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"Mutation (Biology)"
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Why are RNA virus mutation rates so damn high?
The high mutation rate of RNA viruses is credited with their evolvability and virulence. This Primer, however, discusses recent evidence that this is, in part, a byproduct of selection for faster genomic replication.
Journal Article
Mutants in nature
\"This photo-illustrated book for elementary readers describes the types of mutations that can happen to animals and plants. Highlights how outside forces or random genetic mishaps can cause extra or missing limbs, color variations such as albinism, and other abnormalities\"-- Provided by publisher.
Book
PremPS: Predicting the impact of missense mutations on protein stability
Computational methods that predict protein stability changes induced by missense mutations have made a lot of progress over the past decades. Most of the available methods however have very limited accuracy in predicting stabilizing mutations because existing experimental sets are dominated by mutations reducing protein stability. Moreover, few approaches could consistently perform well across different test cases. To address these issues, we developed a new computational method PremPS to more accurately evaluate the effects of missense mutations on protein stability. The PremPS method is composed of only ten evolutionary- and structure-based features and parameterized on a balanced dataset with an equal number of stabilizing and destabilizing mutations. A comprehensive comparison of the predictive performance of PremPS with other available methods on nine benchmark datasets confirms that our approach consistently outperforms other methods and shows considerable improvement in estimating the impacts of stabilizing mutations. A protein could have multiple structures available, and if another structure of the same protein is used, the predicted change in stability for structure-based methods might be different. Thus, we further estimated the impact of using different structures on prediction accuracy, and demonstrate that our method performs well across different types of structures except for low-resolution structures and models built based on templates with low sequence identity. PremPS can be used for finding functionally important variants, revealing the molecular mechanisms of functional influences and protein design. PremPS is freely available at
https://lilab.jysw.suda.edu.cn/research/PremPS/
, which allows to do large-scale mutational scanning and takes about four minutes to perform calculations for a single mutation per protein with ~ 300 residues and requires ~ 0.4 seconds for each additional mutation.
Journal Article
Secret weapons
The government has dispatched Amanda McKee - the technopath codenamed Livewire - to investigate the ruins of a secret facility formerly run by Toyo Harada, the most powerful telepath on Earth and her former mentor. In his quest for world betterment at any cost, Harada sought out and activated many potential psiots like himself. Those who survived, but whose powers he deemed to have no value to his cause, were hidden away at this installation. But Livewire, having studied Harada's greatest strengths and learned his deepest weaknesses, senses opportunity where he once saw failure. A young girl who can talk to birds... A boy who can make inanimate objects gently glow... To others, these are expensive disappointments. But, to Livewire, they are secret weapons...in need of a leader. Now, as a mechanized killer called Rex-O seeks to draw them out, Livewire and her new team of cadets will be forced to put their powers into action...in ways they never could have imagined
Book
The coronavirus is mutating — does it matter?
Different SARS-CoV-2 strains haven’t yet had a major impact on the course of the pandemic, but they might in future.
Different SARS-CoV-2 strains haven’t yet had a major impact on the course of the pandemic, but they might in future.
Journal Article
Roadside picnic
Red Schuhart is a stalker, one of those misfits who are compelled, in spite of extreme danger, to venture illegally into the Zone to collect the mysterious artefacts that the alien visitors left scattered around. His life is dominated by the place and the thriving black market in the alien products. Even the nature of his mutant daughter has been determined by the Zone. And it is for her that he makes his last tragic foray into the hazardous and hostile territory.
Book
Sheltering of deleterious mutations explains the stepwise extension of recombination suppression on sex chromosomes and other supergenes
Many organisms have sex chromosomes with large nonrecombining regions that have expanded stepwise, generating “evolutionary strata” of differentiation. The reasons for this remain poorly understood, but the principal hypotheses proposed to date are based on antagonistic selection due to differences between sexes. However, it has proved difficult to obtain empirical evidence of a role for sexually antagonistic selection in extending recombination suppression, and antagonistic selection has been shown to be unlikely to account for the evolutionary strata observed on fungal mating-type chromosomes. We show here, by mathematical modeling and stochastic simulation, that recombination suppression on sex chromosomes and around supergenes can expand under a wide range of parameter values simply because it shelters recessive deleterious mutations, which are ubiquitous in genomes. Permanently heterozygous alleles, such as the male-determining allele in XY systems, protect linked chromosomal inversions against the expression of their recessive mutation load, leading to the successive accumulation of inversions around these alleles without antagonistic selection. