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

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Does biotin affect downstream experiments, such as RT-qPCR?

I have two biotins--one of which is binding my RNA with cleavable bonds, and the other with irreversible bonds. Does biotin have an effect if it keeps its bonds with RNA? If it does, why is this the ...
5
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1answer
51 views

What method would you use to genotype SNPs in low quality samples?

What method would you use to genotype SNPs in low quality samples? I ideally want to genotype hundreds of SNPs in hundreds of scat samples (very low amount of target DNA, potentially degraded and ...
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1answer
80 views

Should I design a primer to detect virus based on NCBI genebank?

When I searched HIV on NCBI gene bank, I found 2 results from 1997: http://www.ncbi.nlm.nih.gov/genome/?term=HIV. HIV can change every day, so I think the sequence from 1997 is not useful. Is it?
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1answer
84 views

Hardy-Weinberg applied to three alleles and stimation of allele frequencies

I have this equation: Corresponds to HW in equilibria with three alleles: $(p+q+r)^2=1$ Expanding the square results: $p^2+2pq+r^2+2pr+q^2+2qr = 1$ I need to separate homozygous and ...
2
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1answer
54 views

Elution of biotinylated RNA

I am using Neutravidin Agarose beads to isolate biotinylated RNA. The thing is, in the manual it says to use 8M Guanidine-HCl, pH 1.5 for elution biotinylated molecules. As far as I know it is a very ...
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2answers
48 views

What is the impact of prolonged electromagnetic exposure on human health?

What are the health effects of being exposed to a very strong electromagnetic field caused by two resonating superconductive coils (not static magnets) for a period of years?
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1answer
39 views

In vitro transcription, contamination problem

I am using a RNA which is in vitro transcripted before I started my project. It turned out it is not prepared properly and has DNA contamination. Instead of perform the in vitro transcription again, ...
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1answer
37 views

Dilution question about RNA

I have a basic and probably silly question. I am isolating RNA with TRIzol. I have performed the basic steps and dissolved the pellet in 50 uL water. I ve measured the concentration and it was 3313 ...
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20 views

How do you amplify a specific AFLP marker?

I'm trying to clone a specific AFLP marker out of Medicago truncatula. I know the selective bases I need for the end of the primers. My problem is that all the AFLP cloning kits I have found are ...
6
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2answers
613 views

why is AUG the initiation codon?

Is there any reason why AUG is the initiation codon ? Why is there a need for an initiation codon ? Can't translation start with different codons?
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25 views

Do you know a learning by research platform for biology?

I work in a university in Europe and I'm looking for new communities of biology enthusiasts. I'm very interested in the "synthetic biology" field and I'm searching good, innovative, if possible ...
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1answer
63 views

Transcribing DNA to mRNA with introns

I have a problem in my bioinformatics class that I thought I was doing right, but someone else is getting a different answer. Here is the problem: Given the following DNA sequence, ...
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1answer
181 views

Effect of single nucleotide deletion or insertion on primer annealing

How is primer annealing, and, consequently, PCR amplification affected by single nucleotide deletion or insertion inside the primer ? Imagine a primer like this: GCGTCATAAAGGGGACGTG (primer) and ...
3
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1answer
77 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 ...
2
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1answer
46 views

Transition/Transversion ratio

I'm taking a bioinformatics class and at this point we are just going over basic stuff about molecular biology. Half of the class is doing reading/research on our own, so there isn't much class time ...
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5answers
434 views

What is a good miniprep protocol for the class room?

I'm trying to find a good protocol for plasmid minipreps and I'm looking at 3 preps I've found: Using phenol/chloroform extract with phenol:chloroform:isoamylalcohol, isopropanol precipitation, ...
6
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2answers
888 views

Very high 260/230 absorbance ratio of an RNA sample

After my most recent RNA extraction, the RNA samples had very high 260/230 absorbance ratios, (ranging from 5 to 25). I've never gotten numbers like this and I know the ratio is supposed to be ~2 in ...
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3answers
2k views

How long can E. coli stocks be stored at -20°C?

I'm volunteering for a biohacker lab - biocurious in Sunnyvale. The have a pretty good set of equipment - gel boxes, incubators, but they don't have a -80°C freezer yet. I'd like to set up some ...
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0answers
42 views

DNA content in seeds vs. fruit flesh

Is there a publication comparing DNA yield and / or PCR-amplifiability after extraction from fruit flesh (like apples, oranges, cherries etc) in comparison to seeds of the same fruits ? I would prefer ...
5
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1answer
589 views

Difference in length of Okazaki fragments

The length of Okazaki fragments in the lagging strand is about 100-200 nucleotides in eukaryotes and about 1000-2000 nucleotides in prokaryotes. What (molecular mechanism, enzyme type ) ...
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1answer
21 views

Vesicular and non vesicular transport

I have to classify them either as transported in vesicles or without vesicles. What I think - Non-vesicular 2.vesicular 3.vesicular 4.vesicular 5.non-vesicular 6.vesicular 7.vesicular ...
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1answer
51 views

DNA ligase mechanism

I am unable to understand what happens to the phosphates from ATP. What are they used for ?Charging 3' end or 5'end ?
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1answer
74 views

How can Southern blotting be used to establish gene copy number?

