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Questions tagged [mutations]

A change in an organism's genomic sequence.

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Has anyone tried site-directed mutagenesis aimed at deleting >10 amino acids of a protein using overlapping primers?

I am trying to use primer pairs with overlapping and non-overlapping regions to create deletions within a protein sequence (https://bmcbiotechnol.biomedcentral.com/articles/10.1186/1472-6750-8-91). I ...
Malka D'Malke's user avatar
2 votes
1 answer
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What is the probability distribution of a neutral mutation's allele frequency after k-generations? (in asexually reproducing organisms)

I've had trouble finding info on how to model this problem, so figured I'd ask it here. I'm trying to figure out what the probability distribution is of the frequency of a mutation in a population ...
mrz123456's user avatar
5 votes
3 answers
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What has caused my oxeye daisies to mutate?

Some oxeye daisies (Leucanthemum vulgare) in my garden are showing strange mutations. I have a few oxeye daisy plants around my garden in different areas, but only one plant's flowers are showing ...
cerys's user avatar
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DNA slippage as the cause of insertion mutations in cancer cells?

I'm a computer science student who has started working with DNA. I know the basics but not everything. While working on the ICGC data, I found a weird pattern in the insertions: In around 60% of the ...
Wassim Jaoui's user avatar
2 votes
1 answer
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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 ...
aquaporin'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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How did the fusion of Chromosome 2 spawn a separate smarter species?

I’m familiar with the evidence that two primate chromosomes fused into human Chromosome 2, and I understand that primates with such a mutation could still breed with those without it. My question is, ...
Jerry Guern's user avatar
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1 answer
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What causes the activation of "Late acting deleterious genes" in late age but not in young age, whose accumulation causes ageing according to Medawar?

Sir Peter Medawar proposed that aging is the byproduct of "late acting deleterious genes". Evolution is good at weeding out genetic mutations that are harmful at an young age, before the ...
Sanjay Biswas's user avatar
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Is there potential to modify GM crops to inhibit their reproduction with non-GM crops?

I've been reading on terminator gene sequences and was wondering whether the same technology could be applied to GM crops to prevent transgene flow. Turns out Monsanto had developed the technology but ...
pesky_nightjar's user avatar
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Can co-mutations be potential expression quantitative trait loci (eQTLs)?

I'm wondering if it is possible to test this and how? Usually we do this for single SNPs, I wanted to know if it was plausible for pairs of SNPs. Which method would you suggest? I want to test whether ...
Caterina's user avatar
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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
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Ames Assay Confusion: Aren't the odds of spontaneous revertants too low to be able to accurately test the mutagenicity of certain compounds?

I am a student conducting a test with the Ames Assay. This assay uses a strain of bacteria that has a mutation in an amino acid synthesizing operon, which doesn't allow it to synthesize its protein. ...
Kyotiq's user avatar
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Can someone with albinism have red hair with very pale skin and blue eyes?

I have heard of a type of albinism that occurs in races with darker skin that can give people red hair, but in the pictures I've seen, they usually have reddish-brown hair, a medium skin tone, and ...
Apollo's user avatar
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Are mutation rates normally distributed? If not, what are they?

On average, there are 64 mutations per generation in the human genome. Is this constant, or can we expect variation in the number of mutations?
Shannon T's user avatar
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Is there an example in evolution where a huge jump in evolution happened due to a dramatic mutation?

Here is a chicken that due to a mutation got 4 legs: I wonder, are there examples, where such one-time dramatic mutational chages gave rise to a new species? Are there species that appeared not due ...
Anixx's user avatar
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What is the nature of seedless fruits?

Can seedless fruit be produced in nature without humans interfering with the fruit? And would that be considered a spontaneous mutation?
Flora561's user avatar
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How did birds reduce their tail and fuse the last caudual vertebrae into a pygostyle?

I was just looking at the phylogeny of Avialae and saw that birds go from having long tails made up of many caudal vertebrae (ex: Archaeopteryx, Jixiangornis, Jeholornis) to ones with very few ...
RenaMoon's user avatar
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Sports of western sword fern: descriptions or resources?

I found a western sword fern (Polystichum munitum) growing in a home garden that appears to be showing a sport. Notably, the sportive fronds come off the same rootstock as more normal-appearing fronds ...
Maximilian Press's user avatar
2 votes
0 answers
28 views

Mutation profiles for Corona viruses in non-human hosts

In this question Mutation rate breakdown by original and mutated nucleotide for Coronaviridae mutation profiles for SARS-CoV-2 in humans are given. It is a known fact that mutation profiles are ...
Sir Cornflakes's user avatar
1 vote
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Is deleting two or three consecutive nucleotides and inserting exactly two or three back more common than two or three consecutive SNP?

