0
votes
0answers
5 views

Why low variant frequency in exomeseq data (ANNOVAR)?

I've got an annotated ANNOVAR file with 300.000 nucleotide variants of 4 genomes. There's one thing I don't understand when looking at the data: Why are the variant frequencies so low in comparison to ...
1
vote
1answer
60 views

History: Building a “Phylogenetic network” of famous evolutionary biologists [closed]

Seems like many of the famous evolutionary biologists are somehow related to each others. For example (and I might be mistaken), Ronald A. Fisher was mentored by a descendent of Charles Darwin. Joe ...
2
votes
1answer
20 views

What are the units of Phylogenetic Independent Contrasts (PICs)

PICs are a popular phylogenetic comparative method and I was wondering what units the actual contrasts are in. I want to say they are unitless but I am not entirely sure.
3
votes
1answer
29 views

How could I identify whether given RNA-seq data is paired end or single end

I need to have a RNA-Seq dataset and therefore, I've visited the following site NCBI-geo C. Elegans In the Supplemantary file part, I clicked the SRP/SRP051/SRP051702 ftp and downloaded sra file. ...
2
votes
2answers
40 views

How to compute the regression of individual fitness on individual phenotype

Consider a population structured in groups of two individuals. Individuals' interactions follow an additive prisoner's dilemma: \begin{array}{c |c |c|} & C & D \\ \hline \text{Cooperate (} C ...
3
votes
1answer
35 views

Mechanism behind negative conductance of ion-channels

I am struggling to understand negative conductance shown on I-V curves on ion channels. Mechanistically negative conductance means that inward (or outward) current increases when voltage across ...
0
votes
1answer
18 views

What does this mutation notation mean: MAP2K41161fs*12

I received a report that had a mutation notated as: "MAP2K41161fs*12". I'm used to seeing this sort of thing: BRAF(V600E) or BRAF(T1799TA). Can someone tell me how to interpret "MAP2K41161fs*12" ?? Is ...
5
votes
1answer
66 views

Influence of eating at late night on sleep

I have often heard the saying that one shouldn't eat a mountain of food because blood will go to the stomach and it'll be difficult to sleep well because the stomach can't rest at night. I see that ...
2
votes
2answers
31 views

How to conceptualize the action potential?

In my AP Biology class, we were taught that action potentials are not electrical impulses in the same way current travels through a wire. Rather, we were taught that action potentials are changing ...
2
votes
0answers
33 views

Colored water uptake by plants [Rainbow Roses]

We all know cut flowers in a vase with water will drink the water. The water is transported by the xylem and by passing through the cellular walls reaches every plant cell and hydrates it or it ...
1
vote
2answers
58 views

Trying to understand the big picture behind DNA sequencing, alignment and searching

I'm about to start a bioinformatics research project but I haven't any biological background. I know my project is in regards to a performance analysis of DNA sequencing and searching "weapons" like ...
1
vote
1answer
21 views

Are there fish with a double circulatory system?

Our courseware materials say there are such fish, but the internet suggests fish only have a single circulatory system. Thanks!
1
vote
1answer
29 views

Identifying the origin of replication of an unknown *E. coli* plasmid

I have attempted a few searches for a list of origins of replication for plasmids in E. coli, but I was only able to find a list of origins, but not their individual sequences. The available plasmid ...
0
votes
0answers
13 views

Linkage Repulsion

"Segregation distorters such as meiotic drivers, involve two loci—a killer (drive) locus and a sensitivity (target) locus—being in strong linkage repulsion to ensure that the drive and ...
9
votes
1answer
64 views

Why some parts of the human body have immune privilege?

Why have the eye and CNS have immune privilege? Why does the body not develop tolerance against their tissue and instead risk their damage in case an accidental immune cell infiltration? Wiki: ...
0
votes
1answer
31 views

Genetic notations

Genetic testing revealed these two mutations (hypothetically): IVS11+6G>A and IVS11-4G>A Could you please explain every part of this notation, especially "+" and "-" signs.
1
vote
0answers
26 views

What will happen to transcription if histone acetyltransferases are removed from a eukaryotic cell?

