2,647 reputation
627
bio website mattdmo.com
location near Boston
age 35
visits member for 1 year, 10 months
seen 11 hours ago

Long-time OSS user/admin, intermediate coder - I heart . Master of Science in Molecular Medicine, many years' experience in biotech working with antibodies and cell-based assays. Science and computer geek. Dad.


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Why Pigimal?

I sometimes call my guinea pig (also known as a cavy) "Pigimal", which is short for "Piggy Animal." Now you know.


Flair, Baby!


Mar
9
comment How is a stem-cell induced to assimilate a knock-in DNA construct?
So, essentially your question is just "How is a transgenic mouse created?", is that correct?
Mar
9
comment Databases for metabolic pathways of human disease
What exactly are you searching for, and how specifically did KEGG and Metacyc fail to meet your requirements? Please edit your question with additional details so we can provide focused answers.
Mar
7
comment what these suffixes mean,-coel,-blast,-cyst?
@WYSIWYG - even if it's short, please post answers to questions as actual answers. Comments should just be used to clarify the question, not answer it. See this meta topic for a discussion regarding this issue. Thanks!
Mar
5
comment How do TLR1/TLR2 activate the MyD88 dependent pathway
Pretty good, but a correction - MyD88 recruits both IRAK1 and IRAK4. 4 then gets phosphorylated, and in turn phosphorylates 1 at Thr209 and Thr387. This in turn activates 1's kinase activity, and it hyper-autophosphorylates. 1 (and maybe 4) then dissociates from the complex, becomes ubiquitinated, and goes on to recruit the membrane-bound TAB/TRAF complex, which facilitates activation of TAK and RIP, leading to the NF-kB, PI3K/Akt, and MAPK pathways.
Mar
4
comment What are the purposes of granulocytes in acute inflammation?
As far as I know they are the same thing. Neutrophilic granulocytes is another term (usually) for neutrophils. All granulocytes (white blood cells with granules in the cytoplasm) are leukocytes (or leucocytes), which literally means "white cells." Another term is polymorphonuclear leukocyte, which refers to neutrophils' unusual nucleus, generally having 2-5 lobes or sections.
Mar
4
comment What are the purposes of granulocytes in acute inflammation?
Have you read the WP article on neutrophilic granulocytes, the most abundant form? Essentially, they are the first infiltrating cells to arrive at the site of injury at the beginning of acute inflammation (bacterial infection, environmental exposure, etc.).
Feb
26
comment Why do we exhale after we hold our breath?
Welcome to the site! While you may have the beginnings of a good answer, it is trapped inside of a gigantic run-on sentence with several misspellings and run-together words that make it very difficult to determine what exactly you're trying to say. Please edit your answer to improve it, highlighting your answer to the question and not just giving a review of the mechanics of breathing, which isn't really relevant.
Feb
25
comment What is immunosuppression? Why would one use it?
Have you read the Widipedia article or done a simple Google search? Please read up on the vast array of publicly available data, then either edit your question to make it more specific, or ask a new question.
Feb
24
comment basic programming and bioinformatics
Python also has interfaces to other languages (R, C/C++, Fortran, Java, etc.) so you can do domain-specific work in the best language for that project, and use Python as the "glue" to piece it all together.
Feb
24
comment basic programming and bioinformatics
What you need to remember is that R is more of a domain-specific language (statistics and related fields like visualization), while Python is more of a "generic" programming language like the C superfamily, Java, Ruby, etc. What sets Python apart is its comparative ease of learning and use, the "batteries included" philosophy of the standard library, and the huge number of 3rd-party modules available for everything from bioinformatics (Biopython, etc.) to visualization (matplotlib) to numerical analysis (numpy/scipy) to web frameworks to natural language analysis and more...
Feb
21
comment Macrophage death by toxin. Little balls inside cell? What type of death?
Also, while I agree that you should first do a DAPI/Hoechst stain, if you're going to be looking at apoptotic markers I'd recommend going for cleaved PARP first. 44 hours is very well along into apoptosis, and there may simply be no cleaved caspase 3 left.
Feb
21
comment Macrophage death by toxin. Little balls inside cell? What type of death?
Is that a cell with "balls" inside it, or is it one or more apoptotic cells clustered together? It's rather difficult to tell just from the one image you have.
Feb
18
comment Sequence analysis software suites
Why do you say that "real" bioinformaticians rarely use GUIs? Is it just some sort of macho "I'm too cool for that user-friendly stuff" attitude? REAL anythings get the job done with the best tools that are available for their particular problem domain. Sometimes it's text-based utilities, sometimes web-based, sometimes GUI-based. It's not about how much pain you can inflict on yourself, but whether you can get the job done correctly, on time, and on-budget.
Feb
7
comment Which of the cell types commonly found in mammals has the greatest number of mitochondria?
Assuming @Remi.b 's correlation between cell size and number of mitochondria, then muscle fibers should win hands down. They are IIRC the largest cells in the body, and they have a need for significant amounts of energy.
Jan
23
comment What happens to our body when we undergo a sudden temperature change?
That depends entirely on the range of temperatures you're talking about. Please edit your question and add some additional details, because as it stands now your question is unclear.
Jan
21
comment How can Southern blotting be used to establish gene copy number?
please edit your question to include a link to the paper, so we can see everything in context.
Jan
16
comment What's the difference between protein and DNA behaviour during agarose gel electrophoresis?
which food coloring dyes will you be using? Most of them are based on small molecules, not proteins.
Jan
14
comment How many species have existed on earth?
Did you read the answer to the linked question? I believe it adequately describes the problems with estimating the number of species (along with the number of individuals) that have ever existed on Earth, and gives some links for further reading.
Jan
13
comment How is the number of histones being related to the number of chromosomes
Hi, and welcome to Biology.SE! If this is a homework question, please give us your thinking on what the answer is, and why. We can certainly help you understand your studies, but we cannot do your work for you. If this is not homework, just let us know too :)
Jan
12
comment Are we inevitable in the evolution?
there is no way to answer this question, because we don't have other systems to observe.