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 is the most appropriate way to normalize gene expression data?

This question comes because reading a paper about normalization of gene-expression data, is not clear if the method for normalize the data is just for RNA-Seq data or could be applied also for ...
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3answers
42 views

What is the role of TATA box in transcriptional regulation? [on hold]

I know what is the TATA box, but I wish to know whether it has specific roles in transcriptional regulation.
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3answers
99 views

Following DNA replication during S-phase of the cell-cycle, are all genomic regions subjected to the same stringent level of DNA-Repair?

To my (limited) understanding, there are 2 main ways that mutations can occur in DNA: Environmental (UV, etc) and mistakes during cell division. I was wondering if there is a mechanism that can give ...
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1answer
32 views

Why does pETDuet-1 only have one T7 terminator but two T7 promoters?

Why does pETDuet-1 only have one T7 terminator but two T7 promoters (vector map below)? Is there any advantage of having only one terminator? There are going to be two mRNAs transcribed from this ...
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1answer
39 views

How big advantage had a trait have to bring to evolve in the human evolution? [closed]

Yes, I've heard that we have evolved from the common ancestor with primates as intesively, as the chimpanzees. Sometimes I read about some enormously complex traits, evolutionary psychologists think ...
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41 views

What further research can the result of gene variation detection be used for [closed]

We do a research on a particular cancer (for e.g. breast cancer). Now, we have a result for the gene variation detection (VCF file). What next steps do we need to do? We don't have a clear picture ...
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2answers
33 views

How do biologists quantify “gene expression” in experiments?

I've read papers which contain statements such as "control of gene expression is critical in biological processes". How exactly does one quantify "gene expression"? Isn't gene expression an umbrella ...
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1answer
24 views

Genes that exist in old Affymetrix platform but not in the newer one

I am using two gene expression datasets from an Affy U95Av2 platform and an Affy U133 Plus 2.0 platform. When I map the Affy probe names to HUGO gene names, there are thousands of genes which exist in ...
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1answer
23 views

differentially expressed genes of the treated with estradiol samples

I did differential analysis on samples treated (G1E-ER4) with estradiol (differentiation induced by estradiol) and control (G1E). The genes that I gor as differentially expressed in G1E-ER4 showed ...
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1answer
29 views

Pooling for qPCR

I am comparing miRNA expression levels in 3 different groups but I am low on money and time. I have to get some preliminary results to get the actual research going so I decided to pool my samples and ...
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0answers
17 views

TCGA Array Data Interpretation - why is PTEN up when I know it shouldn't be in RCC?

I am trying to make some sense of the KIRC (clear cell renal cell carcinoma) gene expression microarray data (level 3). I am a little bit confused by the expression levels of PTEN which are elevated ...
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2answers
105 views

Is the increased/decreased enzyme activity (tyrosinase) caused by an environmental factor (UV radiation) considered to be gene expression?

My AP Bio assignment asks that I research the effects of UV radiation on melanin production, but the directions and questions suggest that UV radiation influences gene expression. From what I could ...
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1answer
35 views

How much time do the different mechanisms of gene regulation need to take effect?

I am thinking of the major regulatory mechanisms, like general transcription factors, activators, repressors, and RNA interference. If non-active regulator genes using each of the different ...
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1answer
25 views

What's the difference between CREs and DHSs?

I would like to know what's the difference between cis-regulating elements and DNase I–hypersensitive sites, in order to produce a meaningful segregation of non coding elements affecting gene ...
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0answers
28 views

mitochondrial gene upregulated in F1 cross

I am doing RNA-Seq data analysis from ovarian samples that represent two pure breeds (high prolific vs low prolific) and their F1 cross. Flushing diet has been shown to affect ovulation rate in some ...
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0answers
52 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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1answer
35 views

Does a zygote express all genes?

If a zygote has all the cytoplasmic determinants and all the specific transcription factors, does that mean that all genes in the genome are expressed?
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29 views

Is the zygote the only totipotent cell?

I’ve been told that the unfertilized egg contains cytoplasmic determinants (e.g. proteins, transcription factors, mRNAs) that are divided unevenly during the early stages of cell division in an ...
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1answer
19 views

Using PGAL10 promoter to overexpress specific yeast genes: How to?

I was reading a poster about expression boosting for Artemesinin production in yeast and it had this line: PGAL1 and PGAL10 have been used for the overexpression of all genes from the ...
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0answers
31 views

Are all genes transcribed in differentiated cells?

My textbook tells me that it’s specific transcription factors that allow for a different set of genes to be expressed in different cells (differential gene expression). My book gives the example of ...
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3answers
172 views

Why don't housekeeping genes have TATA Box regions in their promoter sequences?

