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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Genetic expression in interspecific hybrids

Referring to interspecific hybrids, I have the following two questions:- Quoting from wikipedia:- The offspring of an interspecific cross are very often sterile; thus, hybrid sterility prevents ...
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Optimization of Signal Peptides

We are looking at modifying the signal peptide of a receptor in a common immortalized human cell line. The cell line already expresses an unusually high amount of the protein, but much of it is not ...
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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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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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56 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 ...
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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 ...
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What is the difference between “dysregulation” and “deregulation” of miRNA?

I've started to study the role of miRNA in cancer. Wikipedia says: Just as miRNA is involved in the normal functioning of eukaryotic cells, so has dysregulation of miRNA been associated with ...
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How are oncogenes targeted for therapy?

How would oncogenes be targeted for therapy and are there any examples of existing therapies for such cancers if the gene was upregulated (i) as a result of copy number variation and (ii) due to ...
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84 views

How do sex biased genes evolve?

I am wondering how do genes become sex-biased? that is, how does a gene evolve expression which is regulated in a sex-specific manner (assuming no effect from sex-limited Y/W chromosomes). I ...
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138 views

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 ...
3
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1answer
1k 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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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 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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28 views

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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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 ...
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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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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 ...
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55 views

Can elementary alternative splicing events be combined in more complex events?

I'm a computer scientist who is trying to understand alternative splicing. As the title says, I'm here to ask you if, from a biological point of view, elementary/basic alternative splicing events (...
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538 views

What's the best wat to combine biological replicates in qPCR gene expression analysis? (2^(-∆∆Ct) method; one-way anova, turkey's test)

I am measuring the levels of gene x after transfection of cells with a plasmid and I want to compare them to the levels in mock-transfected cells. I did three different transfection experiments, in ...
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Gene products of recessive/mutated alleles

I probably would not cite a specific example, but some recessive allele work by encoding for the non-functional form of an enzyme. While the dominant allele encodes for sufficient levels of functional ...
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55 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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25 views

How to automate this custom gene expression microarray chip?

I have 16 gene sequences that I am interested in their detection in clinical samples. I already measured their RNA levels by using RT-qPCR technique and their benefit has already been proven to help ...
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Is it reasonable to assume that RNA polymerase would bind preferentially to the promoter of the long allele of the SERT gene?

I'm trying to come up with an idea for a school project (a hypothetical research study). I'm looking at depression and the serotonin transporter gene, which is highly expressed in the human ...
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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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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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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 ...
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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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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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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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63 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 ...
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77 views

What determines the differences between differentiated cells?

Given two multi-cellular species with obviously different phenotypes. The reason for the different phenotypes reflects their different DNA. However two types of cells in an adult organism may have ...
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24 views

why should someone study mRNAs instead of miRNAs as a biomarker

why should someone study mRNAs instead of miRNAs as a biomarker from liquid cell-free biopsy like from exosomes? Is it wrong to do it? Does it offer you something different? Thank you in advance
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585 views

How to preprocess htseq counts for gene expression (TCGA)

I want to prepare a matrix of gene expression to analyse TCGA LAML data. The required data is available at TCGA LAML - Gene expression quantification. The following is an example of the kind of data ...
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123 views

Why is the total length of Introns greater than the total length of exons?

I have just been reading that typically the total length of the Exons of a split gene is very much smaller than to total number of its Introns. Could anyone please explain why this is the case if its ...
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RNA-Seq library normalization and experimental setup

I'm working on an RNA-Seq project and I am trying to figure out library normalization. I'm aware of using the geometric means (e.g. cuffdiff) of the fpkm for the normalization. However, I was ...
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How to specify a promoter in de novo gene synthesis service?

I am trying to use a de novo gene synthesis service (Genscript) and one part confuses me: Where do I pick the choice of promoter? Or is the promoter choice automatic based on my plasmid choice? e.g....
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Serotonin activity with short 5-HTT promotor region and depression

So after reading a few studies (1,2) it seems that a shorter promotor region for the serotonin transport protein may be associated with increased likelihood of developing depression after stressful ...
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761 views

Interpretation of qPCR results for low expression genes

I am attempting to validate existence of a transcript using 40 cycle qPCR. I designed primers for a unique feature of this transcript, and also designed primers for a sequence in the transcript that ...
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56 views

Would it be possible to create a gel, holding viruses, that could alter the human genome 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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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 PARADIGM."...
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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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water stress expression markers in arabidopsis thaliana

So far I found papers that show studies using RNA arrays on whom they categorized water stress gene markers in root. Water stresses were reproduced by different protocols (manitol...) but always on ...
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Root hair formation in Arabidopsis

In arabidopsis, 2 cell types arise in the root epidermis : root hair cells and hairless epidermal cells. The immature epidermal cells that are in contact with 2 underlying cells of root cortex ...
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1answer
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Are there differences between the activation proteins of Eukaryotes and those of Prokaryotes

I'm in BIO 203 (for reference to my skill level), and I noticed the textbook makes a whole section out of transcriptional activator proteins, their function and applications in eukaryotes, but in ...
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Validation of houskeeping genes in a mixture of cDNAs of two species

I have a parasite sample (mixed with host blood) and I need to check gene expressions of parasite using relative quantification (RT_qPCR). For this, I need a good housekeeping gene. I chose 10 genes (...
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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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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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What is the expected relative RNA concentration level using T-REx Flp-In?

I need to understand the level of RNA over-expression that is normally reached with HEK293 T-REx Flp-In cells. This over-expression system is widely used in PAR-CLIP experiments, which is why I want ...
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Transgenic plants with multiple genes?

I have in mind, as a hypothetical project, to generate a transgenic plant capable of synthesizing vitamin B12. This could be consumed by vegans, for instance, as an alternative to B12 supplements or ...
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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 ...