in the control condition. If the signal area is increased but signal density is not increased, this would imply that the cells which expressed detectable levels of mRNA in the control condition did not increase their expression after treatment. The failure to increase mRNA levels in cells that already express the gene could be due either to insensitivity to the treatment or to a “ceiling” of maximal possible expression.

Note that the ceiling or maximal level of expression may vary across regions, even for the same gene product. For example, the MR has a lower and sparser expression of 5HTT and Pet-1 mRNA than the DR under baseline conditions. Thus the dynamic range of MR cells may be lower than cells in the DR, and an increase in expression within the MR may be detected as an increase in area rather than in density. The physiological bases for the heterogenity in baseline and stimulated levels of gene expression within the raphe nuclei is a profound topic, to which this paper makes a small contribution with respect to estrogen effects.

[[Category:Protocols]]

Serine Racemase

2024-01-14T14:39:12Z

Chuck: Update IUPAC link because it has moved to its own subdomain

Serine Racemase is the enzyme that interconverts between the two enantiomers of serine, D-serine and L-serine. (the nomenclature for chiral amino acids is well explained on the [https://iupac.qmul.ac.uk/AminoAcid/AA3t5.html IUPAC site].

=Regulation of SR gene expression=

There are three approaches to examining changes in SR expression in vivo: by pharmacological manipulaton, by characterization across development, and by pathological conditions.

==Pharmacological manipulations==

MK-801: Hasimoto et al. PMID 17109841 used qRT-PCR and HPLC to detect changes in SR and DAAO in adult rat brain after acute or chronic injections of MK-801, the non-competitive NR antagonist. Changes in mRNA were only seen at 400 ug/kg and above, Very large changes (5x - 10x at 1 h, still elevated 2-3x at 4 h) were seen in all brain regions examined (striatum hippocampys, cortex, diencephalon, midbrain, pons/medulla and cerebellum (although absolute levels were lower in more caudal brain regions.) DAAO mRNA levels were decreased by MK-801 at 1 h, but increased at 4 h (and absolute levels of DAAO mRNA were high in more caudal brain regions.) DAAO showed a more dose-dependent response. Chronic MK-801 (400 ug/kg for 14 days) also increased SR mRNA (2x in forebrain) but did not affect DAAO expression. There is little discussion of the possible mechanisms, aside from pointing out that MK-801 can induce c-fos and there is an AP-1 element in the SR promoter, and a CRE element in the DAAO promoter.

MK-801: Yoshikawa et al. PMID 15337321 using qt-PCR showed an increase in SR mRNA at 2-6h after systemic administration of MK-801 (0.4 mg/kg). Very nice description of qRT-PCR controls and calibration.

Ketamine Takeyama et al. PMID 16716293 using qRT-PCR showed an increase in SR mRNA and DAAO at 4 h (but not 2 h or 6h) after systemic ketamine (50 mg/kg) A dose response curve at the 4 h time point showed a dose dependent increse in SR and DAAO at 50 and 100 mg/kg

Morphine Yoshikawa et al. PMID 16256980 using qRT-PCR found a small increase(25-50%) in SR mRNA and DAAO at 4 h (but not 2 h or 6 h) after systemic morphine ((20 mg/kg, i.p.) A dose response curve at the 4 h time point showed no change after 10 mg/kg, but a dose dependent increase in sR and DAAO at 20 (2x) and 40 mg/kg (5x). Again, discussion focussed on morphine inducing AP-1 and CREB transcription factors.

Beta-Amyloid Wu et al. PMID 15285800

inflammatory stimuli Wu and Barger PMID 15681805

==Developmental changes==

Aging Mothet et al. PMID 16842499 found a decrease in d-serine and serine racemase expression in the aged hippocampus. (Don't have access to the original article)

Postnatal Puyal et al PMID 16739185 found low levels of d-serine (by chemiluminescent assay) at PO, then a surge of d-serine at P7 that declined until a very low level at P45. Western blot analysis of SR and DAAO showed that SR declined from birth to P45, while DAAO increased from P14 and later. Some nice colocalization by fluroescent double-labeling showed that d-serine was mostly in glial cells at P0-P21, but after P28 the d-serine was mostly in neurons. No discussion of what regulates SR or DAAO expression.

Postnatal Wang and Zhu PMID 14531937

==Pathological conditions==

ischemia Wang and Zhu PMID 15066209

schizophrenia

alzheimers Wu et al. PMID 15285800

=Probe for in situ hybridization=

Primer sequences taken from Yoshikawa et al., PMID 16973158

Rat serine racemase. Genbank Ascension # NM_198757

PCR product Length: 295 bases (+22 bases for T7 promoter]

Forward Primer 664 to 683
:ATT GCA AGA AAC TGG CCA TC

Reverse Primer [with T7 promoter] 958 to 939
:[CTT AAT ACG ACT CAC TAT AGG G] TC AGC AGC GTA CAC CTT CAC

Amplification conditions (from Yoshikawa et al, PMID 15337321):
:10-min predenaturation at 95 °C
:15-s denaturation at 95 °C.
:20-s at 58 °C for serine racemase
:followed by a 20-s extension at 72 °C.

=Probes for real time PCR=

Primer sequences taken from Yoshikawa et al. 2004, PMID 15337321 (did not use BioRad system)

Rat [actually mouse] serine racemase. Genbank Ascension # NM013761

Forward (bases 784-803)
:CCT GCA GTG ATA GCT GGA CA

Backward (bases 1052-1033)
:AAG CCA ATG CTG GAT TTG AC

Primer sequences taken from Yoshikawa et al. 2006, PMID 16973158 (did not use BioRad system)

Rat serine racemase mRNA (accession number NM198757)

forward primer 664 - 683
:ATT GCA AGA AAC TGG CCA TC

reverse primer, 958-939
:TCA GCA GCG TAC ACC TTC AC

[[Category:Taste_Aversion]]

Water Maze

2023-12-12T15:17:58Z

Chuck: Fix water tank perm redirect

Reference site: https://web.archive.org/web/20180317100212/http://watermaze.com/

==FSU setup for Mice==

===Currently have:===

Wading pool (approximate 2m diameter x 20 cm deep, dark blue)

Tripod and stand for video camera (could replace with ladder, or with ceiling mount)

Sony Digitial8 Camcorder

Heat lamps

Pump to empty pool

===Need to Get===
Platform for mice

White tempora or latex for making water opaque

geometric shapes or posters on walls to serve as visual cues

Heater for water

insulation to cover pool to prevent heat loss

drainage system (e.g. a spigot on side)

===Nice to get in future===

Ceiling mount for video camera or mount mirror on ceiling

Realtime tracking software

Table to get water maze off the floor.

==Sources of Water Mazes and Equipment==

[https://www.any-maze.com/mazes/water-maze/ ANY-maze] $1195 for 6-foot diameter, metal, with wheels and side drain

[https://sandiegoinstruments.com/product/water-maze/ SD Instruments] 6ft x 30" deep, polyethylene blue or white, drain kit

[https://hvsimage.com/information/3rd_party_pools.htm List of suppliers] HVS Image has a list of places that sell galvanized or polyethylene tanks

[https://www.bioseb.com/en/learningmemory-attention-addiction/1323-circular-pool.html Bioseb] French company

[https://www.tse-systems.com/products/behavior/maze-systems/water-maze.htm TSE Systems]

[https://muromachi.com/en/ Muromachi] Japanese company, I think they sell their own water maze pool.

==Aquaculture Tanks==

[http://www.solar-components.com/aqua.htm Solar Components] Transparent fiberglass tanks

[https://dolphinfiberglass.com Dolphin Fiberglass Products] located in Homestead, FL . They list 6' by 2' round tanks [https://www.aquaculturetanks.com/pricelist2.gif here]. Note that you can get feet put on the tanks. (see their picture catalog].

[https://web.archive.org/web/20090118141101/http://aquaticeco.com:80/categories/Tanks--Liners/97/0 Aquatic Eco-Systems] (now [https://pentairaes.com Pentair]) Located in Apopka, FL. Large selection.

[https://www.plastic-mart.com/water-tanks/plastic-stock-tanks-water-troughs/ Plastic-Mart] Livestock watering tubs.

==Tracking Software==

[https://web.archive.org/web/20180317100212/http://watermaze.com/ Watermaze Software (Edinburgh)] also sold by [https://web.archive.org/web/20220810202835/https://www.coulbourn.com/category_s/291.htm Coulbourn Instruments]

[https://actimetrics.com Actimetrics]

[https://hvsimage.com/ HVS Image]

[http://www.biobserve.com/products/viewer/plugins/watermaze.html?gclid=CLDQwIDU144CFRVBgAodVgbo6A Biobserve]

[https://www.viewpoint.fr/product/rodent/rodents-behavior-monitoring/videotrack Viewpoint]

[https://muromachi.com/archives/item/191 DV-Track] from Muromachi

[[Tracker]] from the [https://houptlab.org/ Houpt Lab]

[[Category:Magnetic_Fields]]
[[Category:Laboratory]]

Selenium

2023-11-10T02:29:24Z

Chuck: Replaced DOD Chem Warfare link with archive link

Selenium is an essential micronutrient. Recently, a specific selenium salt, sodium selenate, was discovered to be a specific enhancer of the enzyme protein phosphatase 2A (PP2A). PP2A removes phosphate groups from target proteins, including tau, a protein implicated in Alzheimer’s disease Corcoran 2010a PMID 20537899, van Eersel 2010 PMID 20643941, and many other proteins implicated in the control of cancer (Corcoran 2010b PMID 20648008).

Because phosphatases like PP2A remove phosphate groups that activate other proteins, PP2A can be considered a “brake” on the activity of cells, including neurons involved in learning and memory. We have previously shown that inhibiting phosphatase PP2A with the non-specific blocker okadaic acid increased the strength of learned conditioned taste aversions in rats. In other words, blocking PP2A “cut the brakes” on the learning mechanism, causing the rats to acquire a stronger memory of a toxic fluid (saccharin paired with lithium chloride).

Because sodium selenate can act as an enhancer of PP2A, we hypothesize that administering sodium selenate before a conditioning trial will decrease the strength of conditioned taste aversion learning (i.e., the “brakes” will be enhanced, thus diminishing the learning.)

==Sodium Selenate==

[https://www.sigmaaldrich.com/US/en/product/sigma/s8295 Sigma-Aldrich S8295-10G] $56

CAS Number: 13410-01-0

Linear Formula: Na2SeO4

Molecular Weight: 188.94

EC Number: 236-501-8

MDL number: MFCD00003490

PubChem Substance ID: [https://pubchem.ncbi.nlm.nih.gov/substance/24899787 24899787]

'''Tonicity of Systemic Injection'''

Osmolarity of Na2Se04 at 12 mg/ml (63 mM) = 189 mOsm

So Na2Se04 at 12 mg/ml (63 mM), NaCl at 3.2 mg/ml (55mM) = 300 mOsm

'''Calculation of suggested i.c.v. injection concentration.'''

Assuming a 500 g rat, then systemic dose is 0.25 mg ( 250 µg). A central dose might be 1/100th of the system dose -> 2.5 µg.

Volume of i.c.v injection would be 5 µl; site specific injection 0.5 µl

So central dose would be 2.5 µg / 5 µl = 0.5 µg/ 1 µl = 0.5 g / L.

MW of sodium selenate is 188.94, so 0.5 g = 2.65 mmole

so central injection dose is 5 µl at 2.65 mM.

(Osmolarity is sufficiently low that can be diluted with saline).

==Toxicity of Selenate==

Selenium is an essential micronutrient and is naturally found a wide variety of food stuffs. As an antioxidant, it is frequently used to treat, e.g., heavy metal toxicosis or liver disease. The recommended dietary intake for adults is 55 micrograms/day, and selenium supplements of 200-300 micrograms/day have been recommended for prevention of several types of cancer. High doses of 1.5 to 5 mg/ day are associated with adverse effects (Brozmanova 2010, Reid 2004). The chemical form of selenium also contributes to toxicity. The form we will use, sodium selenate (Na2Se04), is well-tolerated in human trials (Corcoran 2010b).

Corcoran (2010a) administered sodium selenate to mice acutely at 12 mg/kg, and chronically at ~192 mg/kg per day in drinking water, and did not report any aversive or toxic effects on the mice. van Eersel (2010) administered sodium selenate to mice chrionically at ~ 1.9 mg/kg per day in drinking water, and also did not report any aversive or toxic effects.

Abdo (1994) reported on the effects of administering sodium selenate in the drinking water for 13 weeks. It was estimated that the "no-observed adverse level" in rat was 0.4 mg/kg per day of sodium selenate for 13 weeks. Doses of 0.6 mg/kg or 1.1 mg/kg per day for 13 weeks caused changes in mortality, body weight depression, decreased water consumption, and renal papillary lesions. However, these were chronic studies so that rats received a total dose of 54.6 mg/kg or 100.1 mg/kg sodium selenate over 13 weeks.

Aasif Mandvi ran a [https://www.cc.com/video/jucn2a/the-daily-show-with-jon-stewart-a-simple-plot story] on selenium pollution of Idaho rivers as a consequence of phosphate mining.

==Selenium Ingestion and Aversions==

Selenium is an essential micronutrient. The mammalian selenoproteome consists of some 2 dozen selenocysteine-containing proteins (24 in rodents, 25 in human) including the glutathione peroxidase, thioredoxin reductase and iodothyronine deiodinase enzymes [PMID 12775843]. However, at doses not much higher than the dietary requirement, selenium is also toxic [PMID 3527390]. Selenium toxicity is due to the generation of superoxide and other reactive oxygen species, the oxidation of thiols, and by substituting for sulfur in methionine to form selenomethione which then may be incorporated into many sulfur containing proteins [PMID 11879936].

Reduced intake and avoidance of toxic diets containing selenium compounds has been demonstrated in many species. Because selenium is concentrated by certain species of plants in selenium-rich geographies, selenosis is a potential hazard for livestock and native herbivores. Waste from mining or agricultural run-off can also introduce selenium into the environment and hence into the food-chain. It has therefore been of interest to determine whether species can avoid selenium-rich food sources due to an aversive taste or odor of selenium compounds, or acute toxic effects, or learned food aversions. Aphids [PMID 17831208, JSTOR 1514562], crickets and grasshoppers [PMID 17635224], southern armyworms [PMID 10467057] mallard ducks [Heinz 1990], owls [Wiemeyer 1996], prairie dogs [PMID 21628258], sheep [Pfister 2010, PMID 3527390], and cattle [PMID 3527390] have been shown to reduce intake of selenium-containing foods, or show reduced preference for selenium-containing foods over control diets.

In laboratory studies, rats show a preference for control or low selenium-diets over high selenium diets [PMID 17788901][Franke and Potter 1935]. Consistent with the effects of other selenium compounds, selenate adulteration also causes a reduction of food [Franke and Moxon 1937] [Smith Stohlman Lillie 1937] or water intake [PMID 6053743, PMID 1255264] Acute injection of selenate can also reduce food intake and body weight gain [PMID 2609019]

Only a few of these studies (e.g. [Pfister 2010, PMID 3527390, Heinz & Sanderson 1990] ) have determined if animals were responding to an acute perception of selenium compounds, or if the animals used food-associated cues, to avoid consumption, after acquiring a selenium-induced conditioned food aversion. Selenium absorbing plants may themselves have salient taste or odor: for example, Provenza et al. have demonstrated that the odor of Astragalus bisulcatus, a sulfur-containing selenium-absorbing plant, can serve as a CS that reduced preference for CS+barley-straw after pairing with oral-intubation of LiCl. [Oikos 88(2000)424-432.] Selenium compounds may also present distinctive cues, e.g., the volatile dimethyldiselenide, a major metabolite of selenite and selenate, has a pungent garlic odor to humans, that may be innately aversive or serve as an indicative CS in learned selenium aversions.

==Government Documents on Selenium Safety==

National Toxicology Program / NIEHS: [https://ntp.niehs.nih.gov/sites/default/files/ntp/htdocs/st_rpts/tox038.pdf NTP Technical Report on Toxicity Studies of Sodium Selenate and Sodium Selenite] (1994)

CDC/NIOSH: [https://www.cdc.gov/niosh/idlh/7782492.html Selenium compounds (as Se)] from NIOSH Documentation for immediately dangerous to life or health concentrations (IDLHs)

WHO: [https://inchem.org/documents/ehc/ehc/ehc58.htm Environmental Health Criteria 58: Selenium] (1987) from International Programme on Chemical Safety

HHS: [https://www.atsdr.cdc.gov/ToxProfiles/tp92.pdf Toxicological Profile for Selenium] (2003)

Agency for Toxic Substances and Disease Registry: [https://wwwn.cdc.gov/TSP/ToxFAQs/ToxFAQsDetails.aspx?faqid=152&toxid=28 ToxFAQs for Selenium] (2003)

Agency for Toxic Substances and Disease Registry: [https://www.atsdr.cdc.gov/toxguides/toxguide-92.pdf ToxGuide for Selenium]

Division 9 of NRDC: [https://web.archive.org/web/20220504131238/https://apps.dtic.mil/sti/pdfs/AD0234270.pdf Chemical Warfare Agents and Related Chemical Problems, Parts I-II, Chapter 11] (1946)

==References==

Abdo, K.M. 1994. NTP Technical Report on Toxicity Studies of Sodium Selenate and Sodium Selenite (CAS Nos. 13410-01-0 and 10102-18-8) Administered in Drinking Water to F344/N Rats and B6C3F1 Mice. NIH Publication 9a4-3387. National Toxicology Program. Toxicity Report Series Number 38.

Brozmanova et al., 2010. Selenium: a double-edged sword for defense and offence in cancer, Arch. Toxicol. 84:919–938. PMID 20871980.

Corcoran NM, et al., 2010a. Sodium selenate specifically activates PP2A phosphatase, dephosphorylates tau and reverses memory deficits in an Alzheimer's disease model. J Clin Neurosci. 8:1025-33. PMID 20537899

Corcoran NM et al. 2010b. Open-label, phase I dose-escalation study of sodium selenate, a novel activator of PP2A, in patients with castration-resistant prostate cancer. Br J Cancer. 103:462-8. PMID 20648008

Mandvi, A. A Simple Plot. The Daily Show with Jon Stewart, aired June 14, 2012. https://www.cc.com/video/jucn2a/the-daily-show-with-jon-stewart-a-simple-plot

Reid ME et al. 2004 A report of high-dose selenium supplementation: response and toxicities. J Trace Elem Med Biol 18:69–74 PMID 15487766

van Eersel J et al. 2010. Sodium selenate mitigates tau pathology, neurodegeneration, and functional deficits in Alzheimer's disease models. PNAS 107:13888-93. PMID 20643941

False Color Mapping

2023-11-10T02:24:26Z

Chuck: Fix ImageJ perm redirects

References for constructing False Color Maps for image analysis. I'd like to add tables of RGB values for constructing maps, because those numbers seem to be rarely posted.

