Hot answers tagged molecular-genetics
17
There is still a lot to be learned about the roles introns play in biological processes, but there are a couple of things that have been pretty well established.
Introns enable alternative splicing, which enables a single gene to encode multiple proteins that perform different functions under different conditions. For example, a signal the cell receives ...
11
GMO foods have a huge potential to make food cheaper to produce and more nutritious.
The most common GMO foods have at least one gene added to them - an enzyme that makes the plant resistant to RoundUp - an herbicide made by the same company (Monsanto). this makes the farmers able to grow their crops with much less intensive labor to keep the plants ...
10
Different genes will serve different purposes. For example, if you want to perform colocalization studies, then fluorescent genes like eGFP and DS-Red (or any variation of those, namely Emerald, mCherry, etc) will be quite useful, since you can use different filters on your microscope for the various fluorophores. For morphological assessments, perhaps a ...
10
Hanahan and Weinberg's "Hallmarks of Cancer" articles should answer your question.
Their original, highly cited (14k+ citations), [Six] Hallmarks of Cancer article list these six common attributes of all cancers:
Sustaining proliferative signaling
Evading growth suppressors
Activating invasion and metastasis
Enabling replicative immortality
Inducing ...
9
This is a great question as I just made my own "homebrew" chemically competent cells.
There are a vast variety of E. coli strains that are commonly used for cloning. They may be transformed chemically by heat shock method, or electrically by electroporation (a brief summary may be found here). These can be made in the lab manually, or purchased commercially ...
8
Perhaps you can draw inspiration from classic paper on lambda cloning: Maniatis T, Hardison RC, Lacy E, Lauer J, O’Connell C, Quon D, Sim GK, Efstratiadis A. 1978. The isolation of structural genes from libraries of eucaryotic DNA. Cell 15: 687–701.
Try selecting tissues from the animal which you think is "enriched" (i.e. highly expressed) for the specific ...
8
You should check out Howald C, et al[1]. This is one of the many recent papers tied to the ENCODE data. They've used RT-PCR to amplify exon-exon junctions and then sequenced the results. Supplemental table 2 shows 3076 validated exon-exon junctions in putative processed transcripts which, in the main body of the paper may be sub-classified as:
...
7
On the example of "golden rice" already raised here I took the liberty of looking up some literature about this GMO varietal. This article by Beyer et al. describes the introduction of the beta-carotene biosynthetic pathway into the strain of rice. About a decade later, Tang et al. followed this up with a clinical trial to measure how much beta-carotene a ...
6
There are two mechanisms of transcriptional termination in prokaryotes. The one shown here is "rho-dependent" because it involves rho, a DNA-RNA helicase that loads on and unwinds the RNA from the DNA, terminating the elongation by the polymerase. Check out [1] which shows a model for how rho multimers move through the RNA.
The other mechanism involves ...
6
The core histones are H2A, H2B, H3, and H4, and the linker histones are H1 and H5. The structure of the nucleosome is well explained in wikipedia:
Two of each of the core histones assemble to form one octameric nucleosome core particle, and 147 base pairs of DNA wrap around this core particle 1.65 times in a left-handed super-helical turn. The linker ...
6
There is a lot of information at OMIM - too much to summarize here - regarding the genetics of handedness and links to which hemisphere of the brain dominates (in an individual), to schizophrenia (slight association with non-right-handedness), and to hair whorl patterns on the scalp. References are provided at the above link. Basically, hand skill appears ...
6
I have heard that Epi300 electrocompetent cells (1) from Epicentre are very efficient: > 1 x 1010 cfu/µg of pUC19. Dan Gibson used them in his paper for the synthesis of the mitochondrial genome (2). We were also thinking of using them for our assemblies, but they are pretty expensive.
1. TransforMax™ EPI300™ Electrocompetent E. coli
2. Chemical synthesis ...
6
Cancer is such a diverse group of diseases that they really only share one commonality, unregulated cell growth with the potential ability to invade or transfer to other tissue types.
Many types of cancer share certain characteristics and can thus be grouped, but as a whole the only characteristic all cancers share is that they are classified as cancer. ...
6
My attempt to find an answer has suggested that no-one knows how the DNA gets into the nucleus.
This fairly recent paper reports attempts to track the pathway of DNA entry and transfer to the nucleus.
Le Bihan et al. (2010) Probing the in vitro mechanism of action of cationic lipid/DNA lipoplexes at a nanometric scale. Nucl. Acids Res. 39:1595-1609
...
5
OMIM (online mendelian inheritance in man) is a good example to explain how complicated heritability usually is. Simple Mendelian traits, where smooth or wrinkly peas will have wrinkly offspring, allow us to segregate individuals with pure dominant / heterologous and pure recessive traits. When we have done so the chance of inheriting the trait can be ...
