Genetics is the branch of biology that deals with the transmission and variation of inherited characteristics, particularly chromosomes and DNA.
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TCGA data, and bioinformatics design questions for SNP/ mirna analysis
It's my first time posting to this forum but was looking for some help on the data aspects of this project.
My tools of choice would be in python/R .
Goal: I'm looking to create a disease specific ...
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Primer design for Gibson assembly
I'm trying to design a primer for Gibson assembly. My gene of interest is on a plasmid, and I want to copy that gene, and put it into a different plasmid.
I am unsure how to design my primers for ...
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Knockdown of long noncoding RNA (lncRNA) - how is it done?
I don't work at the wet lab and don't know all the details about the knockdown techniques.
My question is:
How lncRNA knockdown is done?
For example - you have lncRNA that is functional in the ...
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What is solid-phase bridge amplification?
During Illumina sequencing there is a step called bridge amplification by which DNA is amplified by isothermal enzymes. What is this stage, and how does it work?
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What's the difference between shotgun sequencing and clone based sequencing?
What are the main differences between shotgun sequencing and clone based sequencing?
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DNA replication Okazaki fragments
I understand multiple origin bubbles; DNA polymerase only synthesizes DNA from 5' to 3' and all that. But what I don't understand is why it has to be in fragments. Yes, DNA is anti parallel, and so ...
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What is an epistasis group?
I have been trying to wrap my head around the concept of epistasis for a couple of days now, and I think I understand it, at least at a basic level, but I still don't understand some of the ways that ...
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Which X-Y chromosomes have the developmental genes for mammals?
I know that for a given mammal, half the chromosomes come from father and half from mother. This is typically denoted as x-y. I've recently read about "toolkit" genes that control how a cell develops ...
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Are there more descriptive ways of naming genes and gene interactions?
I couldn't help but notice just how non-descriptive the gene names that modern genetics is using. Currently I'm reading "The new science of Evo Devo" by Sean B. Carroll and here are some examples of ...
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Detecting Introns and Exons
I know that when RNA is transcribed from the original strand of DNA it contains introns and exons, and that the introns are spliced out of the strand to provide genetic diversity. However, what I ...
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Low complexity region and relaxed selection
I'm reading a text (Wagner, 2007) on identifying positive selection. In paper, the author says that low complexity regions are known to be associated with relaxed selection. I'm trying to understand ...
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How is gene expression estimated?
I'm reading this fantastic article on estimating body time: Molecular-timetable methods for detection of body
time and rhythm disorders from single-time-point
genome-wide expression profiles and one ...
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What is the mechanism of regulation of PER /CRY genes?
I've read multiple descriptions of biological/circadian clocks and they all mention PER, CRY and CLOCK genes. While I kinda get how they are connected, what interests me is how these actually regulate ...
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How do mutations come to be shared by all cells?
It's my understanding that various hazards can damage the DNA in our cells, causing mutations.
But whenever I picture this, I see the damage being done to one of our tissues (for example, our lungs ...
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Hardy-Weinberg Equilibrium: To compute probability of finding two siblings (random mating)
I've been working a little with M. G. Bulmer's Principles of Statistics (Dover, 1979) and cannot see how to properly compute half of one question. This should be a basic probability computation, but I ...
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67 views
Results of a complete DNA sequencing - are they 100% reusable?
Is that correct that a complete DNA sequencing (the whole genome) need only to be done once (per person)?
After that is done, it the complete genome can be stored and once the new genes (and they ...
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Two brown-haired people have two children, P and Q. P has blond hair. Q has brown hair. What is the probability that Q is heterozygous?
Two brown-haired people have two children, P and Q. P has blond hair. We therefore believe that each parent is heterozygous and that blond hair is a recessive trait.
Q has brown hair. What is the ...
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What factors govern the variable age of onset in Huntington's Disease?
"Huntington's disease (HD) is a neurodegenerative genetic disorder that affects muscle coordination and leads to cognitive decline and psychiatric problems." As we all know, this genetic disease ...
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What are polytene bands, and why are they there?
Drosophila polytene chromosomes have been particularly useful in genetic research, as it made cytogenetic gene mapping possible with very little effort. This was primarily accomplished due to polytene ...
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How is the exogenous DNA protected from degradation during bacterial transformation?
During transformation, a bacterium can take up DNA from its environment. A small fraction of bacterial species are known to be naturally competent, meaning that they can engage in this sort of ...
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Definition of Dye- Reduction Test?
Can some one give a simple explanation or definition on what a dye-reduction test is.
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Are there eukaryotes without introns?
This question on the function of introns in eukaryotic genes made me think: I know that more basal organisms have smaller introns and fewer alternatively spliced exons compared to mammals. But are ...
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How are geneticists able to isolate gene functions?
As an example, this Scientific American article describes a known area in the dog genome that metabolizes carbohydrates.
How is it that researchers are able to determine specific functions such as ...
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Can mammals from different species reproduce?
I'm curious on how genetically different can two animals be in order to reproduce. Could they belong to different species?
One example is the mule which is the offspring of a donkey and a horse, in ...
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What's the difference between a free chromosome fragment and an extrachromosomal array?
This is reference to a review on C. elegans mosaic analysis by Yochem and Herman, in which the authors make a distinction between free chromosome fragments and extrachromosomal arrays.
For the ...
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What is the biological mechanism underlying caffeine intolerance? (CYP1A2 or other?)