==General References==

[https://web.archive.org/web/20190614182049/http://www.efg2.com/Lab/Library/Color/AndComputers.htm Extensive bibliography] of false color schemes.

==Luminance-Based Color Maps==

Based on this work: Stevens, S. S. Matching Functions Between Loudness and Ten Other Continua. Perception and Psychophysics, 1, pp. 5-8, 1966.

IBM on false color maps as used in the IBM Visualization Data Explorer system:
:https://web.archive.org/web/20180308150711/https://research.ibm.com/people/l/lloydt/color/color.HTM
:https://web.archive.org/web/20120928080636/http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm
:https://sites.google.com/site/bernicerogowitz/publications

:[https://www.mathworks.com/matlabcentral/fileexchange/28982-perceptually-improved-colormaps Mathlab perceptual colormaps]

==Discussions of Different Color Maps==

[https://doi.org/10.1109/MCG.2007.46 Rainbow colormap still harmful]

[https://colorbrewer2.org/ A webtool for testing colormaps]

[https://en.wikipedia.org/wiki/HSL_and_HSV HSL and HSV] entry in Wikipedia

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

==Calculation of color maps==

[https://www.fourmilab.ch/documents/specrend/ Colour Rendering of Spectra] for calculating the RGB value of different wavelengths of light. By John Walker, the co-founder of AutoDesk.

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

[http://www.midnightkite.com/color.html Color Science] referenced by Igor for algorithms for calculating rainbow spectra, blackbody, etc.--- in Fortran!

==Collections of color maps==
[https://geography.uoregon.edu/datagraphics/color_scales.htm Color schemes for improved data graphics]. Based on Light, A and P.J. Bartlein (2004) The end of the rainbow? Color schemes for improved data graphics. EOS Transactions of the American Geophysical Union 85(40):385

[https://www.wavemetrics.com/products/igorpro/creatinggraphs/colortab Igor's color tables]

[https://www.nws.noaa.gov/wwamap-prd/faq.php National Weather Service Map Colors] (keys to different phenomena, so not the same as a color map!)

[https://www.ncl.ucar.edu/Document/Graphics/color_tables.shtml National Center for Atmospheric Research (NCAR) Command Language]

[https://www.kennethmoreland.com/color-maps/ Diverging Color Maps]. Based on Kenneth Moreland. "Diverging Color Maps for Scientific Visualization." In Proceedings of the 5th International Symposium on Visual Computing, December 2009.

NIH ImageJ Lookup Tables (".lut" files) are available as a [https://imagej.net/ij/download/luts/luts.zip zip file], although the directory holds a smattering of other LUTs as well. According to the [https://imagej.net/ij/docs/menus/file.html ImageJ documentation], "The raw LUT file must be 768 bytes long and contain 256 reds, 256 blues and 256 greens."

[[Category:MindsEye]]

Raspberry Pi Kiosk

2023-10-24T13:23:54Z

Chuck: Add etymology

[https://languagelog.ldc.upenn.edu/nll/?p=56607 Kiosk Etymology]

==Raspberry Pi Setup==

Modified procedure at [https://pimylifeup.com/raspberry-pi-kiosk/ Raspberry Pi Kiosk using Chromium].

1. Follow default setup of the RPi, including updates.

sudo apt full-upgrade

2. Install <code>unclutter</code> to hide the mouse when idle

sudo apt-get install unclutter

You might need to install <code>sed</code> as well, but that was pre-installed on my RPi.

3. Enable auto-login at

sudo raspi-config

Arrow down to "3 Boot Options" then "B1 Desktop / CLI" then "B4 Desktop Autologin". (I set "B2 Wait for Network at Boot" as well).

4. Create a bash script at <code>/home/pi/kiosk.sh</code>. (Note that "chromium-browser" may have changed name to just "chromium")

<syntaxhighlight lang=shell>
#!/bin/bash
xset s noblank
xset s off
xset -dpms

unclutter -idle 0.5 -root &

sed -i 's/"exited_cleanly":false/"exited_cleanly":true/' /home/pi/.config/chromium/Default/Preferences
sed -i 's/"exit_type":"Crashed"/"exit_type":"Normal"/' /home/pi/.config/chromium/Default/Preferences

/usr/bin/chromium-browser --noerrdialogs --disable-infobars --kiosk https://www.bio.fsu.edu/grad/kiosk/kiosk.html?kiosk=Unit%20I
</syntaxhighlight>

This script:

* disables the screen saver (the xset commands)

* hides the mouse (unclutter)

* deletes any chromium crash notice settings (the sed commands)

* Points the pi to the kiosk.html webpage, with the physical location of the kiosk as a query parameter, eg <code>https://www.bio.fsu.edu/grad/kiosk/kiosk.html?kiosk=King%20Atrium</code>

5. Create a system daemon service file <code>kiosk.service</code>, and copy it to <code>/lib/systemd/system/kiosk.service</code> (don't forget to use <code>sudo</code> to do the copying).

<syntaxhighlight lang=ini>
[Unit]
Description=Chromium Kiosk
Wants=graphical.target
After=graphical.target

[Service]
Environment=DISPLAY=:0
Environment=XAUTHORITY=/home/pi/.Xauthority
Type=simple
ExecStart=/bin/bash /home/pi/kiosk.sh
Restart=on-abort
User=pi
Group=pi

[Install]
WantedBy=graphical.target
</syntaxhighlight>

To copy the service file:

sudo cp kiosk.service /lib/systemd/system/kiosk.service

Enable and start the service:

sudo systemctl enable kiosk.service
sudo systemctl start kiosk.service

6. Reboot the Pi. Note: use <code>sudo reboot</code> to restart the pi from the command line.

To exit kiosk mode, use alt-space bar or alt-F4.

===Chromium update pop-up fix===

In February 2020 a bug in Chromium caused an update popup to appear. The following commands will delay displaying the update popup for 1 year (from [https://www.raspberrypi.org/forums/viewtopic.php?f=63&t=264399&sid=ff83b4376c348fb72379b97eab5be07b&start=25 Raspberrypi.org forum posting] by ShiftPlusOne.

sudo touch /etc/chromium-browser/customizations/01-disable-update-check;echo CHROMIUM_FLAGS=\"\$\{CHROMIUM_FLAGS\} --check-for-update-interval=31536000\" | sudo tee /etc/chromium-browser/customizations/01-disable-update-check

==Network Connectivity==

Get the RPi ethernet MAC address with <code>ifconfig eth0</code>. If the RPi is on a DHCP setup, then you should see the assigned ip with <code>ifconfig -a</code>.

Wireless MAC address is found with <code>ifconfig wlan0</code>.

===Remote Screensharing===

For remote screensharing, follow procedure at [https://pimylifeup.com/raspberry-pi-screen-sharing/ Raspberry Pi Screen Sharing with TightVnc] or [http://4dc5.com/2012/06/12/setting-up-vnc-on-raspberry-pi-for-mac-access/ Setting up VNC on Raspberry Pi for Mac access] and [https://learn.adafruit.com/adafruit-raspberry-pi-lesson-7-remote-control-with-vnc/mac-screen-and-file-sharing Mac Screen and File Sharing].

==Google Docs==

1. Create a number of Google Presentations, with 1 slide per presentation. Only 1 slide per presentation, as the kiosk cycles through multiple '''presentations''', and '''NOT''' the slides within a presentation.

2. Set share permissions on the presentation so that anyone with the link can edit the presentation (or however you want to control editing). Keep this link secret if anyone can edit it.

3. Via "File" -> "Publish to the Web" -> "Publish" button, get the public key for displaying the presentation, which is in the middle of the presentation link, eg:

https://docs.google.com/presentation/d/e/2PACX-1vTKawnqr671l-BcVQP0_dwK2pQDFdtM5RQZwxsF6hLOGZBk4kRIjcTwF6mCP_sknF12ZzEuBlm6aX1i/pub?start=false&loop=false&delayms=3000

(this is a public page which just displays the slide: this link can't be used for editing the presentation).

4. Set up a Google Sheet, with each row listing one of the Google Presentations, with columns for each of your kiosks.

* Column A: "Display" -- the name of each presentation (eg "Upcoming Event", "Public Service Announcement", "This Week's Seminar", etc.) You can link the name of the presenatation with it's shared editable link for convenience if desired, but not required.

* Column B: "URL" -- the public key of each presentation used in the "Publish to the Web" link (just the key, the kiosk page will fill in the rest of the url).

* Columns C-?: "<kiosk name>" -- The query key for each of your kiosks, eg. "Lobby", "Dept Office", etc. The cells in these columns indicate the number of seconds used to display each slide on that particular kiosk. Enter zero seconds to hide the slide from that particular kiosk.

Get the "Publish to Web" key for this Google Sheet via "File" -> "Publish to the Web" -> "Publish" button. This key (which is NOT the same as the shared link for editing) will be used by the website php script to get access to the sheet contents.

==YouTube Video on the Kiosk==

Google Slides makes it pretty easy to embed a YouTube video in a slide. Some tips to get them working on the kiosk:

1. Get the URL of the youtube video you want to display, eg. [https://www.youtube.com/watch?v=B6suC_pPfqg https://www.youtube.com/watch?v=B6suC_pPfqg] . (NB: The "watch?v=" seems to be critical).

2. If you want closed captions /subtitles on the kiosk (because you probably won't want sound playing in the hallway), the captions HAVE TO BE EMBEDDED in the video: there does NOT appear to be way to have the youtube captions/subtitles displayed in the video embedded in a Google Slide without user interaction.

2. In Google Slides, set the Video Format -> Video playback -> check "Autoplay", so that the video plays automatically when the slide presentation starts (not sure if "Mute" needs to be checked)

3. On the Raspberry PI, you need to run the desktop version of Chrome to Preferences (chrome://settings) to Advanced -> Privacy and Security -> Site Settings -> Sound -> Allow -> Add -> add your kiosk site (eg. https://www.bio.fsu.edu/grad/kiosk), to whitelist your site so that videos will autoplay.

IMPORTANT: as far as we can tell, there is NO way to use the command line to set Chrome to autoplay a video inside a Google Slides inside an iframe, which is how the kiosk displays the slides. That means that the kiosk.sh script can't set this up for you, you have to use the desktop version of Chrome "in the real" to make the setting.

==Kiosk Webpage==

1. On the public website, install the following <code>kiosk_slides.php</code> file

<syntaxhighlight lang=php>
<?php
header("Content-type: text/csv");

readfile('https://docs.google.com/spreadsheets/d/e/<google_sheet_key>/pub?gid=0&single=true&output=csv');
</syntaxhighlight>
where <code><google_sheet_key></code> is the "Publish to Web" key for the google sheet listing the slides and display times (keep this a secret if there are shared links to the presentations in this sheet).

2. In the same directory as <code>kiosk_slides.php</code>, create the <code>kiosk.html</code> page. Each Pi kiosk will look at this page, which cycles through the presentations as specified in the google sheet. Note that there is nothing private (ie no secrets) in the webpage itself. Even accessing the <code>kiosk_slides.php</code> file will only display the google sheet contents with the public presenation keys (but not any shared editable links).

<syntaxhighlight lang=html>
<!DOCTYPE html>
<html lang="en">
<head>

<meta http-equiv="refresh" content="3600" />
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="">
<meta name="author" content="">
<title>Pi Kiosk</title>

<script src="https://code.jquery.com/jquery-3.4.1.min.js" crossorigin="anonymous"></script>



</head>

<body>

<style>

html,body {
padding: 0;
margin: 0;
}
iframe {
display: block;
width: 1980px;
height: 1114px;
position:relative;
left:-28px;
top:-4px;
}

.slide {
width:1920px;
height:1080px;
overflow:hidden;
border:solid 1px gray;
}

</style>

<div id="slide0" class="slide">
<div style="text-align:center;margin-top:300px;"><h1>Announcements</h1></div>
</div>
<div id="slide1" class="slide"></div>
<div id="slide2" class="slide"></div>

<div id="slide3" class="slide"></div>
<div id="slide4" class="slide"></div>
<div id="slide5" class="slide"></div>

<div id="slide6" class="slide"></div>
<div id="slide7" class="slide"></div>
<div id="slide8" class="slide"></div>

<div id="slide9" class="slide"></div>
<div id="slide10" class="slide"></div>
<div id="slide11" class="slide"></div>

<div id="slide12" class="slide"></div>
<div id="slide13" class="slide"></div>
<div id="slide14" class="slide"></div>

<script>

/*
look up list of google presentations from a google sheet (retrieved by kiosk_slides.php)
filter the list by our kioskName, taken from ?kiosk=<kioskName> parameter
construct iframe based on "publish to web" url of the google presentation
assign each slide iframe to one of the predefined slide divs (#slide0-#slide<max_slides>)
based on display time in the google sheet, show then hide each slide div in sequence

*/

function getParameterByName(name, url) {
if (!url) {
url = window.location.href;
}
name = name.replace(/[\[\]]/g, "\\$&");
var regex = new RegExp("[?&]" + name + "(=([^&#]*)|&|#|$)"),
results = regex.exec(url);
if (!results) return null;
if (!results[2]) return '';
return decodeURIComponent(results[2].replace(/\+/g, " "));
}

function ParseGradPhileFormQuery(query) {

// note that fsuid, eval_year, eval_term, default_eval_year, default_eval_term, qr_abbr and auth are globals

var kiosk_param = getParameterByName("kiosk", query);

if (kiosk_param) {
kioskName = kiosk_param;
}

}

var kioskName = "_none";
const max_slides = 15;
var slides = [];

// get kioskName from query
ParseGradPhileFormQuery(window.location.search);

jQuery.get("kiosk_slides.php", function(slides_csv) {

var rows = slides_csv.split("\n");

var my_column_index = rows[0].split(",").indexOf(kioskName)

if (-1 == my_column_index) {
// unknown kiosk
return;
}
// remove header row
rows = rows.slice(1);

rows.forEach(function(r) {
var cells = r.split(",");
var display_time = parseInt(cells[my_column_index], 10);

if (0 != display_time) {
slides.push({
// url to display first slide of a google presentation
'url': "https://docs.google.com/presentation/d/e/" + cells[1] + "/embed?start=true&loop=false&delayms=60000",
'display_time': display_time * 1000

})
}

}); // next rows

if (slides.length == 0) {
// no slides allocated to this kiosk
return;
}

// we only have max_slides number of divs allocated for slides,
// so discard the excess slides
while (max_slides < slides.length) {
slides.pop();
}

var current_slide = 0;

// initialize content of slides
// TODO: put in status check before switching to this url
for (var i = 0; i < slides.length; i++) {
// iframe to display slide from google presentation
// width="2016" height="1134"
$("#slide" + i).html('<iframe src="' + slides[i].url + '" frameborder="0" allowfullscreen="true" mozallowfullscreen="true" webkitallowfullscreen="true"></iframe>');
}

// cycle through the slides, delaying for the associated display_time before going to next slide
function updateSlide() {
current_slide = (current_slide + 1) % slides.length;

console.log("curent_slide: " + current_slide + " display_time: " + slides[current_slide].display_time);

$(".slide").hide();
$("#slide" + current_slide).show();
setTimeout(updateSlide, slides[current_slide].display_time);
}

// start the display cycle
updateSlide();

}); // get php callback

</script>

</body>
</html>
</syntaxhighlight>

14-3-3

2023-08-08T14:28:07Z

Chuck: Simplify 2587 link to reduce perm redirects

==14-3-3==

https://medlineplus.gov/genetics/gene/ywhae/

Ywhae gene = 14-3-3 epsilon = tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (Ywhae)

Mus musculus tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (Ywhae), mRNA
NCBI Reference Sequence: NM_009536.4

==Dr. Yi Zhou's 14-3-3 FKO (Thy1-YFP-DIfopein) Transgenic Mice==

See SFN abstracts (2010) 53.1/M17 and (2011) 790.09/FF16

From Kourtney Graham's Honor's Thesis:

<blockquote>
In order to study the role of 14-3-3 proteins in the nervous system_ in
vivo_, we have successfully created lines of neuronal-specific
transgenic mice that may inhibit 14-3-3 dependent cellular processes.
These transgenic mice express a YFP-fused peptide (R18) which binds to
endogenous 14-3-3, and thus blocking its capability to interact with its
binding partners; and are therefore considered to be a functional
knockout. The transgenes are expressed under the control of the Thy-1
promoter which is neuronal-specific and produces variation of transgene
expression in different brain regions, which is great among founder
lines but minimal among descendants of a single founder (Feng et al.
2000). To minimize strain-dependent genetic variation, we have
backcrossed the founder lines with wild-type C57BL/6 mice for at least 8
generations.
</blockquote>

From Sun et al PMID 23861400 :
Glutamatergic kainate receptors (KAR) KAR-EPSCs at mossy fiber-CA3 synapses decay significantly faster in the 14-3-3 functional knock-out mice (but no difference in NMDA-R or AMPA-R EPSC in same synapses)

==R18 peptide ==

PMID 11577088

R18 is a synthetic 21 amino acid unphosphorylated peptide (MW 2309.6) which binds to the same amphipathic groove on the surface of 14-3-3 as phosphorylated peptides, with high affinity for all 7 mammalian isoforms of 14-3-3 PMID 10493820. Commercial source of peptide [https://www.enzolifesciences.com/BML-P214/r18-peptide/ Enzo #BML-P214-0001].

Difopein is a construct with two R18 monomers in a single 62 amino acid peptide PMID 11577088. Commercial source of peptide: [https://www.tocris.com/products/difopein_2145 Tocris #1245]

R18 Sequence:

Pro-His-Cys-Val-Pro-Arg-Asp-Leu-Ser-Trp-Leu-Asp-Leu-Glu-Ala- Asn-Met-Cys-Leu-Pro-OH

PHCVPRDLSWLDLEANMCLP

Difopein sequence (with individual R18 monomers in parentheses):

SADGA (PHCVP RDLSW LDLEA NMCLP) GAAGL DSADG A(PHCV PRDLS WLDLE ANMCL P) GAAG LE

C54 (consisting of the carboyl-terminal 54-amino acid region of theHMG-box binding protein Ste11p ) is another 14-3-3 inhibitor that is structurally unrelated to R18/difopein. The C54 region permits sequestration of Ste11p in the cytoplasm to inhibit nuclear localization PMID 12697825.

==Thy-1 Promoter==

PMID 11086982

==YFP==

YFP is 239 amino acids long (717 bp) according to plasmid map of Invitrogen [https://www.thermofisher.com/order/catalog/product/V35820 Vivid ColorsTM pcDNATM/6.2 N-terminal EmGFP/YFP-DEST vectors] see p, 28 of the manual. Difopein is 62 amino acids long (186 bp), so total YFP-difopein fusion protein should be ~ 301 amino acids (903 bp).

== 14-3-3 FKO papers==
Vogt, Peggy, [https://diginole.lib.fsu.edu/islandora/object/fsu:204445 "Exploring the Function of 14-3-3 Proteins in Neurodegenerative Disease"] (2011). Honors Theses. Paper 42.

