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Questions tagged [molecular-genetics]

The scientific study of the structure and function of genes at the molecular level, particularly chromosomes and DNA.

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Do cells know or imagine how each part of the DNA influences body structure and function? How else would evolution happen in specific ways?

Consider how an octopus looks at a rock and it's entire body blends in to resemble the rock. Consider how insects evolved to resemble leaves or twigs. Even frogs, butterflies and other creatures ...
Nav's user avatar
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Can the mechanism behind changes in protein expression be inferred by the timing of those changes?

My question relates to the timing of protein expression changes, and whether there is a literature-based consensus as to how long changes in protein generally take. For example, if protein changes 24h ...
Ryan Ellison's user avatar
1 vote
1 answer
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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 ...
Shivam Agarwal's user avatar
2 votes
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Is Regenerative Brain Tissue Technology In The Near Future?

I got 99% of my information from articles I found in NIH's library; I can't cite anything now because I am on a timed session in a public library. I've been reading material from research papers in ...
Salus's user avatar
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How do you find the template strand for a sequence where start codon is in both strands?

Maybe I'm missing something very obvious but I can't seem to understand how to find the template strand given a sequence and its complementary strand if both strands contain ATG from 5' -> 3'. ...
Naumhat's user avatar
1 vote
2 answers
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Preserving a sample for mtDNA and nuclear DNA analysis

Imagine a person in the early half of the 20th century (1900 to 1950) took some kind of sample(s) from a living human body using any technology of the era. They then stored it using any technology ...
CXJ's user avatar
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With CRISPR-mediated gene editing, can the PAM for the guide RNA also be site of the desired edit?

I'm hoping to use CRISPR-Cas9 in yeast to change a single nucleotide in a gene of interest. While there are a couple potential guide RNA sequences I could use, the best option's PAM sequence (TGG) it ...
PigweedHater's user avatar
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Why is the expected time to coalesce the same as the ploidy times inbreeding effective population size?

The expected time to coalesce, in generations, is the same as the ploidy (e.g., 2 for humans) times Nef, the inbreeding effective population size, under coalescent theory. Why? Both ploidy * Nef and ...
BigMistake's user avatar
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3 answers
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Have there ever been "half-twins" who were halfway between siblings and twins?

Have there ever been two human siblings who were 75% or more genetically related?
BigMistake's user avatar
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Has perturbation theory been applied to mutation process frameworks?

For example, imagine this Feynman diagram: This is analogous to mutational homoplasy. When comparing haplotypes, there are many possible tree topologies. Under maximum parsimony, we ignore suboptimal ...
BigMistake's user avatar
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Sequencing a PCR product with no band

I did a PCR that successfully showed the appropriate bands one time, but when I tried to re-do the same PCR just at a larger quantity to send for Sanger sequencing, very faint or no bands were seen. ...
Nalonda's user avatar
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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, ...
Andrew Roots's user avatar
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2 answers
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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 ...
Amit Kumar's user avatar
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What is the most accurate polygenic score for Alzheimer’s disease?

To date, which polygenic score (i.e. which study) has produced the largest effect size for Alzheimer’s prediction in out-of-sample validation?
BigMistake's user avatar
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Why do many plasmids for Flp-mediated Flip-Excision only flanked by one FRT site on each side and not two non-homologous?

I'm trying to build some molecular gene switches into a model, and want to use both Cre and Flp. I understand how to invert gene segments with Cre, double floxing (e.g. with loxP and lox2272, like in ...
immunoLogical's user avatar
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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
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Gene Name Finding

X8HS20 - please help, I am not able to find the proper name or function of this gene in any database - can someone kindly help to figure out what it is ? I hypothesize that it is some gene of ...
Stack Man's user avatar
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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&...
Doug Null's user avatar
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How pitch of a DNA Helix is 3.4 nm?

How pitch of a DNA Helix is 3.4 nm? In the image that I have attached, the numbers with prime represent the number of base pair and normal numbers represent the number of gap elements between two base ...
Peter swift's user avatar
1 vote
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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 ...
arsy's user avatar
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3 answers
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What is the exact definition of a "gene"?

