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

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41 views

Plasmid gene knockout

How do delete a single gene encoded in an operon on a plasmid using E. coli? Could you use the same principle as when knocking out a gene from the bacterial chromosome which is e.g. suicide ...
6
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2answers
142 views

How does LCR compare to Assembly PCR

The question pretty much explains itself. How do the two methods compare? I've always used Assembly PCR but the method is prone to mistakes and I'm curious how it compares to Ligase Chain Reaction ...
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0answers
14 views

MIN 6 cell culture [on hold]

I am trying to culture MIN 6 cell line. After one passage and about 5 to 8 days later the cells show round morphology,however I did not found any linkage between them they look all apart from one ...
6
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1answer
54 views

What is the biochemical explanation for tingling and burning sensation in brain due to certain food?

Consumption of mustard (spicy English Mustard), wasabi and horseradish based food dressings usually result in a burning, tingling or freezing sensation in the brain/scalp and nostrils as the vapour ...
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0answers
62 views

Why do some medicines induce sleep? [closed]

I have seen lot of people sleep or say that they are feeling sleepy after taking some medicines. Why? I mean, if a medicine acts on some cell of the body because that cell has got its receptors and ...
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1answer
52 views

Why does my anti-ubiquitin antibody visualization not work on my PAGE gel?

I am using 2D gel electrophoresis to visualize polyubiquitinated proteins. However, while I can see actin and heat shock protein using when appropriate antibodies, I cannot visualize them using ...
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0answers
10 views

What is the concentration of leptin in white adipose tissue in mice? [closed]

I am trying to perform an ELISA experiment and for this I need to know the physiological concentration of the hormone leptin in white adipose tissue in mice.
6
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1answer
256 views

How bad is ethidium bromide in your plasmid for downstream applications?

I want to transfect Adipose Derived stem cells using a clone of my own. My problem is that I get a lot of contamination (not only genomic, but due to the nature of the technique, I get undesired ...
3
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1answer
111 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
208 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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0answers
48 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?
6
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3answers
61 views

Mutation That Loses Stop Codon

Someone asked this in my class and my instructor wasn't sure in her answer, doesn't anyone know what happens in protein synthesis if a mutation causes mRNA to not possess a stop codon? Would the ...
4
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2answers
64 views

Does suffocation pain involve nociceptors?

I never suffocated myself so not entirely sure, but when you suffocate, it's painful, right? But of course different kind of pain than being injured or sick. What I'm wondering is, if the "painful" ...
3
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1answer
107 views

Restriction sites

I would like to know: how many restriction sites does a restriction enzyme use on a DNA molecule? In other words: If a sequence on a plasmid contains the following bases: ATTGCAGTCTG and I want ...
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1answer
40 views

What is a selectively neutral genotypic change?

I am reading the paper "Neutral evolution of mutational robustness". Because I am new to neutral evolution, I have a few questions. Firstly, from my understanding, genotypic neutrality means the ...
3
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1answer
39 views

What makes a strong polyadenylation signal a strong signal?

I was wondering why is it that "AAUAAA" is a strong Polyadenylation signal whereas the rest of the polyadenylation signals show reduced cleavage and polyadenylation efficiency?
3
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2answers
51 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 ...
4
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1answer
33 views

Why do some protocols require prewarming a liquid medium before inoculating?

For example, in this protocol for E. coli competent cell preparation, it says: Plate 10 uL E. coli BL21(DE3) cells on a LB-agar plate; incubate overnight (12 hours). Prepare 500 mL SOB medium ...
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3answers
21k views

Why is SOC medium recommended for transformations?

In pretty much every transformation protocol I've seen SOC medium is used to grow the bacteria for a short while after the tranformation and before plating. I've usually substituted LB medium for ...
3
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0answers
31 views

Can I leave BL21(DE3) cells in room temperature?

I am preparing competent cells, and I finished inoculating a single colony in SOB. It has been incubating at 37 degrees Celsius for almost 16 hours since, and it's getting very late where I live. I ...
1
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1answer
27 views

specific numbers of neucleotides in okazaki fragments

Why there is specific number of nucleotides in okazaki fragments...? Okazaki fragments are form in lagging strand during the process of DNA replication.
2
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1answer
30 views

Workspace preparation and cleanup for DNA work [duplicate]

What steps should be taken in a molecular lab environment to help ensure that DNA samples/stocks are not contaminated, or contaminate other objects in the lab?
3
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3answers
67 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
58 views

Walk me through microsatellite markers and PCR

Three polymorph microsatellite markers are used to try and narrow down the location of a disease locus, with the use of PCR with 2 flanks on each side of the actual polymorphic area. The PCR ...
4
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1answer
94 views

Do mitochondria use ATP in order make another ATP from glucose?

Do mitochondria use ATP in order make another ATP from glucose, or does it use another source of energy to convert glucose to ATP?
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27 views

Primer heterodimer problem

I design my primers in Primer3PLUS and analyze them in Oligoanalyzer3.1, A big problem that I have this is that I got very nice output in NCBI-Primer BLAST for their specificity but a very negative ΔG ...
3
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1answer
48 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 ...
1
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1answer
120 views

Hypothetically, what is the smallest functional form of human?

