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

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255 views

Is the amount of dNTPs rate limiting for very long PCR products?

I'm using the Q5 system and I'm PCRing a product that will have a final length of around 9500 bases. I have noticed that the product is there but very faint. The primer seems to be used up. So my ...
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3k views

Does sample buffer require EDTA for protein separation on SDS PAGE?

In sample buffer preparation we add EDTA, but if SDS-PAGE is for protein then is it necessary to add EDTA in sample buffer? What is role of EDTA in sample buffer for protein separation for SDS-PAGE.
3
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1answer
104 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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2answers
101 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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2answers
163 views

Immunodominant Peptide

Can someone please explain me the concept of Immunodominant peptide in simple language?? I did read the wiki article but did not understand it clearly. Please help! (I have not studied biology since ...
3
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1answer
109 views

Propensity Score for amino acid

What is the meaning of propensity score of amino acid? How is it calculated? (I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if ...
3
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1answer
390 views

Efficiency of plasmid DNA isolation from frozen E. coli cell cultures

Has anyone isolated plasmid DNA from frozen (at -20degrees) E. coli cell cultures (not pellets)? Has that worked and if so, with what yields? What would be the quality of the isolated plasmid DNA if ...
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2answers
49 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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754 views

What is “bacto” peptone?

Standard recipes for yeast medium often include "bacto-peptone". Is this the same as bacteriological peptone? Is there an authoritative source that spells it out?
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208 views

Do macrophages engulf mtDNA?

Let us assume that in a human body, a mitochondrial DNA is released to extracellular environment. We know that mtDNA inheritance is solely matrilineal. So the question is, If your mitochondrial DNA ...
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739 views

Role of isopropanol in plasmid isolation

In plasmid isolation, isopropanol is used to renature only the plasmid macromolecules after we precipitate all macromolecules(DNA, RNA, plasmids) using sodium acetate solution. How does it do that? ...
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785 views

Why does methylation not occur in viral DNA?

Why does methylation not occur in viral DNA? Can viral DNA undergo the process of methylation? If not then why does this process does not occur in viruses?
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63 views

How do you express and detect GLP-1 receptors?

I am currently working with a peptide which is an analogue for glp-1, but during invitro studies am not able to detect for the presence of GLP1- receptors. The cell line used is Min-6. How do I detect ...
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328 views

Why did Fair Meiosis evolve?

How and why did Fair Meiosis evolve? I can hardly think that it provided a fitness advantage to the individual carrying the mutation. Why would it? Or did it evolve through lineage selection? Or was ...
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3answers
2k views

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 nucleus....
3
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1answer
211 views

What molecular processes are involved in pseudopodial extension?

I am curious as to the processes and mechanisms involved in the extension of pseudopodia in amoeba. How does the cell know and control the direction and extent of pseudopodia formation at a molecular ...
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296 views

How do I create a probe for in situ hybridization?

I tried to make the probe several times but it failed again and again. It usually turns out that the probe after hydrolysis is very very short (maybe around 50nt). I did not check the RNA before ...
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2answers
63 views

Codon tables and the wobble hypothesis

In E. coli, there are only 47 different tRNAs but 61 potential anticodons. This is because, from what I understand, the third base of the anticodon can pair by wobble rules. However, it is known that ...
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24 views

Can a cleaved plasmid “close” without exact matching “sticky ends”?

Say if you have a multiple restriction site and use two restriction enzymes on it to cleave a plasmid, can it recombine with ligase? My concern is that without the small sequence of nucleotides ...
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80 views

Does size matter?

As I compare the morphologic differences between mouse models and the human disease for which they are analogous, I have become interested in what difference interspecies size has on molecular ...
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59 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 ...
3
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62 views

How to predict a mRNA secondary structure with a large sequence?

When I use some web servers to predict a mRNA secondary structure, I find they always required in a small size sequence. If I use a long sequence and cut it into small parts, do these small parts ...
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2answers
251 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 ...
3
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1answer
202 views

What is a functional screen?

I was going through this paper, but did not understand a term. What is the meaning of functional screen? (I am not a biology student, I don't understand much, and a small simple explanation would ...
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239 views

Where do the H+ ions come from in light reactions?

In the light-dependent reactions of photosynthesis, H+ ions pass to the thylakoid space. Where do these protons come from?
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300 views

Neomycin resistance gene in E. coli stb3 cells

We use a lentivirus packaging vector called pLenti_puro_DEST. We use puromycin to select for the cloned gene in 293T cells. However, the pLenti_Neo_Dest has been discontinued, so I'm cloning a ...
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33 views

Authority on Microbiological Definitions

Is there an authority on definitions for molecular microbiology concepts, like an IUPAC book for chemical definitions? The particular definition I am debating is chromatin. Some say it encompasses ...
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113 views

Need help in codon optimization

I want to chemically synthesize a GFP gene for expressing in rice.I am using the IDT Codon Optimization program and found that not all the codons are 100% optimized. Some of them are the 2nd or 3rd in ...
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36 views

Gene Sequencing and Plasmapper

Is there anything similar to this in Java (especially the circular map sequencing along with hover effect)? For information I would like to convey that I am using Plasmapper and BioJava for achieving ...
3
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1answer
117 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 ...
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2k views

What is the exact principle of capillary isotachophoresis?

