0
votes
0answers
2 views

Affymetrix SNP data, how to filter out rows based on rsid

this is my first time on stackexchange (after a history of condescension at biostars.org where almost no one bothered to help a noob) I am new to bioinformatics, and I have some new SNP data from an ...
0
votes
0answers
4 views

How copy number variation thresholds are defined in GISTIC

I am having trouble trying to understand how GISTIC discretize copy number variation to values -2, -1, 0, 1, 2. I am using TCGA copy number variation for ColoRectal Adenocarcinoma. In cBioPortal FAQ ...
0
votes
0answers
10 views

Can light pollution cause cancer?

Impaired circadian rhythm is associated with cancer. Light pollution affects the circadian rhythm and the circadian rhythm affects the metabolism. But what is the (molecular) connection between ...
3
votes
0answers
6 views

What is the connection between sleep requirement and age?

By this question: Is the human biological clock genetically programmed or learnt? we discussed that the sleep requirement depends on the age of the individual. - Figure 1. - Sleep requirements by ...
3
votes
1answer
15 views

What is this insect that has invaded my home in Texas?

After the recent floods in central Texas this past weekend I noticed my that bedroom has suddenly been infested with these small insects that have climbed in through the window. Previously, the hole ...
1
vote
1answer
11 views

Oral allergy syndrom, continuation of continuous consumption of allergen

Wikipedia states on its page that In addition, patients are advised to avoid the triggering foods, particularly nuts. And same thing goes for webmd.com The basic rule: If a food makes you ...
3
votes
0answers
19 views

Do newborns resemble their father?

An often heard theory is that newborns resemble the father more than the mother, a theory apparently ignited by a Nature paper by Christenfeld and Hill (1995). It is suggested that paternal matching ...
2
votes
1answer
23 views

How to calculate the Jaccard index

I want to calculate the Jaccard index between two compounds. What is the algorithm? I have searched for it, it just gives the formula but how to apply it on compounds is not known to me. Can you help? ...
1
vote
1answer
18 views

Y-chromosome and phenotype

I have a male colleague which has a son that does not resemble its father in any degree (apart of being male). The "father" is thin, tan-skinned, brown-eyed and the "son" has blue eyes, blond and ...
11
votes
1answer
632 views

Why do smaller mammals move in “snappy” fashion?

I was watching a nice little video on youtube but couldn't help but notice how snappy smaller animals such as rats and chipmunks move. By snappy I mean how the animal moves in almost discrete states ...
0
votes
0answers
15 views

Is there a consensus on the CaMV 35S minimal promoter sequence?

We have an algal enhancer element and a transcription factor that probably binds it. Basal expression of the enhancer element or full promoter driving luciferase in tobacco protoplast was extremely ...
2
votes
2answers
112 views

Question about cell membrane

I just started learning about the structure and composition of cell's membrane and there is one little detail that I fail to understand. So, the membrane is composed of a phospholipid bilayer. The ...
0
votes
0answers
17 views

Sexually homologous traits

When papers refer to traits as being sexually homologous do they refer to traits which are: a) present in both sexes but can be dimorphic (e.g. body size is sexually homologous because both sexes ...
1
vote
0answers
15 views

Can we stop hearing by ourselves? [on hold]

If we don't want to see we can close our eyes. But if we want to avoid noise we can't do that just then as we don't have such fast reflex action to close our ears with hands like eyes. But like some ...
1
vote
1answer
30 views

What can cause a lump in the middle of the neck? (homework case study)

What can cause an erythematous, fluctuant, nontender mass in the middle of the neck? Full Case Study: (Its the last of 6 cases and I just can't figure this one out, because of all the possibilities, ...
9
votes
1answer
847 views

What kind of memory is “keyboard/keypad memory”?

