Questions tagged [molecular-biology]
The study of the molecular processes underlying life.
1,623
questions
5
votes
1answer
72 views
Methods of investigating the occurrence of non-standard bases in nucleic acids
Recently the popular scientific press gave considerable publicity to three publications in Science (30th April 2021 — see below) relating to the substitution of the nucleic acid base, 2-amino adenine, ...
-1
votes
0answers
16 views
Are liposomes structurally the same as endosomes?
I have recently learnt about liposomes, and from the definition on this site, it states that "A liposome is a spherical vesicle having at least one phospholipid bilayer". I know that ...
6
votes
1answer
112 views
Why doesn't RNA polymerase just rotate?
I read A little help understanding DNA supercoiling , Understanding DNA supercoiling , and Why does underwinding create topological strain of DNA? , but there's still something I don't get. ...
1
vote
0answers
12 views
Question about using primary neuronal cultures from mice to support findings from in vivo models
I am analysing synapse formation during early postnatal development using the brains of postnatal day 2 (P2) and postnatal day 10 (P10) wild-type and knockout mice. Through Western blot analysis, I ...
-3
votes
0answers
16 views
How do binding proteins lead to conformational changes in fluorescent proteins in reporter genes?
Is the protein backbone in many fluorescent proteins really necessary to lead to this conformational backbone, as just a very small portion of the protein is actually fluorescent.
1
vote
0answers
38 views
Is lactic acid build up the cause of muscle fatigue or only a symptom?
If your body could magically instantly remove lactic acid as it is produced, would that make you immune to muscle fatigue, or is the lactic acid only a symptom of muscle fatigue and instead exists, at ...
0
votes
0answers
22 views
Which genes/proteins constitute the core components of the circadian clock?
What the title says.
For instance in Drosophila melanogaster and Mus musculus (see Patke et al. 2020) the CLOCK, CYCLE/BMAL, CRYPTOCHROME, PERIOD setup seems to be conserved. But other components also ...
1
vote
1answer
119 views
Is 'constitutive effect' the proper term for explaining a biological effect that occurs due to the constitutive knockout of a gene in a mouse?
I am working on an experiment involving the analysis of expression of a protein X in wild-type (+/+) and knockout mice (-/-). In the knockout mice, the gene of interest has been constitutively knocked ...
9
votes
2answers
443 views
Tips for longer fragment size and higher purity of insect DNA
Aim
In a pilot experiment I tested three different genomic DNA extraction methods on the non-model organism Pieris mannii (southern small white; Insecta, Lepidoptera, Pieridae). The goal was to ...
2
votes
1answer
65 views
Why are heterologous expression systems such as mammalian cell lines commonly used for studying interactions between neuronal proteins?
I am reading papers about heterologous expression systems and I have seen that they are used a lot in neuroscience to studying interactions between proteins that are normally expressed in the brain.
I ...
-3
votes
1answer
47 views
How does protein knockdown allow a phenotype to be observed?
I am trying to understand how AID2 technology works.
I came across an article that says "Protein knockdown using the auxin-inducible degron (AID) technology is useful to study protein function in ...
1
vote
0answers
51 views
What is the effect of an acidic solution on hydrolytic enzymes?
I'm working on a school research project and my research question is "What is the effect of increasing concentrations of Acid X on hydrolytic enzymes, measured through the loss of mass of leaf ...
-1
votes
1answer
78 views
What are the prospects in synthetic biology, especially in the introduction of biological computers? [closed]
One of the interesting areas of synthetic biology is the so-called biological computers. A biological computer refers to an engineered biological system that can perform computer-like operations. I ...
0
votes
0answers
23 views
Preventing the transcription bubble from occurring in an individual gene
I'm trying to find a way to stop the transcription bubble from occurring over a individual gene in humans. I need the act of transcription to be inhibited, siRNA knock down of the transcript does not ...
0
votes
0answers
39 views
The average of Ct values in real-time PCR
The Ct value is the number of cycles when the "PCR amplification curve with the horizontal axis as the number of cycles" and the "predetermined threshold" intersect, and is not ...
1
vote
0answers
69 views
Will a Kozak sequence within a coding sequence interfere with eukaryotic expression?
I want to make a DNA vaccine for fish by using plasmid pcDNA3.1(+) with a bacterial antigen. Unfortunately, there is a Kozak sequence in the middle of my target gene.
I am concerned that this Kozak ...
0
votes
1answer
26 views
Can Ni-NTA-Atto Conjugates bind to single His-tag
Can I label a protein with a single His-tag with Ni-NTA-Atto conjugates?
