Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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1answer
70 views

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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Does anyone know of any other papers investigating this polymer mechanism idea?

https://www.google.com/amp/s/amp.dw.com/en/german-researchers-are-working-on-a-tissue-that-will-tell-you-whether-youve-got-the-flu/a-17030239 I am having trouble finding any other papers that describe ...
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55 views

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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62 views

"No two cells in an organism have an identical genome sequence"

In Applications of Single-cell DNA Sequencing there is a claim Indeed, it can be safely assumed that no two cells in an organism have an identical genome sequence, in particular, organisms whose ...
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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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Why use GAL4-UAS + anti-GFP when you can just directly stain against your protein of interest? [closed]

When visualising gene expression, you can use UAS-GAL4 to drive expression of GFP in all cells that express the protein and then stain the cell with anti-GFP. But why do this when you could just ...
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1answer
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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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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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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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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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Where in the cell does this enhancer RNA knockdown take place?

In Pneuli et al 2015, they knock down an enhancer RNA using RNAi, testing whether it is a mere byproduct or whether it has a key role in the enhancer's function. They find their system works: the ...
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1answer
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Could p-loop bind fully protonated ATP?

The phosphate tail of ATP binds the p-loop motif, evolutionary conserved, going back to since forever. In the dominant model, the deprotonated hydroxyl groups are complexed with Mg2+, at least two of ...
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What are the additional considerations for primer design in ancient DNA?

I'm familiar with the principles of primer design and have previously designed primers for use in modern DNA. However, in my current project I am working with ancient DNA (nuclear gene) and need to ...
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1answer
51 views

Why is ACE 2 located on the Alveolar side of Pulmonary Epithelium?

Location and Purpose of ACE 2. Given that the primary purpose of the transmembrane enzyme ACE 2 is ostensibly to bind Angiotensin 1 and 2 in order to convert these to derivatives such as Angiotensin [...
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Can a polymer coated with antibodies have enough attraction to wrap around a virus?

Archived source for image Please ignore the signal release. Does anyone know if it’s possible for polymer to wrap around a virus?
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1answer
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How does the hydrophobic amino acid fuse the corona virus with the host cell membrane?

I am reading the article How the coronavirus infects cells — and why Delta is so dangerous. It describes the fusion process of the virus into the host cell as follows right above an animation ...
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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, ...
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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. ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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1answer
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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1answer
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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.
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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 ...
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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 ...
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1answer
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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 ...
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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 ...
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1answer
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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 ...
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1answer
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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 ...
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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 ...
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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 ...
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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 (...
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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 ...
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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 ...
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1answer
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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 ...
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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 ...
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1answer
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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 ...
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1answer
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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?
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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 ...
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1answer
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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-...
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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 ...

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