I work in IT and I have observed many people who cannot remember their iPhone passwords or computer passwords off the top of their head. However, if presented with a keyboard or a phone with a ...
-1
votes
0answers
15 views

How many ATP molecules do stearic acid give rise to in the beta oxidation? [on hold]

Stearic acid is $\ce{C18H36O2}$ How much ATP does one stearic acid molecule give rise to if we assume that all generated $\text{NADH}$, $\text{FADH}_2$ and $\text{acetyl-CoA}$ goes to Kreb's cycle and ...
1
vote
0answers
21 views

Risks in bacterial phage therapy

I just finished reading J. Craig Venter's book Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life. The book is a little over a year old now, and Venter has an optimistic ...
2
votes
2answers
32 views

What is “theae folium”?

I wanted to buy black tea at a pharmacy and the pharmacist told me that russian tea is actually black tea so I bought it instead.It's made out of theae folium leaves and for some reason I can't find ...
2
votes
3answers
31 views

Looking for good reference book in molecular biology [on hold]

I am starting to work in molecular biology/ molecular genetic and I am looking for a really good book containing the main concepts and mostly the more recent techniques. I would be interested in a ...
3
votes
2answers
36 views

How does a virus reach its host, it is always passive? [on hold]

We know that viruses are non motile and cannot metabolise, and that it enters the host cells via binding to the receptors. But how exactly it reaches the host (that is, how it go from the ...
-1
votes
0answers
20 views

Why do we have mostly 3 lines in our palm? [on hold]

Whenever we get sense to feel what's outside us we see we have some particular patterned structures in our palms. What is the reason for that and why mostly it has 3 main lines?
3
votes
1answer
21 views

Insect Identification - Black Cicada

I came across a black cicada in northwest Missouri last week. I am only familiar with brown cicadas. What makes this black one different? Is it a different species, or do the brown cicadas change ...
2
votes
1answer
21 views

In protein-protein interactions what is the difference between a binding site and an interface?

I see binding site and interface used almost interchangeably in the literature, but I'm not sure if it is exactly the same thing or not - what is the difference?
4
votes
1answer
34 views

How do I know which alleles the parents have?

I have the following assignment where I am to look at the "tree" (not sure the english word) and assign whether or not they can be autosomal dominant or recessive as well whether they can be X-linked ...
5
votes
1answer
26 views

Comparison of gene expression time series in vitro and in vivo

I have to analyse two datasets consisting of time-series measurements of gene expression. One set are in vivo data from the expression profiles obtained between a few days before birth to several days ...
2
votes
2answers
162 views

A question on glycolysis

In the first step of glycolysis, the glucose ring is phosphorylated. Phosphorylation is the process of adding a phosphate group to a molecule derived from ATP. As a result, at this point in ...
3
votes
5answers
1k views

Are there any papers arguing against vaccination in French? [on hold]

Disclaimer: This question is NOT about challenging the safety or efficacy of vaccines. It is only asking for tips on providing credible references that may show harmful effects of vaccination, if any. ...
3
votes
1answer
27 views

Why is it difficult to bend the waist while keeping the knees straight?

It's easy to keep your legs straight when you're standing up or laying flat on your back, but as soon as you try to sit up or bend down, you need to bend your knees as well as your waist. (Try it. ...
4
votes
0answers
23 views

How pronounced is the difference if we would change the running direction for runners?

I was jogging when I asked myself this question: In running contests the standard running direction is counterclockwise; I also believe to remember that the regulation is very old (right back to the ...
4
votes
1answer
22 views

Is there a protocol for freezing and thawing Bacillus subtilis cells?

There is a book that says to store Bacillus spores in 50% glycerol at -70 degrees Celsius (doesn't mention if the 50% is final concentration or not). But from what I know, the cells themselves can be ...
4
votes
1answer
30 views

Tree identification from dried branch

I found a very interesting branch last week, and have been trying to identify it but cannot seem to find the answer. If anyone has any suggestion, I would be grateful. I found it near the forest, ...
5
votes
1answer
30 views

Can nociceptors die because of too much mechanical stress?

