The scientific study of the structure and function of genes at the molecular level, particularly chromosomes and DNA.

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What tests can be performed to test the purity and quality of the raw peptide HCG (Human Chorionic Gonadotropin)

What tests could be run to test the purity and type of HCG? We are looking to purchase HCG from China but the purity and quality varies between labs, we are able to receive samples of the raw peptide ...
2
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1answer
92 views

When DNA is at its uncondensed form, what can it do?

I think it can do two things: The cell may be duplicating the genome during S phase. The cell may be transcribing the DNA into mRNA. Question: Can the two activities occur at the same time or one ...
5
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1answer
701 views

Smallest unit on which selection can act

Traditionally, the individual was considered to be the smallest unit on which Natural Selection (NS) acts. Today, we usually consider the gene as being the unit of NS. Of course, we should also ...
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3answers
531 views

Is there variation of AT/CG ratio along species?

Chargaff's rules say that the number of Adenine of the number of Thymine in a genome are equal (nA=nT) and similarly nC=nG. This makes obvious sense knowing that C binds to G and A to T. But what ...
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2answers
437 views

How does the genetic code evolve?

After looking at this question, some other questions poped in my mind. The DNA code is redundant, there are 20 amino acids for 64 possible nucleotide combinations. Therefore some amino acid are coded ...
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2answers
71 views

Collective term for both exons and introns

Is there a term I can use to refer collectively to both exons and introns? By collectively, I don't mean ligated as with an unprocessed transcription product. I'm just writing about exons and introns ...
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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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0answers
180 views

Can Pfx polymerase add only one 3' A overhang?

I am trying to clone a PCR product that was amplified using Pfx polymerase into pGemT vector. I had to A-tail the PCR product using Taq polymerase since Pfx only generates blunt end products. My ...
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2answers
85 views

How does the DNA know which chain has error in repairing?

As we know, the DNA has more stability than RNA, if one chain has broken or accidentally distorted, it can be repaired by the other one. Suppose there is a segment AGTC, its peer is GACT. Now its ...
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2answers
123 views

Prenatal Marketing

This is for a short story idea. Is it possible to modify the DNA of a child to make their metabolism more susceptible (physical response, addiction, etc) to a certain type of chemical i.e. a chemical ...
5
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1answer
240 views

Is there a practical upper limit to amount of nucleotides or genes in a transformed plasmid?

I'm currently working on a synthetic biology project which involves working with lots of different parts. I would ultimately like to integrate these genes by transforming a single plasmid. I've heard ...
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3answers
1k views

Knockdown of long noncoding RNA (lncRNA) - how is it done?

I don't work at the wet lab and don't know all the details about the knockdown techniques. My question is: How lncRNA knockdown is done? For example - you have lncRNA that is functional in the ...
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1answer
469 views

What is solid-phase bridge amplification?

During Illumina sequencing there is a step called bridge amplification by which DNA is amplified by isothermal enzymes. What is this stage, and how does it work?
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2answers
6k views

What's the difference between shotgun sequencing and clone based sequencing?

What are the main differences between shotgun sequencing and clone based sequencing?
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1answer
459 views

How is the exogenous DNA protected from degradation during bacterial transformation?

During transformation, a bacterium can take up DNA from its environment. A small fraction of bacterial species are known to be naturally competent, meaning that they can engage in this sort of ...
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1answer
50 views

How do amino acids become attached to tRNA?

Is there a protein that catalyzes this or does it happen spontaneously? In which part of the cell does this happen?
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2answers
57 views

Cell cycle selection

Is it possible to select from colonies only cells which are at a certain stage in the cell cycle? E.g. if I was trying to analyse expression of a number of genes during different stages of the cell ...
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2answers
2k views

Gene & Protein nomenclature: N-Myc, c-Myc, et. al

Can someone explain (or point me to an explanation of) exactly what is meant by all the different symbols I see used for writing genes and proteins? I think I know that for genes, we use an italic ...
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0answers
102 views

Comparative cost of RNA-seq vs sequencing full length cDNAs

I am in the process of assembling and annotating the genome of a non-model organism, using almost exclusively short read (paired-end Illumina) data. Throughput is one obvious benefit of these data ...
2
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1answer
132 views

Histone marks mechanism

I am slightly confused about the mechanisms that makes histone modifications associate with gene expression. That is, H3K36me3 is believed to be present in actively transcribed genes, H3K27me3 in ...
2
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1answer
52 views

PGC-1β Sod2 limiters/blockers

I'd like to block a percentage of PGC-1β or Sod2 expression. According to the following paper's figure beta-blockers inhibit some expression of PGC-1α. Are there any medicines/chemicals which safely ...
3
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1answer
49 views

mutant down but not out

I am interested in a gene which is null lethal but I need to temporary induce diminished capacity. If a cell is homozygous is it possible to induce heterozygous phenotypes or a partial knockout from ...
2
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1answer
51 views

methods for targetted deletion of genomic regions?

I would like to know what are currently used methods for targeted deletion of genomic regions in mammalian organisms or cell lines. I have heard of Zinc-Finger nucleases as a recent genetic ...
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1answer
58 views

Arabidopsis thaliana RCSB active site gene mutant

I'm looking for an Arabidopsis thaliana gene listed in RCSB with a clear mode of function and active site. In addition it needs to have an obvious phenotype when knocked out like severely retarded ...
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1answer
303 views

Can DNA act as a translation substrate?

I get conflicting answers. One would think if it was true, it would be rather seminal and widely known. There are papers from Khorana[1], Holland[2], and Bretscher[3] (late 60s) that suggest that it ...
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3answers
247 views

Are some non-coding RNA spliced?

