Questions tagged [molecular-biology]
The study of the molecular processes underlying life.
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Need help choosing a plasmid that induces increased trehalose and glycerol production in yeast
I wanted to know how I should go about choosing a plasmid that increases trehalose and glycerol production in yeast or if anyone had any ideas on suitable plasmids.
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What makes viruses like the flu and covid so tolerant of mutations compared to most other viruses?
I was curious about why we benefit from yearly flu shots and apparently will also benefit from yearly covid booster shots too, whereas this doesn't seem to be the case for most other vaccines -- even ...
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#Gateway Cloning How does gene of interest replace ccdB genes?
I knew that Gateway cloning used a site-specific recombination method, but I still cannot figure out how does gene of interest actually replace ccdB genes? Bacteriophage site-specific recombination
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Understanding DNA Fingerprinting
I am a high-school student learning about DNA fingerprinting. I know that satellite DNA is non-coding DNA and has a lot of repetitive sequences, and the length of each repeat can be either short or ...
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Rectangle-like structures and their folding in biology
I've heard that mathematics helps to explain some biological problem. For example gömböc, which was a well hidden body from mathematicians, explains the body structure of some tortoises in relation to ...
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What is H-activation vs. O-activation in the context of cellular respiration?
I was reading this article on Albert Szent-Gyorgyi and on page 7 there's this statement:
Now, I thought myself capable of tackling a biochemical problem. I
embarked on biological oxidations. At that ...
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What is the minimum Ct value that you would consider indicates no gene expression?
I am doing relative quantification to compare gene expression between a control with several mutant backgrounds using qPCR.
Looking online I find several different sources suggesting different values ...
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Do right-handed helices bind to right-handed helices, and vice versa?
I know that B-conformation DNA is a right-handed helix, and most proteins that form helices form right-handed, not left-handed, helices (1). Furthermore, "Many transcription factors have an alpha-...
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Overlapping atomic radii in data of experimentally observed protein assemblies
I am looking at experimentally observed configurations of viral capsid proteins like that of the tobacco mosaic virus. https://www.rcsb.org/structure/6R7M
When taking the atom centers of a monomer and ...
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Correlation of Meselson and Stahl with “multifork” replication in E.coli
Because of the limiting value of the rate of DNA replication, rapidly dividing E.coli use multiple replication forks [1][2]. Thus, DNA replication of one generation has already begun in the previous ...
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Will diffusible protein aggregates coated in cell-free nucleic acids near a depolarizing neuron's soma diffuse along the axon to synapsing neurons?
Edit in response to feedback in comments requesting specific details, etc.: Will aqueously diffusible protein oligomers and protofibrils coated in cell-free nucleic acids in the aqueous interstitial ...
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Receptor tyrosine kinases: Clarification about what is meant by stabilization of the receptor
I am reading a journal paper. This paper focuses on how neural cell adhesion molecule (NCAM) interacts with fibroblast growth factor receptor 1 (FGFR1) and promotes its stabilization.
When FGF binds ...
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Why do we choose to use agar instead of agarose in various microbial applications?
When performing gel-electrophoresis we always use agarose. Is there a reason we can't perform it using Agar?
And in microbial culture Agar is commonly used as solidifying agent, could this be replaced ...
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Best way to predict the effects of deletion mutations on protein function?
I have the coding sequences of a WT gene and several mutants of this gene (deletion mutations varying from 5bp to 50% of the sequence deleted). What is the best method for inferring the impact of ...
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The split in Boroeutheria into Euarchontoglires and Laurasiatheria. Was this due to the opening up of the Atlantic Ocean?
I'm asking this question as a cat owner. I've seen a figure like 94 MA for the most recent ancestor of both cats and humans (this from, I guess, molecular clock arguments), and it kind of lines up ...
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Who discovered that phage phiX174 has a single-stranded genome?
I have recently read that Erwin Chargaff has discovered that the genome of phage phiX174 (ϕχ174) is single-stranded. However I could not find the paper reporting this discovery.
Is there a link to the ...
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Mesh formation in the wells of SDS PAGE. How to solve it?
