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

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31 views

Are there specific non-protein substances that pathogens release into their host?

Reading research articles, I have found out that proteins called effectors get released into the host cell when a pathogen attacks a host. My question is, whether pathogens also release non-protein ...
-1
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0answers
11 views

Band is not available. Why?

I confirmed the GFP-fused protein by fluorescence microscopy. The molecular weight of the protein is 123 KDa. I used 10% SDS-PAGE. I washed the nitrocellulose membrane 3 times with 10 mins each. I ...
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1answer
9 views

Plasmolysis vs Flaccidity in cells

When is a cell said to be flaccid and when is it called plasmolysed? So far I found that there is a specific relation to osmosis.
5
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1answer
87 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 ...
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0answers
51 views

What is the Ramachandran z-score of a denatured protein?

I thought it should be 0, but the professor pointed out I was wrong. What should the Ramachandran z-score of a denatured protein be?
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0answers
34 views

Why do electrophoresis gel boxes only have 1d wire electrodes and not a 2d 'mesh' as used in clarity?

Since the DNA and protein are electrophoresed in a 2D plane (along one dimension, the length of the gel), I am surprised that a 1D wire electrode is used for anode and cathode, and not a 2D mesh-like ...
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0answers
28 views

CRISPR Cas9 most updated paper protocol

I am collecting literature to start a new project on CRISPR Cas9 gene editing. I must put together a protocol to start asap. I am intending to use the following paper as guidance: "Genome ...
1
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1answer
33 views

What is a “noninvasive” biomarker for a disease? [on hold]

What is a "noninvasive" biomarker for a disease? I know what a biomarker is, but what makes it noninvasive?
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0answers
13 views

Optimum gibson assembly overlap length

Does anyone know the optimum length of overlap your primers should have to your vector for gibson assembly. Most manufacturers say to do at least 20 bp on both side but don't give a maximum. Sometimes ...
2
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1answer
25 views

Question about Enzyme Inhibition in relation to Aspirin

I've been trying to learn a bit more about pharmacology, so bear with my ignorance. In short, I see that aspirin (in part) works by inhibiting cycloxygenase isoenzymes and that this inhibiting is ...
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2answers
49 views

What is meant by “Expression” of Non-Coding RNA?

I was having a look at lncRNAdb and its help says: The ENCODE project gene annotation list, GENCODE, has predicted that the human genome contains 14,470 lncRNAs whereas only a small proportion of ...
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0answers
11 views

SSR Association Mapping [closed]

I do association mapping of SSR with the help of the bioinformatics tool "Tassel v 2.1". Can any one tell me about Ls Mean in GLM. Actually, when I click on "add Ls Mean data" for output the software ...
10
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2answers
221 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 ...
2
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2answers
122 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 ...
2
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1answer
53 views

Programs/software to graph biological data [closed]

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
votes
1answer
52 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
53 views

CRISPR/Cas for editing the human genome [on hold]

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
votes
1answer
41 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
73 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
412 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
votes
1answer
184 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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1answer
19 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 ...
12
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2answers
192 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
214 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
26 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
votes
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 = ...
0
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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. ...
2
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1answer
74 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
17 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
45 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
144 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 ...
7
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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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0answers
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
votes
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
789 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
48 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
74 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
35 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
38 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 ...
1
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2answers
39 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
38 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
35 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 ...