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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where can I study the mechanisms of DNA repair in Archaea such as Pyrococcus Furiosus?

Can you provide me some useful and straightforward material where I can study the mechanisms of DNA repair in Archaea such as Pyrococcus Furiosus ?
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Is there a negative correlation between the mRNA produced by the cell and the time of extraction? [closed]

I am doing some data analysis about gene expression time series. When I plot mRNA produced by P. Furiosus cells irradiated by gamma radiation against the time of extraction, it seems that there is a ...
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How do genes determine facial features?

What is known about the genes responsible for inherited facial features — the family resemblances that are so recognizable? Take for example a particular shape of nose: which gene or genes make it ...
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Pet 28a plasmid is obtained from which type of bacterial strain

I want to ask some question which is very confusing Pet28a is a vector.I want to know which strain of bacteria have pet28a plasmid? E.coli DH5 alpha strain have pet28a plasmid? Please help me .......
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Will a nucleic acid sequence deduced from a protein sequence be expressed from a plasmid?

I have a fasta file containing the amino acid sequence of glycogenin-1: https://www.rcsb.org/fasta/entry/6EQJ I want to create a plasmid that produces glycogenin-1. Is it possible to use the ...
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Limits of gene editing

I was reading some articles about CRISPR and the world of gene editing, but then a lot of questions for which I couldn't find any answer online came into my mind. Those are all about how far can we ...
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Help Finding Specific BlaZ Gene Type Sequences on Genbank

I am doing an undergraduate research project that involves blaZ gene typing for different strain types of Staphylococcus aureus bacteria; for reference, here are some of papers on this topic that ...
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Time scale for cAMP-dependent pathway cascades

What is the time scale for cAMP-dependent pathway cascades that start at the level of ligand binding to a G-protein receptor and finish at the level of gene transcription regulation? For example, when ...
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About genomic imprinting

In the context of genomic imprinting, how does a human cell "know" whether a chromosome is paternal or maternal(out of a homologous pair), in order to silence genes?
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What does this mean?

The phenotypic ratio of dihybrid cross 9:3:3:1 can be derived as a combination series 3 yellow: 1 green, with 3 round :1 wrinkled. This derivation can be writtenbas follows: (3 round :1 wrinkled) (...
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Histone Deacetylase Inhibition

So I am trying to brush up on my knowledge of HATs and HDACs. I am reading the just the 1st paragraph of the background of this study I remember learning that HATs turn things on on, and HDACs turn ...
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Can the activity of a specific gene in a cell artficially be increased?

While there are many gene regulation mechanisms from the cell itself, I was wondering whether it is possible to increase the gene activity in a living cell permanently (so that the protein that it ...
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Protein half-life regulating gene expression

Are there any instances in real life of protein half-life regulating gene expression? For example, in a cell, Gene A produces a starting population of protein P, after which the expression of the gene ...
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Vectors for genetic engineering

Well can a bacterium be used as a vector?I have learnt that Agrobacterium tumifacian can be used to deliver a gene of interest in plant cells but on a book in a multiple choice question it says that ...
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Modeling the production of mRNA

I have the following example of how an equation for the production of mRNA in a particular organism could look like: Consider the following equation for the production of mRNA for a gene Y. Gene Y ...
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Mutated and unmutated PCR product

If I have a mutated colony containing the fusion protein, mCherry instead of the stop codon TAA, and an unmutated colony which does not contain the protein. Why will the PCR products of the two ...
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How do substances for gene expression work?

How does amplification of gene expression work? I often find in various articles expressions like "Using substance X or peptide X, we enhanced the expression of gene Z, which led to a certain ...
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Absent gene expression from one of two vectors co-transformed into the BL21(DE3) strain of E. coli

I've been trying to express two proteins in the BL21(DE3) strain of E. coli. One gene is in a pCR2.1 vector and the other in a pET-expression vector. When I induce with IPTG and run on an acrylamide ...
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DNA methylation and the validity of the definition of epigenetics

I am currently studying a textbook that presents the following definition of epigenetics: Epigenetics is defined as heritable changes in gene expression without changes in the DNA sequence. The ...
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Cell type = gene expression spectrum?

I wonder if it is correct to say that the type of a cell is essentially its spectrum of expressed genes, i.e. the rates at which it produces specific proteins. As these rates may change (e.g. during ...
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Convolution and deconvolution in gene expression

I am trying to understand the mathematical concept behind convolution and deconvolution in gene expression. Went through various papers but they are way too complicated. Can anyone provide simple ...
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How do enhancers induce transcription?

DNA response elements are DNA sequences that are could be found upstream, downstream of genes that regulate gene expression at the transcriptional level. One type -Enhancers- bind specific ...
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Is there a difference between “genetic cross regulation” and “crosstalk”?

What is the difference between genetic cross regulation and crosstalk? I'm a physics major and learning about bioinformatics now. So it might seem trivial to many but from the article "Wanner BL. ...
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What does it mean that the transcript is enriched?

I think I don't get the meaning of "enriched" in the context of genes. What's the difference of gene being "enriched" and "expressed" in the cell?
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What are the effect of P. Falciparum on gene expression in humans? Do they have an effect in the first place?

I am looking for names of genes which are affected (if any) and how are they affected, I mean whether the expression levels are lower or higher?
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What prevents mRNAs that are localized to a specific part of the cell from being translated before they reach their destination?