I casted 10% resolving gel and 4% stacking gel and every time a mesh like structure ( polymerisation) in the wells are formed.How to avoid this from happening and how do i get clear wells? If someone ...
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Change of DNA concentration due to restriction digest?
Assume that you perform a restriction digest in a molecular biology lab: you combine genomic DNA, a restriction endonuclease (e.g., EcoRI), and the optimal buffer for that endonuclease and are about ...
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Recovering DNA from an RNA-extraction/purification kit
We are extracting RNA from single insects with the later purpose of performing RNA-seq. We are using the RNeasy Plus Miniki from Qiagen, which involves the use of eliminator columns as you can see ...
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What is meant by the stabilization of a receptor?
I am reading a journal paper, and have a question about the below statement:
PSD-95 is involved in the recruitment, trafficking and stabilization
of N-methyl-D-aspartic acid receptors (NMDARs) and
α-...
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Is the 5% of the oxygen used in the breathing process fully transformed into CO2?
More specific, I found out that the amount of oxygen we inspire is 21% from the total amount, with 0.04% CO2. The expired amount is 16% oxygen, with 4% CO2. Where does the remaining 1% oxygen go? Or ...
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Why are camelid-derived nanobodies called VHH (variable heavy domain of heavy chain)?
Single-domain antibodies (or nanobodies) derived from camelid heavy-chain antibodies are called VHH antibodies, where VHH stands for "variable heavy domain of heavy chain". I assume the ...
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What is the optimal pO2 concentration for automated reactor batch mode EColi expression?
I am wondering what is the optimal pO2 level for an reactor based expression? All protocols I have found indicate for E.Coli pO2 levels just bigger 20%. So, I am wondering what is the optimal level? ...
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Can you store 5% BSA, in TBST, in -20C?
I have stock solution of 5% BSA prepared in TBST I use to make primary antibody dilutions for western blot. I'll admit I just assumed -20C, with freezing and thawing as needed, was an acceptable means ...
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How many GTPs are used in prokaryotic translation?
Here is the question: How many GTP are necessary to synthesize 2 linear peptides of 11 amino acids each using an in vitro prokaryotic system? Assume the tRNAs provided are already loaded with their ...
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Why doesn't treating neurons with a high sodium solution depolarize their membranes?
I am reading a journal paper, and in one of their experiments they treated organotypic hippocampal slice cultures with a high potassium solution to depolarize the neuronal membranes:
We found that ...
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Can a person have different sex at cellular level?
I mean like every cell has a sex chromosome.So does a male with XY chromosomes has all the cells in all the organs inside his body of XY chromosomes only? And vice versa.....
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Storing bacteria in a dry, room temperature long-term storage whilst maintaining viability
I'm quite new to biology, but I'm wondering if there are any methods of storing bacteria in long-term, dry conditions with no climate control. Perhaps they could be dormant in a powder or granule-like ...
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How come SSBPs in RPA don't bind primers?
I've started reading about the recombinase polymerase amplification (RPA). I'm learning that in RPA, recombinase enzyme binds to primers, then makes them anneal to the complementary target DNA strand, ...
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Does recombination occur in both chromatid of a chromosome with homologous chromosome? Or only 1 chromatid participate in crossing over?
A chromosome has two chromatids. In meiosis weather both chromatid participate in crossing over or just only 1 chromatid does?
So, I am asking whether 1 turquoise and 1 purple chromatid participate ...
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Can humans metabolize D-malate?
Only the L-isomer is produced naturally, while racemic mixtures are produced synthetically and used commercially as food additives and energy supplements.
So what happens when we consume D-malate? ...
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Is crossveinless in Drosophila melanogaster example of condition mutant or phenocarpy?
This is the original question -
Ques - A researcher exposed Drosophila larvae to 37°C during their growth. One of the adult flies that emerged had a crossveinless phenotype. When this crossveinless ...
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Induction of IFN-beta in HEK293T
I'm trying to increase expression of a protein we're attempting to study, UBL7, supposedly unregulated by Type I Interferon and particularly IFN-beta.
I've tried treating HEK293T cells (~60% ...
