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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Can co-mutations be potential expression quantitative trait loci (eQTLs)?
I'm wondering if it is possible to test this and how? Usually we do this for single SNPs, I wanted to know if it was plausible for pairs of SNPs. Which method would you suggest?
I want to test whether ...
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How to choose a method for upregulating an endogenous protein?
What factors affect the method that should be chosen to engineer a cell line that upregulates an endogenous protein? I am mostly asking permanent or long-term expression of nuclear proteins in ...
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Ubiquitous overexpression line of a gene expressed higher gene expression in leaf but not in seeds
I tried to make ubiquitous overexpression lines of a gene using a constitutive promoter vector in plant. I got multiple regenerated plants through tissue cultures.
At T0, T1, T2 leaves tissues, the ...
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Gene Name Finding
X8HS20 - please help, I am not able to find the proper name or function of this gene in any database - can someone kindly help to figure out what it is ? I hypothesize that it is some gene of ...
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How does positional memory in fibroblast cells work?
I have a question regarding how positional memory in fibroblasts work, specifically, where the memory comes from/how its made.
For example, the Salamander & other amphibians are able to regenerate ...
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What is a good expression vector for Salmonella enterica subsp. enterica serovar typhimurium
I am interested in expressing custom proteins in a Salmonella strain, however I am facing difficulties in finding the appropriate expression vector for it. It seems that most of the resources provide ...
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What is the best way to learn about gene regulation?
For those of you who already have a decent knowledge of how gene regulation works, how should someone new to the topic acquire a detailed overview?
Is there a particularly good and up-to-date resource?...
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What is the meaning of NF-kB (transcription factor) "activity"?
This article discuss about the NF-kB activity and its mathematical modeling Understanding NF-κB signaling via mathematical modeling. The NF-kB is a transcription factor mainly involved in the ...
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Random X-Inactivation and Duchenne
I'm reading about X-inactivation and I can't reconcile some things with it being truly random. In only a small percentage of female carriers Duchenne's will be expressed. But if this was truly random, ...
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How do DNA methylation canyons/DNA methylation valleys/DMCs differ from CpG islands?
Are these just both regions of the genome that are undermethylated? Is the only difference that for something to be a CpG islands it needs a high level of CpG sites and DMCs don't?
So could a 3.5kb ...
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Function of SMAR in plasmids?
A few years ago, the Thought Emporium published a video (https://www.youtube.com/watch?v=aoczYXJeMY4) in which he refers to a study in which they mix plasmid DNA with Chitosan and feed it to mice to ...
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PCR for gene expression [closed]
Could somebody please explain the basic principle behind how qPCR can detect if a gene is expressed or not? I tried looking at literature on ScienceDirect and other websites but I could not find any ...
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Resources for understanding the basics of cell signaling, gene expression and cell fate determination, for a physics student?
I'm a physics student who will join a theoretical biology/applied mathematics research group this September. I'll link some papers at the end for further context.
The main problem I have is that my ...
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Why do cells use microRNA to break down mRNA, instead of not transcribing it in the first place?
As I understand it, microRNAs are used to ensure that certain genes are only expressed when needed. The way this apparently works is that when the translation products of an mRNA are not required the ...
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Defining cell state and type without calculating distances in expression space
Usually, cell types are found by clustering cells in expression space (or some lower dim. projection of it), and calculating differentially expressed (DE) genes. These DE genes are then used to ...
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Copy number deletion and high expression [duplicate]
I have a region that has significant CNV loss. But the expression for the genes in those regions is high compared to the expression found in the samples that don't have the regions lost. How can this ...
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Are all genes capable of being switched on or off?
Are all genes capable of being switched on or off or only some genes? Are there some genes that permanently do not have the functionality that enables them to be switched on or off?
Everything I have ...
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How I can find the list of transcription factor proteins involved in transcription of a specific gene?
I want to get the list of transcription factor proteins involved in the transcription of the human SIRT1 gene. How can I access that?
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Adh2 promoter in saccharomyces cerevisiae
I'm looking at expressing a protein in saccharomyces cerevisiae using the Adh2 promoter. My understanding is that the gene will be repressed by the presence of glucose, but when glucose runs out it ...
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Do homologous chromosomes have same rates of gene expression in a cell?
I was googling around and found only articles related to XY differences in expression. Can you please clarify if homologous genes/chromosomes have about the same levels of expression in a cell or one ...
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Is it possible to identify secreted metabolites or secondary metabolites from a gene list?
So I have a gene list obtained from differential gene expression analysis of a metabolic disease model, and I was wondering if I can identify metabolites or secondary metabolites that may be produced ...
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what are the nodes and edges in gene regulatory networks
I am trying to find out how one can using gene expression data can infer gene regulatory network applying graph theory concepts. But I could not find a proper reference that
1)explain how one can get ...
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qPCR - different results total RNA vs mRNA
I have performed qPCR on a tissue, where I have extracted total RNA and also purified mRNA. I ran the qPCR samples together, and have therefore been exposed to the same conditions except the ...