If HATs are destroyed in a eukaryotic cell, how will gene expression level be affected? Will all gene expression be affected or just be slowed down and most gene will still be expressed?
3
votes
2answers
56 views

Antibodies stored in freezer instead of fridge

Someone from my lab put the box of antibodies in the freezer instead the fridge. Can I hope that they will still work?
0
votes
3answers
81 views

How does frame-shift mutation not absolutely ruin the organism?

I'm a bit curious as to how frame-shift mutation works. If you shift one amino acid towards another. How does this not affect the entire chromosome? Wouldn't this mean that the organism would be ...
1
vote
0answers
15 views

Linkage Disequilibrium in GWAS

I see a lot of studies on GWAS not filter out for linkage disequilibrium or even make the slightest mention of it. Why is this the case? I would imagine that you want to keep SNPs that are only in ...
0
votes
0answers
28 views

Some kind of better oxygen-transport protein or something… Can you help me find it?

I remember reading about artificial or man-made, oxygen-transport protein that is somehow an improvement on hemoglobin, and that it is possibly immune to sickle-cell anemia, or something... But I ...
1
vote
0answers
46 views

Consuming animals by slaughtering vs injecting barbiturates?

In "Least painful way to die" we get an answer ... Companion animals (e.g., dogs and cats): injected barbiturates are recommended Laboratory animals (e.g., mice and rats): injected ...
6
votes
0answers
64 views

Biopython - Big Discrepancy Calculating RNA melting Temperature over Literature

I experience big discrepancies when calculating melting temperature of RNA 7-mers with Biopython over values generated by a popular algorithm. I tried the nearest neighbour algorithm with RNA and ...
0
votes
1answer
31 views

(Genetics) Is a silencer the same as gene silencing (heterochromatin)?

Is silencer the same as gene silencing? I know that gene silencing refers to those heterochromatin concentrated at the telomeres or centromere. It is also related to methylation. But what about a ...
0
votes
1answer
17 views

Can the Staph streak method be used for culturing Neisseria on blood agar?

What I learned in class: Normally chocolate agar is needed to grow Haemophilus and Neisseria. The Staph streak technique can be used for culturing Haemophilus on blood agar by allowing the Staph to ...
0
votes
0answers
21 views

What is a “NuMA protein”?

I just got out of a lecture on mitosis and this part was incredibly confusing. After searching my textbook it doesn't cover it that well either. The professor mentioned a NUMA protein that is ...
1
vote
0answers
35 views

Importance of organic chemistry in biochemistry/molecular biology? [closed]

I'm halfway through my biochemistry and molecular biology degree in Australia and i'm concerned about a lack of organic chemistry. My friends studying biochemistry back home in Canada take units upon ...
3
votes
0answers
40 views

Neural coupling between Pinsky-Rinzel (reduced Traub) neuron with a Wang-Buzsaki neuron?

I have read two papers related to modeling neurons. The first one is the paper by Pinsky and Rinzel and the second one by Wang and Buzsaki. The first mentioned neuron model is a excitatory neuron ...
1
vote
1answer
39 views

Limited space for animals - how is that bad?

I am writing an English paper wherein I have to appeal for change in the way humans treat wildlife. I was initially given a situation wherein I took a ferry in a certain area and saw a dead baby ...
3
votes
0answers
28 views

Is the number of stamens always 9 for geranium?

We are studing in class the reproduction of plants. We start the lesson by observing some components of flowers, it was the Géranium. First of all we start counting the number of sepals , petals and ...
0
votes
0answers
25 views

Determining the percentage of the query of an alignment from a BLAST output

Given this BLAST output, how can I determine the percentage of the query sequence in the alignment? I know that it's also referred to as 'query cover' but I can't seem to find anything online that ...
0
votes
0answers
13 views

Over what range do Thyroid Stimulating Hormone (TSH) levels tend to fluctuate over the course of a day?

I understand that the majority of doctors consider the TSH test "the gold standard" for measuring thyroid function (examples stating that literally are here and here). The reference range for what is ...
1
vote
1answer
25 views

How does inbreeding depression cause infertility?

