2
votes
0answers
221 views

Best way to automatically link Gene Entrez ID with Gene Symbol in TCGA

I am trying to figure out how to link Gene Entrez ID with Gene Symbol, for TCGA dataset. So far, I have found this ftp directory with Gene info updated daily. But, for Entrez ID 728661, I have found ...
1
vote
1answer
319 views

Mapping a mutation to known SNP, 3' UTR, miR

I've parsed out a very large TCGA cancer ssm (single mutation file) file to give me the essential information. The ssm is in the following format: ...
0
votes
1answer
254 views

How to select genes before log2 ratio on a RNASeq gene expression matrix, based on signal median

I want to transform a TCGA mRNA expression matrix (in linear data format) to log2-ratios and then run a feature (gene) selection, selecting the 1000 most variant genes (genes with higher standard ...
4
votes
2answers
328 views

Relative microRNA comparison from from TCGA data?

I have a conceptual question that I was hoping someone could answer. Can I say that microRNA A is expressed x-fold greater than microRNA B directly from the TCGA miRseq data? Can I do this after ...
1
vote
0answers
92 views

What's a good simple test for cDNA library quality?

How do I assess the quality of a cDNA library? I want to clone CDS copies of genes from a library, but I don't know what's a typical expectation of getting a full length clone even for a shorter ...
6
votes
1answer
875 views

How does the brain cool itself?

Thoughout life everyone tells you that brain is essentially a computer but just like computers your brain would create immense amounts of heat by being in use, so if that's the case how does it cool ...
2
votes
2answers
1k views

TCGA gene expression data are missing matched normal

I'm trying to use the TCGA data portal to get gene expression data for cancer tissues, but I'm not sure what "Tumor matched normal" means. It is unclear to me if the values are already compared to a ...
1
vote
0answers
151 views

How TCGA CNV values are calculated?

When I download CNV SNP array data for ovarian cancer from TCGA data portal, I see some very small numbers like -5, -6 in the "Segment_Mean" column of the segmentation data files. I am very new to ...
9
votes
1answer
142 views

Circadian Clock During a Flight

I am interested to know how does our Circadian Clock respond (and its resultant changes if any) when we are traveling across Time Zones? UPDATE 24th April I am reopening this question as the ...
4
votes
0answers
57 views

Y Chromosome in Ovary Cancer Data

I have been analyzing TCGA Ovary Cancer data. In Somatic Mutation data, there is data of mutations in all the chromosomes (1-22 and X), but amazingly, I have found one (just one) row of Y Chromosome ...
2
votes
1answer
55 views

Why are 2 electrons transported from photosystem II at the same time?

I only know that electrons are captured by the primary electron acceptor and then go through the electron transport chain, ultimately ending up at photosystem I. But why do 2 leave photosystem II in ...
3
votes
1answer
34 views

Does the palate truly house the sense of taste?

Source: Your “palate” is the roof of your mouth, and by extension, your sense of taste. I was reading Etymonline's entry for palatable {adj.}, which cites and derives from palate {noun}: ... ...
4
votes
1answer
5k views

What is the difference between intrinsic and extrinsic apoptosis?

Hello my Professor has been teaching about apoptosis and sometimes makes the distinction between extrinsic and intrinsic. I am not sure if I know for sure what this means. Does this just refer to ...
5
votes
1answer
40 views

Are all protein composed of all the amino acid (in animal) or are there less diverse protein?

I have a question about amino acid composition of proteins: Are there proteins in animals that are made up only from a small subset of amino acids? So instead of all 20 amino acids let's say only 6-14 ...
24
votes
3answers
2k views

Hot water and bacteria

I know that it is common to say, "use hot water when washing your hands" or when you've got a cut, "wash your hands with warm water," etc. I was wondering, why is this the case? Since bacteria grow in ...
5
votes
1answer
66 views

Do non-enzyme catalysed reaction pathways exist?

Can their be a kind of chemical reaction pathway in a cell, that is catalyzed or regulated but NOT necessarily by enzymes? I could not find anything on Google. I have almost no background in biology, ...
2
votes
1answer
260 views

Is cysteine deficiency possible?