Since the my first encounter with doraemon manga, I've been wondering many things, one of them is the small light. Assuming we had an instrument, such as small light, which enabled people to grow and ...
3
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69 views

E. coli not growing in liquid medium

We are regularly doing bacterial transformation and subculture from plate to liquid media to extract DNA. This usually goes very well and is straightforward, but occasionally, the colonies that grew ...
3
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3answers
49 views

Looking for good reference book in molecular biology [closed]

I am starting to work in molecular biology/ molecular genetic and I am looking for a really good book containing the main concepts and mostly the more recent techniques. I would be interested in a ...
2
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1answer
59 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 ...
4
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2answers
92 views

What are the “minimum requirements” for a single cell?

I saw a description of the "minimum requirements" for a cell at http://creation.com/origin-of-life in the section called "What are the minimum requirements for a cell to live?" and I'm wondering if ...
2
votes
1answer
28 views

Why does the inhibition of translation initiation cause the accumulation of 80S ribosomal monosomes?

As I have read in (1), inhibition of translation initiation will increase the number of 80S ribosomes while decreasing the fraction of polysomes due to the polysome-runoff. The net effect is to ...
2
votes
1answer
21 views

What is the protein sequence taken as input in the Path-A prediction system

Considering the Path-A based metabolic pathway prediction (http://nar.oxfordjournals.org/content/34/suppl_2/W714.short). It uses machine learning for pathway prediction. Suppose that the input was a ...
6
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1answer
224 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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0answers
50 views

Recommend any Molecular lab LIMS (Laboratory Information Management System)

We are looking to develop or customize a LIMS for our molecular lab. Do you know of a LIMS that you've used in a molecular lab before, or one that could be used. Thanks for the help (Edit) Some of ...
7
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2answers
219 views

What is the difference between sequence, reads, and contigs of genetic material?

Can someone explain the differences between sequence, reads, and contigs of genetic material such as DNA, if possible with an example? I am new to bioinformatics, and I have not found any conclusive ...
12
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2answers
94 views

How can we predict protein folding in silico?

Currently, there is a lot of research focused on solving the folding patterns of proteins using computers (Folding@Home, https://fold.it/portal/, etc.). The question that I have is: How do you know ...
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1answer
32 views

How is cancer associated with host pathogen interaction?

Does cancer by any chance fall under host pathogen interaction domain? What I mean to ask is that, is there pathogen interaction involved in cancer? I went through this article: ...
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0answers
23 views

Does blood typing still provide a use for ancient tissue analysis?

Modern techniques. In recent years, DNA sequencing has become extremely cheap. This, compounded by the ability to PCR miniscule samples to viable samples for analysis, means that aDNA can be ...
2
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2answers
42 views

How can 3' end polyadenylation protect cellular RNA from ribonuclease degridation?

In this link, it states: It is worth noting that all intracellular RNAs are protected from RNase activity by a number of strategies including 5' end capping, 3' end polyadenylation, and folding ...
7
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1answer
67 views

Double stranded nucleic acids are more 'durable' than single stranded nucleic acids?

I'm struggling with a question I've been asked. "Why is double stranded genetic material more 'durable' than single stranded one?" I know that double stranded genetic material is more stable due to ...
0
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1answer
27 views

What is meant by clonal isolates?

With respect to this website: http://horfdb.dfci.harvard.edu/ what does the term clonal isolates mean?
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0answers
55 views

Storing Taqman plates with polymerase in fridge before running

I'm going to be running some Taqman assays on cDNA generated from RNA collected from various samples, and will end up running a bunch of plates (right now the setup is 1/2 a plate per sample, ...
2
votes
1answer
26 views

Which is the guideline to choose a molecular target to identify vertebrate hosts from arthropod bloodmeals?

There are some molecular targets to identify vertebrate hosts from arthropod bloodmeals including the Cyt b gene and the COI gene. Which are the standards or characteristics that I have to bear in ...
8
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2answers
27k views

What is the function of the RNA primer in DNA replication?

During DNA replication, RNA primase puts an RNA primer in the lagging strand. What is the function of this RNA primer? Why can't the enzymes put DNA fragments directly?
3
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2answers
38 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 ...
1
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0answers
27 views

What will happen to transcription if histone acetyltransferases are removed from a eukaryotic cell?

If HATs are destroyed in a eukaryotic cell, how will gene expression level be affected? Will all gene expression be affected or just be slowed down and most gene will still be expressed?
0
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1answer
35 views

(Genetics) Is a silencer the same as gene silencing (heterochromatin)?

Is silencer the same as gene silencing? I know that gene silencing refers to those heterochromatin concentrated at the telomeres or centromere. It is also related to methylation. But what about a ...
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2answers
6k views

Why is PEG important for efficient yeast transformation?

One way to do an yeast transformation is by using lithium acetate, a single-stranded carrier DNA, and PEG (1). I was wondering why is the polyethylene glycol important for the efficient ...