My textbook states that repetitive self-pollination in the plants cause inbreeding depression which causes infertility thus plants develop techniques called outbreeding devices to encourage ...
2
votes
1answer
57 views

Are there any examples of how to apply evolutionary models?

Apologies if this question it too open-ended; evolutionary biology is not my primary field. I have been reading a lot about the use of statistical mechanics in analyzing evolutionary dynamics. As an ...
1
vote
1answer
28 views

How does the partial pressure of oxygen affect mental focus?

On this Wikipedia page it says that lower oxygen levels can cause light-headedness. Is there evidence that higher partial pressure of oxygen can improve mental focus?
3
votes
2answers
37 views

Macrophages and what they consume

Do macrophages in the dermis consume any foreign invader to the body, or simply pathogens and cellular debris? For example, would macrophages consume vitamins or medications injected into the dermal ...
7
votes
1answer
144 views

Why do only humans commit suicide?

Why is it that only humans commit suicide? Many animals do 'brave' things to protect their children or family, and some male spiders sacrifice themselves so that they can impregnate the females. ...
0
votes
1answer
21 views

Do restriction enzymes on read 3' to 5'?

Every chart of palindromic restriction enzymes I've seen lists their restriction sites from 5' to 3', something like this: EcoR1 cuts GAATTC between the G and A: 5' NNNGAATTCNNN 3' --> ...
3
votes
1answer
141 views

Lentivector biosafety

Lentivectors are widely used in molecular biology, most commonly to transduce in a stable way a desired gene. These vector system takes advantage from the ability of viruses to introduce their own ...
4
votes
1answer
47 views

Multistability in the lactose ultization network

Reading the paper here, I'm confused about the production of figure 4d. The method of production is detailed in the supplementary information under the heading "Theoretical phase diagram". ...
5
votes
2answers
101 views

Proteins that give color (without fluorescence)

Is there proteins that have strong color, that could be seen without the need of UV and with naked eyes (with white light) - in mammalian cells? Searching for reporter, something like GFP, but that ...
-1
votes
0answers
20 views

Regarding benzoic acid and its effects

One of the users on the chemistry s.e. mentioned that when benzoic acid forms in the body in response to other chemicals it might have a mutating effect on one's DNA. Is this true?
2
votes
2answers
75 views

Why do slime molds pulsate when growing into their fruiting body?

An example can be seen in this Youtube video, where the slime mold pulsates as it engulfs a rock in order to form its fruiting body. Why does this pulsing happen?
-1
votes
1answer
30 views

What does a read simulator do?

There are various software for simulating reads for Next Generation Sequencing. Can anyone tell what exactly is done by a read simulator software
1
vote
1answer
19 views

What causes muscle spasms?

What causes muscle spasms with muscles that are not in the heart ? Could it be some sort of stimulus overload that causes a massive contraction?
4
votes
0answers
22 views

What are those visual and auditory reflex controlled by the midbrain?

The midbrain is a centre for certain visual and auditory reflexes. But what are those reflexes exactly? My study book says that these reflexes are, e.g., responsible for moving the eyes to view ...
6
votes
0answers
39 views

Basic Modelling in Quantitative Genetics

I am pretty bad in thinking quantitative genetics models. I am trying to get some basic understanding of modelling the evolution of a quantitative trait. I am therefore asking for help to analyze a ...
3
votes
0answers
24 views

Multiplex PCR, shorter amplicon inhibiting longer amplicon?

I want to run multiplex PCRs for my genotyping, with a primer pair targeting my construct and a primer pair targeting some housekeeping gene (sort of a built-in control). I designed the control ...
4
votes
2answers
49 views

A doctor might give bicarbonate (HCO₃¯) to a patient who is breathing very rapidly. What is the doctor assuming about the patient’s blood chemistry?

The answer is: The doctor is assuming that the rapid breathing is the body’s response to low blood pH. (Source: Campbell Biology) But this answer doesn't make sense. Why would the doctor give the ...
1
vote
0answers
38 views

Drosophila biarmipes gene annotation, transposable element?

When doing an annotation of a contig31 of Drosophila biarmipes genome, the gene predictions(in orange, red, green, tan, blue, brown, and gray) picked up numerous possible genes in the area circled in ...

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