C. Sun, H. Qiao, Q. Zhou, Y. Wang, Y. Wu, Y. Zhou, et al., Modulation of GluK2a Subunit-containing Kainate Receptors by 14-3-3 Proteins, J Biol Chem. 288 (2013) 24676–24690. PMID 23861400

Qiao H, Foote M, Graham K, Wu Y, Zhou Y. 14-3-3 proteins are required for hippocampal long-term potentiation and associative learning and memory. J Neurosci. 34(2014):4801-8. PMID 24695700

==Antisera for IP Experiments==
anti-pan-14-3-3 (K-19) , rabbit polyclonal, Santa Cruz #sc-629, 200 ug/1 ml, $279 [https://www.scbt.com/p/pan-14-3-3-antibody-k-19 datasheet]

anti-HDAC4 (H-92), rabbit polyclonal, Santa Cruz #sc-11418, 200 ug/1 ml, $279 [https://www.scbt.com/p/hdac4-antibody-h-92 datasheet]

anti-Torc1 (C71D11), rabbit mAb, Cell Signaling #2587 $225 [https://www.cellsignal.com/products/primary-antibodies/torc1-crtc1-c71d11-rabbit-mab/2587 datasheet]

Bruker MRI

2023-08-01T13:39:44Z

Chuck: Update Bruker perm redirect

==File Formats==

Description of [https://imaging.mrc-cbu.cam.ac.uk/imaging/FormatBruker Bruker MRI data file formats].

Additional description taken from https://mriresearch.med.ubc.ca/facilities/7t-mri/researchers-guide/naming-conventions/

Each Experiment directory contains another subdirectory called pdata as well as several data files:
:'''fid''': the raw unreconstructed data file (i.e. the “k-space” time-domain data)

:'''method''': text file containing the high-level acquisition parameters (e.g. number of pixels, measurement method, field of view, echo time, repetition time, number of averages, etc.)

:'''acqp''': text file containing the base-level acquisition parameters (the method parameters are derived from these acqp parameters, which are a bit like the “machine-code” variables of the pulse sequence that was used)

:'''pulseprogram''': text file containing the MRI sequence

:'''pdata folder''': only exists for image data. It contains subdirectories corresponding to the different Processed Datasets of the current Experiment – each directory is named after the<ProcNo>(e.g.1,2,etc.). For the majority of cases,the“1”directory contains the processed image data. Files in “1” include the following:

::'''2dseq''': the processed image data, expressed in a raw binary format without header. If there are multiple slices in the dataset, they are usually stored contiguously. The default binary word type is 16 bit signed integer, little endian.

::'''Reco''': text file including all reconstruction parameters

MindsEye

2023-07-30T11:33:38Z

Chuck: Follow Bruker perm-redirect to HTTPS

==Quantification of immunohistochemistry for Methods section==

For the immunohistochemistry and X-Gal staining, cells expressing darkly-positive, nuclear staining were quantified with custom software (MindsEye, T. Houpt; Kwon et al. 2008). Regions were digitally-captured at 40x magnification on a Macintosh computer using an Olympus Provis AX-70 microscope with a Dage-MTI DC-330 CCD camera and Scion LG-3 framegrabber. Cells with dark nuclear staining were automatically detected and counted by the software across each image, based on the relative pixel darkness and circular symmetry of the nuclei relative to surrounding background tissue in the digitized image. To insure a consistent crtieria for the automatic counting, the same threshold parameters were used for all images from all treatments. Counting was restricted to the basolateral amygdala (BLA), central nucleus of the amygdala (CeA), or lateral amygdala (LA) as delineated by a hand-drawn outline. Bilateral cell counts were averaged for 6 sections of the amygdala for each mouse. The individual mean counts for each region were then averaged across mice within experimental groups. Significant effects across treatment groups were detected by one-way ANOVA and Neuman-Keuls post-hoc tests (Kaleidagraph, Synergy Software). All data are presented as the mean ± standard error of the mean.

==Programming Notes==

===MRI files===

Description of [https://imaging.mrc-cbu.cam.ac.uk/imaging/FormatBruker Bruker MRI data file formats]. We need to convert 2dseq file (a 3D block of data) into TIFF slices, probably in 3 different orientations (assuming TIFF can handle 16-bit grayscale. Otherwise may need to convert to RAW image files).

see [[Bruker MRI]] for more details on MRI files

[[Category:Software]] [[Category:MindsEye]]

Extension & Option Samples

2023-07-03T12:08:30Z

Chuck: Update broken Body-in-Question clip, now points to full episode

Here are some simple examples of useful extensions on MagnetoWiki. Edit or View Source to see the markup.

==Infobox==

{{infobox
|title = An amazing Infobox
|header1 = It works!
|label2 = Configured by
|data2 = houpt
|label3 = Web
|data3 = [https://houptlab.org houptlab.org]
}}

{{Infobox experiment|align=right
| Name = Valproate and Ovariectomy
| project = Histone Acetylation
| code = DMB
| protocol = 1917
| funding = Chair's Fund
| investigators = Mukherjee, Houpt
| species = rat
| date = 2022-12-4
| type = CTA
| drugs = valproate, lithium
| artifacts = PMID 23720133
| data = https://houptlab.org/bartab/expt/?id=DMQ
}}

==Raw HTML==

MagnetoWiki allows raw HTML. This is a standard MediaWiki feature, not an extension.

<html>
<a href="#" onclick="alert('Hello! I am here!')">Click here.</a>
</html>

==Magic Links==

Optional [https://www.mediawiki.org/wiki/Help:Magic_links MediaWiki Magic Links]:

* PMID 23720133
* ISBN 1119232767
* ISBN 9781119232766

==SimpleTable Sample==

<tab sep=comma class=wikitable head=top>
A,B,A xor B
0,0,0
0,1,1
1,0,1
1,1,0
</tab>

==EmbedVideo Sample==

{{#ev:youtube|yUBQjnQVJ4U}}

==Cite References Sample==

''[Note: old HarvardReference extension is deprecated]''

MagnetoWiki now includes the [https://www.mediawiki.org/wiki/Extension:Cite Extension]

According to scientists, the Sun is pretty big.<ref name="miller2005" />
The Moon, however, is not so big.<ref name="smith1978" />

===Notes===
<references>
<ref name="miller2005">E. Miller, ''The Sun'', (New York: Academic Press, 2005), 23–25.</ref>
<ref name="smith1978">R. Smith, "Size of the Moon", ''Scientific American'', 46 (April 1978): 44–46.</ref>
</references>

==Category Trees & Clouds==

===Tree===
<categorytree mode="all">Taste Aversion</categorytree>

===Cloud===
<tagcloud></tagcloud>

===Syntax Highlighting of Code===

See [https://www.mediawiki.org/wiki/Extension:SyntaxHighlight SyntaxHighlight Extension]

<syntaxhighlight lang=prolog>
mortal(X) :-
human(X).

human(socrates).
</syntaxhighlight>

==Upgrade Test==

This is a test that Mediawiki 1.23.9 is working.

An image using old Image namespace:

[[Image:HouptLabIcon-flat.png]]

An image using new File namespace:

[[File:HouptLabIcon-flat.png]]

test edit.

__INDEX__

Random Walk

2023-06-06T15:19:27Z

Chuck: Fix broken Einstein link

=Random Walks in NetLogo=

Each tick, generate a random heading from 0-359. Gives an even distribution of headings, and the resulting random walk has lots of backtracing and crossings.

rt random 360
fd 1

[[File: random_walk.png|400px]]

=Triangular Random Walk=

Advance +/- 50 degrees from straight ahead, gives a triangular distribution around 0. As a result, the turtles have a much greater tendency t move forward, and so cover a wider range and show less backtracing and crossing (and visit more unique patches).

rt random 50
lt random 50
fd 1

Distribution:

[[File: triangular_heading.png|400px]] [[File: triangular_walk.png|400px]]

=Some Theory=

In a true random walk (ie Brownian motion) the mean displacement along the x-axis is proportional to the square root of time dx=sqrt (2Dt), where D is the diffusion constant which gives mean radius of a circle covered by the random walk

Einstein, Albert (May 1905). [https://onlinelibrary.wiley.com/doi/pdfdirect/10.1002/andp.19053220806 "Über die von der molekularkinetischen Theorie der Wärme geforderte Bewegung von in ruhenden Flüssigkeiten suspendierten Teilchen" (PDF)]. Annalen der Physik (in German). 322 (8): 549–560. Bibcode:1905AnP...322..549E. doi:10.1002/andp.19053220806. Retrieved 2008-04-10.

Einstein, Albert (1989). [https://einsteinpapers.press.princeton.edu/vol2-trans/137 "On the movement of small particles suspended in a stationary liquid demanded by the molecular-kinetic theory of heat" (PDF)]. Princeton University Press

A random walk constrained to 2 dimensions, the mean displacement is proportional to sqrt(t).

There are supposed to be interesting properties of random walk on a lattice, which is probably the best model of NetLogo movement.

McCrea, W. H. and Whipple, F. J. W. "Random Paths in Two and Three Dimensions." Proc. Roy. Soc. Edinburgh 60, 281-298, 1940.

[[Category:Taste Evolution]][[Category:NetLogo]]

Selenium

2023-05-30T19:56:44Z

Chuck: Follow perm redirect for NTP study

Selenium is an essential micronutrient. Recently, a specific selenium salt, sodium selenate, was discovered to be a specific enhancer of the enzyme protein phosphatase 2A (PP2A). PP2A removes phosphate groups from target proteins, including tau, a protein implicated in Alzheimer’s disease Corcoran 2010a PMID 20537899, van Eersel 2010 PMID 20643941, and many other proteins implicated in the control of cancer (Corcoran 2010b PMID 20648008).

Because phosphatases like PP2A remove phosphate groups that activate other proteins, PP2A can be considered a “brake” on the activity of cells, including neurons involved in learning and memory. We have previously shown that inhibiting phosphatase PP2A with the non-specific blocker okadaic acid increased the strength of learned conditioned taste aversions in rats. In other words, blocking PP2A “cut the brakes” on the learning mechanism, causing the rats to acquire a stronger memory of a toxic fluid (saccharin paired with lithium chloride).

Because sodium selenate can act as an enhancer of PP2A, we hypothesize that administering sodium selenate before a conditioning trial will decrease the strength of conditioned taste aversion learning (i.e., the “brakes” will be enhanced, thus diminishing the learning.)

==Sodium Selenate==

[https://www.sigmaaldrich.com/US/en/product/sigma/s8295 Sigma-Aldrich S8295-10G] $56

CAS Number: 13410-01-0

Linear Formula: Na2SeO4

Molecular Weight: 188.94

EC Number: 236-501-8

MDL number: MFCD00003490

PubChem Substance ID: [https://pubchem.ncbi.nlm.nih.gov/substance/24899787 24899787]

'''Tonicity of Systemic Injection'''

Osmolarity of Na2Se04 at 12 mg/ml (63 mM) = 189 mOsm

So Na2Se04 at 12 mg/ml (63 mM), NaCl at 3.2 mg/ml (55mM) = 300 mOsm

'''Calculation of suggested i.c.v. injection concentration.'''

Assuming a 500 g rat, then systemic dose is 0.25 mg ( 250 µg). A central dose might be 1/100th of the system dose -> 2.5 µg.

Volume of i.c.v injection would be 5 µl; site specific injection 0.5 µl

So central dose would be 2.5 µg / 5 µl = 0.5 µg/ 1 µl = 0.5 g / L.

MW of sodium selenate is 188.94, so 0.5 g = 2.65 mmole

so central injection dose is 5 µl at 2.65 mM.

(Osmolarity is sufficiently low that can be diluted with saline).

==Toxicity of Selenate==

Selenium is an essential micronutrient and is naturally found a wide variety of food stuffs. As an antioxidant, it is frequently used to treat, e.g., heavy metal toxicosis or liver disease. The recommended dietary intake for adults is 55 micrograms/day, and selenium supplements of 200-300 micrograms/day have been recommended for prevention of several types of cancer. High doses of 1.5 to 5 mg/ day are associated with adverse effects (Brozmanova 2010, Reid 2004). The chemical form of selenium also contributes to toxicity. The form we will use, sodium selenate (Na2Se04), is well-tolerated in human trials (Corcoran 2010b).

Corcoran (2010a) administered sodium selenate to mice acutely at 12 mg/kg, and chronically at ~192 mg/kg per day in drinking water, and did not report any aversive or toxic effects on the mice. van Eersel (2010) administered sodium selenate to mice chrionically at ~ 1.9 mg/kg per day in drinking water, and also did not report any aversive or toxic effects.

Abdo (1994) reported on the effects of administering sodium selenate in the drinking water for 13 weeks. It was estimated that the "no-observed adverse level" in rat was 0.4 mg/kg per day of sodium selenate for 13 weeks. Doses of 0.6 mg/kg or 1.1 mg/kg per day for 13 weeks caused changes in mortality, body weight depression, decreased water consumption, and renal papillary lesions. However, these were chronic studies so that rats received a total dose of 54.6 mg/kg or 100.1 mg/kg sodium selenate over 13 weeks.

Aasif Mandvi ran a [https://www.cc.com/video/jucn2a/the-daily-show-with-jon-stewart-a-simple-plot story] on selenium pollution of Idaho rivers as a consequence of phosphate mining.

==Selenium Ingestion and Aversions==

Selenium is an essential micronutrient. The mammalian selenoproteome consists of some 2 dozen selenocysteine-containing proteins (24 in rodents, 25 in human) including the glutathione peroxidase, thioredoxin reductase and iodothyronine deiodinase enzymes [PMID 12775843]. However, at doses not much higher than the dietary requirement, selenium is also toxic [PMID 3527390]. Selenium toxicity is due to the generation of superoxide and other reactive oxygen species, the oxidation of thiols, and by substituting for sulfur in methionine to form selenomethione which then may be incorporated into many sulfur containing proteins [PMID 11879936].

Reduced intake and avoidance of toxic diets containing selenium compounds has been demonstrated in many species. Because selenium is concentrated by certain species of plants in selenium-rich geographies, selenosis is a potential hazard for livestock and native herbivores. Waste from mining or agricultural run-off can also introduce selenium into the environment and hence into the food-chain. It has therefore been of interest to determine whether species can avoid selenium-rich food sources due to an aversive taste or odor of selenium compounds, or acute toxic effects, or learned food aversions. Aphids [PMID 17831208, JSTOR 1514562], crickets and grasshoppers [PMID 17635224], southern armyworms [PMID 10467057] mallard ducks [Heinz 1990], owls [Wiemeyer 1996], prairie dogs [PMID 21628258], sheep [Pfister 2010, PMID 3527390], and cattle [PMID 3527390] have been shown to reduce intake of selenium-containing foods, or show reduced preference for selenium-containing foods over control diets.

In laboratory studies, rats show a preference for control or low selenium-diets over high selenium diets [PMID 17788901][Franke and Potter 1935]. Consistent with the effects of other selenium compounds, selenate adulteration also causes a reduction of food [Franke and Moxon 1937] [Smith Stohlman Lillie 1937] or water intake [PMID 6053743, PMID 1255264] Acute injection of selenate can also reduce food intake and body weight gain [PMID 2609019]

Only a few of these studies (e.g. [Pfister 2010, PMID 3527390, Heinz & Sanderson 1990] ) have determined if animals were responding to an acute perception of selenium compounds, or if the animals used food-associated cues, to avoid consumption, after acquiring a selenium-induced conditioned food aversion. Selenium absorbing plants may themselves have salient taste or odor: for example, Provenza et al. have demonstrated that the odor of Astragalus bisulcatus, a sulfur-containing selenium-absorbing plant, can serve as a CS that reduced preference for CS+barley-straw after pairing with oral-intubation of LiCl. [Oikos 88(2000)424-432.] Selenium compounds may also present distinctive cues, e.g., the volatile dimethyldiselenide, a major metabolite of selenite and selenate, has a pungent garlic odor to humans, that may be innately aversive or serve as an indicative CS in learned selenium aversions.

==Government Documents on Selenium Safety==

National Toxicology Program / NIEHS: [https://ntp.niehs.nih.gov/sites/default/files/ntp/htdocs/st_rpts/tox038.pdf NTP Technical Report on Toxicity Studies of Sodium Selenate and Sodium Selenite] (1994)

CDC/NIOSH: [https://www.cdc.gov/niosh/idlh/7782492.html Selenium compounds (as Se)] from NIOSH Documentation for immediately dangerous to life or health concentrations (IDLHs)

WHO: [https://inchem.org/documents/ehc/ehc/ehc58.htm Environmental Health Criteria 58: Selenium] (1987) from International Programme on Chemical Safety

HHS: [https://www.atsdr.cdc.gov/ToxProfiles/tp92.pdf Toxicological Profile for Selenium] (2003)

Agency for Toxic Substances and Disease Registry: [https://wwwn.cdc.gov/TSP/ToxFAQs/ToxFAQsDetails.aspx?faqid=152&toxid=28 ToxFAQs for Selenium] (2003)

Agency for Toxic Substances and Disease Registry: [https://www.atsdr.cdc.gov/toxguides/toxguide-92.pdf ToxGuide for Selenium]

Division 9 of NRDC: [https://apps.dtic.mil/sti/pdfs/AD0234270.pdf Chemical Warfare Agents and Related Chemical Problems, Parts I-II, Chapter 11] (1946)

==References==

Abdo, K.M. 1994. NTP Technical Report on Toxicity Studies of Sodium Selenate and Sodium Selenite (CAS Nos. 13410-01-0 and 10102-18-8) Administered in Drinking Water to F344/N Rats and B6C3F1 Mice. NIH Publication 9a4-3387. National Toxicology Program. Toxicity Report Series Number 38.

Brozmanova et al., 2010. Selenium: a double-edged sword for defense and offence in cancer, Arch. Toxicol. 84:919–938. PMID 20871980.

