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

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28 views

Programs/software to graph biological data

I am curious about what sort of programs people in my field of academia are using to graph their data. I am a master student in biochemistry, and have more or less only used excel (on rare occasions I ...
2
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1answer
50 views

Difference between the P4 and P5 subtypes of P-type ATPases in plants

In plants there are various kinds of P-type ATPases. What is difference between P4-ATPase and P5-ATPase?
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2answers
48 views

CRISPR/Cas for editing the human genome

I know, that the CRISP/Cas approach for "cutting" the human genome is not completely suitable if we can't say not suitable at all. Because we have many repeats and this approach can bring to our ...
3
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1answer
39 views

What is a regulable promoter? And how does one regulate it?

I'm reading a patent where they (in S. cerevisae YNP5 strain): downregulate the ERG9 gene by replacing the native ERG9 promoter with the regulable MET3 promoter What's a regulable promoter and ...
3
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2answers
68 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 ...
3
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1answer
399 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, ...
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2answers
48 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 ...
4
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2answers
211 views

Randomness in living systems

The point of my question is not to talk about events that are uncontrolled by living organisms. My question is about controlled randomness, or I'd like to say adaptive random process. Process that are ...
4
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1answer
183 views

What do “e” “-” “C” and “E” mean in this output?

I have given an input of this protein sequence: MEPVDPRLEPWKHPGSQPKTACTTCYCKKCCFHCQVCFTTKALGISYGRKKRRQRRRPPQGSQTHQVSLSKQPTSQPRGDPTGPKE from this website along ...
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0answers
14 views

Wrong amount of Glycerol for medium

I need to make agar plates, usually I add 2.5 ml of Glycerol per bottle but I am not sure if I made a mistake and I added 0.5 ml to one bottle and 3 ml to the other one.Would I see diferences if I ...
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1answer
18 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 ...
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18 views

breeding of mice with cre/lox system [on hold]

we are crossing foxp3 mutant/mutant female mice with notch1 lox/lox male mice.please tell me the possibility of getting litters when this cross has done? please specify each litter with what type it ...
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2answers
186 views

How can we verify predictions of 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 ...
3
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0answers
58 views

What Chemical Trigger Causes Ectomycorrhiza To Change From Asexual To Sexual?

I want to know the trigger behind the change of asexual to sexual ectomycorrhiza when symbiosis with a tree root is formed. As ectomycorrhiza attaches itself to a root, it forms a relationship wherein ...
3
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1answer
210 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?
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1answer
25 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 ...
3
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1answer
67 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
54 views

Does adding antibiotic after 5-10 mins of innoculation affect the protein yield or growth?

I've asked a lab colleague the same question. She said, it would loosen the bacterial cells in the LB medium and plasmids would come out. Is that true? and why?
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2answers
61 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 ...
3
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1answer
3k views

What's the physical meaning of Svedberg unit?

Sedimentation coefficients, using a centrifuge, are expressed using Svedberg unit (symbol S, sometimes Sv). Wikipedia states that $S = 10^{-13}$ sec but I also saw in a book that actually $S = ...
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1answer
71 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. ...
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1answer
73 views

Genomic DNA isolation from wheat

Can I use dry seed, wheat for example, in place of young leaves for isolation and purification of genomic DNA for PCR amplification? The goal of my experiment is to validate a novel gene which is ...
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0answers
16 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
44 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 ...
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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? ...
5
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1answer
143 views

enzymes that stabilize DNA loops

As a follow-up of a previous question, I would like to know what enzymes or protein complexes have been used to manipulate DNA samples into stabilizing DNA loops. I have read that cohesin is one of ...
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3answers
13k views

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

In a lecture during my undergraduate degree we were introduced to the race to complete the human genome. Celera were competing with Sanger and collaborators to sequence the human genome. Celera ...
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2 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 ...
4
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1answer
80 views

Why is an A-U bond less stable than an A-T bond?

I have encountered the following fact many times, but have not yet encountered a possible explanation for it. Will you please help me understand the molecular mechanism by which the bond between ...
31
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4answers
786 views

Why are amino acids in biology homochiral?

Why are nearly all amino acids in organisms left-handed (exception is glycine which has no isomer) when abiotic samples typical have an even mix of left- and right-handed molecules?
3
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1answer
47 views

Do only one or both pairs of homologous chromatids exchange genetic material during the process of crossing over?

To be specific: Assume chromosomes A and B are homologous. They've both replicated into A1, A2 and B1, B2 and have formed a tetrad at the equator (synapsis). Most textbooks show either A1 and B1 OR A2 ...
5
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1answer
72 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 ...
1
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1answer
34 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
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1answer
36 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 ...
4
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2answers
83 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 ...
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2answers
114 views

Extending a small fragment of DNA

Is there a way to extend a small fragment of DNA, say 150 bp, by making copies of itself and attaching each copy of that small fragment to the end of that 150 bp sequence? For example, I want a 1 ...
5
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0answers
76 views

Can bacteria, viruses, and cancer cells be destroyed by resonance?

Radiotherapy has been used to treat cancer. Can the resonances by coordinated electromagnetic waves (and/or other forms of waves), of various frequencies, amplitudes and pulse rates, directed from ...
0
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2answers
32 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
35 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 ...
4
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1answer
34 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 ...
7
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1answer
54 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 ...
12
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2answers
1k views

Why is there more variation in proteins than genes?

The Genome of a cell or organism is the same as that of the entire organism. However, the proteome of an organism is much greater than that of each cell (unless the organism is unicellular). How do ...
4
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1answer
46 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 ...
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2answers
91 views

Why mutations in genes involved in general processes like DNA repair increase the risk of developing specific types of cancer?

For example, mutation in MHS2, which encodes a protein involved in the repair of mismatches that occur during DNA replication, dramatically increases the risk of developing colon cancer. (There are ...
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1answer
12 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
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21 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 ...
1
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1answer
74 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 ...
0
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1answer
32 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 ...
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24 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 ...
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0answers
22 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 ...