Housekeeping genes are genes that are continuously transcribed. Like all other genes they have promoter sequences, but they don't have TATA box sequences that are used to specify from where ...
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2answers
156 views

Balanced vs Maximized Codon Optimization

I have worked with the optimization of several viral proteins, from different viruses/families, with different results. When Menzella, 2011 was published I tried that method. I found quite the ...
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0answers
18 views

Transcription profiling analysis software

I am entering now the field of transcription profiling analysis - and looking for good software to work with the data. I got files with list of genes like this for example: 1415751_at 618.9 ...
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0answers
20 views

From DNA to final traits of microorganisms? [closed]

From the answer of this topic, could someone indicate me a book or article about how DNA set the phenotype of microorganisms? For example, showing how DNA changes the shape of such a cell or how DNA ...
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0answers
13 views

How to Download the broadpeak files from the encode chip-seq experiment matrix? [closed]

I have tried the SqlDatabase of Encode opened it trough R ,i have tried other packages in R, i have tried the ENCODExplorer package but none of them seems to do what i want. I have an app that asks ...
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4answers
626 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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45 views

Interpreting soft clipping in a SAM alignment

I am interpreting CAGE data. I have noticed that in the SAM files I am analysing, there are many pairs of lines of the form (e.g.) ...
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1answer
44 views

cell specialisation and their location

When we create new cells, how come they are of the 'right' type at the 'right' place? For example, when I make a new cell on my lips, it's obviously not the same as a new one in my kidneys. Is the ...
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1answer
56 views

Common genes and enzymes involved in pathogen entry into host

Many microbes like Salmonella, E.coli, Legionella pneumophila etc. enter host cells via cystoskeleton remodeling of the host cell. Do all microbes follow the same path or there are any other ways for ...
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2answers
522 views

Using RNA-seq to compare gene expression across patients instead of between Control and Experimental conditions

I am working with RNA-seq data from the Cancer Genome Atlas TCGA and I have been reading about how people have compared gene expression levels measured by RNA-seq. Many of the papers I have read talk ...
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1answer
77 views

What determines whether the maternal or paternal allele is expressed?

I am taking cell biology and have this question: During the process of gene expression, it is possible to express either the maternal allele or the paternal allele. When and how is the determination ...
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2answers
66 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
28 views

ATP to disassembly of nucleotide ratio

DNA Helicase, the enzyme that is responsible for tearing apart the strands before DNA replication, requires ATP to rip apart nucleotides. I have asked this question to several professors and they ...
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15k views

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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2answers
215 views

Can intron become exon in alternative splicing?

From this image We can see several exons that are actually introns in other genes. It's not a really a different gene, it's an alternative splicing of a gene. My background is not biology so is it ...
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1answer
31 views

Transcription of Genes: Are Specific Transcription Factors + Enhancers Necessary?

I learned about transcription in my AP Biology class and we discussed how transcription occurs, but I was wondering whether transcription always requires the enhancers, activators (specific ...
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2answers
822 views

What is the instructional language of DNA?

DNA carries most of the genetic instructions used in the development, functioning and reproduction of all known living organisms and many viruses (Wikipedia). Is it already know how ATCG's ...
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0answers
35 views

Can genes be expressed sequentially?

As I understand it, any gene on an exposed/unpacked region of a chromosome is continuously being expressed. Regulatory genes may increase or decrease the amount of protein synthesised due to its ...
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2answers
41 views

Animal gene in plants

Usually only microbes, specifically bacteria are used to express genes of other species for various functions. But, it is possible to try and express an animal gene into a plant. Bacteria like ...
5
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1answer
343 views

Lac operon: How can lactose enter the cell in the absence of lactose permease?

My textbook states that lactose permease...transports lactose into the cell and When lactose is added to the growth medium, the lactose molecules bind to the other site on the repressor ...
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1answer
33 views

Plasmid Expression Vector [closed]

If I am going to transform a plasmid into a bacterium, which will then be fed to a C. elegans, the expression vector needs to be bacterial correct? The other option is to have a worm expression ...
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1answer
34 views

Question about cutting gene in Plasmid

I am designing a researching proposal for the class. Because it uses microinjection to up-regulate the gene in C. elegans, the plasmid pCFJ104 - Pmyo-3::mCherry::unc-54 sequences has been chosen. But ...
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20 views

Organ secretions

If an animal secrets an enzyme from an organ that is entirely dedicated for the same secretion, can one or cannot one just use the gene coding for that protein to obtain the protein in vitro. How much ...
2
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1answer
146 views

Is there a consensus on the CaMV 35S minimal promoter sequence?

We have an algal enhancer element and a transcription factor that probably binds it. Basal expression of the enhancer element or full promoter driving luciferase in tobacco protoplast was extremely ...
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1answer
25 views

Gene silencing in C. elegans

I am trying to silence the tph-1 (tryptophan hydroxylase) gene in C. elegans using the pLT63 plasmid to check if that particular gene has anything to do with the pharyneal pumping or not. Am I using ...
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2answers
380 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 ...
3
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1answer
129 views

Could fingerprints potentially be changed using a gene gun?

Not to confuse with your "DNA fingerprint" I've read surgery is readily used to not just remove but even to change people's prints through employing very small grafts between opposing hands. About 5 ...
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3answers
654 views

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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0answers
15 views

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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1answer
54 views

What is meant by “the degree to which a gene is expressed” in an individual?

Here is an excerpt from a text that I was reading, Here is an example of microarray data. The idea is to take a group of different individuals and for each of them, you measure how much they ...