Questions tagged [gene-expression]
The process by which information encoded in a gene is converted into a functional protein or RNA, resulting in or contributing to a phenotype.
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Gene silencing in C. elegans
I am trying to silence the tph-1 (tryptophan hydroxylase) gene in C. elegans using the pLT63 plasmid to check if that particular gene has anything to do with the pharyneal pumping or not. Am I using ...
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ATP to disassembly of nucleotide ratio
DNA Helicase, the enzyme that is responsible for tearing apart the strands before DNA replication, requires ATP to rip apart nucleotides. I have asked this question to several professors and they ...
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Common genes and enzymes involved in pathogen entry into host
Many microbes like Salmonella, E.coli, Legionella pneumophila etc. enter host cells via cystoskeleton remodeling of the host cell. Do all microbes follow the same path or there are any other ways for ...
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Serotonin activity with short 5-HTT promotor region and depression
So after reading a few studies (1,2) it seems that a shorter promotor region for the serotonin transport protein may be associated with increased likelihood of developing depression after stressful ...
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What is meant by "the degree to which a gene is expressed" in an individual?
Here is an excerpt from a text that I was reading,
Here is an example of microarray data. The idea is to take a group of
different individuals and for each of them, you measure how much they
do ...
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how do I find the number of bp in chromosome 3 by knowing number of bp in chromosome 1?
If i have a number of bp in chromosome 1 for example(298,295,559 bp) can I use this number to find the number of bp in chromosome 3.
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In which phenomena does one gene pair hide the effect of other unit?
This question was asken in an exam,
The answer they are saying is "Epistasis". But I think "Dominance" fits better, because it is not mentioned whether genes of same allele are to be considered or ...
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What is pQTL and why do we need eQTL?
eQTLs are genomic loci that contribute to variation in expression levels of mRNAs (wikipedia).
There is data out there that shows that ~60% of the time, the amount of mRNA in a cell is directly ...
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Differential gene expression analysis between species
I have RNA Seq data from mouse and human skin ( 2 replicates each) and want to compare the expression of the orthologous genes to find any which are differentially expressed.
I have quantile ...
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How many copies of a gene?
I am studying mathematical models of transcription and translation and I am wondering:
In a particular genome, how many copies of a gene coding for one particular protein should one expect? Are they ...
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Could fingerprints potentially be changed using a gene gun?
Not to confuse with your "DNA fingerprint" I've read surgery is readily used to not just remove but even to change people's prints through employing very small grafts between opposing hands.
About 5 ...
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Are dogs affected by dwarfism?
My husband and I noticed a dog today that looked like a smaller version of a purebred Border Collie, although it didn't appear to be a puppy. It made us wonder if other animal species experience ...
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Gene and Protein isoform
What is the relationship between term "Gene isoform" and "Protein isoform"?
Say a gene can make 3 isoforms, will it produce only (maximum) 3 isoform protein?
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Interpretation of qPCR results for low expression genes
I am attempting to validate existence of a transcript using 40 cycle qPCR. I designed primers for a unique feature of this transcript, and also designed primers for a sequence in the transcript that ...
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How do sex biased genes evolve?
I am wondering how do genes become sex-biased? that is, how does a gene evolve expression which is regulated in a sex-specific manner (assuming no effect from sex-limited Y/W chromosomes).
I ...
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Sex biased gene expression in the X chromosome
It has been shown that the X chromosome is frequently enriched for female biased genes, and has a deficit of male biased genes. For example in this paper, and this one.
However, I'm struggling to ...
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Critical discussion: Gene expression and systems biology allows us to understand the control of complex traits
I'm having a bit of trouble tackling this question. Any help on what I should write about or the points I should mention would be much appreciated. I keep seeing articles about eQTL and QTL are these ...
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Why is polysome loading affected by double stranded structure?
Why polysomes are not able to load properly onto a transcript if a transcript has a double-stranded structure in it?
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Why do Alu repeats form secondary structures?
I've been doing a lot of research on Alu repeats and how they mediate the gene expression. I read the following article "Useful junk: Alu RNAs in the human transcriptome".
And it says that alu ...
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Why do some protocols require prewarming a liquid medium before inoculating?
For example, in this protocol for E. coli competent cell preparation, it says:
Plate 10 uL E. coli BL21(DE3) cells on a LB-agar plate; incubate overnight (12 hours).
Prepare 500 mL SOB medium ...
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Following DNA replication during S-phase of the cell-cycle, are all genomic regions subjected to the same stringent level of DNA-Repair?
To my (limited) understanding, there are 2 main ways that mutations can occur in DNA: Environmental (UV, etc) and mistakes during cell division.
I was wondering if there is a mechanism that can give ...
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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 ...
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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 ...
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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?
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Would it be possible to create a gel, holding viruses, that could alter the human genome when rubbed in?
I was wondering if it could be possible to engineer a virus, that when it comes into contact with human hair follicles, it could alter someones natural hair color.
Naturally blue hair anyone?
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Can intron become exon in alternative splicing?
From this image
We can see several exons that are actually introns in other genes. It's not a really a different gene, it's an alternative splicing of a gene. My background is not biology so is it ...
