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

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43 views

Is galvinoxyl antioxidant assay possible using NMR spectroscopy?

I would like to perform an antioxidant assay using the galvinoxyl protocol. The protocol states that we need EPR spectroscopy, but only NMR spectroscopy is available at my institution. Is there an ...
4
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1answer
127 views

How small does a nanobot have to be to “swim through the brain” and access any neuron it wants to?

I read on this question What is in the space between neurons in a brain? that there is actually not much empty space in a brain. But my question is slightly different. Is there a visual demonstration ...
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0answers
26 views

Can mutation rate be increased for instance by mutagenesis targeting the DNA polymerase?

I am studying a non-cultivable bacterium living in an insect host, and I would like to generate some random mutants of this bacteria while preserving the insect. I am wondering if one way to do so ...
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2answers
1k views

Why is the DNA helix anti-parallel? [duplicate]

Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.
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0answers
93 views

How can we determine the polarity of fat molecules?

I'm trying to solve a question in a biochemistry quiz, which is asking for classifying a set of lipidic derivatives, by increasing polarity. Unfortunately, we didn't cover the classification of ...
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0answers
247 views

How much salt [NaCl] is too much in DNA precipitation?

In DNA extractions, how much is too much salt in a CTAB extraction buffer? Protocols hover around 2.5 molar; if you go over this (e.g. 25 molar), will you saturate your solution, and precipitate the ...
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1answer
61 views

How to synthesize and isolate single stranded cDNA from an RNA template?

I would like to have pure single stranded cDNA of my choice. I am thinking of reverse transcription from RNA (obtained by in vitro transcription), degrading RNA from RNA-DNA hybrid with RNase-H, ...
2
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0answers
31 views

BSA for trouble shooting failed PCRs?

I am using PCR to amplify a 1000bp region of the CytB mt gene. Some of the samples had not amplified and I wish to change the reaction components (or use additives like BSA) to attempt at getting ...
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1answer
31 views

How is Glycophorin A and straphylococcal related to Escherichia coli and what does readily purified mean in this context?

I am reviewing the paper "Glycophorin A Dimerization Is Driven by Specific Interactions between Transmembrane Alpha-Helices." There is a statement in the abstract which I don't understand: "The ...
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0answers
90 views

L-tryptophan in mammalian cell culture

Why must the concentration of L-tryptophan be kept to a relatively low level when culturing mammalian cells? It's an essential amino acid, so I cannot fathom why low concentrations as opposed to ...
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1answer
42 views

Is there a good site or software to see if a primer pair spans an exon junction?

I am going to perform some RT-qPCR tests to validate an experiment.  I'm currently in the process of ordering primers, and I would like to get them from the Harvard Primer Bank since these have been ...
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0answers
28 views

Is a Ribonuclease Inhibitor protein the only mechanism employed by the human cell to protect cellular RNA from degradation by endoribonuclease?

Are there any other methods of protection for cellular RNA from degradation by endonuclease (specifically the Pancreatic Ribonuclease RNase II (Eosinophil-derived neurotoxin) and RNase III (Eosinophil ...
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3answers
6k views

Why is the number of PCR cycles limited?

I've been told that the maximum number of cycles in PCR is between 20 and 30. Is this true, and what are the reasons for this limitation?
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1answer
178 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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1answer
86 views

Is nuclear DNA immuno-privileged?

It is well known that if DNA occurs in the cytoplasm of eukaryotic cells, an immune response may be triggered through a myriad of DNA receptors and pathways as part of the immuno response. Yet, ...
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1answer
106 views

Specific numbers of nucleotides in Okazaki fragments

Okazaki fragments are formed during replication of the lagging DNA strand. What determines the length of these fragments?
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26 views

What is the lifetime of the vasopressin receptor V2?

I was looking at the production of vasopressin receptor 2, also known as V2R or ADH-R. What I found is that it is coded by the AVPR2 gene and degraded by the Alix protein (source). But I did not get ...
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1answer
36 views

Finding a reaction from a KEGG map

I have come across a map and a part of it looks like this: Now I have not been able to locate the reaction that converts alpha D-Glucose to Glucono-1,5-lactone but was successfully able to locate ...
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1answer
1k views

How to secrete a recombinant protein from E. coli?

What are some secretory pathways that can be used to secrete a recombinant bacterial enzyme from E. coli? I have a recombinant protein (29kDa) that I will express in E. coli BL21 cells. For now I ...
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0answers
17 views

What is the effect of the RNA 2' OH group on its structure and stability? [duplicate]

I've read that the 2'-hydroxyl group plays "fundamental roles" in both the structure and the function of RNA, and that it is a major difference between RNA and DNA. I would like to know more ...
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2answers
253 views

How to Extract RNA and perform RT-qPCR from very few cells ( ~5,000)?

I am currently conducting an experiment which involves FACS-sorting a specific population of cells using an antibody of interest. In order to validate the type of cells I have collected using this ...
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2answers
570 views

Does ATP hydrolysis reaction have a high or low activation energy?

I was recently studying about ATP and how it functions as an energy carrier to all biological processes; however, I came across a confusing and paradoxical statement from two sources: (at 7:36) and ...
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2answers
201 views

What happens when we re-start a PCR reaction?

Recently when my PCR reaction was running there was power fluctuation and the entire lab was blacked out for a few minutes and unfortunately PCR that I was running got switched off. So, would it be ...
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1answer
31 views

Presence of reaction module in bacteria but not in Eukaryotas (human)

From the statistics page, I found that the Module-M00008 is present only in bacteria and not Eukaryotes. Why so? I noticed that all the compounds necessary or the reaction are present in human body ...
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1answer
110 views

shRNA knockdown not showing with Western

I've recently been performing shRNA transfections and was hoping to get some advice on why I'm not seeing any knockdown via western blot I transfected by MDAMB468 breast cancer cell lines with shRNA ...
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1answer
19 views

What information does the KEGG Module statistics page show?

While browsing through the home page of KEGG Module, I clicked the button named Module statistics. Can someone tell me what does these numbers signify? What are they the statistics of?
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1answer
57 views

What happens to IP3 molecules after release from IP3 receptors?

IP3 molecules bind to IP3 receptors and open up the calcium channels on the endoplasmic reticulum. I am wondering what happens to IP3 molecules after they have been released from the IP3 receptor? Do ...
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1answer
66 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 ...
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1answer
132 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
73 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 ...
2
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1answer
88 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 ...
6
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1answer
300 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
160 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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1answer
459 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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3answers
689 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 ...
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2answers
143 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" ...
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1answer
62 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 ...
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1answer
49 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
247 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
180 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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2answers
28k 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
141 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 ...
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1answer
39 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
220 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
85 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 ...
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1answer
104 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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0answers
54 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
157 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 ...
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1answer
129 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 ...
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0answers
316 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 ...