Corcoran NM, et al., 2010a. Sodium selenate specifically activates PP2A phosphatase, dephosphorylates tau and reverses memory deficits in an Alzheimer's disease model. J Clin Neurosci. 8:1025-33. PMID 20537899

Corcoran NM et al. 2010b. Open-label, phase I dose-escalation study of sodium selenate, a novel activator of PP2A, in patients with castration-resistant prostate cancer. Br J Cancer. 103:462-8. PMID 20648008

Mandvi, A. A Simple Plot. The Daily Show with Jon Stewart, aired June 14, 2012. https://www.cc.com/video/jucn2a/the-daily-show-with-jon-stewart-a-simple-plot

Reid ME et al. 2004 A report of high-dose selenium supplementation: response and toxicities. J Trace Elem Med Biol 18:69–74 PMID 15487766

van Eersel J et al. 2010. Sodium selenate mitigates tau pathology, neurodegeneration, and functional deficits in Alzheimer's disease models. PNAS 107:13888-93. PMID 20643941

Neurogenesis

2023-03-07T11:57:59Z

Chuck: Updated perm redirects

=Useful Markers=

=='''Ki67''' ==

Ki67 is a marker for proliferating cells, because it is present during all active phases of the cell cycle (G1, S, G2, and mitosis), but is absent from resting cells (G0) PMID 10653597 .

a rabbit anti-rat Ki67 monoclonal antibody (1:750, Biomeda, Foster City, CA) From Corniola et al PMID 18778998

<blockquote>
The nuclear protein Ki67 is expressed during all active phases of the cell cycle. Three weeks of dietary zinc deficiency reduced the number of Ki67-positive cells in the SGZ and GCL of the dentate, suggesting that zinc is required for neuronal precursor cell proliferation in vivo. This conclusion is supported by the finding that zinc restriction of human neuronal precursors in culture decreased the number of cells that entered S-phase, as evidenced by a reduction in BrdU labeling.
</blockquote>

=='''GAD67'''==

anti-GAD67 rabbit antibody from Chemicon. Used by Tamamaki N et al to confirm expression pattern of GAD67-GFP mice PMID 14574680 Used by Stewart et al to demonstate GAD/GABA expression in SVZ progenitor cells PMID 11891665.

Millipore (nee Chemicon) Catalog # AB9706 (broken link: www.millipore.com/catalogue/item/ab9706), Anti-GAD67 affinity purified rabbit polyclonal antibody; described for Western blotting. 100 µg, $239

=='''Doublecortin'''==

DCX is a marker for migrating cells DCX (Santa Cruz) From Imayoashi et al PMID 18758458

Santa Cruz Catalog # [https://www.scbt.com/p/doublecortin-antibody-c-18 sc-8066] anti-DCX goat polyclonal antibody. 200 µg/ml, $259

Found a posting on the interweb that recommended (instead of Santa Cruz) Abcam's anti-DCX antiserum [https://www.abcam.com/products/primary-antibodies/doublecortin-antibody-ab18723.html ab18723], might try that for $325. Requires a heat retrieval step by heating at 60C.

=='''NeuroTrace'''==

Molecular Probes from Bagley et al PMID 17996088

Invitrogen NeuroTrace 435/455 blue fluorescent Nissl stain catalog #[https://www.thermofisher.com/order/catalog/product/N21479 N-21479] 1 ml, $120

Mount Neurotrace with [http://www.thermofisher.com/us/en/home/life-science/cell-analysis/cellular-imaging/fluorescence-microscopy-and-immunofluorescence-if/mounting-medium-antifades/prolong-gold-antifade.html Prolong Gold AntiFade] invitrogen Catalog P36930 10 ml, $114.00

=='''PSA-NCAM'''==

PMID 18945916

AbCys

[[Category:Flavor Preference]]

Water Maze

2023-02-21T20:51:12Z

Chuck: Archive Coulbourn link

Reference site: https://web.archive.org/web/20180317100212/http://watermaze.com/

==FSU setup for Mice==

===Currently have:===

Wading pool (approximate 2m diameter x 20 cm deep, dark blue)

Tripod and stand for video camera (could replace with ladder, or with ceiling mount)

Sony Digitial8 Camcorder

Heat lamps

Pump to empty pool

===Need to Get===
Platform for mice

White tempora or latex for making water opaque

geometric shapes or posters on walls to serve as visual cues

Heater for water

insulation to cover pool to prevent heat loss

drainage system (e.g. a spigot on side)

===Nice to get in future===

Ceiling mount for video camera or mount mirror on ceiling

Realtime tracking software

Table to get water maze off the floor.

==Sources of Water Mazes and Equipment==

[https://www.any-maze.com/mazes/water-maze/ ANY-maze] $1195 for 6-foot diameter, metal, with wheels and side drain

[https://sandiegoinstruments.com/product/water-maze/ SD Instruments] 6ft x 30" deep, polyethylene blue or white, drain kit

[https://hvsimage.com/information/3rd_party_pools.htm List of suppliers] HVS Image has a list of places that sell galvanized or polyethylene tanks

[https://www.bioseb.com/en/learningmemory-attention-addiction/1323-circular-pool.html Bioseb] French company

[https://www.tse-systems.com/products/behavior/maze-systems/water-maze.htm TSE Systems]

[https://muromachi.com/en/ Muromachi] Japanese company, I think they sell their own water maze pool.

==Aquaculture Tanks==

[http://www.solar-components.com/aqua.htm Solar Components] Transparent fiberglass tanks

[https://dolphinfiberglass.com Dolphin Fiberglass Products] located in Homestead, FL . They list 6' by 2' round tanks [https://www.aquaculturetanks.com/pricelist2.gif here]. Note that you can get feet put on the tanks. (see their picture catalog].

[https://web.archive.org/web/20090118141101/http://aquaticeco.com:80/categories/Tanks--Liners/97/0 Aquatic Eco-Systems] (now [https://pentairaes.com Pentair]) Located in Apopka, FL. Large selection.

[https://www.plastic-mart.com/category/41/plastic-stock-tanks-water-troughs Plastic-Mart] Livestock watering tubs.

==Tracking Software==

[https://web.archive.org/web/20180317100212/http://watermaze.com/ Watermaze Software (Edinburgh)] also sold by [https://web.archive.org/web/20220810202835/https://www.coulbourn.com/category_s/291.htm Coulbourn Instruments]

[https://actimetrics.com Actimetrics]

[https://hvsimage.com/ HVS Image]

[http://www.biobserve.com/products/viewer/plugins/watermaze.html?gclid=CLDQwIDU144CFRVBgAodVgbo6A Biobserve]

[https://www.viewpoint.fr/product/rodent/rodents-behavior-monitoring/videotrack Viewpoint]

[https://muromachi.com/archives/item/191 DV-Track] from Muromachi

[[Tracker]] from the [https://houptlab.org/ Houpt Lab]

[[Category:Magnetic_Fields]]
[[Category:Laboratory]]

Fructose

2023-02-19T23:01:34Z

Chuck: Fix typo in Sweetener link

Entries related to our research on Fructose ingestion.

::[[Sweeteners]]
::[[Density of Sugar Solutions]]

A list of our experiments:

::[[:Category: Fructose Experiments]]

Selenium

2023-01-24T20:55:36Z

Chuck: Fix Chem Warfare Agent link.

Selenium is an essential micronutrient. Recently, a specific selenium salt, sodium selenate, was discovered to be a specific enhancer of the enzyme protein phosphatase 2A (PP2A). PP2A removes phosphate groups from target proteins, including tau, a protein implicated in Alzheimer’s disease Corcoran 2010a PMID 20537899, van Eersel 2010 PMID 20643941, and many other proteins implicated in the control of cancer (Corcoran 2010b PMID 20648008).

Because phosphatases like PP2A remove phosphate groups that activate other proteins, PP2A can be considered a “brake” on the activity of cells, including neurons involved in learning and memory. We have previously shown that inhibiting phosphatase PP2A with the non-specific blocker okadaic acid increased the strength of learned conditioned taste aversions in rats. In other words, blocking PP2A “cut the brakes” on the learning mechanism, causing the rats to acquire a stronger memory of a toxic fluid (saccharin paired with lithium chloride).

Because sodium selenate can act as an enhancer of PP2A, we hypothesize that administering sodium selenate before a conditioning trial will decrease the strength of conditioned taste aversion learning (i.e., the “brakes” will be enhanced, thus diminishing the learning.)

==Sodium Selenate==

[https://www.sigmaaldrich.com/US/en/product/sigma/s8295 Sigma-Aldrich S8295-10G] $56

CAS Number: 13410-01-0

Linear Formula: Na2SeO4

Molecular Weight: 188.94

EC Number: 236-501-8

MDL number: MFCD00003490

PubChem Substance ID: [https://pubchem.ncbi.nlm.nih.gov/substance/24899787 24899787]

'''Tonicity of Systemic Injection'''

Osmolarity of Na2Se04 at 12 mg/ml (63 mM) = 189 mOsm

So Na2Se04 at 12 mg/ml (63 mM), NaCl at 3.2 mg/ml (55mM) = 300 mOsm

'''Calculation of suggested i.c.v. injection concentration.'''

Assuming a 500 g rat, then systemic dose is 0.25 mg ( 250 µg). A central dose might be 1/100th of the system dose -> 2.5 µg.

Volume of i.c.v injection would be 5 µl; site specific injection 0.5 µl

So central dose would be 2.5 µg / 5 µl = 0.5 µg/ 1 µl = 0.5 g / L.

MW of sodium selenate is 188.94, so 0.5 g = 2.65 mmole

so central injection dose is 5 µl at 2.65 mM.

(Osmolarity is sufficiently low that can be diluted with saline).

==Toxicity of Selenate==

Selenium is an essential micronutrient and is naturally found a wide variety of food stuffs. As an antioxidant, it is frequently used to treat, e.g., heavy metal toxicosis or liver disease. The recommended dietary intake for adults is 55 micrograms/day, and selenium supplements of 200-300 micrograms/day have been recommended for prevention of several types of cancer. High doses of 1.5 to 5 mg/ day are associated with adverse effects (Brozmanova 2010, Reid 2004). The chemical form of selenium also contributes to toxicity. The form we will use, sodium selenate (Na2Se04), is well-tolerated in human trials (Corcoran 2010b).

Corcoran (2010a) administered sodium selenate to mice acutely at 12 mg/kg, and chronically at ~192 mg/kg per day in drinking water, and did not report any aversive or toxic effects on the mice. van Eersel (2010) administered sodium selenate to mice chrionically at ~ 1.9 mg/kg per day in drinking water, and also did not report any aversive or toxic effects.

Abdo (1994) reported on the effects of administering sodium selenate in the drinking water for 13 weeks. It was estimated that the "no-observed adverse level" in rat was 0.4 mg/kg per day of sodium selenate for 13 weeks. Doses of 0.6 mg/kg or 1.1 mg/kg per day for 13 weeks caused changes in mortality, body weight depression, decreased water consumption, and renal papillary lesions. However, these were chronic studies so that rats received a total dose of 54.6 mg/kg or 100.1 mg/kg sodium selenate over 13 weeks.

Aasif Mandvi ran a [https://www.cc.com/video/jucn2a/the-daily-show-with-jon-stewart-a-simple-plot story] on selenium pollution of Idaho rivers as a consequence of phosphate mining.

==Selenium Ingestion and Aversions==

Selenium is an essential micronutrient. The mammalian selenoproteome consists of some 2 dozen selenocysteine-containing proteins (24 in rodents, 25 in human) including the glutathione peroxidase, thioredoxin reductase and iodothyronine deiodinase enzymes [PMID 12775843]. However, at doses not much higher than the dietary requirement, selenium is also toxic [PMID 3527390]. Selenium toxicity is due to the generation of superoxide and other reactive oxygen species, the oxidation of thiols, and by substituting for sulfur in methionine to form selenomethione which then may be incorporated into many sulfur containing proteins [PMID 11879936].

Reduced intake and avoidance of toxic diets containing selenium compounds has been demonstrated in many species. Because selenium is concentrated by certain species of plants in selenium-rich geographies, selenosis is a potential hazard for livestock and native herbivores. Waste from mining or agricultural run-off can also introduce selenium into the environment and hence into the food-chain. It has therefore been of interest to determine whether species can avoid selenium-rich food sources due to an aversive taste or odor of selenium compounds, or acute toxic effects, or learned food aversions. Aphids [PMID 17831208, JSTOR 1514562], crickets and grasshoppers [PMID 17635224], southern armyworms [PMID 10467057] mallard ducks [Heinz 1990], owls [Wiemeyer 1996], prairie dogs [PMID 21628258], sheep [Pfister 2010, PMID 3527390], and cattle [PMID 3527390] have been shown to reduce intake of selenium-containing foods, or show reduced preference for selenium-containing foods over control diets.

In laboratory studies, rats show a preference for control or low selenium-diets over high selenium diets [PMID 17788901][Franke and Potter 1935]. Consistent with the effects of other selenium compounds, selenate adulteration also causes a reduction of food [Franke and Moxon 1937] [Smith Stohlman Lillie 1937] or water intake [PMID 6053743, PMID 1255264] Acute injection of selenate can also reduce food intake and body weight gain [PMID 2609019]

Only a few of these studies (e.g. [Pfister 2010, PMID 3527390, Heinz & Sanderson 1990] ) have determined if animals were responding to an acute perception of selenium compounds, or if the animals used food-associated cues, to avoid consumption, after acquiring a selenium-induced conditioned food aversion. Selenium absorbing plants may themselves have salient taste or odor: for example, Provenza et al. have demonstrated that the odor of Astragalus bisulcatus, a sulfur-containing selenium-absorbing plant, can serve as a CS that reduced preference for CS+barley-straw after pairing with oral-intubation of LiCl. [Oikos 88(2000)424-432.] Selenium compounds may also present distinctive cues, e.g., the volatile dimethyldiselenide, a major metabolite of selenite and selenate, has a pungent garlic odor to humans, that may be innately aversive or serve as an indicative CS in learned selenium aversions.

==Government Documents on Selenium Safety==

National Toxicology Program / NIEHS: [https://ntp.niehs.nih.gov/ntp/htdocs/st_rpts/tox038.pdf NTP Technical Report on Toxicity Studies of Sodium Selenate and Sodium Selenite] (1994)

CDC/NIOSH: [https://www.cdc.gov/niosh/idlh/7782492.html Selenium compounds (as Se)] from NIOSH Documentation for immediately dangerous to life or health concentrations (IDLHs)

WHO: [https://inchem.org/documents/ehc/ehc/ehc58.htm Environmental Health Criteria 58: Selenium] (1987) from International Programme on Chemical Safety

HHS: [https://www.atsdr.cdc.gov/ToxProfiles/tp92.pdf Toxicological Profile for Selenium] (2003)

Agency for Toxic Substances and Disease Registry: [https://wwwn.cdc.gov/TSP/ToxFAQs/ToxFAQsDetails.aspx?faqid=152&toxid=28 ToxFAQs for Selenium] (2003)

Agency for Toxic Substances and Disease Registry: [https://www.atsdr.cdc.gov/toxguides/toxguide-92.pdf ToxGuide for Selenium]

Division 9 of NRDC: [https://apps.dtic.mil/sti/pdfs/AD0234270.pdf Chemical Warfare Agents and Related Chemical Problems, Parts I-II, Chapter 11] (1946)

==References==

Abdo, K.M. 1994. NTP Technical Report on Toxicity Studies of Sodium Selenate and Sodium Selenite (CAS Nos. 13410-01-0 and 10102-18-8) Administered in Drinking Water to F344/N Rats and B6C3F1 Mice. NIH Publication 9a4-3387. National Toxicology Program. Toxicity Report Series Number 38.

Brozmanova et al., 2010. Selenium: a double-edged sword for defense and offence in cancer, Arch. Toxicol. 84:919–938. PMID 20871980.

Corcoran NM, et al., 2010a. Sodium selenate specifically activates PP2A phosphatase, dephosphorylates tau and reverses memory deficits in an Alzheimer's disease model. J Clin Neurosci. 8:1025-33. PMID 20537899

Corcoran NM et al. 2010b. Open-label, phase I dose-escalation study of sodium selenate, a novel activator of PP2A, in patients with castration-resistant prostate cancer. Br J Cancer. 103:462-8. PMID 20648008

Mandvi, A. A Simple Plot. The Daily Show with Jon Stewart, aired June 14, 2012. https://www.cc.com/video/jucn2a/the-daily-show-with-jon-stewart-a-simple-plot

Reid ME et al. 2004 A report of high-dose selenium supplementation: response and toxicities. J Trace Elem Med Biol 18:69–74 PMID 15487766

van Eersel J et al. 2010. Sodium selenate mitigates tau pathology, neurodegeneration, and functional deficits in Alzheimer's disease models. PNAS 107:13888-93. PMID 20643941

Pica

2023-01-17T22:05:04Z

Chuck: Updated PikaScript to new name, PikaPython

Multiple uses of the word Pica or Pika

=Pika=

rock rabbit

a lagomorph (relative of rabbits) in the mountains of the western United States

=Pica=

eating clay or other nonnutirive subantances to detoxify ingested toxins. Named after the behavior of magpies.

Can be [https://newsfeed.time.com/2013/01/30/japanese-restaurant-serves-meal-of-dirt-for-110/ pricey.]

=Pica Pica=

The European Magpie

=Hyrax=

[https://en.wikipedia.org/wiki/Hyrax Not] a pica. Also not a rodent; related to elephants.

=Puca=

A creature of Celtic folklore, Though the púca enjoys confusing and often terrifying humans, it is considered to be benevolent.

=Pooka=

https://en.wikipedia.org/wiki/Harvey_(film)

=Pica=

A typographic unit of measure corresponding to 1/72nd of its respective foot, and therefore to 1/6th of an inch. .

=Pica, Chile=

[https://en.wikipedia.org/wiki/Pica,_Chile Pica] in the north of Chile is famous for its "small and unusually acidic lemons." Coincidentally, it is also the site of substantial [https://www.mining.com/mammoth-energy-group-continues-to-acquire-chilean-lithium-assets/ lithium concessions] acquired by Mammoth Energy Group's Compania Lithium Investments Limitada, from the dry lake bed of Laguna Lagunilla.

=Pika=

[https://www.pika.dev/about Pika] is a “project to move the JavaScript ecosystem forward.” Allows searching for ES module syntax packages, and integrates ESM packages with npm.

Has an icon of a pika for a mascot.

=Piku=

How I love a verse
Contrived to unhusk dryly
One image nutshell

(count the letters)

=Pika Pika=

[https://nakamotoforestry.com/shou-sugi-ban-siding/ Pika Pika] ( ぴかぴか ) is variant of charred cedar boards (焼杉板 or “yakisugi-ita”) used for siding in Japanese building. The charing helps preserve the boards. Pika Pika boards are scrapped with a wire brush that increases contrast by removing soot from softer grain in the wood.

=PikaPython=

[https://github.com/pikasTech/PikaPython PikaPython] is a cross platform ultra lightweight embedded Python engine.

[[Category:Taste Aversion]]

Water Maze

2023-01-17T16:40:21Z

Chuck: Fix perm redirect

Reference site: https://web.archive.org/web/20180317100212/http://watermaze.com/

==FSU setup for Mice==

===Currently have:===

Wading pool (approximate 2m diameter x 20 cm deep, dark blue)

Tripod and stand for video camera (could replace with ladder, or with ceiling mount)

Sony Digitial8 Camcorder

Heat lamps

Pump to empty pool

===Need to Get===
Platform for mice

White tempora or latex for making water opaque

geometric shapes or posters on walls to serve as visual cues

Heater for water

insulation to cover pool to prevent heat loss

drainage system (e.g. a spigot on side)

===Nice to get in future===

Ceiling mount for video camera or mount mirror on ceiling

Realtime tracking software

Table to get water maze off the floor.

