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

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meaning of the “reads” keyword in terms of RNA-seq or next generation sequencing

I'm an undergraduate student at computer science and currently, I'm interested in bioinformatics. Today, I've started to read a paper about clustering and classification of non-coding RNAs can be ...
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36 views

Telomere and its effect on aging

The cloned sheep, Dolly, was said to have died very soon because the cells used to create it were taken from an adult sheep with an aged telomere. Why doesn't this happen with humans? Why aren't we ...
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115 views

Inbreeding depression and dominance

From this article, second paragraph of the second page A classic theoretical result is that the mean of a character controlled by a single locus i with two alleles Ai1 and Ai2 is only affected by ...
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118 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 ...
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78 views

What is the difference between the mitotic spindle and microtubules?

In mitosis, I understand that the centromeres line up on the spindle. I also know that the centrioles form microtubles between the centromeres during mitosis in the metaphase. But, are microtubles ...
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59 views

How do the major and minor grooves in the DNA helix arise?

I understand that they arise due to the pairing of bases of two opposite stands and are sites through which important proteins needed for replication and transcription of DNA interact. But I don't get ...
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84 views

Crossing over and exon shuffling?

Campbell Biology 10e, in discussing the functions of introns, writes: The presence of introns in a gene may facilitate the evolution of new and potentially beneficial proteins as a result of a ...
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125 views

Do transposons usually jump from one chromosome to another?

If it is usual occurrence, does it mean that my one gene can change its location from one chromosome to another?
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158 views

Why increasing the vector concentration does not increase the effeciency of bacterial transformation?

I was reading some old description of the protocols used for the transformation of bacterial cells. In the description I read that the transformation works best with low amount of DNA, and if we ...
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92 views

Why aren't introns found on the ends of pre-RNA?

We recently learned in genetics class that exons always cap the ends of nascent RNA. I have been trying to figure out the reason why introns can't instead be found on the ends instead of exons. The ...
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135 views

Why do we use DNA sequencing methods such as shotgun?

I am learning about DNA cloning for the first time. What I understand is that, in order to clone DNA, we break-up the original gene into shreds. Then try to piece it back together. Why exactly do we ...
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47 views

Heterochromatin production limitations

Currently playing with some ideas for a project and needed some guidance. I am wondering, both in Drosophila melanogaster and in general, is the amount of heterochromatin a cell/nucleus can produce ...
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Telomere shortening during replication

It is widely know that each cell cycle during DNA replication some fraction of the telomeres is lost, and this phenomenon is called the end replication problem. Well this is due to the fact that the ...
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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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50 views

Does DNA polymerase I require a $3^\prime$ end?

DNA polymerase III adds nucleotides in the $5^\prime \rightarrow 3^\prime$ direction because it can only add nucleotides to the $3^\prime$ end of the previous nucleotide. This is why it requires a ...
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218 views

How does Cro protein expressed by lambda phage kill its host?

I read that the DNA segment of lambda phage integrated in host DNA could switch between lysogenic state where cI represses the expression of Cro and lytic state where Cro expression takes over and ...
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110 views

What is a holocentric chromosome?

I was doing this question that asked: "How many centromeres does a typical chromosome have?" I thought one and the answer was:"One, except for holocentric chromosomes." So then what are ...
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35 views

Exon skipping in mammals

I've heard from several sources that the predominant form of alternative splicing (at least in mammals) is exon skipping. However, my personal evidence is only anecdotal: I've heard it and read it, ...
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50 views

Process of Transcription

During the process of Conversion to Ribonucleoside Monophosphates the various ribonucleoside triphosphates break off their high energy bonds after linkage to the DNA.But the first ribonucleotide ...
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209 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 ...
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79 views

Is sequencing error a function of the nucleotide being read?

Checking out on Google Scholar, I can see that for Illumina (just to consider one example) the sequencing error rate is of the order of 0.001-0.01 per nucleotide. Talking about sequencing error, ...
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57 views

Why do genes with closely related functions often reside on different chromosomes?

Why do genes with closely related products are so often positioned on different chromosomes? To illustrate what I mean, here is an example from immunology: the invariant region of MHC is on ...
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126 views

Problem on number of amino acids that an alien can use

A new life form discovered on a distant planet has a genetic code consisting of five unique nucleotides and only one stop codon. If each codon has four bases,what is the maximum number of unique amino ...
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83 views

What does it mean for the signals for transcription and translation to be “conserved”?

I was reading this article: "Overview of vector design for mammalian gene expression." for an explanation of why mammalian cell lines are used for expressing cloned genes, and one of the reasons ...
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739 views

How does GC-content evolve?

