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

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3
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2answers
81 views

Is “A” inhibiting “B” and vice-versa, a positive feedback loop?

If product A inhibits the expression of product B, and product B inhibits the expression of product A, is this a positive feedback loop? My thinking was to consider the scenario that A starts off ...
1
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2answers
72 views

Why is DNA Shuffling more efficient than Point Mutation?

In a related post on Biology-SE the following insightful comment was made: The advantage of DNA shuffling over introducing single mutations is that you have to screen fewer mutants and the ...
0
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1answer
27 views

Random Mutagenesis vs Directed Evolution as Strategies to boost expression

Do people use random mutagenesis (say using UV) to generate host variants that have high expression of a metabolite / enzyme? I've seen it mentioned as a strategy but it confuses me as to why. How ...
3
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1answer
80 views

Does size matter?

As I compare the morphologic differences between mouse models and the human disease for which they are analogous, I have become interested in what difference interspecies size has on molecular ...
1
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1answer
31 views

Difference between pulse coupling and diffusive coupling In biological oscillators

What are the differences between pulse coupling found among neuron cells and diffusive coupling found in cells that exhibit calcium waves? Moreover, in both methods, is it a strict requirement that ...
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0answers
18 views

Transgenic zebrafish: what are some reasons for the constructs not working?

My Master's project is about generating some zebrafish transgenic lines and for that purpose I've cloned 2 new constructs, taking the promoter from a pre-existing plasmid and the vector backbone (...
4
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1answer
60 views

Directed evolution: Point mutation vs Insertion-Deletion vs Shuffling

When attempting enzyme function improvement via Directed Evolution I can see three different strategies to generating variation for the gene sequence: Point mutations Insertion / Deletions Shuffling ...
0
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0answers
8 views

What is the role of Glycine in SDS-PAGE [duplicate]

We are using glycine in SDS-PAGE running buffer. What does it actually do? I found out that it maintains the pH and prevents sample damage. Does it play any other role and can it have any alternative?
0
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0answers
4 views

Plant symbiosis, alternative regulation pathways to AON and miRNA399?

I am currently studying systemic repression of both arbuscular mycorrhizae and nitrogen fixing bacteria in legumes. I know of the AON pathway (which works through CLE and NARK). I also know of ...
1
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2answers
65 views

Are there proteins that stabilize mRNA:RNA polymerase or mRNA:ribosome complex?

Actinomycetes are known for their ability to produce rich variety of natural products, and particularly, polyketides. Many of the genes that encode the biosynthetic pathways are pretty big, as they ...
1
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1answer
41 views

Yeast Strain with squalene synthase / farnesyltransferase (ERG9) gene deleted

I was interested in obtaining a yeast strain without the enzyme farnesyltransferase (Which catalyses conversion of FPP to Squalene). The Euroscraf database has thousands of yeast strains with ...
3
votes
1answer
60 views

Genomic DNA resuspension after ethanol precipitation

I am having trouble resuspending purified human genomic DNA. The genomic DNA is purified using phenol:chlorofom from ~ 1 mL of blood. After ethanol precipitation, I normally see a large pellet which ...
1
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2answers
49 views

difference between transcriptional activator and general transcription factors?

What is the difference between transcriptional activator and general transcription factors? Are they same or different, and do the transcriptional activators first attract general transcription ...
1
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0answers
65 views

Genomic DNA extraction protocol by salting out with NaCl, how to improve yield

In these papers A rapid non-enzymatic method for the preparation of HMW DNA from blood for RFLP studies A simple salting out procedure for extracting DNA from human nucleated cells Modified salting-...
4
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1answer
38 views

How much time do the different mechanisms of gene regulation need to take effect?

I am thinking of the major regulatory mechanisms, like general transcription factors, activators, repressors, and RNA interference. If non-active regulator genes using each of the different ...
4
votes
2answers
85 views

How to safely conserve my current DNA methylation marks?

I read the Wikipedia article on DNA methylation Let's say I want to extract and then stock my current DNA methylation marks somewhere so that I can use it safely 20 years in the future for a medical ...
4
votes
1answer
48 views

A good software for agent based modelling?