Is there such a thing as cysteine deficiency in humans or other mammals? What effects would such a deficiency have? As I understand it, most cysteine for humans comes from dietary sources, though it ...
4
votes
2answers
196 views

Do acetyl-CoA, acetyl-CoA carboxylase and acetyl-glutamate carry any charge?

Do the following compounds have any charge? If not, then why? If yes, is there any database that would give me this information if the compound is negatively or positively charged? The compounds are ...
5
votes
1answer
267 views

Are HeLa cells edible?

I'm curious if HeLa cells are intrinsically poisonous or dangerous to ingest. My understanding is that some of the contamination in HeLa cells such as HPVs are not readily expressed. I have no plans ...
3
votes
1answer
77 views

Mammal vs Placental Mammal

So for Google Earth Day's quiz I ended up being a "Pangolin." Turns out I had no idea what it was so I looked into it and honestly it reminded me a lot of an Armadillo. So I decided to find out the ...
5
votes
1answer
52 views

what is linkage disequilibrium supposed to measure?

During reading about genetics I came across with the term of linkage disequilibrium, and I do not really understand what it supposed to mean. What is linkage disequilibrium? My current understanding ...
3
votes
1answer
183 views

Why do spiders make their web near the ceiling and near a light source?

Why do spiders make their webs near the ceiling and near light sources ? Is their an advantage for spiders in doing that? For example do they catch more insects when their web is near a light source ...
5
votes
1answer
80 views

Do we instinctially interpret birdsongs as a sign that there are no predators present?

I was outside today thinking how nice it was to hear the birds back from winter when I started thinking about the fact that we like bird song. It makes us happy in a very basic level, the sort of ...
2
votes
2answers
132 views

Help reading chromatogram

A genetic variation is found in this chromatogram: It says that the "reference sequence" is the top line and that I can use the general genetic code to find the reading frame. I can see that there ...
2
votes
1answer
358 views

Why are clementines easier to peel than oranges?

In my experience, clementines have been significantly easier to peel by hand than and orange. The skin of the orange seems to cling to the rest of the orange much more so than the skin of the ...
4
votes
1answer
237 views

blue/white screening - results are opposite as expected

We inserted GFP-gene into plasmid Bluescript SK+, transformed E. coli with this construct, and then plated on an agar plate with Ampicillin and X-gal to do a blue/white screening. We got blue colonies ...
13
votes
1answer
726 views

What is the magnification necessary to see pond life

My daughter is 5 and wants to learn about Biology. I thought a great start is to see life from pond water through a USB microscope. It would be great if she could see organisms like amoebas, ...
4
votes
1answer
2k views

Does DNA polymerase always go the same direction?

I read that mutations are more likely to occur on "the strand that DNA polymerase replicates discontinuously". Does DNA polymerase always go replicate the same strand discontinuously, and if so, how/...
2
votes
1answer
57 views

What does it mean when a protein has a different excitation spectra than wildtype, but the same emission spectra?

We have a GFP mutant that displays a different excitation spectra with emission at 510nm than the WT. However, their emission profiles with excitation at 490nm are the same, and we do not observe the ...
1
vote
1answer
51 views

What are the factors on which protein-protein interaction depend? [closed]

Does protein-protein interaction only happens when one of them is basic and the other acidic? Do protein interactions also depend on the protein structure? Are there more factors?
6
votes
2answers
1k views

GWAS: why is replication in another cohort so crucial?

Almost all the landmark GWAS (Genome-Wide Association Studies) reviews agree that, for a GWAS finding to be valid, it needs to be replicated in an independent cohort. What exactly is the rationale ...
41
votes
3answers
4k views

Why does cracking a joint make noise?

What causes the noise when you crack a joint? Is joint cracking harmful?
8
votes
1answer
822 views

What causes knuckle “popping” and the feeling of relief that comes from it?

