Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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yeast culture live cell extraction

I have been extracting samples for a gene expression assay from yeast. I would like to know how to ensure that the samples I am collecting at 48 hr. culture time, by then culture is probably saturated....
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Why does plasmid cloning efficiency go down with increased size of insert?

I am setting up a cloning experiment. Briefly, I ran PCR on a gene of interest, cloned it into a vector (pGemTeasy) and bulked it up in bacteria. I have been advised to limit the size of my fragment ...
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Nomenclature query about molecule acronyms & hyphens

Are hyphens necessary if the syntax is not a chemical formula? E.g. TNF-α, IL-6, G-CSF
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What would happen if the central dogma was reversed and protein was able to translate to RNA? [duplicate]

During one of my interviews, I have been asked this question. Can somebody please help me with this?
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why are buffaloes black in colour and how would you prove my hypothesis with an experiment? [closed]

I was just wondering why buffaloes are all black, Why not pink or blue? Also if I want to prove this experimentally how would I test my hypothesis. I was thinking in terms of melanin pigment
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Where to archive web citations for molecular biology article?

In 2013 I wrote a scientific paper in the field molecular biology. I needed to quote some webpages which I feared might disappear, e.g. amazon sales offers (it was a food related topic). So I archived ...
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Do complementary DNA sequences/codons produce the same amino acids? [closed]

I haven’t been able to confirm this anywhere. If this were not the case, when transcription occurred, if the transcription were based upon the incorrect side of the DNA molecule, a completely ...
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4 votes
1 answer
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Ischemia-induced deploarization in excitable cells

I have read in many sources that ischemia-induced depolarization is due to the opening of ATP-sensitive potassium channels and inactivation of Na/K exchangers [1,2]. However, K-atp channels are inward-...
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The quality of binding sites?

Can someone please provide a human friendly explanation. to the following: RNAp binds a defined site (a specific DNA sequence) at the promoter (Fig- ure 2.2a). The quality of this site specifies the ...
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Has there been a measurement of a stalling force for myosin molecular motors?

For processive molecular motors like kinesin, in vitro assays have allowed to measure directly a stalling force beyond which they do not progress anymore or detach. As far as I know, the literature ...
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How to make predictions on genes not involved in a particular disease

I have one set of genes which counts about 100 such that every gene of that set is evidence based involved in a particular disease. Let's call this set A. For a machine learning project I need a set ...
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What does rescue mean in the context of biological experiments?

I have come across the term 'rescue' in biological contexts a lot recently and despite reading multiple definitions online cannot seem to get my head around what the word means on its own, and what it ...
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Plasmid Design and Integration events [Single vs Double cross over]

When linearising a vector by restriction digest within the middle of a homologous region can a single cross over integration event only occur if the plasmid is re-ligated within the cell after ...
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How are DNA virus cladograms actually calculated in practice? Is the procedure different for RNA viruses? Are these processes somewhat subjective?

The May 24, 2022 Bloomberg opinion piece Monkeypox Isn’t Looking Like a Covid-Sized Threat; It’s still early, but contact-tracing efforts and analysis of the virus’s genome offer hope that this ...
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Why DNA polymerases don't have helicase activity

RNA polymerases have intrinsic helicase ability, while DNA polymerases don't. I am curious why DNA polymerases evolved in such a way that they lack the ability to unwind DNA.
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How does non-cell autonomous work - how can a mutant cell make other non-mutant cells exhibit a mutant phenotype?

I am reading a journal paper, and I have coming across the following statement: Furthermore, although late-born neurons that take up exogenous Dcc fail to settle in the superficial layer of the ...
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Apparant inconsistency in DNA topology theory in formation of origin of replication [duplicate]

I'm studying an introductory course in genetics and came across something I don't fully understand. I obviously used Google to find where I'm thinking wrong, but I still can't understand it. To ...
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Why would E. coli cultures suddenly start to slow down?