Hello i'm gonna start my master degree in systems biology and i'm thinking of working with agent based modelling, but i really don´t know which platform can be the best to simulate interactions ...
1
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1answer
19 views

When should you use a stringent plasmid

I was wondering if anyone had good examples of when you would want to use a stringent plasmid vs a relaxed plasmid in a research setting. Thanks
0
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0answers
29 views

Do any gaps in DNA during cell division (meiosis in particular) lead to crossover?

I have some gaps in the knowledge abour crossover. I know, that crossover is connected with reparation process. I'd like to know if all gaps in chromosomes lead to crossover (reparation based on 2d ...
7
votes
1answer
56 views

Does copper exacerbate wounds?

There is a three edged stiletto (weapon, not shoe) with a triangular cross-section that is often touted as being "extra dangerous" because of the triangular puncture it makes, and its copper ...
5
votes
1answer
81 views

Can difference in the expression potential of alleles lead to dominance?

Several hour ago I was in thoughts what allele dominance really means on molecular level. As we know from basic genetics, if the organism had Aa type of some gene ...
0
votes
1answer
33 views

Why do RNAi pathway proteins exist in the nematode when they can cause them harm?

When dsRNA is injected in plant, Dicer cuts it and prevents disease. Why would the plant parasite, M. incognita - a nematode, die when dsRNA was injected in it? It should have saved it. Again, to be ...
0
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0answers
28 views

Artificial Synthesis of Animal Cells

If we know the elements with which a certain type of cell is composed of (I am particularly talking about Animals, and Humans more importantly), why aren't we able to make cells on our own then, in a ...
1
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0answers
29 views

UV light-induced mutagenesis during gel extraction

this is a very short question I did not find the answer for online, neither on this nor other fora. At the beginning of my cloning protocol, I extracted the band with the sequence of interest directly ...
1
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1answer
78 views

Goodwin oscillator explained

Hello I have been reading papers about the Goodwin oscillator and I found that the equations are kind of tricky. Specially the part of the hill coefficient. In his paper "An entrainment model for ...
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0answers
17 views

de novo gene synthesis vs cDNA library creation from plant RNA: Pros & Cons

What are the relative pros & cons of the following two approaches when one wants to insert a known, sequenced plant gene into a target host organism: de novo gene synthesis vs plant matter ...
1
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1answer
52 views

What are the problems in using an ssDNA or an mRNA for expression instead of using a plasmid?

Let's say you want to do a gene cloning experiment. You have an empty expression vector (mRNA or DNA) and are looking to clone some gene X into it. Why is it you can only buy X already inside a vector ...
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1answer
57 views

How RNA primer on leading strand is removed during DNA replication and how the gap is filled? [closed]

Please can you explain me how the gap created by the removal of primer on 5'-3' leading strand is filled.
0
votes
1answer
27 views

Synthesis of an additional DNA in Pachytene and Zygotene [closed]

I've read, that in Pachytene and Zygotene additional DNA material is synthesized, about 0,3, 0,1% respectively. Why is it so?
2
votes
1answer
87 views

Techniques to show a protein heterodimer-DNA interaction

It is known that c-Jun and fos dimerize to form AP1 factor that binds to a sequence on DNA containing PyPuGACGTCNNNNGAGGTCPyPU. In esophageal cancer cell lines there is no expression of the fos gene. ...
3
votes
1answer
74 views

Why does Taq polymerase add 3' adenine overhangs?

Is there a mechanism for the preference of Taq polymerase to add a non-templated 3' adenine (overhang) instead of other bases?
3
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0answers
37 views

Are all genes transcribed in differentiated cells?

My textbook tells me that it’s specific transcription factors that allow for a different set of genes to be expressed in different cells (differential gene expression). My book gives the example of ...
1
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1answer
38 views

does life make or break?