Many people like cracking their knuckles. I have always been curious about it. What happens when we crack knuckles? What creates the POP sound? Why do we get a relief-like feeling after doing it?
3
votes
1answer
67 views

Applying kiwis on gelatin

Kiwis have the enzyme actinidain. This enzyme will break the peptide bonds from the gelatin. Making gelatin with raw kiwis will not work, because the peptide bonds in the gelatin will be broken down. ...
5
votes
1answer
207 views

Help me identify this insect

Over the last week or so as warmer weather has arrived, I've noticed small insects crawling around in the bathroom. I'm located in western Europe. They are perhaps 1mm in length, quite difficult to ...
2
votes
1answer
150 views

“bead” on a string theory of genetics, source?

Thomas Hunt Morgan was a pioneer in genetics and proposed the now false model of genes being "beads" on a string. These beads being indivisible and responsible for a single phenotype, if I understand ...
1
vote
0answers
22 views

OCT-1 transport in Enterocytes [closed]

Does Oct-1 transport lactate or any of its products and in which direction (intracellularly to extracellular, the opposite, or inter-nuclear). The literature talks about Oct-1's role in neuronal ...
8
votes
1answer
3k views

Why are pili more common in Gram negative bacteria than in Gram positive?

Although pili have been observed in some species of Gram positive bacteria, the preliminary research that I have done indicates that pili are significantly more common in Gram negative bacteria. Is ...
4
votes
1answer
77 views

Why do plants produce so many hybrids as a kingdom?

Why do plants produce so many hybrids? I have read that they are the largest kingdom of organisms to do so. Does this have something to do with polyploidy events?
7
votes
1answer
1k views

Magnetic-activated cell sorting vs. FACS

When sorting cell populations it is possible to use either magnetic-activated cell sorting or fluorescence-activated cell-sorting (FACS). I am wondering when you would choose either technique and what ...
3
votes
0answers
135 views

Current Trend in Evolution of Human Intelligence

Up front, I am specifically not interested in philosophical or ethical considerations re Eugenics and related concepts. In an effort to receive a concise answer I'll post a narrowly defined question ...
11
votes
1answer
1k views

Why can I see a light flicker when it's in my peripheral vision?

When I'm looking at an old CRT monitor or a worn fluorescent lamp, but not directly in the center of my gaze, the light from it seems to flicker. When I focus my gaze onto the monitor or lamp, the ...
5
votes
2answers
1k views

What has caused life to choose this unfathomably tiny subset of all possible proteins?

I wonder why life uses the particular proteins that it does, about 10^6 different proteins, I think? Evolution cannot explain it because the number of possible proteins is far far too large to ever ...
2
votes
1answer
226 views

If oxygen deficiency is bad even for a short while, why do people swim?

This may be trivia to many of you. Textbook says the oxygen deficiency, even for a short while can injure our cells. Then why do people go for sports like swimming? (where rhythmic breathing is ...
3
votes
1answer
96 views

DNA length and annealing kinetics

I have a mixture plasmids and undesired short linear fragments that share the same sequences. During denaturation and annealing, I would like the plasmids to 'find each other' before annealing to the ...
1
vote
1answer
114 views

Is it possible to knock out a gene in adults?

gene knockout is mainly used in creating newborn animals... right? Well can you do it to already-adult animals or humans so that they themselves would experience change in their body and not just ...
1
vote
0answers
58 views

If I fall into a pond with an algal bloom, could I die from the cyanotoxins? [closed]

Suppose I fell into a pond with an algal bloom, and swam in it for a bit, but did not ingest any of the pond water (this is a hypothetical btw). Some algal blooms are harmful, containing natural ...
1
vote
2answers
1k views

Did cats evolve from monkeys ? or vice versa?

Did cats evolve from monkeys ? or vice versa ? How similar are the genes of cats and monkeys ? What is the proof that they are related or that they are not related ? Most monkeys climb in trees and ...
8
votes
2answers
3k views

Free software for measuring parts of an image? [closed]

Let's say I have a picture of an insect wing and a ruler on the same image. Is there any computer program that I can use to calibrate with the ruler and then get a measurement on the wing length? ...
5
votes
2answers
687 views

How can I text-mine full-text articles from PubMed? [closed]

I want to do a text mining study using full-text versions of articles I find on PubMed. My intended search protocol will be roughly as follows: Search PubMed using a gene name (and any alternate ...

15 30 50 per page