The study of the molecular processes of the nucleus and cell function.

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Clustal X command-line version [on hold]

I downloaded a precompiled executables CLUSTAL software from http://www.clustal.org/clustal2/. When a .dmg file was downloaded, I tried clicking it but then it pops up: ...
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22 views

How does non-homologous end joining (NHEJ) work?

I was reading about non-homologous end joining (NHEJ) in my molecular biology of the gene textbook but the explanation provided in the text was rather vague to me, and I was not able to understand it ...
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Alternatives to trypsin for cell detachment?

I have ran out of trypsin and need to passage my cells (immortalized chondrocytes, C28/I2) today or tomorrow. I have been out of town and forgot to order more trypsin. I was wondering if there are ...
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45 views

How does high-fidelity of DNA replication depend on the formation of hydrogen bonds?

Replication has an error rate of less than 1 in 100 million. DNA polymerase forms H-bond with the H-bond acceptor atoms in the minor groove. <-- enhance fidelity here? Binding of the triphosphate ...
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38 views

What are some of the general characteristics of the DH5 alpha strain?

I can not find some useful sources unfortunately. Please tell me about some important characteristics of DH5 alpha. What makes DH5 alpha suitable for the gene cloning?
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13 views

Cellulase Assay [closed]

I'm doing an investigation on the effect of temperature on cellulase. I have done a cellulase assay twice and it has been a failure both times. Can anyone recommend an assay that will only take ...
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0answers
15 views

how far are SNP's and miRNA related [closed]

Recent findings indicate that SNPs could create, destroy, or modify the efficiency of miRNA binding to the 3'UTR of a gene, resulting in gene dysregulation. How well can we establish a relationship ...
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1answer
22 views

Does adding antibiotic after 5-10 mins of innoculation affect the protein yield or growth?

I've asked a lab colleague the same question. She said, it would loosen the bacterial cells in the LB medium and plasmids would come out. Is that true? and why?
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21 views

Laboratory question about meosis dye [closed]

We are doing the meosis lab in intro bio course. Here are two post lab questions that I couldn't figure them out! In mitosis lab, under the microscope, the toluidine blue appeared as dots inside the ...
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1answer
45 views

Active & passive transport question

If an element, ion or molecule is found in a cell is it possible to tell which method of transport was used? for example if a hydrogen or sodium ion was found in the cell could you tell if it got ...
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165 views

Why proteinase K doesn't degrade itself?

Can anyone tell me why proteinase K doesn't degrade itself? If possible please provide me the source.
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1answer
173 views

How many RNA-binding proteins can simultaneously bind on a single mRNA?

Typically, how many RNA-binding proteins can simultaneously bind to a single mRNA? Or said differently, how many "binding sites" does an mRNA have? What order of magnitude? I am interested in RNA ...
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1answer
30 views

PSI-BLAST website algorithm parameters

http://blast.ncbi.nlm.nih.gov/Blast.cgi In this website, when I want to apply the psi-blast algorithm on a sequence, under the section of algorithm parameters , what does PSI-BLAST threshold mean? ...
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1answer
33 views

protein-binding sRNAs

I am actually a computational biologist, pardon me if my question description is a bit off-note, my curiosity is driving me on A bit of background and context: In bacteria, a regulatory protein ...
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15 views

Sequence based method for prediction of continuous B cell epitope

What is Sequence based method for prediction of continuous B cell epitope? What is the algorithm/procedure of this method? Can someone please explain this to me in simple language?
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0answers
20 views

Receptors for red and far-red light in plants: Shade avoidance

Franklin (2009) describes how plants use the ratio of the red wavelength (660-670nm) over the far-red wavelength (725-735nm) (R:FR) in order to avoid shading. My question is: which receptor is ...
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1answer
45 views

A monkey typing Shakspeare? [closed]

I think that the ultimate and most important question of biology and science is the origin of life. Was it the result of pure probability? Or was it the result of the law of physics? In other words, ...
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1answer
31 views

Determining and Differentiating specific ATPases

In respects to this certain ATPase transporter. What do i look for in respects to determining what specific kind it is out of: F-ATPases V-ATPases A-ATPases P-ATPases E-ATPases Im assuming that ...
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2answers
62 views

peptide MHC microarray

"The recent technology is peptide–MHC microarray or artificial antigen-presenting chip. In this technique, recombinant peptide–MHC complexes and co-stimulatory molecules are immobilized on a ...
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24 views

recombinant peptide MHC complex

What is recombinant peptide-MHC complex??? Recombinant DNA means "to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in biological ...
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2answers
76 views

Transmembrane Protein Problem

Problem A transmembrane protein has 1000 aa. The 5th aa is found on the external side of the cell membrane. It interacts with the aqueous environment outside the cell. Amino acid 90 is inside the ...
2
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1answer
21 views

epitope prediction/ mapping

B-CELL EPITOPE PREDICTION Regarding this article: "Such a molecule can be synthesized or, in case of a protein, its gene can be cloned into an expression vector."----- is a particular line in ...
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11 views

How does Temperature influences the rate of protein turnover?

Question How (quantitatively speaking) does temperature influences rate of turnover of transcription factors? Which protein? As I am not looking for any accurate number I am talking about an ...
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1answer
24 views

aspartame in relation to generating methanol

So I posted another question with respects to methanol and aspartame in metabolism with respects to toxicity. So another question I have is "Why is aspartame used as a dietary component to generate ...
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12 views

Metabolism that generates methanol

I've been looking for help topics about methanol in metabolism. Specifically I wish to know What is a common dietary component that generates methanol following metabolism and comment on its ...
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19 views

What is Colloidal biology and does it have any scientific background?

