Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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1answer
37 views

How much of the genotype-phenotype map do we understand in HIV?

From what I understand, viruses have very small genomes relative to those of standard model organisms used in biological research. For example, according to Wikipedia, "the HIV genome contains nine ...
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1answer
128 views

Why there is no ELISA for SARS-CoV-2?

As far as I know, SARS-CoV-2 tests currently used worldwide are real-time RT-PCR. Why there is no ELISA for SARS-CoV-2? Compared to PCRs, ELISA is: Way cheaper; Way faster; Does not require trained ...
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3answers
152 views

Do proteins contain phosphorous? If its true then how alfred hershey and martha chase used the statement that proteins do not contain phosphorous?

I hv heard about phosphorus that it is a constituent of certain protein, although we know that no amino acids have phosphorus... and if its true then how Alfred hershey and Martha chase experiment got ...
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0answers
26 views

What causes the overactivity of keratin production and expression in the cells of the nail bed/ nail matrix after some traumata?

What is the cellular mechanism of traumatic(sterile) onychodystrophy(hypertrophy)? I.e one hits his toenail and has it removed twice( once after the first trauma and then again 3 years after the first ...
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1answer
23 views

Relationship of RNA-binding proteins to peptidyl-prolyl cis-trans isomerase [closed]

I am studying a Plasmodium gene, known to encode an RNA-binding protein. However a BLAST search brings up mainly peptidyl-prolyl cis-trans isomerases from other species. Why would this be so?
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31 views

Can virus and bacteria move on the surface? [duplicate]

Do viruses/bacteria have some motive mechanism? I mean if the virus/bacteria reach some surface by touching, can it move on that surface? Life example: suppose the cooler is not so clean and has ...
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30 views

Absent gene expression from one of two vectors co-transformed into the BL21(DE3) strain of E. coli

I've been trying to express two proteins in the BL21(DE3) strain of E. coli. One gene is in a pCR2.1 vector and the other in a pET-expression vector. When I induce with IPTG and run on an acrylamide ...
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1answer
58 views

What are some good books on basics of Cell signaling?

I think the title says it all. (self answered, although others' answers requested)
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1answer
123 views

How can I get started in molecular biology? [closed]

I have a background in computer science and math and am interested in learning molecular / synthetic biology - what resources do people recommend?
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1answer
65 views

Can I pellet DNA back from dissolved state?

I have a dissolved plasmid pellet in water. Can I pellet it again by centrifuging it at 13000 rpm? If not, why?
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0answers
17 views

Is downregulation of neurological receptors fully reversible, i.e. complete upregulation and resensitization?

Are down/upregulation truly reciprocal mechanisms? After a binding ligand or agonist is removed, such as a prescription medication, is upregulation and resensitization able to occur to a level that ...
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1answer
605 views

Open Reading Frames vs Coding Sequences (CDS), are they different?

The two terms confuse me for a long time. What is the difference between ORF and CDS. Some people say ORF could contain intron and CDS does not. The wikipedia definition of ORF does not contains ...
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78 views

design and assessment of qPCR primers for COVID19

I read the False Negative of qPCR test for COVID19 is high compare to CT scans. https://pubs.rsna.org/doi/10.1148/radiol.2020200642 I was curious if experts can comment on why and what makes it ...
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1answer
110 views

Expression of eukaryotic ribosomal DNA

The Wikipedia page for rDNA says "Ribosomal DNA (rDNA) is a DNA sequence that codes for ribosomal RNA" Also, the figure next to it says "The gene segment of eukaryotic rDNA contains 18S, 5.8S, and 28S ...
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1answer
29 views

In the notch signaling pathway, what is Fringe activating?

Take a look at the notch signaling pathway in human from KEGG : https://www.genome.jp/kegg-bin/show_pathway?hsa04330 I want to know what is Fringe activating. It is not pointing to another gene or ...
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46 views

Non specific band in EMSA gel?