My E. coli cultures used to take 13.5 hours to reach stationary phase. I have not changed any of the parameters like temperature, shaking speed, media formulation/components or inoculation volume. ...
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How can SNP arrays be used to detect deletions within a gene?

I am reading a journal paper where the researchers are studying the effect of disease-causing mutations in the IL1RAPL1 gene. In the first figure of this paper, they show pedigrees of families where ...
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How do refractive index (RI) matching solutions reverse tissue expansion in CLARITY tissue clearing?

I am learning about the CLARITY tissue clearing technique. I am researching this technique to understand how it works better. I know that this technique can make tissues transparent without severe ...
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What is meant by “global RNA polymerase occupancy”?

I read the following in a paper It provides base-pair resolution and strand-specific information of **global RNA polymerase** occupancy. CDK13 cooperates with CDK12 to control global RNA polymerase ...
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biofilm model scales

I have a question about the meaning of biofilm modelling scales: Are they microscopic, mesoscopic and macroscopic. Microscopic means individual bacteria macroscopic means large number of concentration ...
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How to look for different transcripts for a protein?

I am trying to find all the different transcripts for a protein that translate into different isoforms of the protein. However, when I look it up online, there is no clear organized data on different ...
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Why don't animal cells have both mitochondria and chloroplasts? [closed]

Ancestral eukaryotes had both mitochondria and chloroplasts, why do animal cells only have mitochondria. Why did evolution allow animal cells to give up such a great circle of energy? Where the waste ...
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3 votes
1 answer
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Zayed et al. (2022) "Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA virome"; expressed sequences or transcribed?

Phys.org's Ocean water samples yield treasure trove of RNA virus data summarizes Zayed et al. (April 7, 2022) in Science Cryptic and abundant marine viruses at the evolutionary origins of Earth’s RNA ...
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A question about transposons

I would like to use the plasmid pXen5 (by Xenogen) for a transposon screen. It contains two inverted repeat sequences, with Luciferase, Kanamycin, and the transposase itself in between. (It's tn1409). ...
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Are introns conserved among cells?

To elaborate on the title: Among somatic, post-mitotic cells, would the same intron on a given chromosome have the same sequence among all cells descended from a progenitor cell?
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4 votes
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Use of different biotinylated GTP compounds in molecular biology

In the Cappable-seq technique 3′-Desthiobiotin-GTP can be used to label the 5′ end of mRNA. However in a commercial technical article on biotinylated-RNA affinity probes I encountered the following ...
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When a dog sniffs up organic material that contains DNA, is it possible his genome incorporates it? [closed]

I'm not kidding. Was just watching my German Shepherd sniffing away at a new Amazon box. ...realized she sniffs vast array of DNA from organic material when on a walk: millions of mammalian, plant, ...
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3 votes
1 answer
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Why do eubacterial DNA Ligases use NAD whereas eukaryotic and archaeal DNA Ligases use ATP?

DNA ligases in eukaryotes are ATP-dependent (as is the enzyme from bacteriophage T4) but in Escherichia coli the DNA ligase is NAD+-dependent. I cannot understand the reason for this. An extensive ...
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2 votes
1 answer
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Please explain to me the difference of molecular weight in g/mol versus dalton

From my studies i thought so far that: 1 NA * Da = 1 * NA mu = 1 g, However since 2019 SI says that one dalton is only approximately one gram per mol 1 NA Da ≈ 1 g/mol This makes sense if I consider ...
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What is a gain-of-function assay in neuroscience?

I am reading this paper and I have come across the following statement: "We sought to test whether exogenous Kirrel3 expression induces synapse formation via a gain-of-function assay... Because ...
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In enhanced chemiluminescence in western blots, will the horseradish peroxidase eventually get used up?

I am learning about enhanced chemiluminescence in Western blots. I have read online that in enhanced chemiluminescence that horseradish peroxidase (HRP) catalyses the oxidation of luminol to 3-...
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Why can SPRITE measure many simultaneous interactions?

Why is the SPRITE method not limited to a number of simultaneous interactions that can be measured, while microscopy and proximity ligation are limited to 2-3 interactions?
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2 votes
1 answer
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Can cell adhesion molecules have intrinsic enzymatic activity?

