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

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87 views

Which restriction enzyme would i use?

Plasmid pBr322 includes two genes that confer antibiotic resistance: a gene for ampicillin and a gene for tetracycline. The cutting site for the restriction enzyme BamH1 is in the middle pf the ...
16
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3answers
223 views

What is the reason behind choosing the reporter gene when experimenting on your gene of interest?

I noticed within example experiments in class that different reporter genes are chosen to be inserted near your gene of interest to prove whether or not the gene is being expressed. For example, you ...
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2answers
64 views

How does promoter sequence affect initiation?

I don't know if this might have been highlighted in recent research, but a textbook I have states that "the exact way in which promoter sequence affects [transcription] initiation is unclear" I'm ...
11
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0answers
152 views

paralogue 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 ...
2
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1answer
94 views

Should the length of the electrodes in the electrophoresis chamber be proportional to chamber's size?

I am trying to build a small horizontal electrophoresis chamber from scratch. I want to use it for comet assay and I will be using only 1 slide, so it's going to be about 3cm wide, 10cm long and 4cm ...
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1answer
71 views

DNA and gene activation

As far as the genetic content of each cell is concerned I have read to my satisfaction that all cells of a person's body except the red blood cells (with no nucleus and so no genetic message) and the ...
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0answers
29 views

Transduction with P1 lysate prepared from strain that is proC::Tn10

If I do a transduction with a P1 lysate prepared from a strain that is pro*C*::Tn10 and the recipient is wild type, will all my recombinants be ProC- and Tet resistant since the Tn10 is in the proC ...
2
votes
2answers
1k views

Difference between CDS and cDNA

What is the difference between Coding Sequences (CDS) and cDNA? Are Coding sequences the sequences that is transcribed to mRNA and cDNA in contrast DNA obtained by reverse polymerization of matured ...
4
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1answer
867 views

Difference between mutation and DNA damage

What is the strict difference between mutation and DNA damage? As far as I understand it, a mutation is an alteration in the genetic sequence, having "tricked" the repairing machinery and thus ...
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1answer
48 views

Criteria for the numbering of human chromosomes

What were the criteria devised for the numbering convention employed in human chromosomes? When was it fixed? Correct me if I am wrong; it appears that chromosome pairs 1 to 22 were originally ...
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2answers
107 views

Can you detect if a mutation is spontaneous or induced?

Is it possible to determine if a certain specific mutation had a spontaneous origin (for example from a mistake of the DNA polymerase) as opposed to an induced origin (for example, from some genotoxic ...
6
votes
2answers
508 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 ...
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2answers
153 views

what is knob heterochromatin?

I am reading a paper which discusses Maize Genome Structure. Descriptions of the structure is given in the papers introduction. I know about heterochromatin "heterochromatin stains intensely, ...
7
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2answers
362 views

What exactly happens if during translation, an amino acid is not present?

Lets say that the cell wants to make a particular protein. Transcription of the appropriate gene is done and the mRNA is made. mRNA attaches to the ribosome and the translation is initiated in a ...
5
votes
1answer
41 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 ...
1
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2answers
38 views

Which part of the genome are the developmental sequences of embryogenesis located?

Which part or parts of the the genome are the sequences located. Are they spread across the chromosomes? If so how are they accessed sequentially with precision during embrygenesis?
2
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0answers
117 views

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
votes
1answer
65 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
votes
1answer
412 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 ...
3
votes
3answers
262 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
64 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 ...
2
votes
2answers
119 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 ...
2
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0answers
129 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 ...
3
votes
2answers
77 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 ...
7
votes
1answer
336 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 ...
5
votes
1answer
144 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 ...
3
votes
3answers
849 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 ...
24
votes
3answers
7k 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 ...
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1answer
315 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?
0
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1answer
48 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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0answers
50 views

Polymerase Observations

DNA polymerase I (PolI) contains polymerase, 3'-5' exonuclease, and 5'-3' exonuclease activities in a single polypeptide chain of molecular weight 109 kDa. If E. coli Pol I is exposed to the protease ...
11
votes
1answer
252 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
votes
2answers
54 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 ...
6
votes
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 ...
6
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1answer
102 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? ...
12
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1answer
245 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 ...
3
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0answers
91 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
votes
1answer
48 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
48 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
48 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 ...
1
vote
1answer
55 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 ...
5
votes
3answers
220 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...
6
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2answers
989 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 ...
5
votes
5answers
273 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?
7
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1answer
742 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 ...
10
votes
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 ...
5
votes
1answer
202 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 ...
4
votes
1answer
144 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
votes
1answer
700 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 ...
7
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1answer
61 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 ...