Background GC-content refers to the frequency of base pairs that are either C or G in the genome, or in other words the number of GC base pairs divided by the addition of the number of GC base pairs ...
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Activation Of Embryonic Genome

Embryonic gene activation is a process by which the embryo begins to transcribe its newly formed genome.As the embryonic gene activation occurs during early stages the paternal genome may not have any ...
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104 views

Transposons and the net amount of DNA

The retrotransposons and certain DNA-transposons, are "jumping" sequences which may be incorporated elsewhere in the genomic DNA of an organism, through varying mechanisms. This insertion is almost ...
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861 views

How to calculate virus titre from qPCR

I harvested some lentivirus from 293T cells and want to titre the result. I infected 293T cells on a well plate with 400,000 cells per well which I infected with virus stock, and 1 in 10, 100 and 1000 ...
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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 ...
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31 views

Are all genes transcribed in differentiated cells?

My textbook tells me that it’s specific transcription factors that allow for a different set of genes to be expressed in different cells (differential gene expression). My book gives the example of ...
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How can a mutator gene can cause a mutation when it is shut off? [closed]

defination of "Mutator" - a gene that increases the rate of mutation of one or more other genes. However, in the book "Molecular Biology of the Cell" (bruce alberts) it states that when a mutator is ...
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41 views

Should gene therapy safety protocol include isolation?

In the case of a gene therapy trial where viral vectors are used to deliver genes into mammalian cells, including humans, should biosafety and ethical protocols include isolation of the patient as a ...
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What is the most complex biological organism (or precursors) that we have been able to synthesize from raw materials?

In the Miller–Urey experiment they produced several amino acids. I'm not sure if there were other similar experiments that got further. ...
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31 views

Gibson assembly - primer design with A and T rich regions

I have question about Gibson assembly. I have done it several times and it always worked okay for us, but now I want to assemble together a fragment which has sequence like this: ...
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64 views

Inbreeding Coefficient and Coefficient of Relationship

Wikipedia gives the following formula to calculate a "path of coefficient of relationship" between an ancestor $A$ and an offspring $O$: $$\rho_{AO} = 2^{-n} \left( \frac{1+f_A}{1+f_O} \right)^{1/2} ...
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What metabolic processes do dormant and ungerminated seeds carry out?

What metabolic processes does a dormant embryo in a seed carry out? Seeds will not germinate, either because of a lack of favourable conditions, seed hibernation, or because of a genetically ...
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2k views

Does a woman contain all the genes needed to make a man?

I know the answer of inverse is at here, but how about this question? I also read this question, can I imply to human that a woman also contain all the genes needed to make a man? Edit: ok , I ...
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102 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 ...
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37 views

What separates gene loci?

Introns are sections of noncoding DNA that separate exons within a gene locus. However, between different gene loci, I also would assume there to be noncoding regions of DNA. What are these regions ...
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87 views

What does it mean to clone a gene?

When I look up information related to the identification of disease genes, texts will often refer to the gene being "first cloned." What does "clone" mean in this context? Is it simply a synonym for ...
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117 views

Alternatives to PCR

PCR uses cycles of heating and cooling to denature the strands, calling for special thermostable DNA polymerases. In a cell, during replication, Helicase unwinds the DNA without the requirement of ...
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Why mutations in genes involved in general processes like DNA repair increase the risk of developing specific types of cancer?

For example, mutation in MHS2, which encodes a protein involved in the repair of mismatches that occur during DNA replication, dramatically increases the risk of developing colon cancer. (There are ...
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606 views

Can DNA & RNA be considered as nature's programming language?

The final frontier of Biological Sciences could be considered understanding the effects of variation in the DNA (and RNA). If after fertilization the DNA of the zygote could be genetically ...
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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 ...
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34 views

Why is mRNA used as a biomarker for cancer over tRNA or rRNA?

I cannot find a clear explanation for why mRNA is used as cancer biomarker and not tRNA or rRNA. Is there something peculiar about mRNA which cannot be fulfilled by tRNA or rRNA?
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124 views

What is the point of DNA sequencing?

This is a very very basic question. I've looked at methods such as chromosome sequencing and shotgun sequencing. Wikipedia says that: ...
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67 views

Why do oncogenes show genetic dominance?

As we know that tumor suppressor gene causes cancer only when both the alleles are recessive in nature.But in case of oncogenes if only one allele is dominant it can cause cancer.Why in case of ...
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59 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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67 views

Markers for human genetic mapping

For human genetic mapping several different types of markers are used: RFLPs (Restriction Fragment Length Polymorphisms) VNTRs (Variable Number of Tandem Repeats) such as mini- and microsatellites ...
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125 views

How does alternative splicing work?

I am trying to find out what controls what exons are spliced out, and I keep coming across the term cis regulator, but I cannot seem to find a clear explanation of what happens... Thank you in ...