==Sources of Water Mazes and Equipment==

[https://www.any-maze.com/mazes/water-maze/ ANY-maze] $1195 for 6-foot diameter, metal, with wheels and side drain

[https://sandiegoinstruments.com/product/water-maze/ SD Instruments] 6ft x 30" deep, polyethylene blue or white, drain kit

[https://hvsimage.com/information/3rd_party_pools.htm List of suppliers] HVS Image has a list of places that sell galvanized or polyethylene tanks

[https://www.bioseb.com/en/learningmemory-attention-addiction/1323-circular-pool.html Bioseb] French company

[https://www.tse-systems.com/products/behavior/maze-systems/water-maze.htm TSE Systems]

[https://muromachi.com/en/ Muromachi] Japanese company, I think they sell their own water maze pool.

==Aquaculture Tanks==

[http://www.solar-components.com/aqua.htm Solar Components] Transparent fiberglass tanks

[https://dolphinfiberglass.com Dolphin Fiberglass Products] located in Homestead, FL . They list 6' by 2' round tanks [https://www.aquaculturetanks.com/pricelist2.gif here]. Note that you can get feet put on the tanks. (see their picture catalog].

[https://web.archive.org/web/20090118141101/http://aquaticeco.com:80/categories/Tanks--Liners/97/0 Aquatic Eco-Systems] (now [https://pentairaes.com Pentair]) Located in Apopka, FL. Large selection.

[https://www.plastic-mart.com/category/41/plastic-stock-tanks-water-troughs Plastic-Mart] Livestock watering tubs.

==Tracking Software==

[https://web.archive.org/web/20180317100212/http://watermaze.com/ Watermaze Software (Edinburgh)] also sold by [https://www.coulbourn.com/category_s/291.htm Coulbourn Instruments]

[https://actimetrics.com Actimetrics]

[https://hvsimage.com/ HVS Image]

[http://www.biobserve.com/products/viewer/plugins/watermaze.html?gclid=CLDQwIDU144CFRVBgAodVgbo6A Biobserve]

[https://www.viewpoint.fr/product/rodent/rodents-behavior-monitoring/videotrack Viewpoint]

[https://muromachi.com/archives/item/191 DV-Track] from Muromachi

[[Tracker]] from the [https://houptlab.org/ Houpt Lab]

[[Category:Magnetic_Fields]]
[[Category:Laboratory]]

Sweeteners

2022-11-27T13:06:47Z

Chuck: Fix perm redirect

{| class="wikitable sortable" border = "1" cellspacing="0" cellpadding = "3"
|+'''Sweeteners'''
|-bgcolor="silver"
! width="125" | Chemical Name !! width="150" | Tradename !! Wiki !! width="75" | MW !! width="125" | Formula !! width="100" | CAS !! width="75" | Calories !! width="100" | Sweetness
|-
| [[Saccharin]] || [https://www.sweetnlow.com Sweet n Lo] || [https://en.wikipedia.org/wiki/Saccharin Wiki] || align="center"| 183.18 ||align="center"| C7H5NO3S || align="center"|81-07-2 || calories || rs
|-
| [[Sucrose]] || [https://www.sucrose.com/ Sugar] || [https://en.wikipedia.org/wiki/Sucrose Wiki] || align="center"| 342.29 || align="center"|C12H22O11 || align="center"|57-50-1 || calories || rs
|-
| [[ Fructose]] || [https://corn.org/products/sweeteners/ HFCS] || [https://en.wikipedia.org/wiki/Fructose Wiki] || align="center"| 180.16 || align="center"|C6H12O6 || align="center"|57-48-7 || calories || rs
|-
| [[Xylitol]] || Xylitol || [https://en.wikipedia.org/wiki/Xylitol Wiki] || align="center"| 152.15 || align="center"|C5H12O5 || align="center"|87-99-0 || calories || rs
|-
| [[Aspartame]] || [https://web.archive.org/web/20180721024410/http://www.nutrasweet.com:80/ NutraSweet] || [https://en.wikipedia.org/wiki/Aspartame Wiki] || align="center"| 294.3 || align="center"|C14H18N2O5 || align="center"|22839-47-0 || calories || rs
|-
| [[Steviol glycoside]] || [https://www.truvia.com Truvia] || [https://en.wikipedia.org/wiki/Steviol_glycoside Wiki] || align="center"| 318.45|| align="center"|C20H30O3 || align="center"|471-80-7 || calories || rs
|-
| [[ Sucralose]] || [https://www.splenda.com Splenda] || [https://en.wikipedia.org/wiki/Sucralose Wiki] || align="center"| 397.64 || align="center"| C12H19Cl3O8 || align="center"|56038-13-2 || calories || rs
|-
| [[ Acesulfame K]]||[https://www.celanese.com/food-ingredients/products/sunett.aspx Sunett], [http://www.sweetone.com/ Sweet One]|| [https://en.wikipedia.org/wiki/Acesulfame_K Wiki] || align="center"| 201.24 || align="center"| C4H4KNO4S || align="center"|55589-62-3 || calories || rs
|-
| [[ Dulcin]] || sucrol, valzin|| [https://en.wikipedia.org/wiki/Dulcin Wiki] || align="center"| 180.20 || align="center"|C9H12N2O2 || align="center"|150-69-6|| calories || rs
|-
| [[ Perillartine]] || (Japanese name: ペリラルチン, available from [https://highchem.co.jp/chem/details.php?cas=30950-27-7 HighChem] and others) japanese product page?|| [https://en.wikipedia.org/wiki/Perillartine Wiki] || align="center"| 165.23 || align="center"| C10H15NO || align="center"|30950-27-7 || calories || rs
|}

Notes:

'''Tradename''' links to manufacturer's website

'''Calories''' (kcal/g) is available calories to humans following ingestion

'''Sweetness''' (g/g sucrose) is reported (maximal?) sweetness to humans relative to sucrose (at a particular concentration)?

= USDA Sugar and Sweeteners Data=

[https://www.ers.usda.gov/data-products/sugar-and-sweeteners-yearbook-tables.aspx Recommended Data]

[https://www.ers.usda.gov/topics/crops/sugar-and-sweeteners/readings/ Recommended Readings]

[https://usda.library.cornell.edu/concern/publications/pv63g024f?locale=en Sugar and Sweeteners Outlook] (PDF file)
(January, May, and September) provides an update of current market and policy developments and their impacts on the sugar and corn sweetener industries.

[[Category:Taste Aversion]]
[[Category:Ingestive Behavior]]

False Color Mapping

2022-11-27T13:05:12Z

Chuck: Fix perm redirect

References for constructing False Color Maps for image analysis. I'd like to add tables of RGB values for constructing maps, because those numbers seem to be rarely posted.

==General References==

[https://web.archive.org/web/20190614182049/http://www.efg2.com/Lab/Library/Color/AndComputers.htm Extensive bibliography] of false color schemes.

==Luminance-Based Color Maps==

Based on this work: Stevens, S. S. Matching Functions Between Loudness and Ten Other Continua. Perception and Psychophysics, 1, pp. 5-8, 1966.

IBM on false color maps as used in the IBM Visualization Data Explorer system:
:https://web.archive.org/web/20180308150711/https://research.ibm.com/people/l/lloydt/color/color.HTM
:https://web.archive.org/web/20120928080636/http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm
:https://sites.google.com/site/bernicerogowitz/publications

:[https://www.mathworks.com/matlabcentral/fileexchange/28982-perceptually-improved-colormaps Mathlab perceptual colormaps]

==Discussions of Different Color Maps==

[https://doi.org/10.1109/MCG.2007.46 Rainbow colormap still harmful]

[https://colorbrewer2.org/ A webtool for testing colormaps]

[https://en.wikipedia.org/wiki/HSL_and_HSV HSL and HSV] entry in Wikipedia

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

==Calculation of color maps==

[https://www.fourmilab.ch/documents/specrend/ Colour Rendering of Spectra] for calculating the RGB value of different wavelengths of light. By John Walker, the co-founder of AutoDesk.

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

[http://www.midnightkite.com/color.html Color Science] referenced by Igor for algorithms for calculating rainbow spectra, blackbody, etc.--- in Fortran!

==Collections of color maps==
[https://geography.uoregon.edu/datagraphics/color_scales.htm Color schemes for improved data graphics]. Based on Light, A and P.J. Bartlein (2004) The end of the rainbow? Color schemes for improved data graphics. EOS Transactions of the American Geophysical Union 85(40):385

[https://www.wavemetrics.com/products/igorpro/creatinggraphs/colortab Igor's color tables]

[https://www.nws.noaa.gov/wwamap-prd/faq.php National Weather Service Map Colors] (keys to different phenomena, so not the same as a color map!)

[https://www.ncl.ucar.edu/Document/Graphics/color_tables.shtml National Center for Atmospheric Research (NCAR) Command Language]

[https://www.kennethmoreland.com/color-maps/ Diverging Color Maps]. Based on Kenneth Moreland. "Diverging Color Maps for Scientific Visualization." In Proceedings of the 5th International Symposium on Visual Computing, December 2009.

NIH ImageJ Lookup Tables (".lut" files) are available as a [https://imagej.nih.gov/ij/download/luts/luts.zip zip file], although the directory holds a smattering of other LUTs as well. According to the [https://imagej.nih.gov/ij/docs/menus/file.html ImageJ documentation], "The raw LUT file must be 768 bytes long and contain 256 reds, 256 blues and 256 greens."

[[Category:MindsEye]]

Laser Capture Microscopy (LCM)

2022-10-11T13:02:06Z

Chuck: Fix perm redirect

==Overview==

[https://houptlab.org/talks/LCM_of_VTA-SN.pptx.zip Example Powerpoint] with videos and calibration images.

==Supplies for LCM==

===CapSure Caps===

[https://www.thermofisher.com/us/en/home/life-science/gene-expression-analysis-genotyping/laser-capture-microdissection/laser-capture-microdissection-lcm-slides-accessories/laser-capture-microdissection-lcm-caps.html ThermoFisher LCM site]

* [https://www.thermofisher.com/order/catalog/product/LCM0213 LCM0213 caps] and alignment tray and incubation block (dont know if we need all that)

* [https://www.thermofisher.com/order/catalog/product/LCM0213 LCM0214 32 caps] $560

* [https://www.thermofisher.com/order/catalog/product/LCM0215 LCM0215 160 caps] $2400

===Cryo-Jane System for Adhesive Slides===

<del>[https://web.archive.org/web/*/http://www.instrumedics.com/ Instrumedics Inc.]
5918 Evergreen Blvd.
St. Louis, Mo 63134
Phone: 314-522-8671
Fax: 314-522-6360
email: sales@instrumedics.com</del> 
Now part of [https://shop.leicabiosystems.com/us/histology-consumables/ancillaries/pid-tape-transfer-system Leica Biosystems]

(prices updated 2022)

Adhesive-Coated Slides CFSA 1X Slides White (125/box) item # 39475208 $375

Adhesive Tape Windows 1x3 Slides (RL200per) item #39475214 $114

see also [https://www.emsdiasum.com/cryojane-the-cryostat-frozen-sectioning-aid-system Electron Microscopy Sciences page]

[https://www.emsdiasum.com/microscopy/technical/manuals/62800.pdf CryoJane Manual]

video: [https://youtu.be/nkzGdc0IAEY Univ Vermont]

==Protocol for Amygdala Regions ==

Reference Kwon et al, 2008, PMID 18374904

The frozen brains were sectioned between -2.30 and -3.14 mm from bregma (Paxinos and Watson, 1986) at 5 µm thickness and mounted on slides in a –20 ºC cryostat using the CryoJane system (Instrumedics, Hackensack, NJ). The frozen brain sections were defrosted at room temperature for 30 sec, then stained and dehydrated by the following procedure: 75% ethanol for 30 sec, DEPC-treated deionized H2O (DEPC-dH2O) for 30 sec, Histogene Staining solution (Arcturus, Mountain View, CA) for 3 min, DEPC-dH2O for 30 sec, 75% ethanol for 30 sec, 95% ethanol for 30 sec, 100% ethanol for 30 sec, xylene for 5 min, air dried in a fume hood for 15 min, and then desiccated with Drierite (W.A. Hammond Drierite, Xenia, OH) for 1 h.
LCM parameters were 15 or 30 µm diameter laser spot, a 10 ms laser pulse duration, and a 65 mW laser power. Multiple laser shots (150-200) were required to transfer each amygdala region. Following dissection, tissue sections were stained with methyl green (Vector Laboratories, Burlingame, CA) and coverslipped to verify the specificity of the dissection.

Total RNA was extracted from individual LCM samples with the Total RNA Microprep Kit (Stratagene, La Jolla, CA) according to the manufacturer’s protocols. RT-PCR was performed by using the OneStep RT-PCR Kit (Qiagen, Valencia, CA).

==Protocol for X-Gal Stained Cells ==

Reference Kwon and Houpt 2010 PMID 19925827

In order to confirm mRNA expression and preservation in β-Gal-positive cells, we performed RT-PCR after LCM of single cells. Transgenic mice were injected with LiCl (0.15 M, 40 ml/kg, i.p.). One hour later, they were anesthetized with sodium pentobarbitol, decapitated, and the brains were dissected. The brains were emmersed in M-1 Embedding Matrix (Shandon, Pittsburgh, PA), immediately frozen with dry ice, and stored at –80 ºC freezer until used. The frozen brains were sectioned at 8 µm and mounted on slides in a –20ºC cryostat using the CryoJane tape transfer system (Instrumedics, Hackensack, NJ). The sections were defrosted at room temperature for 30 s and then briefly washed with DEPC-dH2O. The brain sections were fixed in 70% ethanol at room temperature for 5 min and then washed with DEPC-dH2O for 5 min. Brain sections were then stained as above in X-Gal reaction buffer containing 1 mg/ml of X-Gal in DEPC-dH2O. The reaction was performed for 16 h at 37ºC in darkness.

Subsequent to X-Gal staining, the sections were washed in DEPC-dH2O for 5 min and dehydrated by the following procedure: 70% ethanol for 30 s, 95% ethanol for 30 s, 100% ethanol for 30 s, xylene for 5 min, air dried in a fume hood for 15 min, and then desiccated with Drierite (W.A. Hammond Drierite, Xenia, OH) for 1 h. X-Gal stained cells in the CeA, cortex and hippocampus were microdissected using the PixCell II LCM system (Arcturus, Mountain view, CA). A 7 um diameter laser spot, a 10 ms laser pulse duration, and a 85 mW laser power were used for the microdissection. Cells from cortex and hippocampus were included as positive controls, because those areas have previously been reported to have high levels of c-Fos and lacZ expression (Smeyne et al., 1992b and 1993). Total RNA was extracted from the LCM samples with the Total RNA Microprep Kit (Stratagene, La Jolla, CA) according to the manufacturer’s protocols. RT-PCR using primer pairs for c-Fos and β-actin was performed by using the OneStep RT-PCR Kit (Qiagen, Valencia, CA) as described above. The total RNA extract from each LCM sample of single cells was used in each RT-PCR reaction (15-20 single cells for β-actin and 30-40 single cells for c-Fos).

==Houpt Lab LCM Operating Procedure==

===Startup===

1. Turn on power for Samsung monitor, VGA up-converter,and MTI camera

2. Turn on power for PixCell II Microscope

3. turn on power for Controller (very stiff switch!)

===Dissection===

1. Place slide on stage, covering up the "I" shaped vacuum port

2. Engage vacuum on Controller, to secure slide to stage

3. Use "Prep strip" on slide to clean up surface of section

3. Pick up CapSure cap in swing arm, and swing over to place cap on top of slide (by grabbing the "beer can")

4. Turn laser "interlock" key clockwise from noon to 3 o'clock: this unlocks the laser

5. Press "Laser Enable" to get targeting laser. If you decrease microscope lamp illumination, you should see the red dot of the targeting laser. (It will be more less diffuse until the laser is focused).

6. Adjust size and focus of the laser spot with the controls on the left side of the laser mounted on the Microscope

7. Adjust the duration and power parameter of the laser pulse on the Controller.

* use the upper up-and-down arrows to select pulse parameter
* use the lower up-and-down arrows to set the parameter value
* Spotsize is set with the controls on the laser in previous step
* Temperature is read-only

8. Use microscope joystick to maneuver red dot over target region on the slide

9. Press the laser button to fire the laser. Can fire repeatedly to ensure collection.

10. Use microscope joystick to maneuver to an adjacent (or distant) spot to collect more samples.

11. Move cap over to "cap holder" on right of microscope.

[[Category:Protocols]]

False Color Mapping

2022-10-11T13:00:15Z

Chuck: Fix perm redirect

References for constructing False Color Maps for image analysis. I'd like to add tables of RGB values for constructing maps, because those numbers seem to be rarely posted.

==General References==

[https://web.archive.org/web/20190614182049/http://www.efg2.com/Lab/Library/Color/AndComputers.htm Extensive bibliography] of false color schemes.

==Luminance-Based Color Maps==

Based on this work: Stevens, S. S. Matching Functions Between Loudness and Ten Other Continua. Perception and Psychophysics, 1, pp. 5-8, 1966.

IBM on false color maps as used in the IBM Visualization Data Explorer system:
:https://web.archive.org/web/20180308150711/https://research.ibm.com/people/l/lloydt/color/color.HTM
:https://web.archive.org/web/20120928080636/http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm
:https://sites.google.com/site/bernicerogowitz/publications

:[https://www.mathworks.com/matlabcentral/fileexchange/28982-perceptually-improved-colormaps Mathlab perceptual colormaps]

==Discussions of Different Color Maps==

[https://doi.org/10.1109/MCG.2007.46 Rainbow colormap still harmful]

[https://colorbrewer2.org/ A webtool for testing colormaps]

[https://en.wikipedia.org/wiki/HSL_and_HSV HSL and HSV] entry in Wikipedia

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

==Calculation of color maps==

[https://www.fourmilab.ch/documents/specrend/ Colour Rendering of Spectra] for calculating the RGB value of different wavelengths of light. By John Walker, the co-founder of AutoDesk.

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

[http://www.midnightkite.com/color.html Color Science] referenced by Igor for algorithms for calculating rainbow spectra, blackbody, etc.--- in Fortran!

==Collections of color maps==
[https://geography.uoregon.edu/datagraphics/color_scales.htm Color schemes for improved data graphics]. Based on Light, A and P.J. Bartlein (2004) The end of the rainbow? Color schemes for improved data graphics. EOS Transactions of the American Geophysical Union 85(40):385

[https://www.wavemetrics.com/products/igorpro/creatinggraphs/colortab Igor's color tables]

[https://www.nws.noaa.gov/wwamap-prd/faq.php National Weather Service Map Colors] (keys to different phenomena, so not the same as a color map!)