I know it's a type of capillary electrophoresis, but I don't get how does the separation happen exactly.
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88 views

Why not use Cu(OH)2 as a dye for protein electrophoresis?

As I know, $Cu(OH)_2$ $+$ Protein $\rightarrow$ Purple. So why not use $Cu(OH)_2$ as dye in protein electrophoresis?
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1k views

Just how light-sensitive is ethidium bromide?

One lab I was in was paranoid about keeping it in a foil-wrapped conical tube; my current lab leaves it out on the bench (and it works fine for staining gels). It's the same company/concentration in ...
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1answer
1k views

Optogenetics - How do microbial opsins work?

I'm just introduced to the optogenetics method and am having some trouble grasping the genetics (of the optogenteics) part of things. So we have Retinal and Opsin that form Rhodopsin molecule that ...
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1answer
306 views

What are centromeres *really*?

I've gathered that a centromere is a a region* where the DNA is bundles up even tighter (around protein different to Histone) and chromatids are 'joined'. However I'm still mostly in the dark ...
3
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148 views

205 nm UV-Vis readings

Typically we determine the concentration of proteins using a 280 nm reading. However, it is reasonable to use 205 nm. I was curious about the effectiveness of this method.
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22 views

For a recombinant pUC19 plasmid with cut sites at Hind III and EcoO109i, does lactose need to be present for the gene of interest to be expressed?

I am growing E. coli transformed with the plasmid pUC19 with an insert of an enzyme in rat brain between the mentioned cut sites (EcoO109i and HindIII). I have isolated and created the recombinant ...
3
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1answer
88 views

How does a protein reach its substrate within the cell?

After a protein has been synthesized and its the final tertiary/quartenary adopted, how does it reach its substrate within the cell and what causes it to interact with it? The transcription factors ...
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1answer
68 views

Genomic DNA resuspension after ethanol precipitation

I am having trouble resuspending purified human genomic DNA. The genomic DNA is purified using phenol:chlorofom from ~ 1 mL of blood. After ethanol precipitation, I normally see a large pellet which ...
3
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1answer
26 views

How can dopamine modulate synaptic strength?

Does dopamine act on G protein coupled receptor, leading to more Ca2+ channels on the postsynaptic knob? Also, how is the specificity of the location (of the brain) that dopamine acts on controlled? ...
3
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1answer
146 views

In CRISPR bacteria, how does viral genomes get integrated into the spacers of CRISPR? Also, in its use, where does Cas9 cut the DNA?

I've been out of Biology for about a year polishing my programming skills. I know CRISPR/Cas9 allows targeted 'cutting' of DNA via RNA-guidance. Few questions regarding this. Regarding to its ...
3
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1answer
93 views

What is the shortest mRNA the ribosome can read to produce a peptide?

This question came as a comment on a previous question regarding non-ribosomal peptide synthesis, and why Glutathione cannot be synthesized by the ribosome. In general, Glutathione has a "gamma" ...
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46 views

Macrophages and what they consume

Do macrophages in the dermis consume any foreign invader to the body, or simply pathogens and cellular debris? For example, would macrophages consume vitamins or medications injected into the dermal ...
3
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1answer
104 views

DNA length and annealing kinetics

I have a mixture plasmids and undesired short linear fragments that share the same sequences. During denaturation and annealing, I would like the plasmids to 'find each other' before annealing to the ...
3
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3answers
247 views

What physical force attracts the anti-codon on tRNA to the codon on mRNA during translation?

What physical force attracts the anti-codon on tRNA to the codon on mRNA during translation? I know that these two bond together, but what actually makes the tRNA move through the cytoplasm to the ...
3
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1answer
46 views

Why introduction of an extra copy of a gene related to pigmentation causes RNA interference in Petunia?

RNAi became famous after Fire and Mello experiment in C.elegans; however, it had been observed before. In the 80's, Jorgensen was trying to increase pigmentation of Petunia flowers by introducing ...
3
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172 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?
3
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1answer
241 views

Biological meaning/interpretation of clustering coefficience

I have been looking for some time to find an answer to the following question. I would be grateful for any help/advice or directions. I work very frequently with large number of proteins and assess ...
3
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1answer
190 views

Real-time PCR delay in Cq due to insertion SNP in primer

I am collecting evidence, even anecdotal, how does single nucleotide deletion or insertion in primer region affect the outcome of real-time PCR. I am most interested in how much there is a delay in ...
3
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110 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 ...