I am looking at cancer mutations. I found that some of the mutations are e.g. c.1251_1252delGGinsTT c.151_152delGGinsTC c.351_352delCAinsTT I wonder if these are indeed two consecutive single ...
William Wong's user avatar
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Can gene mutations cause Down's syndrome in humans?

I am working on an A levels questions: Which of the following statements about gene mutation is incorrect? A. It can occur in both somatic and sex cells B. It can cause Down's syndrome in humans C. ...
green onion's user avatar
1 vote
1 answer
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Are gene conversions and expansion/contraction of repetitive (satellite) DNA examples of directional, non-random mutations?

Are gene conversions and expansion/contraction of repetitive (satellite) DNA examples of directional, non-random mutations? For some context, it was brought to mind as a result of reading the ...
arara's user avatar
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Cancer: computing the proliferation of DNA mutations in cancer cells

I have a question about cancer. How is it, that in a cancerogenous cell, once a specific gene changes, subsequent DNAs in cells end up exponentially acquiring more and more mutations? Can, these ...
Joselin Jocklingson's user avatar
5 votes
1 answer
137 views

How exactly do mutations cause genetic variation in bilaterians?

I am trying to understand how mutations cause genetic variance, and I'm stuck on one issue that I'm going to try my best to explain. (I am specifically talking about mutations that cause a ...
Luke B's user avatar
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Primer design for site-directed mutagenesis

In our practical course about modern cloning methods, we performed point mutations on a promotor via site-directed mutagenesis. As far as I understand that method you need forward and reverse primers ...
Natalie's user avatar
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Why are precultures done in Luria-Delbruck fluctuation assays?

I looked at a variety of descriptions of the classic Luria-Delbruck fluctuation assay protocol for determining mutation rates in different organisms (e.g. 1, 2, 3) and noticed that they all start from ...
Dahlai's user avatar
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1 answer
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Expected variant allele frequency of mutation present on 2 out of 3 copies of a 70% purity cancer sample

I am reading Nik-Zainal et al., 2012. In such paper, (for sample PD4120a - a 188-fold depth ER+ breast cancer tumor), it is stated that: The sample has 70% tumor purity. The genome has one triploid ...
gc5's user avatar
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226 views

Single flowers and double flowers on the same plant?

A friend of mine found a strange plant of begonia that at first had regular flowers. After a while it started producing double flowers and has now a mixed inflorescence: The double flowers look like ...
alephreish's user avatar
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Calculating bacterial mutation rate

I'm reading Molecular Biology of the Cell by Alberts et. al and at one point, the authors mention: One finds that a single gene that encodes an average-sized protein (~$10^3$ coding nulceotide pairs) ...
An Ignorant Wanderer's user avatar
7 votes
1 answer
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Amino Acid mutation profile for human coronavirus: Why is the mutation from T to I so frequent?

Still watching the emerging lineages of SARS-CoV2 I noticed that the amino acid mutation from threonine to isoleucine seems to be particularly frequent. Counting mutations in a lineage with a lot of ...
Sir Cornflakes's user avatar
1 vote
1 answer
90 views

Do the quantum mechanical properties of the particles that make up DNA affect mutations in the genome?

Do quantum mechanical properties of particles, such as uncertainty, probability, tunneling, and so on, affect mutations in the genome?
Арман Гаспарян's user avatar
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1 answer
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Are introns conserved among cells?

To elaborate on the title: Among somatic, post-mitotic cells, would the same intron on a given chromosome have the same sequence among all cells descended from a progenitor cell?
UD22022's user avatar
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56 views

Colonizing Mars: Is research being done to find the most radiation-tolerant plant species?

Due to Elon Musk's stated objectives to colonize and live on Mars in his lifetime, is there research occurring to determine what plants would be the most hardy to survive in the extreme environmental ...
Dale Mahalko's user avatar
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1 answer
219 views

Why is the genetic code so heavily conserved?

Except some organisms, most organisms follow the same Genetic Code tRNAs, tRNA synthetases, ribosomes, etc. comprise the translational machinery for converting nucleotide codons to proteins. My ...
Asmit Karmakar's user avatar
0 votes
2 answers
110 views

Number of "mutations" in Omicron variant

Currently in the media they say that the Omicron variant has more than 30 "mutations", ie changes in spikes. I find this confusing, because the way I understand a single change in the virus ...
Dirk N's user avatar
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1 answer
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Do mutations in a fundamental structure of a virus [Omicron Variant] make it more transmissible?