5
If I understand the nomenclature correctly, an R plasmid is just any plasmid containing an antibiotic (R)esistance gene (eg. Amp, Kan, Cm, etc.). It's a bit of an outdated name from when people didn't know how exactly the plasmids conferred such resistance.
An F-plasmid is any plasmid that contains the genes necessary for (F)ertility, eg:horizontal gene ...
5
The melting temperature (Tm) of a double stranded DNA tract is defined as the temperature at which 50% of the DNA molecules are dissociated into single strands (and 50% form duplexes). Sure, it has a different meaning than in physics... but it is a really common term in molecular biology and I doubt people will stop to use it anytime soon!
There is a vast ...
5
the devil is in the details here - the logic is okay, but there is no experiment here. Too many unanswered questions.
Are you doing anything specific to see optimize RT activity?
How are you preventing your GFP mRNA from being turned into protein, producing much larger signal than you will ever see from RT activity?
Once its integrated into the ...
5
Evolution - Douglas J. Futuyma, Chapter 19, p. 461
Michael Lynch and John Conery (2003) have pointed out that a variety
of genomic features that appear to have little fitness advantage for
organisms-introns, transposable elements, large tracts of noncoding
DNA-may be more prevalent in species with small effective population
sizes. They have ...
5
DNA is more chemically stable than RNA, which makes it ideal for long-term storage. RNA viruses like HIV have a short lifespan and must replicate to survive, which is why they can get by with a less chemically stable genome.
RNA is a useful format to transcribe since it has multiple forms and functions (e.g. rRNA, mRNA, tRNA, siRNA, snRNA, miRNA, etc.). RNA ...
5
Let's start with a word of caution: on the internet, the terms macroevolution and microevolution (especially together) are usually used primarily in creationist rhetoric. As such, it is usually best to avoid them, especially when talking to a lay audience. The main mistake creationist perpetuate when thinking about micro-vs-macro evolution, is that the two ...
4
In terms of crops, plants that are grown for food, one advantage is the targeted modification of a single gene. Classical plant breeding is slow, imprecise and carries many traits of negative benefit. For example, if you cross plant variety A with variety B for the purpose of obtaining one of B's traits (say oil content of the seed), the resulting progeny ...
4
I'm with @Mad Scientist. Save yourself the trouble and do this in an in vitro system. At the moment, you don't even know if the HIV-RT will express or will be active in E .coli.
Rather, express mutated HIV-RT in T-Cells or Rabbit Lysate. Purify.
Add in a RNA template with the appropriate primer.
Hydrolyze your RNA
Detect your cDNA.
4
According to their website New England Biolabs use a version of the approach pioneered by Wayne Barnes, as described in:
Kermekchiev, M.B., Tzekov, A and Barnes, W.M. (2003) Nucl. Acids Res. 31, 6139–6147
This is basically an assay for the mutation rate in a PCR-amplified lacZ (β-galactosidase) gene, assayed by transforming E. coli, plating on the ...
4
Yes, check out HOTAIR (in human), as well as cyrano and megamind in zebrafish -- they are all spliced.
4
As far as I can tell from the paper you linked to (Damiana et al) it is possible but inefficient:
Naturally, we tried to translate ssDNA, but as previously described
elsewhere, direct DNA translation was not really efficient in absence
of antibiotics such as neomycin [5] and [6]. It seemed that the
elongation phase was the limiting step in the ...
4
I can only provide you with a few pointers from memory, as an ad hoc search for "review of dna cutting techniques" was not prolific.
Please consider the provided information with precaution and only for pointers to help you do literature research.
cre/lox system and variants (best known), belong to SSRs (Site specific recombinases)
various Restriction ...
4
That's a good question, and honestly, the nomenclature for genes and their coded proteins is somewhat abused in scientific literature. For example, when referring to microbes (like E. coli), gene names are all lowercase (eg, lacZ). The problem of protein names is compounded when the protein name is (often) an abbreviation.
With respect to myc, it can refer ...
4
There is a useful set of links to nomenclature guidelines for all of the main genetic systems at this Wikipedia page. Personally, I think that the Saccharomyces cerevisiae system works best: it manages to cover dominant and recessive alleles of a gene, the name of the protein, how to refer to a related phenotype, and the use of a parallel convention for the ...
3
Using a somatic cell in an a ovum is what is typically done in the process of cloning. It was the same process used to create Dolly the Sheep. What you're asking about is something very different:
Consider that somatic cells are properly diploid. Whereas an ovum itself just contains a haploid number of chromosomes. In typical sexual reproduction the sperm ...
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