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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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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51 views

Constitutive mutation in operator gene

If a constitutive mutation happens in the operator of an inducible operon, does that mean that repressors won't be able to bind them ? Or does it mean that even if repressors are bound, they will not ...
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Why do we assume that the first humans were dark-skinned?

According to the article Dark skin and blue eyes: How Europeans once looked: It is widely accepted that Man's oldest common forefather was dark skinned, and that people became more pale as they ...
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Could miniaturization be used to protect endangered large species?

In some animals (like dogs) size seems like it's controlled mostly by just a few genes (IGF1, and the genes that repress it). I'm curious: (1) Does other miniaturization takes a similar route (for ...
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37 views

What is mRNA expression level?

I cannot find clear explanation of what is mRNA expression level, and how to measure it. I would appreciate if someone explained it or gave a reference. Thanks!
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49 views

Epistasis when interacting loci are codons within a single gene

There is epistasis when the effect on the phenotype of one gene is influenced by one or more other genes (called modifiers). Is there a similar concept when the effect on the phenotype of one site ...
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317 views

Shine-Dalgarno sequence and expressing proteins

Shine-Dalgarno sequence present in the prokaryotic mRNA plays a role in initiation of translation. In eukaryotes a Shine-Dalgarno like sequence is present but does not play an important role in ...
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173 views

What are some examples of genes that code for multiple proteins?

The title pretty much says it all. It is widely taught that a gene in a eukaryotic system could produce more than one protein due to post-transcriptional modification, but I do not believe I have come ...
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4answers
256 views

Punnett Square Help

In fruit flies, red eyes are dominant over white eyes. Show a cross between two white-eye fruit flies. My question is... How do I know if the white-eye fruit flies are homozygous or heterozygous?
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How does the colinearity of the HOX genes determine the body plan of an organism?

I was recently reading about colinearity in the HOX genes that give an organism its high-level body plan (where the order of the HOX genes on the chromosome follow the head-to-tail order of body ...
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1answer
54 views

The reason why researchers usually use cell lines from “blast cells”?

What's the reason why researchers usually use cell lines from "blast cells" (so, immature, like lymphoblastoid cells) for measuring gene expression data? Is that they are growing up, which would make ...
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113 views

explanation of conjugation experiment in bacteria

In this paper (On the expression of a structural gene) I am confused about what is being plotted in Figure 6. The x-axis contains the fraction of radioactive day and y-axis contains the enzyme ...
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2k views

Why is the function of lacA (encoding thiogalactoside transacetylase) not clearly understood?

It's almost half a century since the lac operon was discovered but isn't it weird that the precise role of transacetylase isn't clearly understood ? Here a wikipedia article with a link to a journal ...
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167 views

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 ...
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1answer
823 views

Lyonization and X-linked disorders?

Lyonization or X-chromosome inactivation is the conversion of all but one, X-chromosomes in Females into non-coding heterochromatin (i.e. deactivated) leading to the formation of one or more Barr ...
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208 views

Cytoplasmic determinants - protostomes and deuterostomes

Cytoplasmic determinants are spread unevenly in the egg, and so when embryo starts forming (cells start dividing), the determinants are also unequally divided between cell. This unequal distribution ...
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353 views

Negative value on linear gene expression in microarrays

I am starting to use microarrays and maybe this is a dumb question: Using Illumina microarrays, linear gene expression can be negative? Or maybe some artefacts have been introduced? And, in this ...
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167 views

Expression of plasmid genes

Are plasmid genes always expressed? If so, then isn't a bacterium wasting it's resources in expressing genes (like antibiotic resistance) which are not required in "normal" conditions? If not, then ...
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36 views

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
76 views

Expression of bidirectional promoters

How are bidirectional promoters expressed ? (Won't RNA Pol have to go in 3'-5' direction?) Why are they more commonly found in eukaryotes than prokaryotes?
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186 views

How can a continuous RNA be transcribed in the lac operon?

The lac operon has 3 genes: lacZ , lacY and lacA. I have seen that the m-RNA transcript of these genes has stop codons in between. So, how can the RNA be made continuously? Won't the RNA Pol detach if ...
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26 views

Known MicroRNA - Gene Systems?

Have there been any experimentally-verified systems of microRNAs targeting a gene set (e.g., in cancer, perhaps)?
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1answer
31 views

Do the phage repressors CI and Mnt exhibit crosstalk?

I am interested in using the CI and Mnt proteins as well as their respective promoters (pR and Pmnt) within the same synthetic system, but am concerned as to their similarity and potential crosstalk. ...
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2answers
53 views

Is there are practical lower limit to gene length in E. coli?

Question is rather self-explanatory. Putting aside other post-transcriptional factors like rate of degradation of transcript, what is the smallest gene ever reported to have successfully been ...
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302 views

which exact mechanism triggers the first cell differentiation after n divisions?

I would like to understand which mechanism triggers the first cell differentiation after n divisions. I read previous articles on SE and Wikipedia articles on cellular differentiation and ...
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613 views

Optogenetics - How do microbial opsins work?

I'm just introduced to the optogenetics method and am having some trouble grasping the genetics (of the optogenteics) part of things. So we have Retinal and Opsin that form Rhodopsin molecule that ...
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1answer
51 views

What is meant by “alien” probe in a microarray?

In my lab we did a microarray to analyze differential gene expression in S. cerevisiae treated with UV irradiation. We are now analyzing the results and one of the up-regulated genes is labeled ...
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2answers
144 views

How is gene expression estimated?