One of the methods of mRNA localization, for example, is random diffusion of mRNAs where the mRNA binding proteins are localized to a certain part of the cell. However, I was taught that the ribosome ...
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How to design a permanent vaccine to cholera using CRISPR?

I know that Vibrio Cholerae infects the body through the GM1 ganglioside. So, would it be possible to engineer a CRISPR gene editing tool to prevent Vibrio Cholerae from getting into our cells? ...
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Can a bacterium express a virulence gene and not produce toxins and what may be the cause of this?

I am preparing a seminar on viable but non-culturable (VBNC) state in bacteria, mainly foodborne pathogens and I just saw this line in a journal article by Lothigius et al that "the expression of the ...
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How can we say that a gene is spacio-temporally regulated?

Gene expression is depending on the space and time of the cell. How can we distinguish the function of a gene without a chance of changing its expression? And also how is it possible to find the exact ...
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Study on Introns?

I am curious whether there has been a study done on the effects of removing introns. Specifically, what happens if you genetically edit a eukaryote genome to no longer contain introns? Or maybe just a ...
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Why are protein-coding regions rich in GC?

I have been searching for an answer for this question and have some possible solutions, but I am not sure. GC regions are more stable as there are 3 hydrogen bonds instead of 2 with AT, however I am ...
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Linker DNA and Genetic Expression

So I was reading on linker DNA, and the textbook only describes it in terms of structure. I was wondering if linker DNA can ever contain genes, and if it can, whether it will always be expressed or ...
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Where to find a list of genes coding for protein in human

I have raw read counts extracted by htseq from STAR alignment I have both data with both Ensembl IDs and gene symbols, but I need only a latest list of protein coding genes in human; I googled but I ...
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Which one is better to use for water stress experiment GWAS or RNASeq?

This is my first time in this area of research. I am working on 95 varieties of bambara groundnut. I have done the agromorphological characterization of these varieties as well as the genetic ...
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Question about alternative polyadenylation

I know that alternative polyadenylation creates different transcript isoforms. My question is whether alternative polyadenylation ever results in differences in the terminal/last exon? The only case I ...
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Studying the epigenetic variability, can I use SNPs?

So, I'm trying to study the effects of epigenetic variability on the brain structure. Can I use SNPs associated with a gene's higher expression to compute the likelihood of that gene being expressed ...
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Is there natural occurrence of induced pluripotency / expression of Yamanaka factors and what is the evolutionary explanation of that?

Is there natural biological processes in which the full (full reprogramming into pluripotent state) or partial (partial reprogramming, stopped before point-of-no-return, preserving the functional ...
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Is complete dominance actually a genotypic process?

An example often stated for codominance is blood groups, where both alleles version of the protein is expressed and can be found in the cell membrane. An example of incomplete dominance often given ...
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x-linked recessive inheritance and correlation for males

I was inspired by a discussion in this thread. Wikipedia lists a number of disorders linked to recessive genes on the x-chromosome. One typical example is red-green color blindness. Now wikipedia says ...
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Why are there three stop codons but only one start codon?

I was wondering whether there is any specific reason that there are three stop codons but only one start codon in prokaryotic and eukaryotic cytoplasmic mRNAs.
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Why do BRAF mutations appear more in skin cutaneous melanoma?

When looking at the tissue expression of the BRAF protein it seems that BRAF is regularly expressed in almost all of the tissues. There is elevated expression in tissues like the Testis and the ...
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Regulation of LBD33 genes Arabidopsis. If LBD 33 gene is up-regulated by auxin then why does expression decrease when increasing auxin concentration?

I have a question regarding the regulation of lateral boundary domain genes in Arabidopsis (specifically LBD33). I am an undergraduate student trying to understand the results of a lab where I measure ...
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Is there a data base, tool or method I can use to find out which of my genes code for cytokine receptors?

I have a list of over 600 differentially expressed genes from my single cell RNA seq data analyses. I want to proceed to find out which of my genes code for cytokine receptors so that I can show on a ...
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X linked traits expression in females

We all know that females have an inactivated X chromosome (Most of its genes are inactivated). Consider a female who is a heterozygous carrier of an X linked abnormality, If the inactivated X was that ...
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Element of promoter responsible for expression power of gene

I know that there is a classification of promoters like: strong, medium and weak. This shows how a promoter affects gene expression levels. So my question is: what part of the promoter affects it? ...
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Is bi-allelic gene expression random?

Supposing we have the genotypes “Aa”, “AA”, and “aa”... which are not mono-allelic (not imprinted and not X-inactivated). Does the dominance of the “A” allele over “a” allele affect which gene is ...
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What do the haploinsufficiency scores in the clinVar database represent?

I understand that haploinsufficiency occurs when one of the two copies of a gene is mutated to the point of being unusable, and the single copy remaining is unable to cope with the cell's demands for ...
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What are mutator genes which cause copying errors in other genes?

Reading Dawkins' book "The Selfish Gene," I came across this line: "There are even genes--called mutators--that manipulate the rates of copying errors in other genes." (The context is his argument ...
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How can the same transcription factor be both an activator and suppressor of the same gene?

For example, hunchback in moderate concentrations is an activator of kruppel, but a suppressor of kruppel in large concentrations. From what I've seen in literature, that's because the kruppel's ...
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Is there a mechanism of timing or delaying the expression of gap genes?

Summary Gap genes are expressed in presence of the right combination and amount of transcription factors. But is there any additional mechanism of timing the expression of the gap genes to ensure ...

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