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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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What backbone to use for Helper dependent adenovirus (HDAd)

I have been trying to design a plasmid for a helper dependent adenovirus but while looking i wasn't able to see a backbone specifically for HDAds so I was wondering if a general adenovirus backbone ...
Gpgabriel25's user avatar
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How to ensure correct and appropriate gene expression for inserted transgenes?

I know little about genetic engineering . But older (Pre CRISPR) gene therapy involved using a vector to insert a foreign gene (from another species) and its promoter sequence into the target species. ...
Sanjay Biswas's user avatar
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Could you recommend literature regarding non-coding RNA and micro RNA?

I am familiar with the Alberts and Watson textbooks, but they are quite general, not specific. I would be grateful if you wrote down books or even in-depth reviews/papers regarding the topic.
Ármin Horváth's user avatar
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Are there any papers that give examples of what is a "high" and "low" TPM expression value for given gene types?

My question relates to how to interpret TPM gene expression values, and what might be considered as "high" and "low" expression values, based on the gene type. For example, a ...
Ryan Ellison's user avatar
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Can the mechanism behind changes in protein expression be inferred by the timing of those changes?

My question relates to the timing of protein expression changes, and whether there is a literature-based consensus as to how long changes in protein generally take. For example, if protein changes 24h ...
Ryan Ellison's user avatar
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What is the minimum Ct value that you would consider indicates no gene expression?

I am doing relative quantification to compare gene expression between a control with several mutant backgrounds using qPCR. Looking online I find several different sources suggesting different values ...
aquaporin's user avatar
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How exactly are the eye color genes related?

How exactly are the gey (maybe aka EYCL1?), bey(2?) (aka EYCL3?), HERC2, and OCA2 genes related to each other? There are numerous sources that explain eye color in terms of OCA2's role in the creation ...
robertwb's user avatar
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Number of regulators required for specify the total state of genes

My course notes make the following claim: If the regulation of each gene could include all transcription regulators available, then in principle the total state of all genes could be specified with ...
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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 ...
Caterina's user avatar
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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 ...
Gumpf's user avatar
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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 ...
bio's user avatar
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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 ...
Stack Man's user avatar
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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 ...
user105463's user avatar
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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 ...
John Appleseed's user avatar
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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?...
aquaporin's user avatar
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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 ...
Manuela's user avatar
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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, ...
Rommelaar's user avatar
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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 ...
k_1223's user avatar
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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 ...
projective_line's user avatar
1 vote
1 answer
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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 ...
thetrueembodimentofstupidity's user avatar
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1 answer
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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 ...
agaminon's user avatar
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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 ...
Sam's user avatar
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1 answer
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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 ...
Abelaer's user avatar
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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 ...
Kasthuri's user avatar
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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 ...
NetCentric's user avatar
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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?
Mehad's user avatar
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4 votes
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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 ...
Shreyas Patel's user avatar
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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 ...
IlliakaillI's user avatar
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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 ...
Tasneem Qaqorh's user avatar
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1 answer
165 views

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 ...
Raz's user avatar
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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 ...
F.Sal's user avatar
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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 ...
Derek H's user avatar
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1 answer
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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 ...
l0110's user avatar
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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 ...
Bianca I.'s user avatar
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1 answer
138 views

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 ...
HypnoticBuggyWraithVirileBevy's user avatar
4 votes
1 answer
2k views

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 ...
Brad0440's user avatar
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4 votes
2 answers
279 views

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?
Youvan's user avatar
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10 votes
3 answers
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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. ...
Pate Ardealul's user avatar
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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 ...
pew31's user avatar
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11 votes
2 answers
332 views

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 ...
ajhfedorec's user avatar
1 vote
2 answers
171 views

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 ...
Manuela's user avatar
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1 vote
1 answer
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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 ...
CopperKettle's user avatar
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-2 votes
1 answer
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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 ...
Prince Zay's user avatar
2 votes
0 answers
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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 ...
KaPy3141's user avatar
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4 votes
2 answers
84 views

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 ...
LizardMan's user avatar
2 votes
0 answers
323 views

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 ...
CuriousTree's user avatar
26 votes
1 answer
3k views

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 ...
Amarylis Vaselaar's user avatar
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1 answer
102 views

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 ...
TheLast Cipher's user avatar
1 vote
0 answers
24 views

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 ...
bohemian's user avatar
-1 votes
1 answer
879 views

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 ...
Andrew M's user avatar

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