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Is it possible to express the cistrons from a polycistronic insertion fragment in a single plasmid?
I have a insertion fragment that I wish to express from pUC19 in Escherichia coli. The insertion fragment is a sub-section from a larger operon sequence and contains just the last two cistrons from ...
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Correct/complete representation of RTPCR statistics
In papers reporting a relative quantification of gene expression by RTPCR, I often see a bar chart with mean ± standard error or deviation, with the deviation belonging to biological replicates. This ...
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Do The Traces Genetic Diseases Remain in families?
I know that there are certain diseases that are predominant on genes. But, is there any sort of surety that if parents are suffering from a disorder then their offspring has to suffer from the same. ...
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Genetic Imprinting and Cell differentiation
It does not seem possible that these two processes can coexist:
1) Genetic imprinting is the phenomenon where genes are expressed differently depending on the parent of origin:
1a. Methylated ...
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What pattern can be learned from the data of RNA seq counts and HiC matrix? [closed]
I now have some data on the RNA seq counts and related Hi-C matrix of gene segment on a chromosome. My concern is, basically, what can we do with these data so as to establish the connection between ...
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Epistasis Across Chromosomes and Individuals 'Homozygous for Interactions'
Apologies for any failures in nomenclature. I'm a mathematician who is making a foray into genetics for a masters thesis. Specifically, I'm generating artificial diploid genetic sequence data and ...
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Where to find E.coli gene expression data?
I am searching E.coli whole genome expression data with different conditions, any suggestion is appreciated. Condition could be for example different growth temperature, different medias, etc.
I have ...
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Why introduction of an extra copy of a gene related to pigmentation causes RNA interference in Petunia?
RNAi became famous after Fire and Mello experiment in C.elegans; however, it had been observed before. In the 80's, Jorgensen was trying to increase pigmentation of Petunia flowers by introducing ...
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Can molecular genetics make a boolean variable from a continuous variable?
In the same kind of idea than this question. Gene expression are regulated through complex interactions. The concentration of enhancers and repressors is an important aspect that dictate the level of ...
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Comparing gene expression levels between control and disease at different time points
I have a data set with expression levels of a list of genes, measured in replicate at two different time points between two groups; a control group and a disease group.
I want to identify the changes ...
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Do DNA repressors exist?
I know about enhancers and the mechanism that lead them to increase the gene expression of their targets but I was wondering if similarly DNA repressors exist. I know about protein repressors but I am ...
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"Enhancers" of enhancers?
I am looking for examples (if any) of genomic regions which regulates the activity of enhancers, either augmenting or reducing it. Essentially some kind of enhancers (or repressors) of enhancers to ...
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How to correlate the pattern by which CAP activator from E.coli binds to DNA and its mechanism of action?
The catabolite activator protein (CAP) activates the expression of more than 100 genes involved in secondary sugar metabolism in E.coli.
Apparently, it always binds in sites that are away from -10 and ...
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Mechanism by which $lacI^{d}$ is a dominant mutation, impairing the function of normal copies of the Lac Repressor
Jacob-Monod model for the lac Operon was based on experiments using two strands of bacteria which constitutively expressed $\beta$-gal: $I^{c}$(mutation in the gene lacI , which encodes the repressor) ...
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How does alternative splicing work?
I am trying to find out what controls what exons are spliced out, and I keep coming across the term cis regulator, but I cannot seem to find a clear explanation of what happens...
Thank you in ...
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What are microRNA, siRNA and antisense RNA?
From what I understand, microRNA binds to proteins which can cut certain mRNA strands do that this protein is not synthesised. This seems like gene silencing to me, however I have also come across the ...
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Which data format for mRNA expression matrix is necessary to run pathway analysis with Paradigm?
I am running Paradigm on a matrix of mRNA expression. I read
Vaske, Charles J., et al. "Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM."...
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Name two reasons why it is impossible to determine a gene's nucleotide sequence from the amino acid sequence of the polypeptide
I can only think of one reason, which is because different codons can specify the same amino acids. However I am having trouble thinking of another reason.
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How does optogenetics work?
I am aware of the post here 'Optogenetics - How do microbial opsins work?'
however it is a bit too technical for me. I am struggling to understand how the neurons can be genetically engineered to ...
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meaning of the "reads" keyword in terms of RNA-seq or next generation sequencing
I'm an undergraduate student at computer science and currently, I'm interested in bioinformatics. Today, I've started to read a paper about clustering and classification of non-coding RNAs can be ...
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What network motifs or other mechanisms can make the expression of a gene invariable to the environment?
Next to double positive feedback loops and chromatin modification, which other mechanisms can make a gene susceptible to a certain environment in one cell-type but not in another?
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Two heterozygote mice for skin color are reproduced. Find the probability that in 3 children 2 will be dark and one white
Two heterozygote mice for skin color are reproduced. Black is dominant to white color. Find the probability that in 3 children 2 will be dark and one white. How did you do the ordering. Well I found ...
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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 ...
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Why people fear GMOs? Can't we map a plant composition?
My main question is can we map what a fruit is made of? For instance apples are made of 0.0002% of protein X, 0.00001 of protein Y, 0.001% of amino acid Z... etc...
If we can, then my next question ...
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