I am doing EMSA with Thermo LightShift Kit. I have a 150 bp biotin labeled probe which has been PCR amplified, gel eluted and sequenced. When I load samples on 5% native polyacrylamide gel, I see a ...
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1answer
57 views

Circulating Tumor Cell vs Circulating Tumor DNA

I'm a little confused about the wording of these two phrases and under which context the epithelial-mesenchymal transition occurs. For example: Is it the circulating tumor cell that releases the ...
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1answer
28 views

Swing bucket for PCR

I see a swing bucket rotor for PCR trips and don't know what step is using? What difference if I use fixed - angle? In addition, Which step I can use swing bucket instead fix - angle in molecular ...
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1answer
165 views

Peptides neither produced by the ribosome or the non-ribosomal peptide synthase complexes

I read in Wikipedia: While there exist a wide range of peptides that are not synthesized by ribosomes, the term nonribosomal peptide typically refers to a very specific set of these as ...
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0answers
10 views

From a hosts point of view, which comes first, effect of toxins on pathways or identification of toxins by immune system?

From a pure biology perspective, when a pathogen (gram-negative bacteria) affects a host by secreting toxins, what comes first, the effect of the toxin on the pathways or identification of the toxin ...
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1answer
123 views

How to analyze phosphorylation shift by western blot?

I want to see the phosphorylation shift in my protein of interest. I have created a point mutation in my protein. so that it will not able to go for the phosphorylation compare to my control. i want ...
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1answer
68 views

How does an antisense RNA molecule restore protein function in CF patients?

I am researching a treatment for cystic fibrosis (CF) called Eluforsen and I am trying to understand the mechanism by which an RNA molecule can restore proper protein function. In many research ...
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0answers
25 views

How do I identify and then isolate a Gene that codes for a particular observable phenotype

How do I identify and then isolate a Gene that codes for a particular observable phenotype. It is a novel bacteria and I do not know the gene sequence or the protein that it codes for.
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16 views

How many metabolites are in the metabolome of (almost) all eucaryotic cells?

Which small biomolecules (up to the size of amino acids) are present in (almost) every eucaryotic cell and thus part of its biochemical network, constantly and inevitably being produced and ...
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1answer
53 views

Bimodal frequency distribution of size of protein loops

The graph of number of amino acid (AA) residues in a loop Vs the frequency of their occurrence in proteins largely follows a tending-to-zero pattern. However, there appear to be some specific number ...
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1answer
68 views

Selection marker for a cytoplasmic vector that works at low expression levels?

I need to express a selection marker on a plasmid in human cells (e.g. HEK293). However, I am using a cytoplasmic vector derived from a non-human virus with its own mechanism for transcriptional ...
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1answer
147 views

What is the difference between Molecular and Cellular tolerance?

Although I've read that there are three types of tolerance, molecular cellular and behavioural, I cannot seem to find any mechanism of cellular other than desensitization of receptors. If someone can ...
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1answer
151 views

How do enhancers induce transcription?

DNA response elements are DNA sequences that are could be found upstream, downstream of genes that regulate gene expression at the transcriptional level. One type -Enhancers- bind specific ...
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1answer
22 views

what happens to rna length if we have a termination site in additional to the original one [closed]

if we have an RNA transcription and we add an additonal temination site in the middle , will i have two RNA molecules or just a short one ?
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1answer
89 views

How to design the primer when you don't have GC?

I have treated my RNA with sodium bisulfite so all my cytosine is converted into thymine. Then I used that RNA for my RT reaction. I have a cDNA template without Cs. Now I am trying to amplify that ...
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0answers
57 views

Where do methyl groups in the human body come from?

Where do methyl groups in the human body or other mammals come from? Do we synthesize them (where?) Do we get them from our diets (in what? anything beside methionine?) Do our gut microbes produce ...
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1answer
136 views

what is the princlple of using DMS (Dimethylsulphate) for structural analysis of rRNA?

I want to check the secondary structure of rRNA (PTC) in a particular position by using DMS footprinting. I have deleted the modified nucleotide (m5c) which is present in the PTC and it helps in the ...
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1answer
33 views

How does lipoid pneumonia lead to acute respiratory distress syndrome (ARDS)?

How does lipoid pneumonia lead to acute respiratory distress syndrome (ARDS)? The vaping illnesses that have been happening on the news in the United States are being caused by the federal ...
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1answer
43 views

Trade-offs between phage and yeast displays?

