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

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11 views

Similarity between lncRNA and Enhancers

Please read it carefully. Question below is purely based on computational experiments: I have been running an analysis algorithm (pretty new one) on lncRNAs and its showing pretty much the same ...
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1answer
36 views

Lifetime of secondary messengers such as Calcium or IP3

Can anyone suggest me literature on the lifetime of secondary messengers such as calcium or IP3? A book would be preferred. What I am specifically looking for is a validation that secondary messengers ...
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3answers
136 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 ...
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2answers
48 views

How do we find antibiotics?

So the last class of antibiotics were made in 1984 (I think), which makes it appear as though they are hard to find(/design maybe). How is it then they were discovered? Was it by chance? I know some ...
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1answer
29 views

How to isolate two plasmids from E. Coli strand?

I have an E. coli cell line I use to express a protein using a two plasmid system. One confers AmpR and one KanR. For mutagenesis I would like to separate the plasmids to increase efficiency of the ...
2
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1answer
55 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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1answer
479 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, ...
2
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1answer
71 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 ...
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2answers
2k views

Why is the DNA helix anti-parallel? [duplicate]

Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.
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21 views

Western Blot suitable condition [on hold]

I would like to ask you some advice about western blot technique. What should be the best way to running my sample? I'm using a lower voltage, until the packaging into the stacking gel, and then a ...
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0answers
22 views

Why are there so many regulatory mechanisms in gene expression? [on hold]

first time posting here, apologies if this is a stupid question. I am a layman, so I might be ignorant to some already well-known or obvious concepts in biology. From what I understand, gene ...
3
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1answer
80 views

How does a protein reach its substrate within the cell?

After a protein has been synthesized and its the final tertiary/quartenary adopted, how does it reach its substrate within the cell and what causes it to interact with it? The transcription factors ...
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1answer
25 views

Why is tRNA called an adaptor molecule?

All I know about adaptor is that it is a device that converts attributes of one electrical device or system to those of an otherwise incompatible device or system. Thank you.
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11 views

Requirements for In-Fusion Cloning Protocol?

I have some long primers I'd like to repurpose for an In-Fusion cloning project. The In-Fusion manual can be found here. They list a few examples of how the primers should match the vector, with 15 ...
5
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1answer
55 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?
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2answers
328 views

What is the importance of urea in mass spectrometry?

What is the importance of urea in mass spectrometry? We use 8M urea to FASP our proteins prior to mass spectrometry. What is the significance of using 8M urea? and how does it affect the proteins?
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2answers
53 views

Material recommendation: molecular biology for mathematicians and computer scientists [closed]

I am wondering if there are some introductory learning resources on molecular biology designed specifically for scientists with heavily math-oriented curricula (math/physics/computer science). They ...
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0answers
30 views

Why oxidation for energy occurs in the tissue?

Air consists of 20% oxygen while a percentage of dissolved oxygen in water is ~0.005-0.0015% in normal Earth condition. Why do animals use dissolved oxygen for energy production ('aerobic' digestion)? ...
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2answers
6k 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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1answer
79 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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0answers
68 views

Does Cas9 require a nuclear localization signal (NLS) for it to work in a Eukaryote?

I'm trying to establish if it's required to add a NLS to Cas9 when expressed (or transfected) in a Eukaryotic cell. Several papers report using a viral NLS, but is it absolutely necessary? Could ...
4
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0answers
39 views

Does depolymerisation take place at the minus end of microtubule?

Wikipedia says that Dynamic instability refers to the coexistence of assembly and disassembly at the 'ends' of a microtubule. but Karp's Cell Biology, 7th edition says Dynamic instability ...
4
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2answers
60 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 ...
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2answers
63 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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1answer
28 views

What do arranging and assigning mean in sequence annotation?

Please could someone explain these lines to me in a simple way These sequences were then arranged based on some overlapping regions present in them. This required generation of overlapping ...
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1answer
52 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 ...
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1answer
24 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
106 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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59 views

What is the Ramachandran z-score of a denatured protein? [on hold]

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
42 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
36 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 ...
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1answer
37 views

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

What is a "noninvasive" biomarker for a disease? I know what a biomarker is, but what makes it noninvasive?
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0answers
14 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
28 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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0answers
12 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 ...
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2answers
233 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 ...
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2answers
55 views

CRISPR/Cas for editing the human genome [closed]

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
43 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
77 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 ...
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2answers
53 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
213 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
185 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 ...
0
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1answer
21 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
201 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
222 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?
1
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1answer
27 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
votes
1answer
76 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
63 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 ...