Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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Can I use a basic compound microscope to analyze the ploidy of plant chromosomes?

So, I'm not really any kind of trained botanist. But I do have two things: some dandelion seeds from France, and, collecting dust in my garage along with related accessories, this thing. Normally, ...
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Buffer Components affect DNA methylation patterns?

I am using this buffer to preserve blood cells for long term storage. The buffer contains the following: 100 mM Tris, 100 mM EDTA, 10 mM NaCl, and 0.5% SDS. From the literature it seems that EDTA ...
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How to troubleshoot in vitro formaldehyde fixation for nucleosomes?

For an experiment, I am trying to fix the mononucleosomes (100ng) using formaldehyde as crosslinking agent in HEPES buffer. I have been using 2% formaldehyde in a reaction buffer containing 1mM EDTA, ...
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Is there a lac operon like sequence in the eukaryotic genome?

A lac operon regulates the expression of the genes that encode for proteins that decomose lactose into its simpler monosaccharides. It is also known to be an inducible operon. Any similar sequence in ...
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What is the meaning of “Rb is in the active state”?

I am reading about cyclins, cdks and Rb (Retinoblastoma) and some of the terminology is not clear to me. I understand that when CDK phosphorylates Rb, it disconnects from E2F, and E2F can act as a ...
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How do receptors lose their sensitivity?

Recently, I learned that one of the causes of Type II diabetes is that insulin receptors on cell surfaces lose their sensitivity due to long-term high exposure to insulin (which occurs as a result of ...
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What impact does substrate bonding have on GMO’s if one at all

Do GMOs increase the effect of substrate bonding? Does it minimize activation energy? Does it change concentrations or bonding potentials?
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Application of molecular dynamics simulation (or alternatives) for the full pathways of protein interactions?

If one would like to control the biological system (e.g. to treat disease or aging/senescence) then one should introduce the drugs in the system, that initiate complex protein interaction pathways ...
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Can Cas13 be used with multiple crRNAs in the same reaction?

CRISPR-Cas13 equipped with crRNA (complementary to transcripts of interest) can be designed to target ssRNA transcripts in cells. Upon successful crRNA and ssRNA binding, a fluorescent domain on ...
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Does the lack of “mirror life” tell us anything about abiogenesis?

My (extremely rudimentary) understanding of Biology is that many of the building blocks of life are chiral and that life on earth is entirely made up molecules with the same chirality. Does this ...
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140 views

How are single-stranded binding proteins removed from the lagging strand during DNA replication?

The lagging strand, downstream of the Okazaki fragment, is covered in single-stranded binding proteins (SSBPs) during DNA replication. What is the mechanism which ensures that SSBPs are removed from ...
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What is the relationship between Ca- and Na-ions and mucins and why?

According to Wikipedia https://en.wikipedia.org/wiki/Mucin#Secretion mucins (Proteins that form mucus) obtain viscoelastic properties by the Exchange of sodium and Calcium Ions. What is Happening ...
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Haemoglobinic acid

I’ve tried searching for the structure of haemoglobinic acid but it isn’t anywhere. I was trying to find out whether H+ ions bind onto the same site as carbon monoxide and oxygen on haemoglobin or not,...
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Are my plasmids single-stranded?

Hi, in this agarose gel photo (70 volts, 3.5uL Gel Red in 30ml of TBE, 1% Agarose, 1 hour run), I've checked the digestion of a large plasmid (15Kbp, one cut site). The theory says that the digested ...
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1answer
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Is the lac operon repressed in the presence of both glucose and lactose?

In the presence of both sugars (glucose and lactose) will there be repression of the lac operon completely? I know that more glucose means less cAMP --> less CAP --> less positive regulation, and ...
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Why are dietary recommendations for methionine consumption combined with cysteine?