If you wanted to test a peptide you designed, you can do a phage display or a yeast display experiment to assess binding affinity. What are the trade-offs between these two methods? I've heard ...
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1answer
64 views

Photolysis in the Light Reactions of Photosynthesis [duplicate]

I'm a bit confused concerning photolysis. During the light reactions, photons are used to excite the chlorophyll molecules so they are passed to the primary electron acceptor. The electrons initially ...
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1answer
27 views

Why does opening of the Ca-channels trigger the release of neurotransmitters?

I understand that the opening of the Calcium channels trigger the release of stored neurotransmitter in granules, but what is it about the flow of positive ions that makes the vesicles fuse with the ...
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1answer
36 views

Analysis of post transplantation lineage tags

I'm having some trouble understanding some bits of a study, mostly about the Sleeping Beauty system and TARIS model, from this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408613/ I ...
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1answer
100 views

Is p53 a cyclin dependent kinase? [closed]

I've been reading some research papers about p53 and associated tumour suppressor proteins, such as p21. I see them referred to and associated with cyclin-dependent kinases. Is p53,p63 et cetera part ...
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0answers
33 views

Prokaryotes Genome

What function of repetitive sequences of Prokaryote? I see a gap (intergenic region) between 2 coding strand. But just only a single origin region in Prokaryotes. How it can transcription coding ...
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1answer
213 views

Lab technique to distinguish between single stranded and double stranded DNA?

What lab techniques exist to differentiate between single-strand and double-stranded DNA?
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0answers
57 views

Can two proteins activate/inhibit the same gene at the same time?

Suppose there are two proteins inhibiting a particular gene. Its not necessary that both will inhibit the gene at the same time instance right? So if one protein has already inhibited that gene before ...
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3answers
618 views

How is incomplete dominance explained at the molecular level?

What happens at the molecular level between two alleles that demonstrate incomplete dominance? Do the proteins coded by each allele have different functions, or is there an interaction at the RNA ...
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2answers
413 views

Can different proteins be produced during translation of a single mRNA in eukaryotes?

Is there a translational mechanism that eukaryotes can use to produce different proteins from a single transcribed mRNA?
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0answers
95 views

Can enzymes be modeled using classical mechanics?

When enzymes interact with substrates (i.e. a small ADP molecule and the much larger ATP synthase), does quantum mechanics play a significant role? Or can the interactions be relatively accurately be ...
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1answer
84 views

What would be the effect of excess taq polymerase on the PCR?

I just had one question regarding the possible effect of putting to much Taq polymerase in my PCR tube? Instead of 5µl I put 50µl (10x more). Do you think it will have a bad effect on the reaction??...
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1answer
61 views

Where does the number 67 in the nuclear protein/antigen Ki-67 come from? Why not 66 or 68?

I have read in in the original paper that in the year 1983 a research group in Kiel, Germany (that's where the Ki- in the name comes from) developed monoclonal mouse antibodies against Hodgkin ...
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0answers
59 views

Fluorescence assays to identify protein concentration without adding a large peptide sequence?

I'm trying to find a way of tagging a protein with something visually quantifiable to track protein concentration through potential purification steps and screen for the most efficient such steps. ...
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1answer
333 views

During DNA foot-printing, what is the purpose of radioactively labeling only one end of the DNA fragment?

I read that during DNA foot-printing analysis, DNA is radioactively labeled on one end before being cleaved by DNase 1. I understand that it is labeled so in order to locate the fragment on a gel, but ...
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13 views

How do I prepare a Basal medium for autotrophic mutant creation

Minimal medium (MM) was prepared by adding 2.0 g sodium nitrate (NaNO3) to 1 L of basal medium (BM) fol- lowing Correll et al. (1987). Chlorate resistant sectors (CRSs) were generated on two media i.e....
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1answer
29 views

Which one is better to use for water stress experiment GWAS or RNASeq?

This is my first time in this area of research. I am working on 95 varieties of bambara groundnut. I have done the agromorphological characterization of these varieties as well as the genetic ...

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