[http://www.ncl.ucar.edu/Document/Graphics/color_tables.shtml National Center for Atmospheric Research (NCAR) Command Language]

[https://www.kennethmoreland.com/color-maps/ Diverging Color Maps]. Based on Kenneth Moreland. "Diverging Color Maps for Scientific Visualization." In Proceedings of the 5th International Symposium on Visual Computing, December 2009.

NIH ImageJ Lookup Tables (".lut" files) are available as a [https://imagej.nih.gov/ij/download/luts/luts.zip zip file], although the directory holds a smattering of other LUTs as well. According to the [https://imagej.nih.gov/ij/docs/menus/file.html ImageJ documentation], "The raw LUT file must be 768 bytes long and contain 256 reds, 256 blues and 256 greens."

[[Category:MindsEye]]

Water Maze

2022-10-11T12:58:46Z

Chuck: Fix perm redirect

Reference site: https://web.archive.org/web/20180317100212/http://watermaze.com/

==FSU setup for Mice==

===Currently have:===

Wading pool (approximate 2m diameter x 20 cm deep, dark blue)

Tripod and stand for video camera (could replace with ladder, or with ceiling mount)

Sony Digitial8 Camcorder

Heat lamps

Pump to empty pool

===Need to Get===
Platform for mice

White tempora or latex for making water opaque

geometric shapes or posters on walls to serve as visual cues

Heater for water

insulation to cover pool to prevent heat loss

drainage system (e.g. a spigot on side)

===Nice to get in future===

Ceiling mount for video camera or mount mirror on ceiling

Realtime tracking software

Table to get water maze off the floor.

==Sources of Water Mazes and Equipment==

[https://www.any-maze.com/mazes/water-maze/ ANY-maze] $1195 for 6-foot diameter, metal, with wheels and side drain

[https://sandiegoinstruments.com/product/water-maze/ SD Instruments] 6ft x 30" deep, polyethylene blue or white, drain kit

[https://hvsimage.com/information/3rd_party_pools.htm List of suppliers] HVS Image has a list of places that sell galvanized or polyethylene tanks

[https://www.bioseb.com/en/learningmemory-attention-addiction/1323-circular-pool.html Bioseb] French company

[https://www.tse-systems.com/products/behavior/maze-systems/water-maze.htm TSE Systems]

[https://muromachi.com/en/ Muromachi] Japanese company, I think they sell their own water maze pool.

==Aquaculture Tanks==

[http://www.solar-components.com/aqua.htm Solar Components] Transparent fiberglass tanks

[https://dolphinfiberglass.com Dolphin Fiberglass Products] located in Homestead, FL . They list 6' by 2' round tanks [https://www.aquaculturetanks.com/pricelist2.gif here]. Note that you can get feet put on the tanks. (see their picture catalog].

[https://web.archive.org/web/20090118141101/http://aquaticeco.com:80/categories/Tanks--Liners/97/0 Aquatic Eco-Systems] (now [https://pentairaes.com Pentair]) Located in Apopka, FL. Large selection.

[https://www.plastic-mart.com/category/41/plastic-stock-tanks-water-troughs Plastic-Mart] Livestock watering tubs.

==Tracking Software==

[https://web.archive.org/web/20180317100212/http://watermaze.com/ Watermaze Software (Edinburgh)] also sold by [https://www.coulbourn.com/category_s/291.htm Coulbourn Instruments]

[https://actimetrics.com Actimetrics]

[https://hvsimage.com/ HVS Image]

[http://www.biobserve.com/products/viewer/plugins/watermaze.html?gclid=CLDQwIDU144CFRVBgAodVgbo6A Biobserve]

[https://www.viewpoint.fr/en/p/software/videotrack Viewpoint]

[https://muromachi.com/archives/item/191 DV-Track] from Muromachi

[[Tracker]] from the [https://houptlab.org/ Houpt Lab]

[[Category:Magnetic_Fields]]
[[Category:Laboratory]]

Lab Supplies

2022-10-11T12:57:46Z

Chuck: Fix perm redirect

Generic supplies for the lab. For specific chemicals and antibodies, look for that item's specific page or topic

== General Lab ==

Pipette tips, ART P10 (pack of 960) VWR #72830-30 $160

Pipette tips, ART 20P (pack of 960) VWR #53225-764 $205.90 (2021-4-12)

Pipette tips, ART P200 (pack of 960) VWR #72830-044 $164

Pipette tips ART P1000 (case of 3200) VWR #72830-042 $238.28 (2021-4-12)

Serological Pipet (10 ml) (case of 200) VWR #89130-888 $57.39 (2021-4-12)

1.5 ml Microfuge tubes (case of 500) Fisher 05-408-129

0.5 ml Microfuge tubes (case of 500) Fisher 05-408-120

Microfuge tubes with screw top

Plastic scintillation vials (case of 500) VWR

Lab Tape 3/4" , assorted case VWR #89097-990 $110

Weigh boats, Medium (3.5 x 3.5") Fisher #08-732-113 or VWR 89106-766, $106.26
Weigh boats, Large (5.5 x 5.5") WR 89106-770, $188.08

Gloves:

Nitrile gloves

Face Mask (thick): 3M N95 Medium 10/Box ButlerSchein #017354 $20.99

== Histology Chemicals ==

Sodium Phosphate, monobasic, anhydrous VWR #BDH4542-1KGP $69.17

Sodium Phosphate, dibasic, anhydrous VWR #BDH4538-1KGP $57.65

Sodium Nitrite Sigma-Aldrich #S2252-500G $32.80

Paraformaldehyde, Granular (1 kg) [https://www.emsdiasum.com Electron Microscopy Science] #19210 or VWR #100504-162 (supplied by EMS) $18

Heparin Sodium injectable (5ml, 10 MU/ml), 25/pack Henry Schein # 375-6848 (check if there Butler Schein has newer number). $620

M-1 Embedding Matrix by Thermo Scientifc Shandon Fisher Scientific #1310 $22

Triton X-100 Sigma-Aldrich T8787-100ML $28

Bovine Serum Albumin Sigma-Aldrich A2153-100G $266

Biotinylated Anti-Rabbit IgG (made in goat) 1.5 mg, Vector Labs, #BA-1000 $130

Biotinylated Anti-Goat IgG Antibody (made in horse) 1.5 mg, Vector Labs, #BA-9500 $130

Biotinylated Anti-Mouse IgG Antibody (made in horse) 1.5 mg, Vector Labs, #BA-2000 $130

Vectastain Elite ABC kit, standard [https://vectorlabs.com Vector Labs] #PK-6100, $195

Hydrogen Peroxide, 100 ml bottle, VWR EM-HX0635-1, $21.67

Methyl Green (500 ml) [https://vectorlabs.com Vector Labs] #H-3402 $105

Xylene (4 L) VWR #JT9490-33 $239.88; case of 4 $600.93

Ethanol, 200 proof (Anhydrous), VWR #89125-172 1 gallon, case of 4, $116.22 (Tax free?)

Microscope slides, One-end Frosted, One Side, 75 mm x 25 mm x 1 mm, Gold Seal #3050, VWR #48312-068, pack of 72 $22.73 (0.31 each), case of 3600 $758.35 (0.21 each)

Cover Slips (case of 10) Mfg no #3317 VWR #48404-053 $116

Permount Fisher #SP15-100 $31.34

== Western Blotting ==

ECL Plus WB detection kit for 3000 cm2 membrane [https://www.gelifesciences.com GE Healthcare] #RPN2133 $466.00
:(also smaller size #RPN2132, $285)

Hybond ECL membrane (7 x 8 cm) 50 sheets [https://www.gelifesciences.com GE Healthcare] #RPN78D $162

Amersham Hyperfilm MP 8x10" 50 sheets [https://www.gelifesciences.com GE Healthcare] #28-9068-45 $217

Amersham Hyperfilm ECL 8x10" 50 sheets [https://www.gelifesciences.com GE Healthcare] #28-9068-38 $227

== PCR ==

Sybr Safe DNA gel stain 400 ul [https://www.thermofisher.com/us/en/home/brands/invitrogen.html Invitrogen] #S33102 $53.75

Trizol reagent 100 ml [https://www.thermofisher.com/us/en/home/brands/invitrogen.html Invitrogen] #15596-026 $151

Qiagen OneStep RT-PCR kit (25 Rxns) Qiagen #210210 $174

== Surgery ==

Mostly from Butler-Schein 888-691-2724 (now https://northamerica.covetrus.com)
Customer # 7760-866-000
:"Please Reference Customer Account # 7760-866-001 for DOH License"



Isoflurane (Aerrane) 250 ml Henry Schein #2091966TV $26 -- check for Butler Schein catalog & price

Ketofen (Ketoprofen) 100 mg/50 ml vial ButlerSchein #005487 $82

Sleepaway 100 ml bottle ButlerSchein #018877 $60.50 -- has to be ordered via EH&S

Sterile Gloves

Sterile Drapes 50/CTN ButlerSchein #003003 $13.49

Smocks:
:Disposable Cover Gown Blue X-Large 10/Pk ButlerSchein 1005806EZ $21.29
:Disposable Cover Gown Blue Med/Large 10/Pk #1005870EZ $21.29

Scalpel blades

Autoclip wound clip, case of 1000 BD/Clay Adams #427631, from VWR #15431-673 $601.29

Swabs Cotton Tipped Applicators 1000/box ButlerSchein #003263 $5.82

Sponges, Gauze 2x2 pack of 200 ButlerSchein #039187 $1.79

Needle Disposable 25x5/8 Vet Pack box of 100 ButlerSchein #004470 $7.98

Disposable 1ml Syringes with Luer Lock box of 100 ButlerSchein #034491 $42.23

Disposable 3ml Syringes with Luer Lock box of 100 ButlerSchein #017260 $7.77

Disposable 5cc Syringes ButlerSchein #017268 $18.41

Disposable 10cc Syringes ButlerSchein #017270 $12.64

Disposable 20 cc Syringes ButlerSchein #19331 $13.24

== Ingestive Experiments ==

Lithium Chloride [https://www.sigmaaldrich.com/ Sigma-Aldrich] #L4408-500G $120

Sodium Chloride Fisher# BP358-1

Saccharin, Sodium [https://www.sigmaaldrich.com/ Sigma-Aldrich] #S1002-500G $66

Sucrose, Ultrapure VWR ( JTBaker) #4097-06

Fructose Sigma #F0127-5kg or [https://www.bio-serv.com Bio-Serv] #3500

Glucose Sigma #G8270-10kg

Polycose Malto Dextrin (Lo Dex-10) 10 kg [https://www.bio-serv.com Bio-Serv] #3585 $75

Kaolin Pellets(1/2 inch diameter) 12.5 kg [https://www.researchdiets.com/OSD/diets/kaolin.htm Research Diets] #K50001, $375

Laminating Film for bottle labels
:Overlaminating Film 1-1/4” x 3” Labels in roll [https://www.seton.com Seton] #20893 $71.30 per roll

[[Category:Laboratory]]

Submissions

2022-10-11T12:56:27Z

Chuck: Fix perm redirect

'''Submitted: 2012-11-29'''

''Reviews: ''

''Resubmitted: ''

''Accepted: ''

Houpt, T.A., B.S.Kwon, C.E.Houpt, B. Neth, and J.C. Smith. Orientation within a high magnetic field determines swimming direction and laterality of c-Fos induction in mice. AJP-Regulatory, submitted.

MS# R-00549-2012

https://ajpregu.msubmit.net

----
'''Submitted: 2011-5-18'''

''Reviews: 2011-6-7''

''Resubmitted: 2011-8-23''

''Accepted: 2011-8-24''

Houpt, T.A., J. Cassell, L. Carella, B. Neth, and J.C. Smith. Head tilt in rats during exposure to a high magnetic field. Physiol. Behav., submitted.

MS# PHB-D-11-00344

https://www.editorialmanager.com/PHB/default.aspx

----
'''Submitted: 2011-5-2'''

''Reviews: 2011-5-23''

''Resubmitted: 2011-8-17''

''Accepted: 2011-8-18''

Spencer, C.M., L.A. Eckel, R. Nardos, and T.A. Houpt Area postrema lesions attenuate LiCl-induced c-Fos expression correlated with conditioned taste aversion learning. Physiol. Behav., submitted.

MS# PHB-D-11-00310

https://www.editorialmanager.com/PHB/default.aspx

----
'''Submitted: 2010-4-20'''

''Reviews: 2010-6-24''

''Resubmitted: 2011-2-18''

''Accepted: 2011-3-2''

Adam Kimbrough, Bumsup Kwon, Lisa A. Eckel, and Thomas A. Houpt, Systemic 5-bromo-2-deoxyuridine induces conditioned flavor aversion and c-Fos in the visceral neuraxis.

----
'''Submitted: 2010-8-9'''

''Reviews: 2010-9-6 ''

''Resubmitted: 2011-10-4''

''Accepted: 2011-10-31''

Bumsup Kwon and Thomas A. Houpt, Mitogen-activated protein kinase in the amygdala plays a critical role in lithium chloride-induced taste aversion learning.

MS Ref. No. NLM-10-141R1

----
'''Submitted: '''

''Reviews: ''

''Resubmitted: 2010-11-15''

''Accepted: 2010-11-23''

Houpt, Cassell, Hood, DenBleyker, Janowitz, Mueller, Ortega, and Smith Behavioral effects on rats of motion within a high static magnetic field.

Ms. Ref. No.: PHB-D-10-00463

----
'''Submitted: 11-9-09'''

''Reviews: 12-17-09''

''Resubmitted: 2010-2-17''

''Accepted: 2010-2-25''

Houpt, T.A. and C.E. Houpt. Circular swimming in mice after exposure to a high magnetic field. Physiol. Behav., submitted.

MS# PHB

https://www.editorialmanager.com/PHB/default.aspx

----

'''Submitted: 10/5/09'''

''Reviews: 11-2-09''

''Resubmitted 11-30-09''

''Accepted 12-22-09''

Houpt, T.A. et al. Repeated exposure attenuates the behavioral response of rats to static high magnetic fields. Physiol. Behav., submitted.

MS# PHB-D-09-00478

https://www.editorialmanager.com/PHB/default.aspx

----

'''Submitted: 9/22/09'''

''Reviews: 10-29-09''

''Resubmitted: 11-15-09''

''Accepted 11-18-09''

Smith, P., J.C. Smith and T.A. Houpt Interactions of temperature and taste in conditioned aversions. Physiol. Behav., submitted.

MS# PHB-D-09-00450

https://www.editorialmanager.com/PHB/default.aspx

----

'''Submitted 9/3/09'''

''Reviews: 9/30/09''

''Submitted to Brain Res. 11-16-09''

''Reviews: 12-15-09''

Kwon, B.S. and T.A. Houpt. Acute lithium chloride induces c-Fos and phospho-acetylation of histone H3 in the amygdala and is enhanced by inhibition of histone deacetylase. Neurosci., submitted.

MS# NSC-09-1202

https://www.editorialmanager.com/nsc/default.aspx

----

'''Submitted: 6/16/09'''

''Reviews: 7/28/09''

''Resubmitted: 11/9/09''

''Accepted: 11/11/09''

Kwon, B.S. and T. A. Houpt. A combined method of laser capture microdissection and X-Gal histology to analyze gene expression in c-Fos-specific neurons. J. Neurosci. Methods, in press.

https://www.editorialmanager.com/JNEUMETH/default.aspx

----

'''Submitted: 9/12/08'''

''Reviews: 10/9/08''

Rivera, H.M. Oberbeck, D.R. , Kwon, B.S. , Houpt, T.A. , Eckel, L.A. Estradiol increases Pet-1 and serotonin transporter mRNA in the raphe nuclei of ovariectomized rats. Brain Res., submitted.

----

'''Submitted: 5/29/08'''

Golden, G.J. K.A. Houpt, and T.A. Houpt. Quantitative analysis of a clinical canine aggression screen. JAVMA, submitted.

MS# JAVMA-08-05-0307

https://mc.manuscriptcentral.com/javma

----

'''Submitted: 8/20/07'''

''Reviews: 10/23/07''

''Resubmitted: 7/31/08''

''Second Set of Reviews: 8/27/08''

Cason, A.M., B.S. Kwon, J.C. Smith, and T.A. Houpt. Labyrinthectomy abolishes the behavioral and neural response of rats to a high-strength static magnetic field. Physiol. Behav., submitted.

MS# PHB-D-07-00345

https://www.editorialmanager.com/PHB/default.aspx

----

'''Submitted: 8/6/07'''

''Proofs submitted 6/17/08''

Freeman, M.E., D. Grattan, and T.A. Houpt. The Hypothalamus. In "Neuroscience in Medicine", Ed. P.M. Conn, New York: Humana Press

Editor: connm@ohsu.edu, freeman@neuro.fsu.edu

----

'''Submitted: 6/12/07'''

''Reviews: 8/7/07''

''Resubmitted: 9/10/08''

''Second Reviews: 9/19/08''

''Resubmitted: 9/23/08''

''Accepted: 9/26/08''

''Proofs: 10/16/08''

Davenport, R.A. and T.A. Houpt. D-cycloserine enhances short-delay, but not long-delay, conditioned taste aversion learning in rats. Pharmacol. Biochem. Behav. submitted.

MS #PBB-D-07-00173

https://www.editorialmanager.com/PBB/default.aspx

----

'''Submitted: 6/5/07'''

''Rejected 7/6/07''

Cason, A.M., B.S. Kwon, J.C. Smith, and T.A. Houpt. Labyrinthectomy abolishes the behavioral and neural response of rats to a high-strength static magnetic field. J. Neurosci., submitted.

MS# JN-RM-2535-07

https://mc.manuscriptcentral.com/jneurosci

----

'''Submitted: 5/4/07'''

''Reviews: 6/11/07''

''Requested Extension: 9/6/07''

''Revision submitted: 11/19/07''

''Reviews: 12/26/07''

''Revision submitted: 1/2/08''

''Accepted: 1/28/08''

''Proofs submitted: 3/18/08''

Kwon, B.S., M. Goltz, and T.A. Houpt. Expression of AP-1 family transcription factors in the amygdala during conditioned taste aversion learning: role for Fra-2, has been given a new ID. Brain Research, submitted.

MS #BRES-D-07-00784

https://www.editorialmanager.com/brainres/default.aspx

----

'''Submitted: 1/20/07'''

''Reviews: 7/3/07''

''Revision submitted: 9/4/07''

''Copy edits submitted: 6/4/08"

''Proofs submitted: 7/16/08''

Houpt, T.A . and J.C. Smith. Conditioned taste aversion induced by exposure to high magnetic fields. To appear in “Conditioned Taste Aversion: Behavioral and Neural Processes,” edited by Steve Reilly and Todd R. Schachtman, Oxford University Press.

Editors: sreilly@uic.edu, SchachtmanT@missouri.edu

[[Category:Laboratory]]

False Color Mapping

2022-10-04T11:42:08Z

Chuck: Perm redirect

References for constructing False Color Maps for image analysis. I'd like to add tables of RGB values for constructing maps, because those numbers seem to be rarely posted.

