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22

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 ...


13

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 ...


12

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 ...


11

All mutagens are potential carcinogens. Unless the mutagen is highly specific to a site. HPV causes oncogenic transformation of a cell because of certain proteins that it expresses. Its mechanism is directed and specific. Most "carcinogens" are non-specific agents. However according to the definition, HPV can be called a carcinogen. Retroviruses can ...


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 ...


10

A cistron is a gene - here's how the word came about: It's 1955. The proposed double helical structure of DNA has been published and the race is on to understand the implications of this for genetics. Geneticists have been working with genes for decades, but they don't know what genes are. Sanger has sequenced the two polypeptides of insulin, so the idea of ...


9

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 ...


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 ...


9

Yes, these sequences exist and they are called "silencers" (surprising, right?). There are different mechanisms by which this silencing of genes can happen. In the "classical" way the silencer is bound by a transcription factor which either passively suppress the gene by hindering the binding of specific transcription factors or by actively preventing the ...


8

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 ...


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: ...


8

This question is closely related, and the fascinating link posted by @JohnSmith is a good read. In short, with a four-base system, and a codon size of 1, you get four possible amino acids. Silly system. A codon size of 2 gives 16. Not too shabby, but not a lot of room for growth, and not enough for those 20 amino acids. Codons of size 3 gives 64 - ...


8

A woman (assuming no mosaicism) has two X chromosomes in the nuclei of her cells (except for oocytes). A man, in every cell with a nucleus (except for spermatocytes), has only one, pluripotent or not. The only way he could make a female would be to either manipulate cells by duplicating the X chromosome (very difficult to do) or remove/inactivate the Y ...


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 ...


7

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 ...


7

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 ...


7

The pattern we see in B. subtilis is quite common in prokaryotes. The origin of replication is shown at the top of the genome diagram. DNA replication proceeds bidirectionally from this point. In the B. subtilis diagram, most genes are located along the leading strand in each direction. Even in E. coli, by the way, important genes, including all rRNAs, tend ...


7

To be specific: I am talking about adult, somatic gene therapy here, and germline gene therapy experiments is still a landmine when considering ethical reasons. The defective gene codes for a defective protein, that usually plays a part in pathways. Since the protein is also defective, that pathway is also rendered defective because of this protein, and ...


7

It is called conditional mutation. You flox (put lox sites around) gene of interest and express Cre recombinase driven by tissue-of-interest-specific promoter. Illustration from here: Using chemically-activatable variant of Cre recombinase (cre-ER) you can create knock-out in some cells of tissue of interest, not every. Addition: a bit weird but still ...


6

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 ...


6

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 ...


6

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 ...


6

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 ...


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

The smallest unit that can be selected is, of course, the single nucleotide. The most striking examples of this are Single Nucleotide Polymorphisms (SNPs), many of which confer selective (dis)advantages. To take a simple example, imagine a SNP that introduces a frameshift mutation, rendering a gene incapable of producing its protein. If that protein is ...


6

Purified DNA contains negligible amounts of ethidium bromide. PCR and gel clean-up kits remove it quite well. There is, though, a risk of mutation from the fact that you're visualizing the gel in UV light with ethidium bromide. The risk of mutation from UV is minimized by exposing the gel as little as possible, and by using "preparative" transilluminators ...


6

There are several ways you could go about identifying species through DNA. If you want to do everything yourself, the simplest option in terms of equipment needed consists of evaluating fragment lengths observed during gel electrophoresis after amplifying specific DNA sequences using PCR. If you are content with some outsourcing, you can also send DNA ...


6

Genetic code and codons are always used with reference to RNA. When talking about DNA, the the sense strand of a gene is considered its sequence. The anti-sense strand though is the template for mRNA synthesis, does not represent the gene. DNA-codon table has simply U replaced by T. Apart from a wikipedia article, I don't find the term being popularly (not ...



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