I am not a microbiologist, nor a virologist so I had a question - in the new Omicron virus variant, a large number of mutations were reported for the protein spike. From my naïve understanding, the ...
neel g's user avatar
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8 votes
1 answer
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Can the SARS‑CoV‑2 virus mutate in people who have been fully vaccinated?

I am curious to know if the original SARS‑CoV‑2 virus, or any of its variants, can mutate in people who have been fully vaccinated. I am referring to those people who have received all the recommended ...
WaterSparkle351's user avatar
3 votes
0 answers
273 views

Why does mitochondrial DNA have a high mutation rate, even though the mitochondrial function is highly conserved?

My understanding is that genes that are functionally important are more highly conserved. The DNA coding for ribosomal RNA is one example of that. I was surprised to find out that mitochondrial DNA ...
scorpion-eating-frog's user avatar
0 votes
1 answer
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What is an example of a benign or beneficial de novo copy number variation?

Duplication events in particular. In any species. Have enough genomes been sequenced and studied to identify any? It is rather easy to find studies which identify them with diseases but have they ever ...
James Marsden's user avatar
3 votes
3 answers
121 views

New ORFs occurring in SARS-CoV-2 due to mutations

Are there examples of new ORFs in SARS-CoV-2 created by mutations? The ORFs should not be present in the reference virus, but they should occur in a lineage occurring in the wild (at best, being part ...
Sir Cornflakes's user avatar
1 vote
1 answer
48 views

What is the mathematical relationship between selection coefficient and dN/dS

dN/dS is often used as a measure of the intensity of selective pressure on a mutation or gene, but I'm curious about how it can be written as a function of the selection coefficient. I'm specifically ...
mrz123456's user avatar
1 vote
0 answers
72 views

Extensions of proteins in SARS-CoV-2 variants

What lineages of the coronavirus SARS-CoV-2 occurring in the wild show some extensions, i.e., mutations of the stop codons to codons encoding amino acids (mutations to another stop codon don't count ...
Sir Cornflakes's user avatar
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2 answers
59 views

Do the genes for external viral epitopes mutate faster than for viral machinery (e.g. Proteases)?

To fight SARS-COV-2 we use vaccines which train our immune system against viral epitopes like the external S(pike) protein. Since these structures change a lot, would it not have been a better idea to ...
Mourinho_1's user avatar
3 votes
2 answers
136 views

Coronavirus lineages with amino acid insertions

Is there an overview over SARS-CoV-2 lineages that have some insertions in their genomes? Tools based on GISAID sequences do not show them. I am aware of a few lineages with insertions Mu with S:...
Sir Cornflakes's user avatar
1 vote
1 answer
135 views

Mutations in a Petri dish overnight

How long does it take for a bacterial culture in a Petri dish to experience all possible single base pair mutations? Can 12 hours be enough? I want to get an intuition for whether a given mutation is ...
Daniel Darabos's user avatar
1 vote
0 answers
81 views

Monogenic disorders vs multifactorial inheritance disorders

There's a condition called SYNGAP1-related intellectual disability which is caused by mutations to the SYNGAP1 gene. I believe that this is called a monogenic disorder, while disorders that are caused ...
Derek H's user avatar
  • 111
1 vote
1 answer
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Do mutations that cause the loss of a complex trait occur more often than mutations causing gain of a complex traits?

The Wiki entry on the evolution of biological complexity states that "[m]utations causing loss of a complex trait occur more often than mutations causing gain of a complex trait". There is ...
alghazali's user avatar
1 vote
1 answer
115 views

How are random mutations in cells of an organism controlled?

Even in the most stable conditions cells undergo mutations. So in humans(an example) with millions of cells, mutations must be a common affair. But how is that we are still basically the same ...
mani datta s's user avatar
9 votes
1 answer
1k views

Do mutations occur while growing virus for preparing inactivated viral vaccine?

The development of mutations in virus is reported to happen during replication, especially for an mRNA type virus like SARS-COV-2 Viruses that encode their genome in RNA, such as SARS-CoV-2, HIV and ...
karthikeyan's user avatar
0 votes
1 answer
99 views

How to calculate the probability that a mutation occurred?

According to the internet, there is a 7% chance that two brown-eyed parents will have a green-eyed child. However, Dominance says that it is impossible for this to happen. Is the internet correct? If ...
EmmaGao8's user avatar

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