Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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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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2 votes
1 answer
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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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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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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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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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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 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 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
240 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 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 votes
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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1 vote
1 answer
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Transformation and PCR in molecular cloning

After obtaining the recombinant DNA, it is common to transform into E. coli to screen for recombinant DNA and amplify it. But I would like to ask can we amplify it using PCR? I think there will be 3 ...
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2 votes
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Occurrence of the theoretical thymine enol::guanine base pair in DNA [closed]

DNA polymerase has a proofreading exonuclease activity that can remove incorrect tautomers in the DNA template or incoming base. In theory the enol form of thymine can form three hydrogen bonds with ...
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11 votes
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What is, (and what isn't) "kinetic replication" as it applies to molecules and to living organisms?

CNN's World's first living robots can now reproduce, scientists say describes "xenobots"; clusters of stem cells that move around and by this motion occasionally push enough free stem cells ...
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22 votes
3 answers
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Effects of mRNA vaccines on human body processes

I would like to understand the effect of an mRNA vaccine on more complex processes in the human body. To what extent does this "artificial", external addition of mRNA interfere with the body'...
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3 votes
1 answer
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Does DNA ligase have any role to play in replication on leading strand?

Actually I developed this doubt while solving some questions(they are poorly framed I suspect). According to my notes and my institute modules, 1 RNA primer is required on the leading strand as well ...
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4 votes
1 answer
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DNA Design for Multi-Site Restriction Enzymes

I have to use the SacII restriction enzyme, which requires multiple recognition sites to efficiently cut DNA, for a DNA assembly. From my understanding, multiple copies of DNA holding only a single ...
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2 votes
1 answer
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Why are IMAC and gel filtration combined?

In a practical course I used an Biorad Profina system to purify a protein with a histidine tag. The device uses a column for IMAC and one for gel filtration. Why are these two devices combined in one? ...
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-1 votes
1 answer
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What is a downstream target?

For example, in a systems biology analysis, what is a "downstream target" and why are these significant in pathway analyses? I have looked for answers on Google, DuckDuckGo, Wikipedia, etc. ...
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-1 votes
1 answer
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What breaks hydrogen bonds while producing sticky ends using restriction endonucleases?

I am a high school student and I am little confused about the uses of restriction endonucleases. Why do hydrogen bonds(base pairing) break when restriction endonucleases produce sticky ends? If they ...
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1 answer
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Can we view the cross section of dna using electronmicroscope?

Is it possible to find how the cross section of DNA looks using without computer simulations ? All pictures I find on the internet are mainly computer simulations.
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Determine directionality of backbone from electron density map

I am given a polypeptide with three electron density maps at different resolutions; 1.85, 2.5 and 3.5Å. And from this I am to determine at which resolution you could be certain about the ...
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1 answer
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Where is the location of cutin or cuticle in the plant leaf [closed]

Cutin's main role is to prevent the the plant leaf from water loss, cutin is thick in shape , but I need to know where is the location of it ,for example is it in the lower epidermis or in the upper ...
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-1 votes
2 answers
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How can you identify recessive mutations in a gene that has been disrupted by a chromosomal translocation?

I am reading a journal paper about a patient who has intellectual disability. The patient was found to have a balanced chromosomal translocation t(11;16)(q24.2;q24). This chromosomal translocation ...
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2 votes
1 answer
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Are there any online resources for visualising on which band of a chromosome a particular gene is located?

I am studying some genes that are expressed in the brain. I use the online database UniProt to get information about the proteins encoded by the genes of interest. However, I would like to know on ...
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3 votes
1 answer
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How do molecules find their places? [duplicate]

In many molecular biology animations, a molecule just flies in and goes straight to the right spot. It's clearly a useful simplification, but I'm interested in learning more of the full story. I ...
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