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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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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23 views

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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32 views

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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33 views

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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25 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 ...
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39 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 ...
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27 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?
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41 views

Would it be possible to create a gel, holding viruses, that could alter human genetic code 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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33 views

Can intron become exon in alternative splicing?

From this image We can saw several exon that is actually intron in other gene. It's not a really different gene, it's an alternative splicing of a gene. My background is not biology so is it ...
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23 views

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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47 views

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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30 views

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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58 views

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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30 views

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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34 views

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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74 views

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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26 views

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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50 views

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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40 views

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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65 views

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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67 views

“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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22 views

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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60 views

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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66 views

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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92 views

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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What is the control level of activation in Paradigm?

I am trying to use Paradigm for pathway analysis on mRNA expression data. In Sample-Specific Cancer Pathway Analysis Using PARADIGM it is written that Each entity can take on one of three ...
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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 ...
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89 views

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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154 views

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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71 views

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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33 views

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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38 views

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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99 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 ...
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256 views

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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37 views

IPTG and lac operator with e coli for foreign gene question

We did an experiment were we have e coli with a plasmid with a gene from another bacteria in it, and we put in IPTG in for induction. Will after looking up more about IPTG online I see it's related to ...
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41 views

In insects, does the Alanine repeat occur on the homeodomain sequence of the abdomen or does it occur on a different sequence?

By "Alanine repeat", I am referring to the suppression of the formation of extra insect legs due to Ubx gene suppression through Distal-less repression.
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88 views

Plasmid in the nucleus and gene expression

If we insert a plasmid into a human nucleus that contains exact copy of gene and all relevant promoters to produce some human protein, will the cell create functional protein from that plasmid only ...
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21 views

Why does a tumour's genome change depending on the environment?

According to the book "Primer of The Molecular Biology of Cancer" by Vincent, Theodore and Ateven, the tumour cell is changed depending on its environment. performed genome-wide analysis on three ...
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47 views

Can methylation of a promoter induce gene expression in some rare cases?

Can methylation of a promoter induce gene expression in some rare cases? I've read somewhere that methylation of an intron can induce gene expression (eg. Igf2). How is that even possible? Thank ...
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35 views

Why are riboswitches mostly present in bacteria and not in eukaryotes?

Riboswitches are a rather elegant way to regulate gene expression without any additional machinery. A small ligand binds to the mRNA and directly influences transcription or translation. Most of the ...
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53 views

Multi-modal distribution for gene expression data

Why would some genes have more than two modes in their expression distribution? What external factors would cause this anomaly? I'm referring to the expression distribution of a gene across different ...
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545 views

Father with mutated mtDNA- why isn't his offspring at risk?

Mothers transmit their mitochondria (and therefore mtDNA) to their offspring and fathers don't. Lets assume that father had a mutation of the gene that encodes mtDNA, would then be his offspring at ...
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79 views

Balanced vs Maximized Codon Optimization

I have worked with the optimization of several viral proteins, from different viruses/families, with different results. When Menzella, 2011 was published I tried that method. I found quite the ...
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93 views

How to validate the regulatory interactions inferred from gene expression data?

My algorithm learns regulatory interaction between genes using Bayesian Network approach from gene expression data. After the algorithm has converged to a network of interacting genes, how to validate ...
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25 views

If gene differs between chromosome pair does individual get a mixture of protein shapes?

Do diploids such as humans end up with a mixture of two different shaped proteins where the appropriate gene is expressed differently in the two halves of a chromosome pair or is there some governing ...
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61 views

Why we do not use RNAi to control ebola?

As you know using RNAi we are able to prevent gene expression. so why we do not use it to stop viral genes expression?
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47 views

Word denoting genetic state

Is there a single word, or brief phrase, that denotes the state of the total genetic machinery (genome + transcriptome + proteome + ...) of a cell or organ or organism at a particular point in time?
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48 views

Mechanisms of genotype*sex interactions [closed]

I'm looking for suggestions of the mechanistic level at which genotype*sex interactions can occur. These give different phenotypes from the same genotype dependent on the sex they are expressed in. ...
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1answer
50 views

What does it mean for the signals for transcription and translation to be “conserved”?

I was reading this article: "Overview of vector design for mammalian gene expression." for an explanation of why mammalian cell lines are used for expressing cloned genes, and one of the reasons ...
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Imperfect dosage compensation

Dosage compensation is used to make up for different copy numbers of the major sex chromosomes in males and females (One X or Z chromosome in one and two in the other). Two main mechanisms of dosage ...