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

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935 views

Reverse transcription PCR optimization

What is the ideal amount of RNA to use for the RT? and how much cDNA to use then for the PCR? I did RT with a solution of RNA of 0.36 ug/ul. Then for my PCR I used 1 ul of the cDNA obtained and used ...
6
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3answers
752 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 ...
6
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2answers
2k views

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 ...
6
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2answers
123 views

DAM enzyme distances move along the genome

I am fusing a protein with a Dam enzyme (http://en.wikipedia.org/wiki/Dam_(methylase)). The idea is that when the protein binds to the DNA, the Dam enzyme will start methylating nearby GATC sites, ...
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2answers
66 views

Can molecular genetics make a boolean variable from a continuous variable?

In the same kind of idea than this question. Gene expression are regulated through complex interactions. The concentration of enhancers and repressors is an important aspect that dictate the level of ...
6
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1answer
212 views

Why do some bacteria have most genes on the leading strand of the genome?

Genes in the (+) strand are black and genes in the (-)strand are red. The gene distribution in E. coli genome is somewhat expected: transcribed regions would tend to alternate with non transcribed ...
6
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2answers
447 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 ...
6
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1answer
5k views

What causes the colors we see in eyes?

Genetics aside, what are the biochemical reasons the different colours of human irises? Also, related, how does eye colour change, particularly in childhood? (example: my eyes used to be blue, ...
6
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1answer
371 views

Why does not the host produce any immune response to antiserum antibodies?

When an antiserum is injected to a person to protect oneself from a certain disease, the antibodies in the antiserum come from another organism. The question is: Why don't the injected antibodies ...
6
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3answers
136 views

Hebbian theory “fire together” clarification

Donald Hebb states it as follows: "Let us assume that the persistence or repetition of a reverberatory activity (or "trace") tends to induce lasting cellular changes that add to its stability.… ...
6
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1answer
233 views

What's the state of the art in designing and creating your own life forms?

What's the state of the art for solving the following problem. You imagine a set of features that you want a life-form to have. Just to take an arbitrary example, say you want your life-form to have ...
6
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1answer
140 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 ...
6
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1answer
94 views

What regulates the timing of the motion of molecular machines during DNA Replication?

This question is about this video I found on Youtube. I just want to know what is the mechanism which regulates the timing of motion of the parts of these molecular machines. I know that those big ...
6
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3answers
252 views

What does it mean for a distribution to be “consistent with a two rate-limiting stochastic steps”?

I'm reading a study (full text here) that examine the dynamic of nuclear translocation of a transcription factor in budding yeast, in response of calcium stress. They found that it occurs in bursts, ...
6
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1answer
977 views

Does anyone have any TOPO directional cloning tips? [closed]

I'm just about to start working on a TOPO cloning after I couldn't get it to work with standard restriction/ligation. Does anyone have any tips for TOPO cloning?
6
votes
1answer
303 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 ...
6
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1answer
104 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 ...
6
votes
1answer
265 views

In C. elegans, why does knock-down of cco-1 in some tissues increase lifespan, and knock-down of cco-1 in other tissues decrease lifespan?

Full question: In C. elegans, why does knock-down of cco-1 via RNA interference in specific tissues like body wall muscle decreases life span, whereas knock-down in the nervous system and intestine ...
6
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1answer
1k 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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2answers
3k 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 ...
6
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1answer
667 views

Why do most organisms have negative supercoiled DNA?

It has been observed that in nature most organisms have negative supercoiled DNA and that few organisms have positive supercoiled DNA. Some of the organisms that have the positive supercoiled DNA live ...
6
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1answer
734 views

How does Topoisomerase II inhibition affect cancer cells?

Topoisomerase II poisons represent some of the most important and widely prescribed anticancer drugs currently in clinical use. These drugs encompass a diverse group of natural and synthetic ...
6
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1answer
147 views

Bicoid regulation of hunchback

I'm learning about development via the example of Drosophila embryogenesis. I understand that bicoid regulates hunchback, among other genes. My question whether the regulation is direct or indirect? ...
6
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1answer
772 views

How Do Adherent Cells In Culture Attach To A Plastic Dish?

I am particularly interested in MC3T3-E1 cells (mouse fibroblasts), which are adherent cells. Are hemidesmosomes involved in anchoring the cells to the plastic dish? What (if any) other molecules are ...
6
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4answers
140 views

Enzymatic error rate

I am aware that each enzyme generate a certain amount of misproducts. This is well documented, for example, for the DNA polymerase. I am interested in enzyme involved in biochemical processes, so for ...
5
votes
4answers
2k views

What is SDS PAGE gel polymerization time?

I am working on 20% SDS PAGE. I want to know optimum polymerization time for 20% resolving gel and 6% stacking gel. If I increase the time then would it affect the band pattern?
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5answers
458 views

What is the lowest common denominator of cancer?

What is the lowest level attribute that all cancers share? Also, what is the highest level attributes that all cancers share?
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3answers
1k views

How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids?

