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

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Genetic linkage greater than 50 centimorgans

Classically, the linkage between two loci can be measured in centimorgans (cM), which represents the percent chance that these two loci will recombine an odd number of times (generating a recombinant ...
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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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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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XNAs as a Genetic material [closed]

I heard there is a new genetic material called XNAs.I wanted to know more about this.Does anyone about XNAs as genetic material?
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48 views

What came first? The DNA or the DNA polymerases?

I know this sounds a lot like chicken and egg question and while the latter has an answer, I am intrigued about the former. A modified form of the question would be, in the course of abiogenesis, ...
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How does a test like the Natera Panorama distinguish the child's genome from the mother?

Blood tests on an expectant mother, like the Natera Panorama, are now being used regularly to screen fetuses for chromosome abnormalities. At my wife's recent prenatal visit, she wasn't really even ...
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Amplified Fragment Lenth Polymorphism (AFLP) primers

I am trying to blast AFLP primer sequences to the genome to find the locations of the AFLP markers. However, I can't seem to find full alignments for the primers on the genome. For example, in the ...
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40 views

Explain allelic complementation at molecular level

I know that Allelic complementation is a phenomenon where two recessive loss-of-function allele generate a functional gene product by compensating each others' defect. But I don't get how do they ...
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Extending a small fragment of DNA

Is there a way to extend a small fragment of DNA, say 150 bp, by making copies of itself and attaching each copy of that small fragment to the end of that 150 bp sequence? For example, I want a ...
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Following DNA replication during S-phase of the cell-cycle, are all genomic regions subjected to the same stringent level of DNA-Repair?

To my (limited) understanding, there are 2 main ways that mutations can occur in DNA: Environmental (UV, etc) and mistakes during cell division. I was wondering if there is a mechanism that can give ...
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probe amplification in MLPA

I'm reading an article about MLPA (Multiplex ligation-dependent probe amplification) and I got stuck on this sentence: The advantage of splitting the probe into two parts is that only the ...
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317 views

Gene and alleles

This is a multiple choice question: Consider a gene, ABC, which codes for an enzyme involved in the metabolism of sugars. There are two known alleles of this gene, ABC1 and ABC2. Which statement ...
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ChIP-seq for histone modification not in agreement with RNA-seq for expression

I have ChIP-seq for H3K79me2 and H3K36me3 and RNA-seq data for treated and untreated samples. Those two histones mark active genes. Lets say, hypothetically, a peak caller finds differential sites at ...
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Is DNA transcription inactive during mitosis ie no proteins are made? How does the cell survive?

I've read that during mitosis, DNA exists as heterochromatin, a form that is unable to be accessed for transcription. Does this mean no new proteins are made during what can be 20% of a cell's life? ...
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Constant or variable number of chiasmata during recombination?

During recombination, is the number of chiasmata consistent for each gamete and are the chiasmata regions consistent within a single organism?
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Genomic DNA isolation from Wheat

Can I use dry seed, wheat for example, in place of young leaves for isolation and purification of genomic DNA for PCR amplification. The goal of my experiment is to validate a novel gene which is ...
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38 views

Are the genes for transcriptional factors close to their targets in the genome?

Transcriptional factors (activators and repressors) are proteins which regulate transcription. Being proteins, they themselves are also made from expression of certain DNA sequences/genes. For ...
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Why does replication require primers while transcription does not?

In transcription, there is no need for any primer. I guess the basic mechanism of DNA polymerase & RNA polymerase is the same. So why does replication have the need for a primer?
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Chromosomomal walking

I'm having a great deal of trouble understanding chromosomal walking, especially in regards to this article: Control of male sexual behavior and sexual orientation in Drosophila by the fruitless ...
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Operators and Enhancers/Silencers

Wikipedia has two images, of a eukaryotic gene and of a prokaryotic gene. They show the difference that the prokaryotic gene also has an operator while the eukaryotic gene does not. Both also have ...
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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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Degenerate primer designing software

Can any one provide online free degenerate primer designing software. I have tried couple of them like CODEHOP is one where BLOCK formatting step finding difficulty, can anyone help me out....
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Why are fifth order Markov Models, the ones most often used for gene prediction?

As far as we know that smallest polypeptide chain length is 60 amino acids - so if we found an Open Reading Frame (ORF) of about 60 codons without the interruption of stop codon we can consider it to ...
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How many genes does D. melanogaster have?