Are some non-coding RNA spliced like mRNA? I tried to find some information but I don't find anything...
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2answers
623 views

Methods of nuclear transfection - nuclear transport

I am reading through the ENCODE papers, which is taking me well out of my comfort zone in terms of modern laboratory techniques. At the risk of asking a question which may well be thoroughly answered ...
5
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1answer
214 views

How are DNA polymerase error rates measured?

It is well known that the first DNA polymerase, Taq, is quite error prone. Newer generation commercial enzymes that have either been isolated from different thermophile species or have been improved ...
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2answers
1k views

Why do DNA and RNA have the functions they have?

I know that there are two most important directions of genetic information transfer in living organisms: DNA->DNA and DNA->RNA. The first is replication, and the second is transcription. I wonder if ...
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5answers
330 views

What is the lowest common denominator of cancer?

What is the lowest level attribute that all cancers share? Also, what is the highest level attributes that all cancers share?
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1answer
1k views

Is ovum + ovum fertilization possible for human?

In humans is it possible to fertilize a ovum with another ovum from the same female subject? I already found some works in which the ovum is fertilized by a somatic cell (see e.g. this ), but I am ...
14
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1answer
197 views

Paralogous genes in genome-wide association studies?

Has anybody tested if paralogous genes are over-represented among the genes identified by genome-wide association studies (GWAS)? For example, if a GWAS study finds 200 genes associated to the ...
11
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1answer
305 views

Do single crossovers occur in circular polynucleotides?

Single crossovers in circular pieces of DNA do not seem to be a big topic, because if they happened, they would lead to a kind of combined chromosome with two inner strands and one large outer strand. ...
4
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1answer
164 views

Vigorous shaking for HFR interrupted mating

I am trying to reproduce E. coli interrupted mating using an HFR strain, and I read that the cultures should be vigorously shaken at times to interrupt the DNA transfer from the F+(HFR) donors to the ...
4
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1answer
2k views

Co-transformation of plasmids from the same incompatibility group

Can two plasmids with the same origin of replication (for example pBR322 ori) and thus from the same incompatibility group be successfully co-transformed in E. coli? What are the mechanisms that would ...
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1answer
114 views

Bicoid regulation of hunchback

I'm learning about development via the example of Drosophila embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? ...
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1answer
91 views

How do nuclear receptors locate each other to form a DNA loop?

Nuclear receptors can influence transcription far up- or downstream from their own binding sites by looping DNA (Rubina et al.; J Mol Bio 2004). I am not sure how exactly the receptors first attach ...
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2answers
98 views

Consensus codon optimization by organism

Does a public database exist that contains this information? I'm trying to make a simple gene annotation program that will let me input a DNA sequence and then optimize it based on one of these tables ...
8
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2answers
186 views

Is there a dominant gene for right-handedness?

Has there been any definitive research about handedness being genetic? Also, why is right-handedness clearly dominant in humans? I'm interested in evolutionary theories, as well as any molecular ...
10
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2answers
421 views

What is the highest competency possible for E coli?

I am looking to find a highly competent E coli strain. I am making a library of a ~6.6kb plasmid and I am not getting high enough efficiency. Does anyone have a suggestion of a strain/protocol with ...
5
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3answers
143 views

Measuring reverse transcriptase activity in E. coli

Goal: To quantify the HIV-1 reverse transcriptase (RT) activity for a number of mutated RTs. Idea: Put RT into a vector in E.coli. Deliver GFP mRNA to E.coli. RT will process the mRNA. The ...
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4answers
2k views

What's the aim of genetically modifying of foods/organisms?

On news, articles etc. experts talking about Genetically Modified Foods and Organisms often mentions about their disadvantages like, their potential to harm human health allergies may become more ...
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3answers
12k views

Why do eukaryotic organisms have introns in their DNA?

We touched on introns and exons in my bio class, but unfortunately we didn't really talk about why Eukaryotes have introns. It would seem they would have to have some purpose since prokaryotes do not ...
8
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1answer
880 views

How to clone and sequence a gene transcript of unknown sequence?

How might I go about amplifying a gene transcript (mRNA) from animal tissue of which little is known about the genome? In some applications, I have used reverse transcriptase PCR to amplify all mRNA ...
7
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1answer
63 views

Which factors besides the thermodynamic stability are important for the hairpin in intrinsic transcription termination?

Intrinsic termination (rho-independent) relies on a stable hairpin with a subsequent uridine repeat. The common explanation on how these sequences cause the termination of the transcription are based ...
19
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1answer
515 views

Regulation of chromatin structure

Recently, I reviewed the different levels of chromatin structure. The primary level is nucleosomes, where DNA is bound to histones, and has structural similarity to "beads on a string." The secondary ...
5
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1answer
1k views

What is the distinction between F' plasmid and R plasmid?

Is there a difference between an F' plasmid that has taken up a chromosomal gene that conveys antibiotic resistance, and an R plasmid? Is a bacterium containing an R plasmid and yet lacking an F+ ...
7
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1answer
246 views

What is the origin of “melting” in molecular genetics?

I'm reading some papers about prokaryotic transcription mechanisms, and I've come across a term I haven't heard before: DNA melting or promoter melting. After reading a bit, it's pretty clear that ...
10
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1answer
2k views

How does the stem-loop cause intrinsic transcription termination?

In this animation, towards the end (about three quarters) the process of transcription termination is shown. It states that the transcribed RNA forms a hairpin loop (or stem-loop), which halts the ...
10
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1answer
453 views

What is the functional and structural distinction between core (H2A, H2B, H3,H4) and linker(H1/H5) histones?

Many explanations of histone biochemistry isn't quite elucidating for the undergraduate student. How does histone structure (dimers, octomers) relate to their specific functions as core or linker ...