(In this question, I'm only considering the molecular-biology notion of a gene, not the older Mendelian notion.) Wikipedia defines a "gene" as "a sequence of nucleotides in DNA that is ...
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Programs/software used to create illustrations and scientific paper ready figures

I am new to the field of molecular biology. I am finding the need to generate illustrative figures displaying interplay between proteins, DNA and various other molecular constructs at different scales ...
Zebra Fish's user avatar
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1 answer
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How random is genetic recombination?

Two parents can have a very large number of different potential offsprings, and it's common knowledge that the daughter chromosomes in meiosis are produced randomly, i.e. in crossover, the exact spots ...
Alex L's user avatar
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Testing primer for misspriming in 770 Mb lepidopteran genome

I designed primer pairs for a lepidopteran genome (Cydia pomonella, codling moth, ~770 Mb, ~60% transposable elements, Reference Genome Paper). I have around 60 primer pairs that bind to a specific ...
CoDa's user avatar
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CRISPR-Cas9 system, DNA repair

As a critical stage in the CRISPR-Cas9 system, two different mechanisms of DNA repair can occur in the target DNA after RNA has been introduced: non-homologous end joining (NHEJ) and homologous ...
Wayne's user avatar
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1 answer
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Do we need to underline the name of a gene while handwriting?

While teaching about the cry genes and the Cry proteins in Biology class, my teacher told us that the names of genes are always written in lowercase and should be italicized, and the name of protein ...
Juhi Kumari's user avatar
1 vote
0 answers
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Identification of cells containing the gene of interest at a double strand break instead of undergoing recombination

If I tried to knock in a gene for example KANMX and want to swap it with say some gene "x", but, since, there can be double strand break in the DNA and KANMX may get inserted within the ds ...
Adaintyflower's user avatar
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50 views

Is there a word to describe a sample of DNA that can be sequenced?

This is a question about terminology. I want to know if there is a word that is used to describe a sample as "able to be sequenced". My rough guess would be "sequencable". But that ...
Kevin Bowersox's user avatar
6 votes
1 answer
127 views

What are the relative frequencies of dominance and codominance in genes underlying phenotypic characters?

Many questions already exist regarding dominance/recessive relationships, see e.g. here. I am asking this question because I have often wished to have it to refer to, and also genuinely curious ...
Maximilian Press's user avatar
5 votes
0 answers
84 views

Is there a name for this type of diagram?

Is there any commonly used name for this type of diagram / symbology? I have not been able to find them referred to by any name.
tsj's user avatar
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Single-cell subcloning of BV-2 cells?

I am trying to knock-out genes in BV-2 cell line. However, the majority of protocols require cell subcloning and expanding. I tried to subcone these cells and grow clones in DMEM+10% heat-inactivated ...
Monika1223's user avatar
12 votes
1 answer
2k views

How did Mendel know if a plant was a homozygous tall (TT), or a heterozygous tall (Tt)?

I had some issues while studying Mendel’s rules of inheritance. How did Mendel, while running his test crosses, know if the plants in his F0 generation were TT (homozygous tall) or Tt (heterozygous ...
Smarika Singh's user avatar
2 votes
1 answer
43 views

Receptors and their distribution over the human population

For humans it has been reported that there are three vasopressin receptors (AVPR1a) and four dopamine receptors (DRD2). (Source: UNIPROT) Question: Does every human contain all three variants of ...
SK SARIF HASSAN's user avatar
0 votes
1 answer
66 views

When do retinal cells stop differentiating? [closed]

I am having a hard time recalling where I had heard this, but I do recall someone saying (perhaps in a video) that cells in the retina divide very rapidly during infancy due to ongoing development of ...
Zuhair Qureshi's user avatar
0 votes
2 answers
97 views

Is retinoblastoma truly an autosomal dominant condition?

I am getting, in my opinion, very conflicting information from sources about the inheritance of retinoblastoma, a type of cancer. Hereditary retinoblastoma is associated with defects in the gene ...
Zuhair Qureshi's user avatar
1 vote
1 answer
191 views

Do cells not grow during mitotic S phase (synthesis phase of interphase of the cell cycle)?

Both these links mention cell growth during G1 and G2 phase, but not during synthesis phase (only DNA replication is mentioned). Is replication all that happens and is there no cell growth during S ...
vishesh jain's user avatar
1 vote
0 answers
291 views

What precisely is the pairwise Fst calculated in GenAlEx 6.5?

