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Questions tagged [molecular-biology]

The study of the molecular processes underlying life.

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What could be the components of the ddPCR mix here, and what is the meaning of VIC FAM HEX?

Can someone please explain me the procedure shown in this diagram?
Rio's user avatar
  • 1
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Why is there no Ligase in Ligation Independent Cloning?

Ligation Independent Cloning literally says no need Ligation, but it still needs ligase to anneal the fragment to vector. And the Protocol used T4 DNA Ligase for anneal process. What does this mean &...
Gordon Chao's user avatar
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Setting up lab at home [closed]

I'm considering doing some plant bioengineering at home for fun. From what I have read, the most dangerous part is the usage of Agrobacterium. I saw another thread (Is it possible to genetically ...
psubodiosa's user avatar
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0 answers
9 views

How much data to expect from metabarcoding? [migrated]

I am about to conduct my first metabarcoding study. We will be using the ITS amplicon to look at fungal community composition in soil samples. I need to write a data management plan before I actually ...
Rendzina's user avatar
-1 votes
0 answers
15 views

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.
helpdaworld's user avatar
7 votes
2 answers
86 views

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 ...
Mikayla Eckel Cifrese's user avatar
1 vote
0 answers
16 views

#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 ...
Gordon Chao's user avatar
1 vote
1 answer
47 views

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 ...
Shivam Agarwal's user avatar
1 vote
0 answers
44 views

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 ...
Mikhail Gaichenkov's user avatar
3 votes
2 answers
124 views

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 ...
imrobert's user avatar
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1 answer
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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 ...
aquaporin's user avatar
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1 answer
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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-...
OdinTheDO's user avatar
3 votes
1 answer
66 views

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 ...
Ivan Spirandelli's user avatar
2 votes
1 answer
52 views

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 ...
Hdje's user avatar
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0 answers
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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 ...
OdinTheDO's user avatar
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0 answers
15 views

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 ...
ceno980's user avatar
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1 answer
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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 ...
Jayanth Vegesna's user avatar
2 votes
1 answer
53 views

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 ...
aquaporin's user avatar
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1 vote
1 answer
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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 ...
Emanuel Landeholm's user avatar
1 vote
2 answers
49 views

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 ...
Gigiux's user avatar
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1 answer
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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 ...
user78810's user avatar
3 votes
2 answers
132 views

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 ...
Michael Gruenstaeudl's user avatar
0 votes
0 answers
27 views

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 ...
CaroZ's user avatar
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1 answer
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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-...
ceno980's user avatar
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1 vote
1 answer
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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 ...
me1234's user avatar
  • 13
1 vote
1 answer
94 views

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 ...
mgarort's user avatar
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0 answers
12 views

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? ...
raptorlane's user avatar
1 vote
0 answers
87 views

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 ...
Tom Murphy's user avatar
0 votes
0 answers
98 views

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 ...
ninja_fun's user avatar
0 votes
1 answer
43 views

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 ...
ceno980's user avatar
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3 votes
1 answer
128 views

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.....
PAWAN's user avatar
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1 vote
2 answers
61 views

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 ...
Lee's user avatar
  • 11
0 votes
1 answer
65 views

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, ...
Andrew Roots's user avatar
0 votes
2 answers
123 views

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 ...
Amit Kumar's user avatar
2 votes
1 answer
402 views

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? ...
ManRow's user avatar
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0 votes
0 answers
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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 ...
Deepesh Bhatt's user avatar
0 votes
1 answer
37 views

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% ...
Tom Murphy's user avatar
2 votes
1 answer
173 views

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 ...
Mathew's user avatar
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4 votes
0 answers
121 views

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 ...
Lauri's user avatar
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0 answers
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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 ...
bio's user avatar
  • 1
0 votes
0 answers
38 views

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 ...
Jaston's user avatar
  • 1
5 votes
1 answer
647 views

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 ...
Ben Zelnick's user avatar
0 votes
0 answers
30 views

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 ...
TheChymera's user avatar
  • 1,336
0 votes
0 answers
265 views

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....
Felix H.'s user avatar
  • 318
0 votes
1 answer
108 views

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&...
Doug Null's user avatar
  • 115
1 vote
1 answer
39 views

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 ...
jettosutorimu's user avatar
0 votes
0 answers
22 views

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 ...
Ke Keiss's user avatar
0 votes
1 answer
171 views

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? ...
Growing6884's user avatar
1 vote
0 answers
71 views

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 ...
arsy's user avatar
  • 19
1 vote
1 answer
55 views

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 ...
Ryan's user avatar
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