==General References==

[https://web.archive.org/web/20190614182049/http://www.efg2.com/Lab/Library/Color/AndComputers.htm Extensive bibliography] of false color schemes.

==Luminance-Based Color Maps==

Based on this work: Stevens, S. S. Matching Functions Between Loudness and Ten Other Continua. Perception and Psychophysics, 1, pp. 5-8, 1966.

IBM on false color maps as used in the IBM Visualization Data Explorer system:
:https://web.archive.org/web/20180308150711/https://research.ibm.com/people/l/lloydt/color/color.HTM
:https://web.archive.org/web/20120928080636/http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm
:https://sites.google.com/site/bernicerogowitz/publications

:[https://www.mathworks.com/matlabcentral/fileexchange/28982-perceptually-improved-colormaps Mathlab perceptual colormaps]

==Discussions of Different Color Maps==

[https://doi.org/10.1109/MCG.2007.46 Rainbow colormap still harmful]

[https://colorbrewer2.org/ A webtool for testing colormaps]

[https://en.wikipedia.org/wiki/HSL_and_HSV HSL and HSV] entry in Wikipedia

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

==Calculation of color maps==

[https://www.fourmilab.ch/documents/specrend/ Colour Rendering of Spectra] for calculating the RGB value of different wavelengths of light. By John Walker, the co-founder of AutoDesk.

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

[http://www.midnightkite.com/color.html Color Science] referenced by Igor for algorithms for calculating rainbow spectra, blackbody, etc.--- in Fortran!

==Collections of color maps==
[https://geography.uoregon.edu/datagraphics/color_scales.htm Color schemes for improved data graphics]. Based on Light, A and P.J. Bartlein (2004) The end of the rainbow? Color schemes for improved data graphics. EOS Transactions of the American Geophysical Union 85(40):385

[https://www.wavemetrics.com/products/igorpro/creatinggraphs/colortab.htm Igor's color tables]

[https://www.nws.noaa.gov/wwamap-prd/faq.php National Weather Service Map Colors] (keys to different phenomena, so not the same as a color map!)

[http://www.ncl.ucar.edu/Document/Graphics/color_tables.shtml National Center for Atmospheric Research (NCAR) Command Language]

[https://www.kennethmoreland.com/color-maps/ Diverging Color Maps]. Based on Kenneth Moreland. "Diverging Color Maps for Scientific Visualization." In Proceedings of the 5th International Symposium on Visual Computing, December 2009.

NIH ImageJ Lookup Tables (".lut" files) are available as a [https://imagej.nih.gov/ij/download/luts/luts.zip zip file], although the directory holds a smattering of other LUTs as well. According to the [https://imagej.nih.gov/ij/docs/menus/file.html ImageJ documentation], "The raw LUT file must be 768 bytes long and contain 256 reds, 256 blues and 256 greens."

[[Category:MindsEye]]

ICV Cannulation

2022-09-20T13:05:32Z

Chuck: Update Bosworth link to Keystone.

[[File:ICV cannulation.png|thumb|Cross-section schematic of cannula attached to skull with dental acrylic and screws.]]
For other stereotaxic coordinates, see also [[Amygdala]], [[JA Lateral Hypothalamus Lesions]].

==Lateral Ventricular Cannula==

1.2 mm caudal to bregma

1.5 mm lateral to the midline

4 mm below the skull surface

Under isoflurane anesthesia, each rat was stereotaxically implanted with a 22-gauge, stainless steel, guide
cannula (model C313G, Plastics One, Roanoke, VA) aimed towards the lateral cerebral ventricle (1.2 mm caudal to bregma, 1.5 mm
lateral to the midline, and 4 mm below the skull surface; Houpt 1998 PMID 9437750). Guide cannulas were held in place with dental acrylic bonded to
stainless steel screws anchored to the skull. A 28-gauge obdurator was inserted into each guide cannula and remained in place
except during injections when it was removed and replaced with an 28-gauge injector that extended 1.0 mm beyond the tip of the guide cannula.

To test the patency and placement of the cannula in the lateral ventricle, water-replete rats were injected with
100 ng human angiotensin II (Ang II; Sigma Chemical Co, St Louis, MO) dissolved in 5 µl volume of saline (0.15 M).
The volume of all icv injections was 5 µl, delivered over 30s with a handheld 50 µl syringe (Hamilton Co, Reno, NV).
Immediately after the ICV injection, rats were returned to their home cage with access to a water bottle.
The latency to drink was recorded; rats that failed to drink within 2 minutes of the angiotensin II injection were
dropped from the study. Cannula placements were also verified postmortem by sectioning through the brain.
ICV injections of 5 µl volume were given by hand to lightly restrained rats using a 50 µl Hamilton microsyringe.

==Fourth Ventricular Cannula==

3.2 mm caudal to lambda

0 mm lateral to the midline

7.2 mm below the skull surface

Under isoflurane anesthesia, each rat was stereotaxically implanted with a single 22-gauge stainless steel guide cannula
(model C315G; Plastics One, Inc., Roanoke, VA) aimed towards the fourth ventricle (4V). The tip of the guide cannula
was positioned on the midline 3.2 mm caudal to lambda and 7.2 mm below the skull surface (stereotaxic coordinates
taken from (Baird et al. 2009 PMID 19008313)). Guide cannulas were held in place with dental acrylic bonded to stainless
steel screws anchored to the skull. A 28-gauge obdurator extending 1.0 mm beyond the guide
cannula was inserted into each guide cannula and remained in place except during injections when it was removed and
replaced with a 28-gauge injector that extended 1.0 mm beyond the tip of the guide cannula.

To test the patency and placement of the cannula in the lateral ventricle, water-replete rats were injected with
XXX ng bombesin (California Peptides) dissolved in 5 µl volume of saline (0.15 M). The volume of all icv injections
was 5 µl, delivered by hand over 30s to lightly restrained rats using a 50 µl Hamilton microsyringe (Hamilton Co, Reno, NV).
Immediately after the ICV injection, rats were returned to their home cage with access to a water bottle.
The latency to initiate and duration of grooming was recorded; rats that failed to groom within 2 minutes of the
bombesin injection or groomed for less than XXX minutes were dropped from the study. Cannula placements were
also verified postmortem by sectioning through the brain.

==Supplies==

===Plastics One Cannulas and Screws===

:[https://www.p1tec.com P1 Technologies (née Plastics One)]
:6591 Merriman Rd
:Roanoke VA 24018
:Tel: 540-772-7950
:Fax: 540-777-5900

''Check prices on annual price list.''

====22 gauge guide cannulas for ventricular injections====

Use C313 components, which provide 28 gauge dummy and injectors.
e.g., for guide cannula(G) projecting 5 mm below skull surface,
with large-cap dummy cannulas (DC) and injectors (I) projecting 1 mm beyond tip of the guide cannula:

:C313G/SPC 5 mm
:C313DC/SPC(LG) for 5 mm C313G with 1 mm projection
:C313I/SPC for 5 mm C313G with 1 mm projection

====26 gauge guide cannulas for site-specific injections====

Use C315 components, which provide 33 gauge dummy and injectors.
e.g., for guide cannula(G) projecting 8 mm below skull surface,
with small-cap dummy cannulas (DC) and injectors (I) projecting 0.5 mm beyond tip of the guide cannula:

:C315G/SPC 8 mm
:C315DC/SPC(SM) for 8 mm C315G with 0.5 mm projection
:C315I/SPC for 8 mm C315G with 0.5 mm projection

====Screws for skull====

We use screws of 0-80 size with shaft length 3/32 inches (2.4 mm).
These are a little long, but they are stronger and easier to work with than 1/16 inch (1.6 mm) long screws.
Also need the small drill bit.

:0-80 X 3/32 (packages of 100)
:D#56 1.18 mm Drill Bit for 0-80 screws

----

===Other supplies needed - more detail to come===

====Pin Vise for hand drilling the screws====

Most pin vises are nickel plated, and so cannot be autoclaved but must be sterilized e.g. with 70% EtOH.
:VWR 63041-530 Pin Vise - Double-Ended, stainless steel

Little tubing for washer around top of guide cannula?

Superglue

Size of screwdriver? source of SS screw drivers?

Trephin drill bits

Hamilton microsyringe and needle

PE-50 tubing to connect with injector

Syringe Pump

====New Truliner Denture Lining Standard Kit, Pink====

From either Henry Schein Dental, #2502527EZ, $105.29, or,
[https://dental.keystoneindustries.com/product/new-truliner/ Bosworth #0921970] $45.00

:Harry J. Bosworth Company
:7227 North Hamlin Avenue
:Skokie, Illinois 60076 USA
:Toll-Free: 800-323-4352
:Phone: 847-679-3400
:Fax: 847-679-2080
:E-Mail: HJBinfo@bosworth.com

[[Category:Taste_Aversion]][[Category:Protocols]]

False Color Mapping

2022-09-07T19:26:12Z

Chuck: Update HTTP to HTTPS

References for constructing False Color Maps for image analysis. I'd like to add tables of RGB values for constructing maps, because those numbers seem to be rarely posted.

==General References==

[https://web.archive.org/web/20190614182049/http://www.efg2.com/Lab/Library/Color/AndComputers.htm Extensive bibliography] of false color schemes.

==Luminance-Based Color Maps==

Based on this work: Stevens, S. S. Matching Functions Between Loudness and Ten Other Continua. Perception and Psychophysics, 1, pp. 5-8, 1966.

IBM on false color maps as used in the IBM Visualization Data Explorer system:
:https://web.archive.org/web/20180308150711/https://research.ibm.com/people/l/lloydt/color/color.HTM
:https://web.archive.org/web/20120928080636/http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm
:https://sites.google.com/site/bernicerogowitz/publications

:[https://www.mathworks.com/matlabcentral/fileexchange/28982-perceptually-improved-colormaps Mathlab perceptual colormaps]

==Discussions of Different Color Maps==

[https://doi.org/10.1109/MCG.2007.46 Rainbow colormap still harmful]

[https://colorbrewer2.org/ A webtool for testing colormaps]

[https://en.wikipedia.org/wiki/HSL_and_HSV HSL and HSV] entry in Wikipedia

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

==Calculation of color maps==

[https://www.fourmilab.ch/documents/specrend/ Colour Rendering of Spectra] for calculating the RGB value of different wavelengths of light. By John Walker, the co-founder of AutoDesk.

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

[http://www.midnightkite.com/color.html Color Science] referenced by Igor for algorithms for calculating rainbow spectra, blackbody, etc.--- in Fortran!

==Collections of color maps==
[https://geography.uoregon.edu/datagraphics/color_scales.htm Color schemes for improved data graphics]. Based on Light, A and P.J. Bartlein (2004) The end of the rainbow? Color schemes for improved data graphics. EOS Transactions of the American Geophysical Union 85(40):385

[https://www.wavemetrics.com/products/igorpro/creatinggraphs/colortab.htm Igor's color tables]

[https://www.nws.noaa.gov/wwamap-prd/faq.php National Weather Service Map Colors] (keys to different phenomena, so not the same as a color map!)

[http://www.ncl.ucar.edu/Document/Graphics/color_tables.shtml National Center for Atmospheric Research (NCAR) Command Language]

[https://www.kennethmoreland.com/color-maps/ Diverging Color Maps]. Based on Kenneth Moreland. "Diverging Color Maps for Scientific Visualization." In Proceedings of the 5th International Symposium on Visual Computing, December 2009.

NIH ImageJ Lookup Tables (".lut" files) are available as a [https://rsb.info.nih.gov/ij/download/luts/luts.zip zip file], although the directory holds a smattering of other LUTs as well. According to the [https://imagej.nih.gov/ij/docs/menus/file.html ImageJ documentation], "The raw LUT file must be 768 bytes long and contain 256 reds, 256 blues and 256 greens."

[[Category:MindsEye]]

False Color Mapping

2022-09-07T19:22:58Z

Chuck: Switch EFG2 biblio link to Archive.org, since it is now domain squatted

References for constructing False Color Maps for image analysis. I'd like to add tables of RGB values for constructing maps, because those numbers seem to be rarely posted.

==General References==

[https://web.archive.org/web/20190614182049/http://www.efg2.com/Lab/Library/Color/AndComputers.htm Extensive bibliography] of false color schemes.

==Luminance-Based Color Maps==

Based on this work: Stevens, S. S. Matching Functions Between Loudness and Ten Other Continua. Perception and Psychophysics, 1, pp. 5-8, 1966.

IBM on false color maps as used in the IBM Visualization Data Explorer system:
:https://web.archive.org/web/20180308150711/https://research.ibm.com/people/l/lloydt/color/color.HTM
:https://web.archive.org/web/20120928080636/http://www.research.ibm.com/dx/proceedings/pravda/truevis.htm
:https://sites.google.com/site/bernicerogowitz/publications

:[https://www.mathworks.com/matlabcentral/fileexchange/28982-perceptually-improved-colormaps Mathlab perceptual colormaps]

==Discussions of Different Color Maps==

[https://doi.org/10.1109/MCG.2007.46 Rainbow colormap still harmful]

[https://colorbrewer2.org/ A webtool for testing colormaps]

[https://en.wikipedia.org/wiki/HSL_and_HSV HSL and HSV] entry in Wikipedia

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

==Calculation of color maps==

[http://www.fourmilab.ch/documents/specrend/ Colour Rendering of Spectra] for calculating the RGB value of different wavelengths of light. By John Walker, the co-founder of AutoDesk.

[http://www.vendian.org/mncharity/dir3/blackbody/ What color is a blackbody?] (for constructing the "heat" color map.)

[http://www.midnightkite.com/color.html Color Science] referenced by Igor for algorithms for calculating rainbow spectra, blackbody, etc.--- in Fortran!

==Collections of color maps==
[http://geography.uoregon.edu/datagraphics/color_scales.htm Color schemes for improved data graphics]. Based on Light, A and P.J. Bartlein (2004) The end of the rainbow? Color schemes for improved data graphics. EOS Transactions of the American Geophysical Union 85(40):385

[http://www.wavemetrics.com/products/igorpro/creatinggraphs/colortab.htm Igor's color tables]

[http://www.nws.noaa.gov/wwamap-prd/faq.php National Weather Service Map Colors] (keys to different phenomena, so not the same as a color map!)

[http://www.ncl.ucar.edu/Document/Graphics/color_tables.shtml National Center for Atmospheric Research (NCAR) Command Language]

[https://www.kennethmoreland.com/color-maps/ Diverging Color Maps]. Based on Kenneth Moreland. "Diverging Color Maps for Scientific Visualization." In Proceedings of the 5th International Symposium on Visual Computing, December 2009.

NIH ImageJ Lookup Tables (".lut" files) are available as a [http://rsb.info.nih.gov/ij/download/luts/luts.zip zip file], although the directory holds a smattering of other LUTs as well. According to the [https://imagej.nih.gov/ij/docs/menus/file.html ImageJ documentation], "The raw LUT file must be 768 bytes long and contain 256 reds, 256 blues and 256 greens."

[[Category:MindsEye]]

Polygon Area

2022-09-07T19:19:06Z

Chuck: Update MathWorld links to HTTPS

To calculate the area of a non-self-intersecting polygon:

see Polygon Area at :
:Weisstein, Eric W. "Polygon Area." From MathWorld--A Wolfram Web Resource. https://mathworld.wolfram.com/PolygonArea.html

If the polygon is a lattice polygon, then area can be calculated from the number of interior lattice points by Picks theorem:
:''A = I + B/2 - 1, where I = # of interior lattice points, B = # of border points''
SInce all the outlines in MindsEye are on a pixelated grid, this may be the fastest way to calculate the area.

:Weisstein, Eric W. "Lattice Polygon." From MathWorld--A Wolfram Web Resource. https://mathworld.wolfram.com/LatticePolygon.html

see also Randall Crandall Projects in Scientific Computation ISBN-10: 0387950095 (but I forget why this book is relevant)

[[Category:MindsEye]]

Sweeteners

2022-08-30T12:58:55Z

Chuck: Update link to https

{| class="wikitable sortable" border = "1" cellspacing="0" cellpadding = "3"
|+'''Sweeteners'''
|-bgcolor="silver"
! width="125" | Chemical Name !! width="150" | Tradename !! Wiki !! width="75" | MW !! width="125" | Formula !! width="100" | CAS !! width="75" | Calories !! width="100" | Sweetness
|-
| [[Saccharin]] || [https://www.sweetnlow.com Sweet n Lo] || [https://en.wikipedia.org/wiki/Saccharin Wiki] || align="center"| 183.18 ||align="center"| C7H5NO3S || align="center"|81-07-2 || calories || rs
|-
| [[Sucrose]] || [https://www.sucrose.com/ Sugar] || [https://en.wikipedia.org/wiki/Sucrose Wiki] || align="center"| 342.29 || align="center"|C12H22O11 || align="center"|57-50-1 || calories || rs
|-
| [[ Fructose]] || [https://corn.org/products/sweeteners/ HFCS] || [https://en.wikipedia.org/wiki/Fructose Wiki] || align="center"| 180.16 || align="center"|C6H12O6 || align="center"|57-48-7 || calories || rs
|-
| [[Xylitol]] || Xylitol || [https://en.wikipedia.org/wiki/Xylitol Wiki] || align="center"| 152.15 || align="center"|C5H12O5 || align="center"|87-99-0 || calories || rs
|-
| [[Aspartame]] || [https://web.archive.org/web/20180721024410/http://www.nutrasweet.com:80/ NutraSweet] || [https://en.wikipedia.org/wiki/Aspartame Wiki] || align="center"| 294.3 || align="center"|C14H18N2O5 || align="center"|22839-47-0 || calories || rs
|-
| [[Steviol glycoside]] || [https://www.truvia.com Truvia] || [https://en.wikipedia.org/wiki/Steviol_glycoside Wiki] || align="center"| 318.45|| align="center"|C20H30O3 || align="center"|471-80-7 || calories || rs
|-
| [[ Sucralose]] || [https://www.splenda.com Splenda] || [https://en.wikipedia.org/wiki/Sucralose Wiki] || align="center"| 397.64 || align="center"| C12H19Cl3O8 || align="center"|56038-13-2 || calories || rs
|-
| [[ Acesulfame K]]||[https://www.celanese.com/food-ingredients/products/sunett.aspx Sunett], [http://www.sweetone.com/ Sweet One]|| [https://en.wikipedia.org/wiki/Acesulfame_K Wiki] || align="center"| 201.24 || align="center"| C4H4KNO4S || align="center"|55589-62-3 || calories || rs
|-
| [[ Dulcin]] || sucrol, valzin|| [https://en.wikipedia.org/wiki/Dulcin Wiki] || align="center"| 180.20 || align="center"|C9H12N2O2 || align="center"|150-69-6|| calories || rs
|-
| [[ Perillartine]] || (Japanese name: ペリラルチン, available from [https://highchem.co.jp/chem/details.php?cas=30950-27-7 HighChem] and others) japanese product page?|| [https://en.wikipedia.org/wiki/Perillartine Wiki] || align="center"| 165.23 || align="center"| C10H15NO || align="center"|30950-27-7 || calories || rs
|}

Notes:

'''Tradename''' links to manufacturer's website

'''Calories''' (kcal/g) is available calories to humans following ingestion

'''Sweetness''' (g/g sucrose) is reported (maximal?) sweetness to humans relative to sucrose (at a particular concentration)?