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Monogenic disorders vs multifactorial inheritance disorders
There's a condition called SYNGAP1-related intellectual disability which is caused by mutations to the SYNGAP1 gene.
I believe that this is called a monogenic disorder, while disorders that are caused ...
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Relative abundance of transcription factors and protein kinases
Are transcription factors and protein kinases only expressed at low levels in eukaryotes?
As regulatory proteins, I would expect their abundance to be lower than most other proteins, but I cannot find ...
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What is a good book to start with if I'm interested in Gene clustering analysis?
As a beginner, I would like to learn more about gene clustering analysis, namely discovering groups of correlated genes potentially coregulated or associated to some conditions or finding patterns in ...
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Why can a gene lack of a binding site be expressed in skin cells? [closed]
In order for a specific gene to be expressed in the mammal’s cells, all of the gene’s binding sites must be bound by transcriptional activators. The mammal’s skin cells contain activators that bind to ...
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Forward or Reverse Strand: Is there a difference when encoding genetic devices?
Background:
In synthetic biology, and also in nature, there are lots of examples of genes in both the forward and reverse orientation. It seems in synthetic biology/bioengineering, most genetic ...
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What genes are required to make E. coli photosynthetic?
"All" of the genes for bacterial photosynthesis were discovered in a gene cluster almost 40 years ago. Marrs, J.Bact. What more is needed to make E. coli photosynthetic?
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Can a blood type O be born from AB and A parents?
I have a basic understanding of genetics, and I'm really puzzled by this. My grandma's blood type is A (I don't know if it's heterozygous or homozygous) and my grandpa is AB. Yet my mother is type O.
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Does the two-state gene expression model apply to constitutive genes?
Wikipedia defines constitutive genes as
a gene that is transcribed continually as opposed to a facultative gene, which is only transcribed when needed.
I don't have a strong theoretical background ...
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Can I use multiple bicistronic RBS sequences in a synthetic biological circuit?
The bicistroninc RBS sequences (BCDs) developed by Mutalik et al. [1] aim to remove context sensitivity from translation and therefore ensure more predictable gene expression. However, I have been ...
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Why do genes, encoding the same proteins and in the same conditions, have different expression?
Is it possible that two genes, which come from two different cell cultures and which encodes the same protein, produces different quantity of mRNA? If yes, why?
My question comes from the fact that I ...
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Meaning of the word "targeted" in a description of chromatin immunoprecipitation
From a research paper:
The ChIP assay demonstrated that CIC physically binds to the promoter region of FOLR1, PCFT and RFC1.
Compared with IgG control antibody, CIC antibody enriched 4.1-fold more ...
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How could I make my fish gold?
I'm doing research on how the pigmentation of fish. I want to know how could you change it with the help of genetic modification. I have some Silver Dollar fish (Metynnis argenteus) and I want to make ...
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How many copies of RNA per cell are usually reached through overexpression in human cell-lines? (any technique)
After 8 hours of online-research I was unable to find any info at all..
I was able to get some concrete copy numbers of DNA (e.g. plasmid) per cell after transfection of diverse transfection ...
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Does the magnitude of gene-expression changes decrease the more downstream a gene is from the origin of change?
If I have a decrease or increase in expression in one gene, will the decrease/increase in expression in the downstream genes always be of a magnitude lower than the previous ones, or can they be ...
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Does glycerol in E.coli culture media somehow inhibit the lac-operon?
I have have been taught that one should induce protein expression with IPTG at an OD of about 1.0 - 2.0 when E.coli grows it TB media (terrific broth). As a reference point, one typically induces ...
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Specific mechanism behind lethality of yellow coat color in mice
Our high school genetics chapter has some extra information about L.Cuenot. It only covered his research, and the fact that mice homozygous for yellow coat color would die before birth. It was an ...
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Meaning of “gene expression heterogeneity” of embryonic stem cells
What does it mean if a gene has a heterogeneous expression? Does it describe the differences of patterns of expression of that particular gene in a population of cells that are identical? The papers I ...
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Are the controls for RT-PCR the same as those for RT-qPCR?
I am searching for negative and positive controls for RT-PCR but all the results seem to point towards RT-qPCR. Are the controls the same for both?
I have found
-RT control
No template control
...
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Can we change the Eye/Hair color by knocking out the OCA2, HERC2 and MC1R genes using CRISPR in an adult human?
This paper seems to describe the use of a plasmid delivered by a gene gun to depigment rat skin;
https://www.nature.com/articles/3302264
Published: 27 May 2004
Seeing the gene therapy: application of ...
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Quantifying Gene Expression
I have found that many studies use the mRNA concentration as a “proxy” for protein activity because there should be correlation between mRNA levels and proteins expression levels. How is protein ...
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Why are there different gene expressions that are refered to the same gene in microarray experiments results?
I am studying gene expression profiling considering a dataset available on NCBI website. I do not understand the following: why are there some genes that have different profile and different ID ...
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Is the mRNA produced constant during time?
I am doing a statistical data analysis of a dataset of P. Furiosus cells exposed to gamma radiation.
For the samples exposed to gamma radiation, I have the values of mRNA produced over time. For the ...
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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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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 ...