A professor of population genetics informed me that there is not a unique notion of pairwise Fst scores in the literature. This information has made me more cautious about what may be implemented by a ...
Galen's user avatar
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1 vote
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Genetic modifications to produce blue hair

The following animals are known to produce blue pigmentation: Linckia laevigata (blue star, study reveals blue carotenoprotein, linkiacyanin) Nessaea batesii (obrina olivewing, study reveals blue ...
Dave Jarvis's user avatar
1 vote
0 answers
22 views

What is the relationship between stress granules and circular RNAs?

I have read that circRNAs act as sponges for miRNAs and that stress granules help reduce chronic cellular stress and they are composed of proteins and RNAs. I'm interested in the relationship between ...
Shadan Alrawi's user avatar
2 votes
0 answers
49 views

What forms a mutation hotspot?

From https://en.wikipedia.org/wiki/Recombination_hotspot#:~:text=Recombination%20hotspots%20are%20regions%20in,that%20of%20the%20surrounding%20region. I understand that hotspots may arise when certain ...
AnethOthbo's user avatar
3 votes
1 answer
83 views

How is a haploblock defined with only one SNP location?

I am reading Impact of estrogen receptor gene polymorphisms and mRNA levels on obesity and lipolysis – a cohort study and am looking at Figure 1. I understand that haplotypes are associated with ...
neurosciencecalc's user avatar
0 votes
0 answers
35 views

Biology (DNA electrophoresis with agarose)X

I'm researching a polymorphism using restriction fragment length polymorphism (RFLP) and gel electrophoresis. After RFLP, I should see fragments at 141bp and 111bp, but I can not see in 2% agarose, ...
seyed farhad sadr tabatabaie's user avatar
7 votes
2 answers
1k views

How are DNA virus cladograms actually calculated in practice? Is the procedure different for RNA viruses? Are these processes somewhat subjective?

The May 24, 2022 Bloomberg opinion piece Monkeypox Isn’t Looking Like a Covid-Sized Threat; It’s still early, but contact-tracing efforts and analysis of the virus’s genome offer hope that this ...
uhoh's user avatar
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2 votes
0 answers
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Apparant inconsistency in DNA topology theory in formation of origin of replication [duplicate]

I'm studying an introductory course in genetics and came across something I don't fully understand. I obviously used Google to find where I'm thinking wrong, but I still can't understand it. To ...
cDirac's user avatar
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3 votes
1 answer
100 views

How can SNP arrays be used to detect deletions within a gene?

I am reading a journal paper where the researchers are studying the effect of disease-causing mutations in the IL1RAPL1 gene. In the first figure of this paper, they show pedigrees of families where ...
ceno980's user avatar
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1 vote
4 answers
232 views

How to look for different transcripts for a protein?

I am trying to find all the different transcripts for a protein that translate into different isoforms of the protein. However, when I look it up online, there is no clear organized data on different ...
Ramil's user avatar
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1 vote
1 answer
54 views

What is the importance of radiation hybrid (RH) mapping in terms of genes?

I'm currently reading about radiation hybrid mapping with a TSP (traveling salesman problem) application in order to find an ordering of the genetic markers (i'm a mathematics student) and was ...
PianoMath's user avatar
1 vote
1 answer
276 views

Time required for DNA replication in E. coli

In a particular strain of E. coli, it was observed that DNA polymerase could add nucleotides to a growing chain of DNA at the rate of 600 per second. If the genome of this organism is 1.1mm long ...
Neerav Singla's user avatar
0 votes
1 answer
56 views

Why can SPRITE measure many simultaneous interactions?

Why is the SPRITE method not limited to a number of simultaneous interactions that can be measured, while microscopy and proximity ligation are limited to 2-3 interactions?
katara 's user avatar
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3 votes
1 answer
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Problem involving genetic interactions in yeast

I'm having difficulty with the following problem: In yeasts, genes MEC1 and SGS1 favor survival in response to HU (hydroxyurea). In the figure below, Δ indicates homozygosis for the mutant allele ...
Horacio Bertorello's user avatar

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