In martial art people hit their body (e.g., with small bean bags) to become more insensitive to pain. Can the sensory neurons die during this procedure? I think this is just an urban legend. Instead, ...
-2
votes
2answers
43 views

Primers for human tissue? [on hold]

If I wanted to examine human tissue samples, such as hair, blood, fingernails, etc, for their DNA, what primers would I use for the amplification of the DNA when extracted(PCR)? edit: To look at the ...
7
votes
0answers
35 views

Was the recent “conservation hunt” of a black rhino supported by science?

CNN recently covered a sanctioned black rhino hunt in Namibia by Texan Corey Knowlton, who bid US$350,000 for the license. In the story, he claims that the hunt was actually supporting conservation of ...
3
votes
0answers
63 views

Restriction sites

I would like to know: how many restriction sites does a restriction enzyme use on a DNA molecule? In other words: If a sequence on a plasmid contains the following bases: ATTGCAGTCTG and I want ...
4
votes
1answer
526 views

What is this Tree?

What is this plant? Location: Bangalore, India
2
votes
1answer
17 views

Do females retain oogonia after puberty?

Oogonia are the precursors of oocytes in females present during embryonic development. I was wondering whether these stem cells are still present in the ovaria at puberty?
11
votes
1answer
723 views

Species ID: Buckyball-like fungus

Previous research A friend of mine shared a link of some beautiful fungi: http://imgur.com/a/Dii3H. I was intrigued by the curious critter below -- it seems to have honed the power of buckyball ...
-1
votes
1answer
39 views

What are these pathways called in Biology?

Considering the pentose phosphate pathway and the sulfate reduction pathway in bacteria; What are these types of reactions called in biology? Bio degradation reactions or bio transformation reactions ...
5
votes
2answers
49 views

What ways are there to determine how big genera are?

I want to look at genera as a whole, across the animal kingdom to determine the range of sizes of genera. I have examined species richness and genetic diversity (pairwise distance from sequence data ...
4
votes
1answer
49 views

How is genetic speciation defined?

What determines speciation at a molecular level? At what point does a scientist determine two lineages are different enough to be considered separate species? Does it have a margin of error?
2
votes
1answer
21 views

What does the energy in an energy pyramid represent?

Suppose the energy at the second trophic level as given in an energy pyramid is 100 kcal per square metre. It could mean either of the two following things: 100 kcal is the energy this primary ...
0
votes
0answers
7 views

What is isomeric threshold and isomeric count?

Found the terms isomeric point and isomeric threshold in the following paper: http://lib.gen.in/ocean/9064caa3202a71977f338ecb430280a7/10.1007%40s12539-012-0119-8.pdf It siad that the isomeric point ...
5
votes
2answers
223 views

What's the name of this flower?

I photographed this flower in Central Europe. I looked in online databases but can't really identify the actual flower, since there are so many that look quite similar. Can you help me? What's the ...
1
vote
1answer
40 views

Is the amount of dNTPs rate limiting for very long PCR products?

I'm using the Q5 system and I'm PCRing a product that will have a final length of around 9500 bases. I have noticed that the product is there but very faint. The primer seems to be used up. So my ...
-1
votes
0answers
18 views

Solidification of coconut water

At first, the coconut is filled with liquid endosperm. Later when it ripens, the outer layers form brown fibrous covering, and the inner solid layer turns brown and hardens. Within that, a white layer ...
1
vote
1answer
29 views

Why do we do nested PCR?

Wikipedia: Nested polymerase chain reaction (Nested PCR) is a modification of polymerase chain reaction intended to reduce non-specific binding in products due to the amplification of ...
1
vote
0answers
28 views

Why Pan_troglodytes-2.1.3 Assembly renamed as a Pre in ENSEMBL?

I began working with panTro3 assembly of the UCSC. This assembly corresponds to CGSC Build 2.1.3. See here: https://genome.ucsc.edu/FAQ/FAQreleases.html Now, I have to cross annotations with ENSEMBL ...
-3
votes
0answers
21 views

What are the rules for primer design [on hold]

I am looking for a (most complete, not to say ultimate) set of rules that one should follow to achieve the best performing PCR primers (aside from being compatible to the desired target sequence). ...

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