Papers generally use this technique to label 6His-tag.
0
votes
0answers
24 views
Why bananas exposed in UVC light turn brown afterwards?
We have this research, where we test if our germicidal disinfection box is working and is functional by doing the banana test, where we expose the green banana to UVC and if the exposed peel turns ...
0
votes
0answers
56 views
How does auxin-inducible degron technology make it possible to observe an immediate phenotype? [duplicate]
I am having trouble understanding this paper, which says
Protein knockdown using the auxin-inducible degron (AID) technology is
useful to study protein function in living cells because it induces
...
3
votes
1answer
51 views
Polymerase Cycle Assembly (PCA) is not working (Only primrs in EF Gel)
Helllo All 👋!
I am working trying to assemble dsDNA fragments (for further golden gate domestication) via polymerase cycle assembly (PCA). After designing the required oligonucleotides with overlap ...
0
votes
0answers
28 views
Can a Gi GPCR receptor be equivalent to a Gs one?
Doesn't a Gi receptor agonist produce the same effects as a Gs receptor inverse agonist thus making them opposite and usable to achieve the same effects? I speculate this considering that one inhibits ...
0
votes
1answer
43 views
Is there any way to identify if chromosomes are inherited from the same parent?
I'm a PhD student in bioinformatics working on genomic data, and I was wondering:
If I have access to a person's chromosomes, is there an assay that can determine that two chromosomes come from the ...
2
votes
1answer
51 views
What is the point of calculating extinction coefficients of a protein without Cys residues?
ProtParam computes various physico-chemical properties that can be deduced from a protein sequence. One of these parameters are "Extinction coefficients". They provide two values. One value ...
4
votes
1answer
71 views
What is meant by “unique ligand” on the RCSB Protein Data Bank website?
I went to the https://www.rcsb.org/ site, and searched for some proteins. For each entry, “unique ligands” are listed.
I understand a ligand is a molecule or ion that binds to a metal atom. I don’t ...
1
vote
1answer
50 views
In plasmid-based transient transfection of mesenchymal stem cells, do I have to select for transfected cells and verify GOI expression via a reporter?
I am transiently transfecting mesenchymal stem cells with a mammalian plasmid-based expression vector that does not contain any mammalian selection marker and also the gene of interest will be cloned ...
0
votes
1answer
24 views
colocalization by IFA?
I have done IFA (immunofluorescence assay) previously but i targeted only one protein or i tagged my endogenous protein with GFP/RFP then i performed IFA. I want to do the IFA in parental cell line (...
8
votes
0answers
47 views
What actually kills a plant that requires winter dormancy if it is kept indoors all year?
In bonsai practice, beginners will commonly purchase a juniper (often Juniperus procumbens 'Nana'), which is an outdoor tree, and keep it inside all year. The tree invariably dies. It is commonly ...
4
votes
1answer
42 views
Genomic library preparation: Why does the restriction enzyme not cut into the gene?
I am currently trying to understand creating a genomic library more profoundly. In most textbooks I read (as well as wikipedia), they mentioned that the genomic library is created by isolating the DNA ...
2
votes
1answer
52 views
Is it possible to use two forward primer and one reverse primer?
I have eGFP and the gene fragment i assembled by pcr.The next step is that i have to join my fragment fragment into 3'p end of the eGFP.I have three primers FP1 is forward primer for eGFP, FP2 has ...
8
votes
2answers
437 views
Why do OX5034 GM mosquitos require the presence of tetracycline to survive? What does the drug do in this case?
I'm confused. Debug Fresno; why are the released mosquitos said to be sterile? from 2017 addresses male mosquitos released with a bacteria that will affect fertility of females after mating. They are ...
1
vote
1answer
39 views
Can a constitutively active kinase be highly regulated?
I am studying the protein kinase GSK3 and I am learning about the regulation of its activity. Many journal papers that I have read have stated that GSK3 is unique because it is a constitutively active ...
2
votes
1answer
36 views
Can oxytocin travel from one cell to another via gap junctions?
Oxytocin is a 9-residue secreted peptide. As a hormone, can it travel through gap junctions, assuming that it is stored in pre-synaptic neuronal vesicles?
0
votes
0answers
29 views
Is there “stem” organelles in plant meristems?
Two cytoplasmic genomes exist in plant in addition to the nuclear one. As far as I understand, they divide more or less during the entire life of the plant along with cell proliferation/growth in ...
1
vote
1answer
45 views
Can GFP reporting be used to track localization of peptides in the ER, Golgi, and plasma membrane?
