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

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Effect of histidine on the binding affinity of HisP

I was asked the following question by my teacher: A gene regulatory protein called HisP regulates the enzymes for histidine biosynthesis in the bacterium E. Coli. HisP is a protein whoes ...
6
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1answer
114 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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2answers
170 views

Why do mitochondria fuse together?

Contrary to all of the textbook images of mitochondria that I have seen over the years, I had just learned that the mitochondria within a cell form a dynamic branching network along microtubule ...
6
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1answer
87 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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1answer
970 views

How much does the distance between a transcription factor binding site and a promoter influence transcription?

Assume we have a synthetic construct with a minimal (inducible) promoter that requires activation for significant transcription to occur. Realistically, how important is the distance between an ...
6
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3answers
242 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, ...
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2answers
11k views

What's the difference between shotgun sequencing and clone based sequencing?

Whilst I appreciate this is a large topic, what are the main differences between shotgun sequencing and clone based sequencing?
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1answer
929 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?
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1answer
288 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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98 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
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1answer
262 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
965 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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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
428 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
666 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
138 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
682 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 ...
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4answers
114 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 ...
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2answers
209 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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4answers
1k 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
425 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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2answers
14k 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
381 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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2answers
301 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?
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1answer
104 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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463 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 ...
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2answers
187 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 ...
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1answer
3k 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 ...
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1answer
3k 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 ...
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4answers
684 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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1answer
102 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
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1answer
1k 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 ...
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2answers
5k views

What is the difference between transformation and transfection?

What is the difference between transformation and transfection? How do both of these methods work?
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3answers
144 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 ...
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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 ...
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268 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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2answers
142 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
84 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
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1answer
100 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
570 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 ...
5
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1answer
70 views

MHC restricted peptide

What is an MHC restricted peptide? I got this definition from wikipaedia, but cannot exactly extract what the phrase MHC restricted peptide means. MHC-restricted antigen recognition, or MHC ...
5
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1answer
182 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
130 views

What are some atypical examples of positive transcriptional cooperativity?

Cooperativity in gene expression is an important feature of many regulatory networks. Described using the Hill function, the most common example is a transcription factor (TF) that when bound to its ...
5
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1answer
176 views

Synthetic construct with multiple ORFs not expressing

I designed a synthetic construct on paper and got it synthesized from a company. The objective was to make a vector which can be used to study both transcriptional and post-transcriptional regulation ...
5
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2answers
2k views

Is wiping with RNAse Zap enough to destroy RNAse activity?

From the RNAseZap MSDS, it is an SDS at some unknown concentration, maybe with some NaOH? Some other links suggest there is some NaOH as well. The Ambion site states that RNAseZap destroys RNAse ...
5
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1answer
260 views

What is the extent of the effect of Tris on E. coli?

I was a fool and dissolved my antibiotic (Kanamycin) into Tris Buffer rather than H₂O. The Kanamycin still seems to be active but a fellow labmate mentioned that Tris messes around with the membrane ...
5
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1answer
247 views

Why is E.coli used as a model?

Is there a reason for the choice of E.coli as a model for many bacterial systems? Other bacteria such as B.subtilis are also used, but why is E. coli preferred?
5
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1answer
254 views

Western blotting with multiple antibodies

Normally I wash/detect with one primary/secondary-HRP antibody pair, strip, then wash/detect with the other primary/secondary-HRP pair which works well. However, I recently started working with a ...
5
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1answer
84 views

What is Colloidal biology and does it have any scientific background?

There is the following bulletin published for the History of Chemistry Vol. 32: 105-118 in 2007: “MOLECULAR” VERSUS “COLLOIDAL”: CONTROVERSIES IN BIOLOGY AND BIOCHEMISTRY, 1900–1940* written by PhD ...