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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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Is retinoblastoma truly an autosomal dominant condition?

I am getting, in my opinion, very conflicting information from sources about the inheritance of retinoblastoma, a type of cancer. Hereditary retinoblastoma is associated with defects in the gene ...
Zuhair Qureshi's user avatar
2 votes
2 answers
88 views

Examples of passive membrane transport proteins that only transport in one direction and their mechanism

I would like to know about those transporters with alternating-access-type mechanism, that can only efficiently shuttle molecules in one direction but the other direction is severely kinetically ...
symmetrickittens's user avatar
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1 answer
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What specific molecules cause the difference in spectral sensitivity in the cones?

What causes the difference in their spectral sensitivity of the S, M and L cones. I'm guessing that the opsin or photopigments are different, but haven't been able figure out conclusively from my web ...
vxs's user avatar
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4 votes
2 answers
335 views

Primer design for site-directed mutagenesis

In our practical course about modern cloning methods, we performed point mutations on a promotor via site-directed mutagenesis. As far as I understand that method you need forward and reverse primers ...
Natalie's user avatar
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2 votes
1 answer
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Does beta-actin have to be consistent in Western Blots?

I have been running Western Blots on rat brain tissues from rats that have been subject to neurological disorders. I loaded the samples on the gel to ensure that for each tissue, I had a constant mass ...
mayurimahes6's user avatar
11 votes
1 answer
1k views

Human Evolution Chromosome 2: Fusion or Break?

I have a question regarding Chromosome 2. I've heard that there is evidence that the Human Chromosome 2 is a fusion between the two ancestral chromosomes 2a and 2b, but could it be possible that it ...
Diego's user avatar
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1 answer
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How do you do Polymerase Chain Reaction (PCR) if you don't have a thermal cycler?

PCR has three steps: Denaturation, Annealing, and Primer extension. Let's say you do not have a thermal cycler in the lab, how would you mimic similar conditions and perform PCR?
user71072's user avatar
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Endosymbiosis Probability

What is the probability of endosymbiosis occurring? I remember seeing it in my AP Biology textbook but haven't been able to find it anywhere after forgetting it. I want to say I remember it being ...
Louis Moon's user avatar
5 votes
1 answer
177 views

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 ...
Olaf's user avatar
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8 votes
1 answer
237 views

How does tetracycline transactivator localize to the nucleus? Where is the nuclear localization signal?

Proteins typically use a nuclear localization signal (NLS) to localize to the nucleus. Tetracycline transactivator (TTA) needs to work in the nucleus, but I did not find an NLS in the structure. ...
bud.dugong's user avatar
1 vote
0 answers
21 views

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 ...
Barbara's user avatar
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1 answer
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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 ...
Toasted Uranium's user avatar
4 votes
1 answer
78 views

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-...
kljiuklk 1's user avatar
0 votes
1 answer
49 views

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 ...
yaya10's user avatar
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3 votes
0 answers
26 views

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 ...
Joce's user avatar
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1 vote
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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 ...
user996159's user avatar
6 votes
2 answers
3k views

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 ...
aquaporin's user avatar
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3 votes
1 answer
392 views

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 ...
Milney's user avatar
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7 votes
2 answers
1k views

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 ...
uhoh's user avatar
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0 answers
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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.
Son of Sevenless's user avatar
2 votes
1 answer
165 views

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 ...
ceno980's user avatar
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2 votes
0 answers
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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 ...
cDirac's user avatar
  • 29
4 votes
1 answer
143 views

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. ...
John Flamour's user avatar
3 votes
1 answer
100 views

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 ...
ceno980's user avatar
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0 votes
1 answer
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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 ...
Arash Salehi's user avatar
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0 answers
38 views

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 ...
yaya10's user avatar
  • 19
1 vote
4 answers
225 views

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 ...
Ramil's user avatar
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-1 votes
1 answer
159 views

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 ...
Christian Chirgwin's user avatar
2 votes
1 answer
139 views

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 ...
uhoh's user avatar
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3 votes
1 answer
72 views

Use of plasmid pXen5 for transposon screening

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). ...
Julius's user avatar
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0 votes
1 answer
66 views

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?
UD22022's user avatar
4 votes
1 answer
117 views

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 ...
DanK's user avatar
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-1 votes
1 answer
73 views

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, ...
Doug Null's user avatar
  • 115
3 votes
1 answer
190 views

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 ...
Masrat Shaikh's user avatar
2 votes
1 answer
1k views

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 ...
user12256545's user avatar
1 vote
1 answer
65 views

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 ...
ceno980's user avatar
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0 votes
1 answer
70 views

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-...
ceno980's user avatar
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0 votes
1 answer
56 views

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?
katara 's user avatar
  • 131
2 votes
1 answer
153 views

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 ...
ceno980's user avatar
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7 votes
2 answers
1k views

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 ...
ceno980's user avatar
  • 1,741
1 vote
1 answer
210 views

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.
Reverend Class Nought's user avatar
1 vote
1 answer
255 views

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 ...
Ryan Ellison's user avatar
4 votes
1 answer
173 views

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 ...
ceno980's user avatar
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0 votes
0 answers
173 views

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 ...
Danyn Patel's user avatar
0 votes
1 answer
158 views

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 ...
Joe's user avatar
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0 votes
0 answers
72 views

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 ...
mathematicalbiologist's user avatar
0 votes
0 answers
58 views

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 ...
Elio Lee's user avatar
1 vote
1 answer
514 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 ...
Agne's user avatar
  • 19
0 votes
1 answer
28 views

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 ...
Ali Pedram's user avatar
0 votes
1 answer
81 views

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 ...
ceno980's user avatar
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