Ok, this question seems like it may be impossible to answer, but would be interesting to see if anyone has an idea. Throughout the course of a human life, do we make more molecular bonds than we ...
1
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1answer
19 views

Molecules, Targets and Isoforms

I have a question. Given a molecule A and two isoforms of a gene X, Y, and the knowledge that A targets X. Can I infere from this anything about whether A targets Y? As a motivation think about ...
0
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0answers
10 views

Are there in biololy specific QM-phenomena which are necessary for their processes?

Of course QM should be every where, because that is how nature is. But for example if you take the fusionprocess of our sun it appears that the sun wouldn't give any heat and light without making use ...
1
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1answer
113 views

An experiment to test if a bacterial resistance gene is on the plasmid or chromosome?

So I have an E.coli strain phenotypicall resistant to the antibiotics ampicillin and rifampicin. How do I test if the AmpR gene is carried on a plasmid and not on the chromosome? In summary, I ...
4
votes
0answers
35 views

Artificial reduction of NADP into NADPH by means of an electrical current

I've recently been attempting to artificially drive the formation of NADPH via the NADP reduction mechanism utilized by Ferredoxin-NADP Reductase in the Light-Dependent Reactions of Photosynthesis in ...
10
votes
1answer
348 views

Restriction enzymes, how are the recognition sequences determined?

How were the recognition sequences (e.g. GAATTC of EcoRI, GGATCC of BamHI) characterised? Text books only list the recognition ...
2
votes
1answer
50 views

Why does protein kinase C activated by different means have different effects?

I could be way off base but I think I remember learning that Protein Kinase C has some effects when activated by one pathway and other effects when activated by another. How does this happen? Is it ...
1
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0answers
216 views

Construct a restriction map of a linear fragment of DNA using the following data?

I've attempted to do the single digests, and the double digests, but cannot complete the map.... I've attached what I've done so far DNA Sizes of Fragments (bp) uncut DNA 900 DNA cut with EcoRI ...
4
votes
2answers
112 views

Is it possible to create a restriction map using python? [closed]

I have some fragments of DNA from single and double digests using three different restriction enzymes. I'm trying to construct a restriction map of a linear fragment of DNA. The map needs indicate the ...
3
votes
0answers
57 views

How can a mutator gene can cause a mutation when it is shut off? [closed]

defination of "Mutator" - a gene that increases the rate of mutation of one or more other genes. However, in the book "Molecular Biology of the Cell" (bruce alberts) it states that when a mutator is ...
3
votes
1answer
75 views

Is a bone marrow transplant limited by sex?

Can a female patient get transplanted with bone marrow of a male donor and vice versa?
1
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0answers
20 views

Enzyme immobilization: Factors that help or hurt success

Are there any factors to consider that can help / hurt the chance to get a successful immobilized enzyme catalyst? i.e. The relative attractiveness of a live host synthesis vs an immobilized enzyme. ...
1
vote
1answer
45 views

Lookup for transporter locations in humans

I am interested in several transporters and cotransporters (eg SLC12A1/2 and many others), more precicely, in (human) organism that are made of cells containing those transporters. So does anyone know ...
1
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0answers
23 views

Computer Models of E Coli / Saccharomyces cerevisiae metabolite pathways

Are there mathematical models one can use to predict the expression levels of a foreign gene inserted into a well studied host organism like E Coli or S cerevisiae? I'm not, obviously, looking for ...
1
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0answers
18 views

codon optimization / enzyme active site improvement

Does one necessarily have to use de novo synthesis of DNA when attempting protein expression improvement by codon optimization? Or are there other ways? e.g. Say the gene coding for the enzyme needed ...
1
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0answers
21 views

Do you have a comprehensive protocol using xGen blocking oligo? [closed]

Specifically used with genomic DNA and to help prevent non-specific binding
2
votes
1answer
53 views

What is the P in LogP? [closed]

How does this value actually get calculated? Logarithms are usually written as log(base 10) of x So what is the 'P' equivalent of 'base 10'? I know it stands for octanol/water, but what does that ...
1
vote
1answer
96 views

What is two-start or zigzag model of 30 nm chromatin fibre?

I read some webpages describing the two-start model but could not get it. I'll be obliged if someone helped me understand the topic. The websites I have been through are: 1.http://www.nature.com/nrm/...