There is the following bulletin published for the History of Chemistry Vol. 32: 105-118 in 2007: “MOLECULAR” VERSUS “COLLOIDAL”: CONTROVERSIES IN BIOLOGY AND BIOCHEMISTRY, 1900–1940* written by PhD ...
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28 views

What keeps resting potential of neurons constant at -70mV?

I know the sodium-potassium pump pumps out 3 Na+ ions and pumps in 2 K+ ions per reaction so the negative charge in the axon increases. However, once the voltage (difference of charge inside and ...
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transfection of expression library made from cDNA into cells expressing the desired MHC haplotypes

http://www.sciencedirect.com/science/article/pii/S0167569997800205 If anybody has access to this paper, can you please explain me the process to find TAA based on transfection of expression library ...
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53 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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1answer
50 views

Knowledge about Organelles

As we know, there are various organelles present inside a cell. Let's consider mitochondria for example. My questions are -> Do we understand the composition, structural and functional features of ...
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1answer
26 views

Difference between sequential and conformational epitope

Is the difference only in its structure? Like conformational epitope has 3D structure while sequential has a linear structure?(I have not studied biology since last 8 years and now I am going through ...
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21 views

MHC restricted peptide

What is an MHC restricted peptide? "MHC-restricted antigen recognition, or MHC restriction, refers to the fact that a given T cell will recognize a peptide antigen only when it is bound to a host ...
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60 views

Manufacturing of Bio Molecules [closed]

Can we Manufacture bio molecules say e.g. the simplest Sugar, C12,H22,O11 the way we do with any other mechanical component. So, we know all about the Structure and arrangement of Atoms in Sugar - so ...
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44 views

How does temperature influence the rate of protein degradation?

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on biochemical reactions. Question In particular, my question is: How does ...
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1answer
13 views

What are the molecular mechanisms behind tachyphylaxis (downregulation of receptors in response to an agonist?)

Anyone know of a good source which explains this? Or is this still an open question? This wikipedia article describes some molecular biology behind morphine tolerance, but it sounds like its newer ...
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41 views

Simulating Drug Entry in Protein and binding?

Is there any simulation protocol or paper which can simulate the dynamics of drug entry and interaction with the target protein?
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1answer
33 views

How is the rate of transcription influenced by temperature?

How is the rate of transcription influenced by temperature? More precisely, I am looking for an article who quantitatively measured the rate of transcription of an "average gene" and show how this ...
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1answer
47 views

Influence of temperature on protein binding and decay rates

For computer modeling purposes, I am looking for some referenced quantitative measurements of the effect(s) of temperature on the dynamic of biochemical reactions. Question In particular, my ...
2
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1answer
26 views

Transcription rate expressed in microarray per hour

This article gives measurement of transcription rate and the unit they're using is microarray per hour. For example, at 27°C the average expression of their genes is 236.1 microarray per hour (page ...
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1answer
55 views

Influence of temperature on transcription, protein binding and decay rates

I am the kind of biologist who doesn't know much about molecular genetics and about the dynamic of biochemical reactions. Question My question concerns the influence of temperature on the dynamic of ...
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23 views

Enzyme Assay - pectinase

During assaying an enzyme at high temperature, the substrate (Pectin) is degraded by the high temperature rather than by enzyme, so, how can I minimize degradation of the substrate by the temperature? ...
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19 views

Difference in structure of B-cell epitope and T-cell epitope

What is the difference in the structure of B-cell epitope and T cell epitope? Also please enlighten me with the fact of discontinuity or conformation of the b or t cell. Went through a number or ...
3
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1answer
32 views

SEREX serological analysis of cDNA expression library

What is Serological Analysis of cDNA expression library? I went through this article:http://cancerimmunity.org/serex/introduction/ but could not really make out. Can someone please explain this to me ...
5
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1answer
146 views

Importance of knowing GC Content of an organism

I was looking at the GC content percentages of few organisms. I also know calculating the GC content percentage. But, what I want to know is, what information would we get., let us suppose if human ...
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1answer
97 views

What is the difference between second and third generation sequencing

I am writing the section about history of DNA sequencing in the introduction chapter and after reading quite a few research papers, I am still confused about them. Here I compile some questions to ...
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1answer
39 views

Complementarity Determining Regions (CDR)

Complementarity determining regions (CDRs) are part of the variable chains in immunoglobulins (antibodies) and T cell receptors, generated by B-cells and T-cells respectively, where these molecules ...
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1answer
22 views

Degenerate Alignment Analysis

Can someone please tell me what is Degenerate alignment analysis? Could not find a good article on the internet that could help me understand what it means? (I have not studied biology since last 8 ...
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22 views

TAA- Tumor associated antigen

An approach to find Tumor associated antigens is based on transfection of expression library made from cDNA into cells expressing desired MHC haplotypes. Can someone please explain what this line ...
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1answer
20 views

Microarray probe and target

In a microarray, which one is called a target and which one is the probe? the one that is added later , is that the probe or the one present in the slots of the microarray, that is the probe? (I have ...
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1answer
19 views

Why can't NMR be used on large RNA molecules?

While reading my Molecular Bio textbook, I came across a sentence that stated that NMR cannot be used on large RNA molecules to determine their structure. Why is this? Is it because RNA is single ...