The scientific study of the structure and function of genes at the molecular level.
22
votes
3answers
2k 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 ...
19
votes
1answer
193 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 ...
16
votes
2answers
150 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 ...
11
votes
1answer
126 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 ...
10
votes
2answers
187 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 ...
10
votes
1answer
731 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
votes
1answer
157 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 ...
9
votes
1answer
142 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. ...
7
votes
2answers
135 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 ...
7
votes
1answer
286 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
votes
1answer
65 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 ...
7
votes
1answer
39 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 ...
7
votes
0answers
57 views
paralogue genes in genome-wide association studies?
Has anybody tested if there is an over-representation of significant paralogous copies of genes -- either tandemly-arranged or in different chromosomes -- in the list of significantly associated genes ...
6
votes
4answers
173 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 ...
6
votes
5answers
185 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?
6
votes
2answers
167 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
votes
1answer
182 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 ...
6
votes
1answer
115 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 ...
6
votes
1answer
68 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? ...
6
votes
1answer
59 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
3answers
102 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...
5
votes
3answers
100 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 ...
5
votes
2answers
421 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
1answer
541 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+ ...
5
votes
1answer
120 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 ...
4
votes
1answer
125 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
475 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 ...
4
votes
1answer
91 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 ...
3
votes
1answer
43 views
What's the difference between shotgun sequencing and clone based sequencing?
What are the main differences between shotgun sequencing and clone based sequencing?
3
votes
2answers
44 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 ...
3
votes
1answer
42 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 ...
3
votes
0answers
59 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
2answers
65 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 ...
2
votes
1answer
65 views
Macroevolution vs. microevolution
Where is the line usually drawn between macroevolution and microevolution?
I thought that, although similar processes govern both, the line was at the species level, with macroevolution being changes ...
2
votes
1answer
37 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 ...
2
votes
3answers
47 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 ...
2
votes
0answers
37 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
votes
1answer
38 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 ...
2
votes
1answer
40 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 ...
1
vote
1answer
21 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?
1
vote
0answers
41 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 ...
0
votes
1answer
33 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?
0
votes
0answers
99 views
Text Book on Cancer Genomics/Biology [closed]
Could anyone of you suggest few of the best text book(s) for Cancer Genomics/Biology from basic to advance level.
-1
votes
2answers
41 views
What are some basic drosophila methods? [closed]
I'm a grad student rotating in a drosophila neurobiology lab. I'd like to do a little self-study to bring myself up to speed. What are some basic, essential drosophila methods and applications? And ...