As far as I can tell, caffeine metabolism occurs primarily via the CYP1A2 enzyme. I am curious as to whether mutations in the CYP1A2 gene are associated with caffeine intolerance. Some site that is ...
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What is the minimum population size that Hardy-Weinberg calculations can be applied to?
I'm trying to find out if a particular allele is in Hardy-Weinberg disequilibrium, but the data is poor. What's the minimum population number that you can use to get any sort of respectable ...
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Recombination-based vs. Sequence-based genetic mapping
Now that sequencing is becoming increasingly cheap, what is the value of recombination-based genetic mapping against the sequence-based genetic mapping?
I think that in the past recombination-based ...
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How many nucleotide pairs code one gene?
As I know three nucleotide pairs (triplus) code one gene. But I have found next information in the "Molecular biology of the cell" by Bruce Alberts:
Mycoplasma genitalium: it has only about 480 ...
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What causes XYY Syndrome?
It's obvious how a misdisjunction can result in klinefelter's syndrome (XXY) but I don't see how this can result in XYY syndrome. Your parents have a collective total of only one Y chromosome so how ...
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What makes a gene dominant or recessive
We all carry two copies of each gene (outside of male sex chromosomes). If the two differ from each other often one is dominant and one recessive. How does this mechanism work on a molecular level? ...
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Chromosomes are of different size but why do all chromosomes have similar GC percentage?
When I browsed NCBI I saw a pattern: even if the chromosome sizes, number of genes, and number of proteins are different, GC% in chromosomes tend to be similar. The examples are linked below.
Yeast,
...
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Why doesn't recombination occur in male Drosophila?
"Males do not show meiotic recombination, facilitating genetic studies."
For a while I have known that this phenomenon occurs, this quote comes from the Wikipedia page on Drosophila melanogaster, ...
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When can I assume individuals marrying into a pedigree are non-carriers?
If I'm not told that they're non carriers, and if I don't have proof of their geneotype based off of progeny, when can I assume they're non carriers for a trait?
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How do circulating androgens contribute to higher rates of hirsuteness in some women?
I was reading up on ethnic groups in which the women are naturally more hirsute (such as South Asian women) in the context of evolving standards of beauty. I came across this statement on a forum:
...
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What is the point of being selection-free?
I'm reading "Highly efficient endogenous human gene correction using designed zinc finger nucleases" by Urnov et al. They propose a way to use zinc finger proteins for gene therapy. They repeatedly ...
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What accounts for size variation in breeds of dogs?
My assumption is that dogs vary so much in size because of artificial selection pressures coming from human breeders, but are there genetic loci that roughly determine approximate size? Do other ...
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How can a three-base codon evolve from a two-base codon?
Inspired by this question among others.
It's widely suggested that the current 3-base codon system of encoding protein sequences in DNA evolved from an earlier 2-base codon system. This makes sense ...
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Mathematical Modelling of Natural Selection
I'm a math undergrad looking for some papers on modelling the process of natural selection. The only paper I've been able to find is by the pre-eminent mathematician Herbert Wilf from 2010,
There's ...
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Are all chromosomes equally susceptible to mutation?
The humans have been around for a few million years, other organisms longer yet. Changes that occur in the genome and propagate (may) eventually throw a new species ... or atleast branch off the old ...
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Papers linking telomeres and aging [closed]
I'm currently writing a piece of work about telomeres and aging, and wondered if you could share some good papers you've either read or know of.
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What is the inbreeding coefficient for the female offspring of a sib-mating in a haplodiploid system?
The inbreeding coefficient of a sibling mating for a diploid organism is 0.25 (each allele has a 25% of being identical by descent in the offspring).
In haplodiploid organisms, males result from ...
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Historical recovery from mass extinction events
Is there a way to generally characterize how species "regrew" after the various mass extinction events happening periodically from 450 Ma to 65 Ma. Would the surviving species just start back where ...
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Can a new Y-chromosome be created?
The major gene of the Y-chromosome is SRY. Would it be possible to get the X-chromosome and add SRY to create a "fuller" Y-chromosome?
What advantage does the skinny Y-chromosome give an individual ...
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Have any genetically altered organisms actually become abundant in a natural environment?
Most of the things that come up in Google and Google Scholar for this question have a mostly/completely speculative tone, or at best use models instead of measurements. This report describes some ...
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Why Can't A Male Mule Have Offspring?
I've read that female mules can sometimes have offspring, but that male mules are incapable of doing so. Why is that the case? Is their sperm not capable of entering the egg or is their a genetic ...
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Chromosome 2 fusion?
I read this article by Jeffrey Tomkins and Jerry Bergman claiming to debunk chromosome 2 fusion. Is there anything wrong with these conclusions?
" 1.The reputed fusion site is located in a ...
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How many people are required to maintain genetic diversity?
Imagine humans were to colonize a distant planet and it was a single one-way trip. How many people would they need to bring?
Obviously 2 is the minimum, but that would result in a lot of inbreeding.
...
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How does a tiger have stripes?
A vague question, but let me try to explain. My friend explained to me that in females, some cells use one X chromosome, while all others use the other X chromosome. This can result in some ...
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Hershey and Chase experiment
http://www.youtube.com/watch?v=3QJ4CjFsflA
This is a link to Hershey and Chase experiment. According to this experiment, we conclude that DNA is the genetic material. But how do we conclude that DNA ...