I am learning about cell adhesion molecules (CAMs), and I know that they mediate cell-cell and cell-extracellular matrix adhesion via homophilic and heterophilic interactions. I have read that CAMs ...
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7 votes
2 answers
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How do geneticists determine if a gene mutation is pathogenic?

I am analysing information about patients with neurodevelopmental disorders using the DECIPHER genomics database. I am looking for patients who have only a specific gene deleted and no other mutations ...
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Why do transcription factors have to be inserted genomically?

Instead of inserting the DNA to synthesize transcription factors into the genome in order to reprogram a cell into an induced pluripotent state, why can't you already synthesize the transcription ...
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1 vote
1 answer
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In enzyme kinetics, Can the Kp be greater than K1 in any way? [closed]

Enzyme reacts with substrate to produce a complex. And finally the products in a catalysis reaction.
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1 vote
1 answer
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Western blot trouble shooting - low voltage and yellow sponges during/after transfer

I have a western blot troubleshooting question that I haven't been able to find the answer to in manufacturer troubleshooting guides. As a bit of background, I was transferring 2 western blots ...
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4 votes
1 answer
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What does the 'y' mean in CHL1−/− / L1−/y double mutant mice?

I am reading a journal paper and I have come across the following statement: To investigate this, $CHL1^{−/−}$ / $L1^{−/y}$ double mutant mice were generated and analyzed for thalamocortical axon ...
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Cloning in a large DNA fragment into a plasmid

I need to clone in a 30kb DNA fragment into my plasmid (~7kb). Working with such a large fragment I have run into a few problems. The first was purifying it from the PCR mix used to amplify it out of ...
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can mammalian expression vector be used in e coli to produce plasmid

I would like to use this plasmid (mammalian expression Flag-HA-USP53 (Plasmid #22606) - Addgene) to produce plasmid in e coli to purify plasmid. Would this work? I am starting out with this vector ...
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Recommendations for good books on bacterial genetics & molecular biology?

I'm starting a new phase of my PhD soon, and am feeling very under-prepared with respect to my general bacteriology knowledge. I was recommended to read up on basic bacterial genetics and molecular ...
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Interactive molecular machinery visualisation software?

If I want to manually feed mRNA through a ribosome to actually see what happens step by step which software can I use to do that? I'd like to be able to see changes in geometry and orientation at an ...
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1 vote
1 answer
244 views

how to extract garlic fructan?

can anyone tell me a not complicated way to extract fructans from garlic (i have access to highschool lab). I need this to be able to make an experiment on garlic extract and just fructan from garlic ...
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Is Signal Transduction Unidirectional from the Stimuli to the Final Receptor?

I wonder if signal transduction in biological systems including visual, olfactory, tactile or any other biological system, is unidirectional. Suppose that $X_i$ is the $ith$ cell in the signal ...
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-1 votes
1 answer
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What has a more negative impact: Having only a partial deletion of a specific gene or the having entire gene deleted?

I am looking through a genomics database to see whether patients who have intellectual disability have deletion of only a specific gene of interest and no other mutations (e.g. deletions or copy ...
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1 answer
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Multicellular but uninucleate?

The "standard" biological setup is one cell-one nucleus (with one or more chromosomes and zero or more plasmids). Multinucleate cells are a thing (e.g., in fungi)--a situation wherein a ...
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Why does Meiosis produce 4 daughter cells instead of 2? Won't splitting the initial diploid cell into two haploid cells be easier?

At first, I thought it was because of crossing-over, but when I thought more about it, that didn't seem reasonable. Why don't cells just do meiosis like this? (I know that we don't understand all the ...
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How many non-pairing bases can a PCR primer have in directed mutagenesis?

I'm not including a lot of details here, because the problem I'm working with is actually more complex. Say you have the DNA sequence 5'-...tct gcg gtg gtt ggc att ctg ctg...-3' Could this sequence ...
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