Obviously there is no 100% exact number, but I came across this on flybase, the gold standard for annotation. I am confused now. "Genes located to the genome", is that what I am looking for? If so, ...
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ATP to disassembly of nucleotide ratio

DNA Helicase, the enzyme that is responsible for tearing apart the strands before DNA replication, requires ATP to rip apart nucleotides. I have asked this question to several professors and they ...
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“Signal Advance”: Unsure of meaning or contextual use

I am reading through Recombinant DNA; Genes and Genomes - A Short Course - Third Edition by James D. Watson, et. al. and I came across this paragraph in the discussion about discrete factors of ...
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How to find conserved residues across species?

I want to identify if certain phosphorylation sites are conserved for protein X across humans and yeast. I know from MS data that there are 4 phosphorylation sites in Human protein X. In order to ...
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gene transformation from plant to plant - transgenic plant

I want to know if the expression of a transfered gene depends on source of the gene, if e.g.: 1] I isolate a gene from plant and transfered it to the same plant? 2] I isolate a gene that is highly ...
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Does a man contain all the genes needed to make a woman?

This question is brought on by a Sci Fi novel I am thinking about writing. The plot device involves a colonist in charge of building a population on a new planet who loses his supply of embryos and so ...
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Degree of complementarity

Apologies in advance for asking bit naive question. I have looked up for this concept a lot but didn't find anything. The wikipedia (I know its not authentic all the time, but I think works well for ...
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When performing mutagenesis for an assay, how do you decide on the sample size of individuals to be mutated such that all genes are covered?

If I want to study, say, gustatory response of salmons to a bile acid, I need to mutagenize a sample of salmon males. However, given that there are many genes involved in this response, what is ...
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59 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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PCR that worked previously is now only showing primer dimers and a smear on gel

PCR amplification of a promoter sequence for gel extraction worked beautifully using Phusion HF enzyme with GC (higher error but less picky) buffer. However, DNA concentration from the gel extraction ...
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genetic complementation problem

I've attached the picture of the problem. SO, based on the information I managed to assemble two large cistrons. (if the combination of two mutants yield (-) mutations are on the same chromosome) ...
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Can genes be expressed sequentially?

As I understand it, any gene on an exposed/unpacked region of a chromosome is continuously being expressed. Regulatory genes may increase or decrease the amount of protein synthesised due to its ...
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What's the difference between shotgun sequencing and clone based sequencing?

Whilst I appreciate this is a large topic, what are the main differences between shotgun sequencing and clone based sequencing?
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Lac operon: How can lactose enter the cell in the absence of lactose permease?

My textbook states that lactose permease...transports lactose into the cell and When lactose is added to the growth medium, the lactose molecules bind to the other site on the repressor ...
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Calculating number of amino acids in mRNA

Assuming there were 20 different amino acids and less than 40 types of different tRNAs found in this alien organism. How many amino acids would be found in the translational product of a ...
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How can I find the mRNA sequence for a specific prokaryotic gene?

What I want to find out is the start of the transcription for a specific gene, how long the UTR is before the actual coding sequence starts. I've looked at various databases like NCBI Gene, Refseq or ...
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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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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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tandem repeat sequence; causes of contraction and/or expansion question

Question: Which of the following events, occurring within a tandem repeat sequence, will cause an expansion or contraction of the array? A) Endoduplication B) homologous recombination C) ...
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mutations induced by transposons

Question: In contrast to chemically-induced mutations, mutations induced by transposons are more likely to ... be lethal de dominant be stable revert to wild types be a gain of function The ...
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recombination between DNA segments question

In the diagram shown above, segments A and C are copies of a repeated DNA sequence, flanking a unique stretch shown as B. A and C are in an inverted orientation relative to each other, as indicated ...
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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 ...
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Abbreviations for molecules: What are CheW, CheA, CheY?

I've encountered the abbreviations such as "CheW" and "CheA" for certain organic molecules. For example: Proteins associating with the Tar complex include the autophosphorylating protein kinase ...
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Double stranded breaks in E. coli

What could be a possible reason why no enzymes have been found that make double stranded breaks in the RecBCD pathway?
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how do I find the number of bp in chromosome 3 by knowing number of bp in chromosome 1?

If i have a number of bp in chromosome 1 for example(298,295,559 bp) can I use this number to find the number of bp in chromosome 3.
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How does RNA transcription know which half of the DNA to use?

I feel that I might have a complete misunderstanding here. If DNA has two strands, how does RNA transcription know which one to choose?