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.
360
questions
0
votes
1
answer
35
views
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 ...
1
vote
0
answers
18
views
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 ...
1
vote
0
answers
30
views
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 ...
- 221
2
votes
2
answers
122
views
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 ...
- 131
4
votes
1
answer
246
views
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 ...
- 65
0
votes
0
answers
86
views
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. ...
- 257
0
votes
2
answers
834
views
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?
- 44
1
vote
1
answer
60
views
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 ...
- 65
0
votes
1
answer
71
views
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?
...
- 15
3
votes
2
answers
99
views
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 ...
- 31
1
vote
0
answers
45
views
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 ...
- 37
0
votes
0
answers
31
views
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 ...
- 191
3
votes
1
answer
76
views
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 ...
-1
votes
1
answer
56
views
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 ...
- 103
0
votes
1
answer
30
views
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 ...
- 1
2
votes
1
answer
64
views
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 ...
- 21
0
votes
1
answer
43
views
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 ...
- 1
1
vote
2
answers
108
views
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 ...
- 103
2
votes
2
answers
66
views
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 ...
- 328
-2
votes
1
answer
115
views
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 ...
- 552
1
vote
3
answers
2k
views
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.
- 11
2
votes
0
answers
132
views
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 ...
- 61
3
votes
0
answers
201
views
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 ...
- 221
0
votes
1
answer
56
views
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 ...
- 111
0
votes
1
answer
45
views
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 ...
- 35
0
votes
1
answer
71
views
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?
...
1
vote
0
answers
34
views
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 ...
- 407
1
vote
1
answer
572
views
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 ...
- 2,721
2
votes
1
answer
31
views
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 ...
- 129
1
vote
0
answers
47
views
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 ...
- 71
2
votes
0
answers
129
views
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 ...
- 71
0
votes
1
answer
61
views
Cloning a coding gene into a non-expression vector
Does it make any sense to clone a CODING gene into a NON-expression vector?
doing this will only give us multiple copies of the gene, while we could run PCR instead (Let's say we know the gene ...
- 1
-1
votes
1
answer
80
views
Are modern gene-editing techniques capable of creating genetically-superior versions of humans? [closed]
Can we alter the DNA in, say, a small-framed, low muscle mass male to those of elite bodybuilders?
Can we alter the DNA sequence that stops balding and hair loss? How about the genes responsible for ...
0
votes
1
answer
24
views
Question: What is CINWntUp and CINnormL?
What is CINWntUp and CINnormL?
I read a paper that uses this two things as classes but Im not sure what they represent. I imply that CIN is referring to Chromosomal instability but I don't know what ...
- 11
0
votes
1
answer
37
views
Gene expression: which allele is considered?
For human beings, we have two copies of each gene inherited from the parents. The question is, when referring to gene expression, which copy (or allele) is considered?
- 111
2
votes
1
answer
83
views
Is there a resource to query gene expression similarity? Stratified by sex?
We developed such a resource. The editors of "Bioinformatics" (at OUP) rejected the paper on the grounds that we did not run a comparison with "state-of-the-art" [similar] resources. Can someone help ...
0
votes
1
answer
66
views
How is the timing of gene expression controlled in developing embryo? [closed]
I understand how cell differentiation works in general (gradients of homeobox proteins etc), but how is timing controlled? Why do some genes switch on at a very specific moment of development and then ...
- 133
0
votes
2
answers
72
views
identification of differentially expressed genes in RNA-seq analysis [closed]
I am using four different packages (viz. EBSeq, DESeq2, edgeR, LPEseq) for identification of differential genes. Now I am confused whose fold change value should I take for further downstream ...
4
votes
2
answers
622
views
How does transcription end?
In rho-dependent termination in prokaryotes, how does RNA polymerase “know” that it has reached the end of a gene and that it has to stop so that the rho-factor can bind mRNA’s rut site? Is there a ...
- 407
0
votes
1
answer
35
views
About Frameshift Mutation
I am coding a DNA translater, based on the homosapiens genome, & i knowing that the data provided from NCBI is surely not 100% precise (there may be some base changes / removes etc...)
, & i ...
- 11
1
vote
1
answer
83
views
What is the role of CRISPR-dCas9 in gRNA-dCas9 transcription regulator complexes?
In this paper1, I read that mutant versions of Cas proteins such as a deactivated Cas9 (dCas9) are used alongside a guide-RNA (gRNA) to form variants of CRISPR tool that can function as transcription ...
- 407
2
votes
0
answers
25
views
Preprocessing microarray data to detect increased male expression variance due to dosage compensation?
I am currently working with a dataset from a large microarray experiment where one of the aims is to look for evidence of the predicted doubling of variance in expression on the X chromosome in ...
- 21
2
votes
2
answers
110
views
What happens to the complementary base when the other undergoes a base substitution mutation?
From what I know only the base pairs A and T/U, or G and C can occur due to hydrogen bonding. So if a base substitution mutation occurs, say an A is replaced by a C on the strand, does it affect only ...
- 21
3
votes
0
answers
71
views
How are animal patterns encoded in the dna?
After seeing the patterns on the feathers of a argusianus argus pheasant (shown below), I am curious where is the information that encodes a pattern for a particular bird, and what form is this ...
- 131
1
vote
0
answers
78
views
qPCR: Huge variation in fold change of genes between biological replicates
I am trying to validate my RNAseq data by doing qpcr for which I am looking at the fold change of few genes across various timepoints of treatment conditions. I am getting huge amount of variation (in ...
- 11
-1
votes
1
answer
269
views
Can the environment affect genes and adaptation in offspring?
I recently read several articles that believe that environment can affect gene expression and this change will transfer down to the children. Some theorists believe that random mutations are more rare ...
- 99
2
votes
1
answer
56
views
Why don't cells double gene expression after S-Phase?
In the cell cycle (G1-S-G2-M), all of the DNA is replicated during the S or Synthesis stage. The cell may then spend some considerable time in the G2 phase before splitting in the M phase. Since there ...
- 525
2
votes
2
answers
89
views
Can gene-gene interactions result in gene expression?
I am building a project on Inferring Gene Regulatory Networks using ARACNE and PCA-CMI algorithms, and the input to these algorithms is taken from the DREAM3 challenge.
The format of the input data ...
- 123
3
votes
0
answers
71
views
Low cost cell free expression system
I am a graduate student looking to incorporate some protein engineering into my training. I have been reading a lot about E coli lysate based systems, but they still require 3rd party additives like ...
- 133
3
votes
2
answers
139
views
When does genetic randomization happen?
When two parents (regardless of species) reproduce in sexual reproduction each offspring is generally a random combination of genetic traits from each parent. Their developed traits then depend on the ...
- 165