I am reading a paper on a certain marine microorganism that can eat alkanes and therefore might be useful for cleaning up oil spills, etc. This sentence struck me as odd (although I am sure that the ...
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0answers
112 views

Can I heat Trizol?

I wonder if I can heat Trizol reagent for 30 min 65C. The goal is to disrupt protein-RNA complex while inhibiting nucleases. (I can't use RNasin cause it's inactivated in 65C, and can't use RVC cause ...
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1answer
110 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 ...
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1answer
328 views

Regulation of chromatin structure

Recently, I reviewed the different levels of chromatin structure. The primary level is nucleosomes, where DNA is bound to histones, and has structural similarity to "beads on a string." The secondary ...
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282 views

What is the functional and structural distinction between core (H2A, H2B, H3,H4) and linker(H1/H5) histones?

Many explanations of histone biochemistry isn't quite elucidating for the undergraduate student. How does histone structure (dimers, octomers) relate to their specific functions as core or linker ...
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1answer
121 views

Histone marks mechanism

I am slightly confused about the mechanisms that makes histone modifications associate with gene expression. That is, H3K36me3 is believed to be present in actively transcribed genes, H3K27me3 in ...
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35 views

How is the number of histones being related to the number of chromosomes [closed]

Please name me at least one reason. I am referring to rats and to humans, as well.
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0answers
57 views

The mechanism of mechanoreception?

I am interested in knowing the molecular mechanism behind mechanoreception/mechanotransduction (i.e. mechanism behind receptor potential generation on mechanical stimulation). I know that most ...
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4answers
793 views

Why we have no enzyme to digest cellulose?

As we know, cellulose is the most abundant polysaccharide in nature. Why don't we have any enzyme to digest cellulose?
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0answers
37 views

What are the lifetimes of cellular components on organelle or molecular level?

I was thinking that even though I know how generally the cell works, I don't really have a feeling of how volatile it is. I want to know what is the lifetime/turnover rate of different constituents of ...
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1answer
37 views

Identifying mutations in a yeast strain

Cells of a triple-mutant yeast strain (leu- his- trp-) were spread either on minimal medium or on minimal medium supplemented with various combinations of histidine, leucine, or tryptophan. The ...
4
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1answer
75 views

poor RNA quality from zebrafish embryos

Does anyone routinely do RNA isolation from zebrafish embryos? I have embryos from different stages but all below 24hpf. This is the protocol I follow: Take 10-20 embryos Wash once with milliQ ...
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2answers
180 views

On which strand does the promoter sit?

My book keeps giving different indicators as to whether the promoters are on the coding or template strand. It says the -35 region in prokaryotes must be on the coding strand. It also mentions, that ...
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1answer
73 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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1answer
327 views

Why is ATP the preferred choice for energy carriers?

Why is ATP the most prevalent form of chemical energy storage and utilization in most cells?
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1answer
63 views

Shine-Dalgarno sequence and expressing proteins

Shine-Dalgarno sequence present in the prokaryotic mRNA plays a role in initiation of translation. In eukaryotes a Shine-Dalgarno like sequence is present but does not play an important role in ...
2
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2answers
39 views

Molecular simulations without capping n- and c-terminus of polypeptide

When running molecular simulations, what is the consequence of not capping the n- and c-terminus? I have been following gromacs tutorials and haven't come across any that deal with capping the ...
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2answers
163 views

How are antibodies designed?

Antibodies have the ability of recognising highly specific peptide sequences and bind it at their antigen-binding site. This ability is harnessed as a tool in research to purify target structures in ...
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0answers
27 views

What is a phospho-protein binding domain?

Is this just a domain that binds proteins that have been phosphorylated? And it mediates signalling between an activated/phosphorylated protein? How is this significant with BRCA1?
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1answer
40 views

Photosynthesis: Splitting Water

The splitting of water is an endergonic (non-spontaneous) reaction, and thus would require energy (chemical work to be done) in order to happen. In Photosystem II, an enzyme catalyzes this splitting, ...
2
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1answer
72 views

Determining sequence of oligoribonucleotide

Oligoribonucleotide X was treated with phosphatase (for removal of 3' and 5' - terminal phosphates), then with RNAase T1, which cleaves all phosphodiester bonds located in a 3' position of ...
6
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2answers
113 views

More variation in proteins than genes. Why?

The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular). How do ...
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1answer
46 views

Clarification of the procedures to amplify cDNA needed

The typical procedure to obtain cDNA from genomic extracted DNA is the following: RNA is extracted from desired tissue, RNA/DNA hybrid is obtained by virtue of reverse transcriptase RNA dependent DNA ...
3
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2answers
72 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?
4
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1answer
118 views

How much does the Hayflick limit/telomere length vary across taxa and within humans?

Since they seem to be quite connected, I'm curious if anyone knows of research comparing the Hayflick limit (and presumably by extension telomere length) between different taxa. I've heard the ...
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2answers
55 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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1answer
48 views

Isoprenoid Diphosphate Concentration in Yeast saccharomyces cerevisiae

Isoprenoid Diphosphate(IPP) is an important metabolites which is precursor in lot of secondary metabolites like Dolichol diphosphate, ubiquinone, prenylated proteins and carotenoid (not synthesized ...
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1answer
41 views

Protein Structure Statistics [closed]

Could you show me references of any works you know of where, 1- they take all the known protein structure data (that is the coordinate data of all the proteins in PDB database lets say or elsewhere) ...