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Chemistry (including Biochemistry)/Bioassay/Biomonitoring Help

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Question
Hello! I am currently working on a science project but have seem to hit a bit of a roadblock in creating the experiment. I am trying to biomonitor/bioassay local water systems. I will run tests throughout different sites and compare the microbiological biodiversity to see and compare the health of each system. The problem is, I do not know what equipment exactly I would need. My teacher is not an expert in microbiology and can not offer any help. Do you by any chance know what technology/tools/equipment I need to be able to identify the different forms of microbiological life? And how exactly I would get the data? Thank you in advance!

Answer
Hello Giorlando,

What a fun idea! I am excited for you.

First up - Microscope access. Is one available?

Also, Do you, or someone who trusts you, have a smartphone?

There are many smartphone camera adapters to convert a smartphone into a microscope.

http://tinyurl.com/q8deuka

Is one of the more inexpensive varieties, although you can make your own.
http://www.instructables.com/id/10-Smartphone-to-digital-microscope-conversion/

This will let you take pictures and video of the microbial life in the field, as well as at home.

Your Shopping List

Some useful solutions:

Methyl cellulose (Protoslo) will increase the solution viscosity, slowing down your microbes so you can see them. A microscope stain, clear nail polish, and microscope slides will let you create permanent slides.

http://tinyurl.com/Protoslo (To look at living little guys. Hopefully your teacher can order this for you.)

Good quality stains. You'll have to put each name into Google to learn what they're best for, but hopefully again your teacher can help with this. You may also want to check the links on identifying critters to see what stains they use, and try those instead - they could be cheaper, too!
http://tinyurl.com/Slidestains

I'd also get cheap microscope immersion oil and lens paper from Amazon or another purveyor. (Don't forget eBay!)

Some basic equipment
Cheap slides
http://tinyurl.com/Amazonslides

Somewhere to put them
http://tinyurl.com/AmazonSlideBox

Labels and a pen, and cheap drugstore clear nail polish. (Whatever you can find on sale is great.)

A lab notebook. I suggest a small sewn or wire bound one you can take along easily. You'll want to carry it in a plastic bag when you're not writing in it, just in case you fall in a pond. :)

Optional equipment

Specimen jars:. Of course, baby food jars or old spice jars work great also!
http://tinyurl.com/qeg2szh
http://tinyurl.com/BMSclear5g

A marker that can write on plastic, to note where you took what sample and the date. (Sharpies are nice)

Some kind of bag to tote your notebook and specimens. (An army surplus canteen bag might do nicely, such as http://tinyurl.com/psfgpa2)

a clicker counter http://tinyurl.com/o7avtnt

Eye dropper

USB drive to store your pictures

Making Slides

Instructions on how to make slides, temporary and permanent
http://www.hometrainingtools.com/a/microscope-slide-making-ideas
http://www.microscope-microscope.org/basic/preparing-microscope-slides.htm
http://tinyurl.com/Sciencefairslideshowto

Now, how to identify?
This web site is a great beginning -
http://www.microscopy-uk.org.uk/pond/

As is this one
http://www.microscope-microscope.org/applications/pond-critters/pond-critters.ht

Those sites may also have good alternate information on what kinds of stains work best.

Data Collection
I'd talk with your teacher about good sites to collect data from. If there are sites you can get to easily you might monitor those over time to observe seasonal changes. You will probably want a few samples from each site - near surface and near the pond bottom at least for stationary water. For a stream, middle of current and something from a still area near the stream should give you a nice variety. If you can get to deep areas, you might find those interesting as well.

After collection, you'll want to plan on spending some time with the microscope looking at critters. After you familiarize yourself with the critters in your area, you'll probably want to build a standard table, establish a number of wet mount slides to count per sample (at least 3, and swirl the sample before taking one)  and then note what kind and how many of each critter was observed per sample. Be sure to take at least the minimum number each time, even though sometimes counting can be dull after a bit. :)

Critters can probably survive for 1-2 days at refrigerator temperatures. It's best to count them when they are fresh. :)

After you are done looking at wet mounts, slides can be cleaned with dish washing liquid and re-used *if handled carefully*.

You'll want to think about what kinds of critters you're interested in, and how best to measure diversity. Talk with your teacher about how best to go about sampling things to design the best experiment and use your time wisely. :)

Be sure to design a file naming system for your pictures that includes the date and sample site, and write down how you came up with it in your notebook. We all think we won't forget... Until we do. :)

Good luck!  