I'm reading this fantastic article on estimating body time: Molecular-timetable methods for detection of body time and rhythm disorders from single-time-point genome-wide expression profiles and one ...
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1answer
156 views

What is the mechanism of regulation of PER /CRY genes?

I've read multiple descriptions of biological/circadian clocks and they all mention PER, CRY and CLOCK genes. While I kinda get how they are connected, what interests me is how these actually regulate ...
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1answer
581 views

Manipulation of gene expression using VP16 fusion and engrailed fusion to a transcription factor?

Today, a presenter briefly mentioned that gene expression in sea urchins during development might be manipulated using VP16 and engrailed fusions. On a slide, it said that expression might be ...
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1answer
597 views

Where to put the gene after eukaryotic promoter for best expression levels?

As far as I know there is an optimum distance between a promoter and the gene for the best expression levels. What is that distance for common promoters like CMV, SV40? If you have a first hand ...
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1answer
89 views

Confusion related to a term probe-by-background interaction

I was reading a paper related to bioinformatics where it uses the drug response on the cancer cells and the gene expression of the individual cells are studied to find any useful insights. Specially, ...
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208 views

What is the best way to express two proteins in a mammalian cell?

I have two proteins and I will be preparing a vector with both genes for stable transfection. Each protein will have their own promoter and I will use piggyBac vector to insert a single cassette with ...
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1answer
205 views

One flybase gene number (FBgn), many Affymetrix Id's

I am trying to convert a set of Affymetrix ID's, like this one 143053_at_3745, to Flybase Gene Numbers (FBgn) like this one FBgn0000015. I have downloaded the Flybase file required to do so (as ...
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48 views

Complexity in creating transgenic animals (e.g., mice)

Many papers I have seen describing transgenic rodent models (and presumably applicable to other model organisms) involve the knock-in, or modification to, a single gene, possibly two genes. With ...
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Combining gene expression data from two species

I currently have two sets of gene expression data. The first is a dataframe of genes identified by Annotation id CG numbers (for example "CG10005") in one column and a numerical variable of interest ...
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1answer
141 views

What is benjamini

I was doing some gene expression analysis using this tool http://david.abcc.ncifcrf.gov/summary.jsp. However, I have a confusion about what benjamini is. I fed it some gene list and it gave me some ...
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1answer
58 views

Confusion related to the DAVID tool

I am trying to use the DAVID tool to do some gene analysis. I have some probe set intensities for some cancer cell lines. I found this link in the DAVID tool http://david.abcc.ncifcrf.gov/tools.jsp. I ...
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1answer
139 views

How to determine the direction of regulation of a gene by comparing gene expressions?

I am just learning about the gene expressions and regulation. Several researches focus on finding the genes of altered gene expressions on a microarray to claim that they have a correlation to a ...
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760 views

How to map the Gene name to its Gene Symbol?

I am learning in Gene data lately so I apologize for the silly questions in advance. I read a paper for a cancer on human which found some important genes. For example, the paper listed one of genes ...
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53 views

What do breeders call the effect when a breed resists modification?

It is impossible to breed a blue rose or a cat with a bulldog shape. This is because breeding is limited by gene variations in the population. What do breeders call this effect? UPDATE I guess ...
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A mathematician's confusion regarding parametric $t$ tests for gene expression data

I'm a mathematician trying to test some things on gene expression data, and I'm thus skimming over various articles such as Sotiriou et. al. to understand what is typically done with such data sets. ...
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87 views

Average number of gene products in (a) eukaryote(s)

Due to alternative RNA splicing, it isn't uncommon to ultimately find multiple gene products expressed from one gene in eukaryotes. I'm looking for a reference value for the average number of final ...
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1answer
47 views

circulating microRNAs are functional?

In plasma and other body fluids, miRNAs can be found. They not only originate from dying cells but also from active secretion and are usually 'packed' into vesicles/lipo-proteic structures (i.e. ...
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1answer
330 views

Does DNA contain information beyond protein synthesis?

It's well known that genetic information is stored in DNA. As far as I know, DNA only has information at the protein level. What about higher levels, such as organelles, cells, tissue, organs? Is ...
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312 views

Where can I find the tissue-specific protein expression levels for hTERT (telomerase subunit)?

I find a number of contradictory sources regarding the tissues in which hTERT - the protein - is expressed. Does anybody know some resource that authoritatively (as authoritative or widely-accepted as ...
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88 views

Expression of an ancestral gene

Why would the expression of an ancestral gene and comparing the product to a modern protein give misleading conclusions about heredity? Update: By ancestral gene I mean a gene which was used by an ...
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1answer
54 views

Where can I find histograms and tables of prevalence of mutations in cancer?

At some point in the past I found a cancer portal site which had aggregated data for the relationships between various mutations and their prevalence in cancer types and tumor data. The data was ...
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1answer
63 views

variation in expression accounted for a SNP — what's a usual percent?

I am reading a GWAS paper that found a SNP associated to predisposition to colon cancer and was assessed for gene expression of the nearby gene. They found that the genotype accounted for 55% of the ...
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387 views

T7 promoter leakiness

Can a gene be expressed under the T7 promoter in an E. coli strain (e.g. DH5 alpha), which does not have the T7 polymerase gene encoded in its genome? In other words, is T7 promoter leaky? To be ...