How many different kinds of polypeptides, each composed of 12 amino acids, could be synthesized using the 20 common amino acids? The book's answer is $20^{12}$. However, I disagree. This result ...
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2answers
17k views

DNA as an acid? [duplicate]

Possible Duplicate: Does DNA react in all of the ways most other acids do? Even if DNA is made up of nucleotide bases, it is said to be an acid. Why is this?
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3answers
408 views

In what sense is the “histone code” a code?

Since I started learning about molecular cell biology, I have witnessed an increasing amount of attention to this thing called a "histone code." However, unlike the central dogma of molecular cell ...
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1answer
2k views

How to avoid air bubbles while pipetting?

I get air bubbles while pipetting small volumes. How can I avoid them ?
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4answers
1k views

Photosynthesis: What Powers the Splitting of 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, ...
5
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2answers
336 views

Can PCR tubes be made of different materials than plastic?

Does it matter if I replace the PCR tube (usually made of plastic) with another material like aluminum, glass, or something similar?
5
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1answer
107 views

What are the different ways an exon gets spliced?

Exons are produced by more than one mechanism, e.g. splicing out introns after transcription, if I remember correctly. Please list all mechanisms.
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2answers
482 views

Evolution of endosymbionts?

Mitochondria and plastids in eukaryotes evolved through a process of endosymbiosis. How does an event like a eukaryote engulfing a bacteria, become a part of the genome? Some of these primitive ...
5
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2answers
217 views

The meaning of RNA-seq data

many papers I read mentioned "RNA-seq data". While searching for the meaning of this word, I could not find any layman's definition. As far as I understand, RNA-seq data is the complete RNA ...
5
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1answer
6k views

Why does high pH result in the denaturation of DNA?

In the Southern blot method, for example, a solution of NaOH is used to denature the DNA in the sample. I find this counterintuitive since I expected that $\text{Na}^+$ cations would neutralize the ...
5
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1answer
4k views

What is the definition of a stringent/relaxed plasmid?

I have found a publication which proposes some definitions, including a definition for strict and relaxed replication. The definitions are: Relaxed control of plasmid replication. Relaxed control ...
5
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1answer
137 views

Is it possible to express a mutant gene only in a specific tissue?

Imagine that someone tries to develop a knockout mouse for a gene, but this result in lethality for the homozygous. Is it possible to express that mutant gene only in a specific tissue of interest to ...
5
votes
1answer
2k views

What is our skin made up of?

Again, it is a basic question. What is our skin made up of? is it made up of many cells arranged in a systematic way or is it just like any layer say of a book?? what is the difference? where is the ...
5
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3answers
147 views

Finding a template/oligo combination for my first PCR experiment

I'm an information technology engineer. I love biology so I research biological topics and have an interest in PCR. That's why I have decided to create a PCR machine. Everything is done now and I ...
5
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2answers
3k views

Primer design for introduction of restriction sites flanking a gene of interest

I am wondering what the correct method for primer design to introduce restriction sites. Specifically between two methods. 1) Primer first partially hybridises to the gene, has a mis-match where the ...
5
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2answers
328 views

What is the IC50 exactly?

I am reading the paper "Activity of the bcr-abl kinase inhibitor PD180970" but I don't understand how IC50 works on table 1. Can you tell with simple words and give me an easy example?
5
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1answer
195 views

High frequency human genetic oscillators?

The most well studied genetic oscillators in human genomes are involved in regulating the circadian clock (which operates on an approximately 24-hour cycle) and cell cycle activity (with single cycles ...
5
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2answers
150 views

There are linear and rotary molecular motors in the cells. Do any of them have a fixed or stable frequency or speed?

Are there any linear, rotary or oscillatory molecular motors in the cells which can have fixed frequeny and which can be used as a reference for elapsed time timer? This question is with relevence to ...
5
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1answer
44 views

Do two compatible tRNA codons bond together?

Can two tRNA with complementary anti-codons link together? For instance UUU with AAA. If not, why not?
5
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1answer
129 views

How is adrenaline a ligand?

I keep reading that adrenaline is a ligand, however from what I understand a ligand is a molecule or ion which donates a pair of electrons to a central transition metal ion in a complex. How then is ...
5
votes
2answers
662 views

How does optogenetics work?

I am aware of the post here 'Optogenetics - How do microbial opsins work?' however it is a bit too technical for me. I am struggling to understand how the neurons can be genetically engineered to ...
5
votes
1answer
119 views

what does Pro→Glu substitution mean?

Considering the paper: A single amino acid in E-cadherin responsible for host specificity towards the human pathogen Listeria monocytogenes in the abstract portion, what does Pro→Glu mean? Does it ...
5
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1answer
849 views

Restriction Mapping - Homework question

I have trouble in solving this exercise. Exercise A circular plasmid of 10,000 base pairs (bp) is digested with two restriction enzymes,A and B, to produce a 3000 bp and a 2000 bp bands when ...