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Why is the codon size three, rather than four? [duplicate]
The genetic code consists of triplets, each of which (apart from the stop codons) yields an amino acid when the mRNA is translated.
But why did triplets evolve, rather than a longer or shorter codon ...
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Does the molecules in nerve cell membrane change 100% during the life of the nerve cell?
In their lifespan nerve cells do not divide and so they stay the same. They do get damaged sometimes and require some maintenance and change their axons a bit. They also require a lot of energy so ...
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Ubiquitous overexpression line of a gene expressed higher gene expression in leaf but not in seeds
I tried to make ubiquitous overexpression lines of a gene using a constitutive promoter vector in plant. I got multiple regenerated plants through tissue cultures.
At T0, T1, T2 leaves tissues, the ...
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Effects of oxygenated water on bacteria
I was curious if any of you would happen to have any experience with this but any hypotheses regarding how this would turn out would be much appreciated.
I’m wondering if water fully aerated with ...
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According to an online course, ribose and adenine can bond to make ATP. Is this true?
I recently came across this question in the MIT Open Learning Library Pre-7.01 Biology Course. It is question 2d in Problem Set 1 (archived link).
The question, as well as the correct answers and ...
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Transfecting cocoon or chrysalis
Do you know whether anybody tried to transfect insects during their cocoon/chrysalis stage, and if so do you have a link to such studies?
I was thinking it would be easier to do given that it's a more ...
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Migration of cut vs. non-cut plasmid on gel
As you might know there are 3 common forms of a plasmid:
ccc-form (CCC), being supercoiled.
oc-form (OC), being nicked and therefore relaxed.
linearized form (L), being cut on both strands and linear....
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What is the approx. diameter of a completely "folded up" human DNA molecule, in inches?
The human DNA molecule would be about 6ft if stretched out to a straight line.
I'm curious what the diameter of the DNA molecule normally is when it is "all scrunched up" or "bundled&...
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ddT-tailed TA cloning, and the fate of a double nicked plasmid in E. coli
In an undergraduate lab class on TA cloning, it was explained that ddNTPs are used as the substrate for terminal transferase when making the T overhangs of the vector. I was told this was to ensure ...
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Live cell imaging using confocal microscope - Question about the microscope settings and laser wavelength
I am doing some calcium imaging to measure calcium levels in HeLa cells. To do this I have expressed cameleon calcium indicator (YC3.60) in the cells and I am using confocal microscope Fluoview for ...
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Why is There a Necessity for Two Rounds of Cell Division and Four Daughter Cells in Meiosis
Why does meiosis involve two rounds of cell division instead of stopping after meiosis I, where each daughter cell would have one chromosome randomly selected from each pair of homologous chromosomes? ...
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Does blunt end have a hydrogen bond?
I am an undergraduate student of biology.
I saw a lecturer online, who said that sticky ends makes phosphodiester and hydrogen bonds cut. (also here).
But why blunt end just makes phospodiester bonds ...
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modify PCR steps to include a ligation
Imagine a multiplex PCR in which after the extension step, the dsDNA is nicked and requires a ligation reaction to repair the nick before the next denaturation step. So the steps would be:
Denature
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What should be considered a GC clamp in a qPCR primer?
Hello there!
After reading different sources regarding designing of qPCR primers, I'm a little confused regarding the concept of GC clamp.
Can you help me by telling which of these cases below is ...
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Why am I getting a large horizontal band spreading across my native gel?
On every gel of this type that I've ran so far, I'm getting this large band interfering with my gel analysis no matter how much troubleshooting I've done. This is a Novex Wedgewell 6% Tris-Glycine Gel ...
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Are all proteins translated by the RER ribosomes destined for the Golgi apparatus?
The proteins translated by the free ribosomes can fold in the cytoplasm and never go through the endomembrane system. But when the endomembrane system is described, it is always stated that the ...
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What is meant by 20 ul final concentration of polyacrylamide?
I am performing a phenol-chloroform extraction in which precipitation is enhanced by linear polyacrylamide. The SDS for linear polyacrylamide mentions that it should be used such that its final ...
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