I want to understand the amino acids missing in certain vegetables. I looked up the US recommendations for amino acids (source: wikipedia). I don’t understand why they pair Methionine + Cysteine: ...
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Ligation without purifying insert

I am planning to insert a 45 bp sequence in a vector. After restricting my insert to create compatible sticky ends, I am finding no way to clean it up. Is there any way for cleaning this fragment ...
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Is it possible to target the same (Protein) region for silencing and tagging? [closed]

The stem loop constructs for silencing mRNAs (~500nt) having no homology (>18nt) to other transcripts in T. brucei genome was used to generate the stem–loop constructs using primers listed above. ...
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How are multiples transmembrane proteins translocated or embedded in the membrane?

This image is in the textbook, Molecular Biology of the Cell. I understand why the start and stop transfer sequences must alternate, but why is there 2 consecutive start transfer sequences at the N ...
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What does the gene name “lexA” stand for?

It is an important gene expressed in E. coli that represses the SOS response and also the expression of lambda lytic phase genes. UV light and damage to DNA is responsible for its breakdown and hence ...
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What is the typical concentration of Calcineurin (PP2B) in CA1 dendritic spines?

I am trying to find the concentration of CaN (PP2B) in dendritic spines, there is a computational model (doi:10.1073/pnas.0804672105) that uses the quantity of 1uM in the dendritic spine. I think this ...
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Why did nature decide to make plasma membrane of animal cell hydrophobic?

I am taking Introductory Human physiology course on Coursera. The teacher said and I quote " the membrane of the cell is a hydrophobic barrier that prevents any charged ions or molecules from moving ...
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Could Wobble Base Pairing ultimately yield an amino acid that was originally uncalled for or not expected?

How does the cell choose which amino acid to attach to tRNA when there is wobble base pairing involved (not the other way around)? Consider the example below. For the purpose of this question I'm ...
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What is the difference between DNA vs RNA Editing in the context of gene therapy?

As a someone with beginner knowledge on biology, I have come across the terms "RNA editing". Take this paper for example : RNA Editing with CRISPR-Cas13 From my understanding, DNA -> RNA -> Proteins ...
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Why do NK cells not destroy bacteria, even though bacteria don't have MHC-I?

Part of the function of NK cells is to destroy cells that are unable to bind their KIR receptors. Or in other words, cells that don't express MHC class I. This is why they can kill MHC supressed ...
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Dna based question [duplicate]

We know that dna is an acid which is elaborated by deoxyribo nucleic acid.It has 4 nucleo bases.Now,the question arises, why dna has no uracil base?
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Can a lentivirus expressed protein that is undetectable by western blot be detected by BioID?

Cloned a single herpesviral gene into pCDH-EF!-GFP and see phenotypic effect on cells of interest and viral gene transcripts BUT unable to detect ANY protein using HRP boosted western blot. Even with ...
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Need help in identifying and understanding the origin of an expression variant

We usually denote the origin of a mutation as either somatic or germline. This information is usually available in certain databases such as CIVIC, ClinVar, COSMIC etc. But when we come to variants ...
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How to map the N6-dimethyladenosine by primer extension?

I am trying to map N6-dimethyladenosine on rRNA using primer extension (low dNTPs assay) method. But i am not able to detect map my position. I went through some articles they mentioned like they ...
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Insight on HPV vaccine to prevent/control reactivation of latent infections in those already infected

Some women experience reactivation of HPV infection in their 50's due to weakened immune system and weakened immune memory. Is it outside the realm of possibility that giving the HPV vaccine to those ...
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Protein misfolding [closed]

Protein misfolding is usually prevented by molecular chaperons. Rarely, the chaperons are not able to prevent the misfolding as a result of which the infectous molecules called prions will form. My ...
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3answers
530 views

Getting PCR amplification at annealing higher than Tm!

I am amplifying a gene where in a gradient pcr i am getting amplification at an annealing temperature about 5 degrees (67) higher than Tm (62.5)? What is wrong here? Also, I am getting a very strong ...
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Are all genes transcribed in differentiated cells?