Suppose I want to study the trafficking of a peptide throughout the ER, Golgi, and plasma membrane. An idea I had was labeling a secreted or plasma membrane integral protein with GFP and using time-...
1
vote
0answers
17 views
How does flow rate of Ion channels depend on the length of the selectivity filter?
The length of the selectivity filter of ion channels such as the potassium channel commonly is only half of the thickness of the membrane. Some book such as MBoC says this can benefit the transfer, so ...
0
votes
0answers
69 views
How can I clone a gene into a plasmid vector with an N-terminal his tag and TEV cleavage site between the tag and the start of the sequence?
I'm a scientist who has significant experience in chemistry but am relatively new to molecular biology and biochemical techniques. I'm trying to make an isolated domain of a protein (166 residues, 19....
1
vote
1answer
89 views
Why is DNA replication not 100% accurate
I've been reading about DNA mismatch repair (MMR) and how this process improves DNA fidelity. However, I was wondering, what is stopping MMR from correcting all mistakes in the daughter DNA with 100% ...
6
votes
3answers
385 views
Does the term 'protein expression' refer to the production of proteins only or also their regulation?
I am learning about molecular biology and I have come across the term 'protein expression' in a research paper. I have searched the definition of this term online and on the Thermo Fisher Scientific ...
0
votes
1answer
57 views
What are the uses of centrioles and matrix of centrosomes?
In centrosomes, the gamma-tubulin ring complexes (gamma-TuRC) located on the surface are essential as the nucleation site for the growing (with polarity) of microtubules.
However, I see that there is ...
1
vote
0answers
26 views
How do cilia beat?
From what I have learnt, the mechanism of the beating of cilia is: movement of dynein towards the (-)-end i.e. towards the microtubule-organizing center (MTOC), causing the 2 pairs of microtubules to (...
1
vote
0answers
21 views
When transmembrane proteins destined for the plasma membrane are in the ER membrane are they in their final folded form?
I am studying how transmembrane proteins are made and I have read that proteins that are destined for the plasma membrane are initially in the ER membrane and do not get translocated into the ER lumen ...
0
votes
1answer
32 views
What is meant by 'topologically continuous' in the context of cell compartmentalisation? [closed]
I am reading the textbook 'Molecular Biology of the Cell', and I am reading the chapter about the compartmentalisation of cells. I have come across the following statement:
The nucleus and the ...
6
votes
2answers
229 views
Can we dilute PureExpress Cell Free Mix to increase number of reactions?
Since the PureExpress Cell Free mix is so expensive, I was wondering if it might be possible to just dilute the mix to increase the number of reactions we need to use.
From this image I found:
It ...
0
votes
0answers
19 views
Why do molecular generation models maximize “penalized logP” as a measure of drug-likeliness?
I found that Lipinski's rule of five states that Log P (octanol-water partition coefficient, lipophilicity measure) usually should not exceed 5.
Many papers about drug discovery machine learning ...
0
votes
0answers
29 views
How to incerase the efficiency of co-immunoprecipitation?
immunoprecipitation recently. My main problem is i am getting very clean and my target protein only (as you see in the lane 3,4,5,6) but when i reduced the NP40 concentration to 0.05 percentage i ...
0
votes
0answers
27 views
Low Density Lipoprotein (LDL) in the endosome
I am learning vesicular transport of LDL endocytosis. I understand as pH of the endosome is lower (around 6.0) than cytosol (around 7.2) due to the H+ pump, so LDL disassembles from the LDL receptor ...
1
vote
1answer
77 views
How broad are the conclusions that one can make from a heterologous expression experiment?
I am studying whether a neural protein regulates the activity of the protein GSK3. I am using heterologous expression systems where I am overexpressing the neural protein in CHO cells (via ...
3
votes
1answer
111 views
How can I change the payload of a bacteriophage used to transform E. coli?
I was looking at bacteriophages and how they're used to transform E.coli. While the whole process of how a bacteriophage works makes sense theoretically, I wanted to know how one goes about changing ...
2
votes
1answer
166 views
Can restriction enzymes (Type II) displace single-stranded binding proteins (SSB)?
Many type II restriction enzymes have been shown to be able to cut ssDNA.
If single-stranded binding proteins are bound to single-stranded DNA (ssDNA), does this prevent restriction enzymes which cut ...
-2
votes
1answer
82 views
Does anyone have a tutorial or some guide to get started with Rosetta protein modeling and design tool? (I am a Mac user) [closed]
I have been trying to get started with Rosetta protein modeling and design software bundle. I searched online but the tutorials in the Rosetta website are difficult follow. I have the binaries already ...