Chemistry (including Biochemistry)

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Trista Robichaud, PhD

Expertise

No homework questions, especially ones copied and pasted from textbooks. I will answer questions about principles or give hints, but I do not do other's homework. I'm comfortable answering basic biochemistry, chemistry, and biology questions up to and including an undergraduate level of understanding. This includes molecular biology, protein purification, and genetics. My training/inclination is primarily in structural biology, or how the shapes of things affect their function. Other interests include protein design, protein engineering, enzyme kinetics, and metabolic diseases such as cancer, atherosclerosis, and diabetes. My chemistry weaknesses are that I do not know organic or inorganic synthesis well, nor am I familiar with advanced inorganic reactions. I will attempt quantum mechanics and thermodynamics questions, but primarily as they relate to biological systems. Furthermore, I cannot tell you if a skin photograph is cancerous, or otherwise diagnose any disease. I can tell you how we currently understand the basic science behind a disease state, but I cannot recommend treatment in any way. Please direct such questions to your medical professional.

Experience

I hold a PhD in Biomedical Science from the University of Massachusetts Medical School in Worcester. I specialize in Biochemistry, with a focus on protein chemistry. My thesis work involved the structure and functions of the human glucose transporter 1. (hGLUT1) Currently I am a postdoc working in peptide (mini-protein) design and enzymology at the University of Texas Health Science Center in San Antonio, Texas. I am in Bjorn Steffensen's lab (PhD, DDS), studying gelatinase A and oral carcinoma.

Organizations
2001 American Association for the Advancement of Science
2007 American Chemical Society
2007 Protein Society
2011 UTHSCSA Women’s Faculty Association


Publications
Levine KB, Robichaud TK, Hamill S, Sultzman LA, Carruthers A. Properties of the human erythrocyte glucose transport protein are determined by cellular context. Biochemistry 44(15):5606-16, 2005. (PMID 15823019)
Robichaud TK, Appleyard AN, Herbert RB, Henderson PJ, Carruthers A “Determinants of ligand binding affinity and cooperativity at the GLUT1 endofacial site” Biochemistry 50(15):3137-48, 2011. (PMID 21384913)
Xu X, Mikhailova M, Chen Z, Pal S, Robichaud TK, Lafer EM, Baber S, Steffensen B. “Peptide from the C-terminal domain of tissue inhibitor of matrix metalloproteinases-2 (TIMP-2) inhibits membrane activation of matrix metalloproteinase-2 (MMP-2)” Matrix Biol. 2011 Sep;30(7-8):404-12. (PMID: 21839835)
Robichaud TK, Steffensen B, Fields GB. Exosite interactions impact matrix metalloproteinase collagen specificities. J Biol Chem. 2011 Oct 28;286(43):37535-42 (PMID: 21896477)

Poster Abstracts:
Robichaud TK, Carruthers. A "Mutagenesis of the Human type 1 glucose transporter exit site: A functional study." ACS 234th Meeting, Boston MA. Division of Biological Chemistry, 2007
Robichaud TK, Bhowmick M, Tokmina-Roszyk D, Fields GB “Synthesis and Analysis of MT1-MMP Peptide Inhibitors” Biological Chemistry Division of the Protein Society Meeting, San Diego CA 2010
Robichaud TK; Tokmina-Roszyk D; Steffensen B and Fields GB “Catalytic Domain Exosites Contribute to Determining Matrix Metalloproteinase Triple Helical Collagen Specificities” Dental Science Symposium. UTHSCSA 2011
Robichaud TK; Tokmina-Roszyk D; Steffensen B and Fields GB “Exosite Interactions Determine Matrix Metalloproteinase Specificities” Gordon Research Conference on Matrix Metalloproteinase Biology, Bristol RI 2011


Education/Credentials
Oakland University, Auburn Hills MI BS, Biochemistry 1998
University of Massachusetts Medical School, Worcester MA PhD, Biochemistry & Molecular Pharmacology 2001-2008
University of Texas Health Science Center, San Antonio TX Postdoc, Biochemistry 2009-Present


Awards and Honors
1998 Honors College Graduate, Oakland University
2009 Institutional National Research Service Award, Pathobiology of Occlusive Vascular Disease T32 HL07446
2011 1st Place, Best Postdoctoral Poster, Dental Science Symposium, UTHSCSA, April 2011


Past/Present Clients
Invited Seminars:
Robichaud TK, Fields GB. “Synthesis and Analysis of MTI-MMP Triple Helical Peptide Inhibitors” Pathology Research Conference, University of Texas Health Science Center San Antonio Pathology Department (June 18th, 2010)
Robichaud TK & Hill, B “How To Give A Great Scientific Talk” Invited Lecture, Pathobiology of Occlusive Vascular Disease Seminars, UTHSCSA (Nov 11th 2010), Cardiology Seminar Series, Texas Research Park (Feb 21st, 2011)
Robichaud TK; Tokmina-Roszyk D; Steffensen B and Fields GB “Exosite Interactions Determine Matrix Metalloproteinase Specificities” Gordon-Keenan Research Seminar “Everything You Wanted to Know About Matrix Metalloproteinases But Were Afraid to Ask” Bristol, RI (Aug 6th, 2011)

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