= USDA Sugar and Sweeteners Data=

[https://www.ers.usda.gov/data-products/sugar-and-sweeteners-yearbook-tables.aspx Recommended Data]

[https://www.ers.usda.gov/topics/crops/sugar-sweeteners/readings/ Recommended Readings]

[https://usda.library.cornell.edu/concern/publications/pv63g024f?locale=en Sugar and Sweeteners Outlook] (PDF file)
(January, May, and September) provides an update of current market and policy developments and their impacts on the sugar and corn sweetener industries.

[[Category:Taste Aversion]]
[[Category:Ingestive Behavior]]

Ibotenic Acid

2022-08-30T12:57:40Z

Chuck: Update to https

Sources:

[https://www.tocris.com/products/ibotenic-acid_0285 Tocris Bioscience], Item #0285, 5mg for $229 (May 2011).

M.Wt: 158.11 Formula: C5H6N2O4 CAS No:[2552-55-8]

=Ibotenic Acid Lesion Surgery=

Ibotenic acid (10 mg/ml in saline) will be infused over 5 min for a total volume of 0.1 µl.

Rats will be stereotaxically injected with ibotenic acid (Natural Products Co., Vashon, WA) to destroy cell bodies within specific brain subnuclei while sparing fibers of passage. Under isoflurane anesthesia and following aseptic surgical preparation, the rat's head is immobilized in a stereotaxic apparatus. An incision is made longitudinally along the midline of the head, to expose the skull. A 1.8 mm hole is drilled in the skull with a Dremel motortool and a Fine Science Tool trephine bit. Injections will be made through a blunt 33 gauge needle attached to a 2 µl Hamilton microsyringe under the control of a syringe pump. Ibotenic acid (10 mg/ml in saline) will be infused over 5 min for a total volume of 0.1 µl. The injector needle will be left in place for 10 min after the infusion and before withdrawal to minimize back flow along the needle track. Sham lesions will be produced by injection of phosphate-buffered saline (0.1 µl) into the same areas, thus controlling for non-specific damage from lowering the injector through overlying tissue. All lesions will be produced bilaterally.

'''Note on Infusion Pump:'''
The KD Scientific 200P pump has a table of syringe sizes, but the settings for Hamilton microsyringes only go down to 10ul. To get 0.2 microliters from a 1 ul syringe, set the pump to a Hmailton 10 ul syringe, but put in the volume of 2.2 ul at 0.44 ul per minute, which will dispense 0.2 microliters over 5 minutes from the 1 ul syringe. (Should probably recalibrate these settings every so often.)

The skull hole is packed with gel foam, and the incision closed with wound clips. Wound clips are removed 7-10 days after surgery. Antibiotics (dose to be determined in consultation with the veterinary staff) are administered 1 h prior to cranial surgery, and buprenorphine (0.2 mg/kg i.p.) is given immediately post-surgery as an analgesic. Antibiotics are given once daily for 7 days after surgery. Body weight and water intake are measured daily, along with other signs of stress, irritability, or pain. Reduced water intake or the appearance of dehydration will be treated with continued antibiotics, and replacement and maintenance of body fluids with warmed 0.15M NaCl or 0.3 M dextrose as recommended by the veterinary staff.

Prior to experimental testing, coordinates for injector placement will be determined in a group of test animals based on Paxinos and WatsonInjector placement will be verified by injections of Sudan Black (0.4 µl). A series of preliminary studies will be conducted to determine the extent of cell damage by cresyl violet staining. Animals will have injections performed, then be euthanized. Sections will be cut through the remainder of the brain and stained with Weil myelin stain to visualize degenerating neurons that may project through the lesion site. Based on these preliminary studies, the concentration and volume of ibotenic acid injections will be adjusted to maximize cell death without damaging fibers of passage.

=Verification of Lesion Site=

Following Jongen-Relo, A. L., & Feldon, J. (2002) PMID 12126979 and in the gustatory cortex, Geddes et al. (2008) PMID 18823161, we will determine loss of neurons using a mouse monoclonal [https://www.emdmillipore.com/US/en/product/Anti-NeuN-Antibody-clone-A60,MM_NF-MAB377 anti-NeuN, clone A60], from Millipore, catalog MAB377, price $259.00. Jongen-Relo used a primary concentration of 1:5000 with a 48-h incubation at 4 C.

[[Category:Taste Aversion]]

14-3-3

2022-08-30T12:55:00Z

Chuck: Update to https

==14-3-3==

https://medlineplus.gov/genetics/gene/ywhae/

Ywhae gene = 14-3-3 epsilon = tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (Ywhae)

Mus musculus tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide (Ywhae), mRNA
NCBI Reference Sequence: NM_009536.4

==Dr. Yi Zhou's 14-3-3 FKO (Thy1-YFP-DIfopein) Transgenic Mice==

See SFN abstracts (2010) 53.1/M17 and (2011) 790.09/FF16

From Kourtney Graham's Honor's Thesis:

<blockquote>
In order to study the role of 14-3-3 proteins in the nervous system_ in
vivo_, we have successfully created lines of neuronal-specific
transgenic mice that may inhibit 14-3-3 dependent cellular processes.
These transgenic mice express a YFP-fused peptide (R18) which binds to
endogenous 14-3-3, and thus blocking its capability to interact with its
binding partners; and are therefore considered to be a functional
knockout. The transgenes are expressed under the control of the Thy-1
promoter which is neuronal-specific and produces variation of transgene
expression in different brain regions, which is great among founder
lines but minimal among descendants of a single founder (Feng et al.
2000). To minimize strain-dependent genetic variation, we have
backcrossed the founder lines with wild-type C57BL/6 mice for at least 8
generations.
</blockquote>

From Sun et al PMID 23861400 :
Glutamatergic kainate receptors (KAR) KAR-EPSCs at mossy fiber-CA3 synapses decay significantly faster in the 14-3-3 functional knock-out mice (but no difference in NMDA-R or AMPA-R EPSC in same synapses)

==R18 peptide ==

PMID 11577088

R18 is a synthetic 21 amino acid unphosphorylated peptide (MW 2309.6) which binds to the same amphipathic groove on the surface of 14-3-3 as phosphorylated peptides, with high affinity for all 7 mammalian isoforms of 14-3-3 PMID 10493820. Commercial source of peptide [https://www.enzolifesciences.com/BML-P214/r18-peptide/ Enzo #BML-P214-0001].

Difopein is a construct with two R18 monomers in a single 62 amino acid peptide PMID 11577088. Commercial source of peptide: [https://www.tocris.com/products/difopein_2145 Tocris #1245]

R18 Sequence:

Pro-His-Cys-Val-Pro-Arg-Asp-Leu-Ser-Trp-Leu-Asp-Leu-Glu-Ala- Asn-Met-Cys-Leu-Pro-OH

PHCVPRDLSWLDLEANMCLP

Difopein sequence (with individual R18 monomers in parentheses):

SADGA (PHCVP RDLSW LDLEA NMCLP) GAAGL DSADG A(PHCV PRDLS WLDLE ANMCL P) GAAG LE

C54 (consisting of the carboyl-terminal 54-amino acid region of theHMG-box binding protein Ste11p ) is another 14-3-3 inhibitor that is structurally unrelated to R18/difopein. The C54 region permits sequestration of Ste11p in the cytoplasm to inhibit nuclear localization PMID 12697825.

==Thy-1 Promoter==

PMID 11086982

==YFP==

YFP is 239 amino acids long (717 bp) according to plasmid map of Invitrogen [https://www.thermofisher.com/order/catalog/product/V35820 Vivid ColorsTM pcDNATM/6.2 N-terminal EmGFP/YFP-DEST vectors] see p, 28 of the manual. Difopein is 62 amino acids long (186 bp), so total YFP-difopein fusion protein should be ~ 301 amino acids (903 bp).

== 14-3-3 FKO papers==
Vogt, Peggy, [https://diginole.lib.fsu.edu/islandora/object/fsu:204445 "Exploring the Function of 14-3-3 Proteins in Neurodegenerative Disease"] (2011). Honors Theses. Paper 42.

C. Sun, H. Qiao, Q. Zhou, Y. Wang, Y. Wu, Y. Zhou, et al., Modulation of GluK2a Subunit-containing Kainate Receptors by 14-3-3 Proteins, J Biol Chem. 288 (2013) 24676–24690. PMID 23861400

Qiao H, Foote M, Graham K, Wu Y, Zhou Y. 14-3-3 proteins are required for hippocampal long-term potentiation and associative learning and memory. J Neurosci. 34(2014):4801-8. PMID 24695700

==Antisera for IP Experiments==
anti-pan-14-3-3 (K-19) , rabbit polyclonal, Santa Cruz #sc-629, 200 ug/1 ml, $279 [https://www.scbt.com/p/pan-14-3-3-antibody-k-19 datasheet]

anti-HDAC4 (H-92), rabbit polyclonal, Santa Cruz #sc-11418, 200 ug/1 ml, $279 [https://www.scbt.com/p/hdac4-antibody-h-92 datasheet]

anti-Torc1 (C71D11), rabbit mAb, Cell Signaling #2587 $225 [https://www.cellsignal.com/products/primary-antibodies/torc1-crtc1-c71d11-rabbit-mab/2587?Ntk=Products&Ntt=2587 datasheet]

Water Maze

2022-08-30T12:52:20Z

Chuck: Downgrade non-HTTPS sites

Reference site: https://web.archive.org/web/20180317100212/http://watermaze.com/

==FSU setup for Mice==

===Currently have:===

Wading pool (approximate 2m diameter x 20 cm deep, dark blue)

Tripod and stand for video camera (could replace with ladder, or with ceiling mount)

Sony Digitial8 Camcorder

Heat lamps

Pump to empty pool

===Need to Get===
Platform for mice

White tempora or latex for making water opaque

geometric shapes or posters on walls to serve as visual cues

Heater for water

insulation to cover pool to prevent heat loss

drainage system (e.g. a spigot on side)

===Nice to get in future===

Ceiling mount for video camera or mount mirror on ceiling

Realtime tracking software

Table to get water maze off the floor.

==Sources of Water Mazes and Equipment==

[https://www.any-maze.com/mazes/water-maze/ ANY-maze] $1195 for 6-foot diameter, metal, with wheels and side drain

[https://sandiegoinstruments.com/product/water-maze/ SD Instruments] 6ft x 30" deep, polyethylene blue or white, drain kit

[https://www.hvsimage.com/information/3rd_party_pools.htm List of suppliers] HVS Image has a list of places that sell galvanized or polyethylene tanks

[https://www.bioseb.com/en/learningmemory-attention-addiction/1323-circular-pool.html Bioseb] French company

[https://www.tse-systems.com/products/behavior/maze-systems/water-maze.htm TSE Systems]

[https://muromachi.com/en/ Muromachi] Japanese company, I think they sell their own water maze pool.

==Aquaculture Tanks==

[http://www.solar-components.com/aqua.htm Solar Components] Transparent fiberglass tanks

[https://dolphinfiberglass.com Dolphin Fiberglass Products] located in Homestead, FL . They list 6' by 2' round tanks [https://www.aquaculturetanks.com/pricelist2.gif here]. Note that you can get feet put on the tanks. (see their picture catalog].

[https://web.archive.org/web/20090118141101/http://aquaticeco.com:80/categories/Tanks--Liners/97/0 Aquatic Eco-Systems] (now [https://pentairaes.com Pentair]) Located in Apopka, FL. Large selection.

[https://www.plastic-mart.com/category/41/plastic-stock-tanks-water-troughs Plastic-Mart] Livestock watering tubs.

==Tracking Software==

[https://web.archive.org/web/20180317100212/http://watermaze.com/ Watermaze Software (Edinburgh)] also sold by [https://www.coulbourn.com/category_s/291.htm Coulbourn Instruments]

[https://actimetrics.com Actimetrics]

[https://hvsimage.com/ HVS Image]

[http://www.biobserve.com/products/viewer/plugins/watermaze.html?gclid=CLDQwIDU144CFRVBgAodVgbo6A Biobserve]

[https://www.viewpoint.fr/en/p/software/videotrack Viewpoint]

[https://muromachi.com/archives/item/191 DV-Track] from Muromachi

[[Tracker]] from the [https://houptlab.org/ Houpt Lab]

[[Category:Magnetic_Fields]]
[[Category:Laboratory]]

Water Maze

2022-08-30T12:48:14Z

Chuck: Use archive link for watermaze.com

Reference site: https://web.archive.org/web/20180317100212/http://watermaze.com/

==FSU setup for Mice==

===Currently have:===

Wading pool (approximate 2m diameter x 20 cm deep, dark blue)

Tripod and stand for video camera (could replace with ladder, or with ceiling mount)

Sony Digitial8 Camcorder

Heat lamps

Pump to empty pool

===Need to Get===
Platform for mice

White tempora or latex for making water opaque

geometric shapes or posters on walls to serve as visual cues

Heater for water

insulation to cover pool to prevent heat loss

drainage system (e.g. a spigot on side)

===Nice to get in future===

Ceiling mount for video camera or mount mirror on ceiling

Realtime tracking software

Table to get water maze off the floor.

==Sources of Water Mazes and Equipment==

[https://www.any-maze.com/mazes/water-maze/ ANY-maze] $1195 for 6-foot diameter, metal, with wheels and side drain

[https://sandiegoinstruments.com/product/water-maze/ SD Instruments] 6ft x 30" deep, polyethylene blue or white, drain kit

[https://www.hvsimage.com/information/3rd_party_pools.htm List of suppliers] HVS Image has a list of places that sell galvanized or polyethylene tanks

[https://www.bioseb.com/en/learningmemory-attention-addiction/1323-circular-pool.html Bioseb] French company

[https://www.tse-systems.com/products/behavior/maze-systems/water-maze.htm TSE Systems]

[https://muromachi.com/en/ Muromachi] Japanese company, I think they sell their own water maze pool.

==Aquaculture Tanks==

[https://www.solar-components.com/aqua.htm Solar Components] Transparent fiberglass tanks

[https://dolphinfiberglass.com Dolphin Fiberglass Products] located in Homestead, FL . They list 6' by 2' round tanks [https://www.aquaculturetanks.com/pricelist2.gif here]. Note that you can get feet put on the tanks. (see their picture catalog].

[https://web.archive.org/web/20090118141101/http://aquaticeco.com:80/categories/Tanks--Liners/97/0 Aquatic Eco-Systems] (now [https://pentairaes.com Pentair]) Located in Apopka, FL. Large selection.

[https://www.plastic-mart.com/category/41/plastic-stock-tanks-water-troughs Plastic-Mart] Livestock watering tubs.

==Tracking Software==

[https://web.archive.org/web/20180317100212/http://watermaze.com/ Watermaze Software (Edinburgh)] also sold by [https://www.coulbourn.com/category_s/291.htm Coulbourn Instruments]

[https://actimetrics.com Actimetrics]

[https://hvsimage.com/ HVS Image]

[https://www.biobserve.com/products/viewer/plugins/watermaze.html?gclid=CLDQwIDU144CFRVBgAodVgbo6A Biobserve]

[https://www.viewpoint.fr/en/p/software/videotrack Viewpoint]

[https://muromachi.com/archives/item/191 DV-Track] from Muromachi

[[Tracker]] from the [https://houptlab.org/ Houpt Lab]

[[Category:Magnetic_Fields]]
[[Category:Laboratory]]

Water Maze

2022-08-30T12:43:41Z

Chuck: Upgrade links to https

Reference site: https://www.watermaze.org/

==FSU setup for Mice==

===Currently have:===

Wading pool (approximate 2m diameter x 20 cm deep, dark blue)

Tripod and stand for video camera (could replace with ladder, or with ceiling mount)

Sony Digitial8 Camcorder

Heat lamps

Pump to empty pool

===Need to Get===
Platform for mice

White tempora or latex for making water opaque

geometric shapes or posters on walls to serve as visual cues

Heater for water

insulation to cover pool to prevent heat loss

drainage system (e.g. a spigot on side)

===Nice to get in future===

Ceiling mount for video camera or mount mirror on ceiling

Realtime tracking software

Table to get water maze off the floor.

==Sources of Water Mazes and Equipment==

[https://www.any-maze.com/mazes/water-maze/ ANY-maze] $1195 for 6-foot diameter, metal, with wheels and side drain

[https://sandiegoinstruments.com/product/water-maze/ SD Instruments] 6ft x 30" deep, polyethylene blue or white, drain kit

[https://www.hvsimage.com/information/3rd_party_pools.htm List of suppliers] HVS Image has a list of places that sell galvanized or polyethylene tanks

[https://www.bioseb.com/en/learningmemory-attention-addiction/1323-circular-pool.html Bioseb] French company

[https://www.tse-systems.com/products/behavior/maze-systems/water-maze.htm TSE Systems]

[https://muromachi.com/en/ Muromachi] Japanese company, I think they sell their own water maze pool.

==Aquaculture Tanks==

[https://www.solar-components.com/aqua.htm Solar Components] Transparent fiberglass tanks

[https://dolphinfiberglass.com Dolphin Fiberglass Products] located in Homestead, FL . They list 6' by 2' round tanks [https://www.aquaculturetanks.com/pricelist2.gif here]. Note that you can get feet put on the tanks. (see their picture catalog].

[https://web.archive.org/web/20090118141101/http://aquaticeco.com:80/categories/Tanks--Liners/97/0 Aquatic Eco-Systems] (now [https://pentairaes.com Pentair]) Located in Apopka, FL. Large selection.

[https://www.plastic-mart.com/category/41/plastic-stock-tanks-water-troughs Plastic-Mart] Livestock watering tubs.

==Tracking Software==

[https://www.watermaze.com/ Watermaze Software (Edinburgh)] also sold by [https://www.coulbourn.com/category_s/291.htm Coulbourn Instruments]

[https://actimetrics.com Actimetrics]

[https://hvsimage.com/ HVS Image]

[https://www.biobserve.com/products/viewer/plugins/watermaze.html?gclid=CLDQwIDU144CFRVBgAodVgbo6A Biobserve]

[https://www.viewpoint.fr/en/p/software/videotrack Viewpoint]

[https://muromachi.com/archives/item/191 DV-Track] from Muromachi

[[Tracker]] from the [https://houptlab.org/ Houpt Lab]

[[Category:Magnetic_Fields]]
[[Category:Laboratory]]

MediaWiki:Sidebar

2022-08-30T11:52:27Z

Chuck: Update guide link to https