My textbook tells me that it’s specific transcription factors that allow for a different set of genes to be expressed in different cells (differential gene expression). My book gives the example of ...
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In HIV-1, what produces Tat?

The Trans-activator of transcription (Tat) plays a crucial role in regulating the transcription process of HIV-1. But which state of the Long Terminal Repeat (LTR) produces Tat? Is it the "...
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Do molecular motors have a life time?

Most of the enzymes have a certain lifetime. I want to know that do molecular motors have a certain lifetime after which they degenerate? Any reference will be appreciated. Basically, I just want to ...
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What is the difference among biochemistry, molecular biology, molecular genetics and structural biology?

I have never heard of straigthforward definitions of these fields in my college lectures, and the Internet searches were not very helpful. However, from what I have learned at different subjects, this ...
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1answer
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Why magnesium ion is needed for activity of G-proteins?

I was studying about G-protein coupled signaling sysytem, somewhere they have mentioned about need of Mg$^{2+}$ for acticty of G-protein and related it to increase of cyclic AMP production. On further ...
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51 views

Immunoprecipitation compared to western blotting

Immunoprecipitation and western blotting are both used to locate a specific protein within a sample and to isolate it. In immunoprecipitation, a specific antibody and agarose beads ( or other ...
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Design rules for DNA linkers

I want to use double stranded DNA linkers to physically bind two "things" together, by grafting ssDNA on each one of them and using DNA hybridization as the locking mechanism. I do not expect the ...
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Endocytic pathway: Macropinocytosis

So I'm trying to understand this phrase: Unlike other endocytic pathways, macropinocytosis is acutely induced by growth factors From the following paper The 4 endocytic pathways I know of are ...
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Can cysteine alone change pigmentation?

According to this graph (from here): cysteine contributes to pheomelanogenesis, and having a high enough concentration of cysteine makes the shift towards pheomelanin instead of eumelanin. So my ...
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4answers
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How to find suitable qRTPCR reference gene for a inflammatory response experiment?

I have tried several housekeeping genes – Hprt, β-actin and GAPDH, to analyze the relative expression of a cytokine for measuring the inflammatory local response in mice ears. However, all ...
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Is NMDA produced in the body?

On the wiki page for NMDA it says that NMDA is a synthetic substance that mimics glutamate. So why does the body not use glutamate instead of NMDA? Also how is it possible that our body can produce ...
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Will DNA nanostructures be useful for medical applications?

There is a lot of work being done on developing small nanomechanical structures and even small nanomechanical actuators built with DNA. I have heard researchers motivate this research with claims ...
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What is an acceptable qPCR efficiency when adjust using the Pfaffl equation?

I have efficiencies of 76% and 85%. THis is clearly below what is normally acceptable. But the pfaffl equation corrects this, doesnt it? However is it acceptable to publish this data?
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Emergence of novel protein interactions by mutation of amino acids

Are there any examples of proteins that, without coming from a recent duplication event, underwent a mutation(s) that caused it to have a novel interaction with a new ligand, substrate, other protein ...
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Can Dpn1 digest hybrid PCR product with only one methylated strand?

In Site directed mutagenesis using PCR, after a cycle we obtain a hybrid molecule with one parental strand and other newly synthesized unmethylated strand. This is followed by Dpn1 digestion. Does ...
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Gene cluster of interest not being amplified in PCR

In a lab, I currently have a sample of Rhizobium sp. NT-26. This bacteria is a chemolithoautotrophic arsenite-oxidizer, and I want to clone the arsenite oxidase genes into another bacteria strain in ...
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Can mRNA be used by ribosomes more than once?

Can mRNA be used by ribosomes more than once? I mean can mRNA be translated more than one time? If not what will happen to it after translation?
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Does the molecular composition of human body change after a period of time?

I was discussing change in human biology over time and my two in-laws charged in saying, "we're molecularly different after x". I didn't pay attention to what time period they exactly mentioned (hence ...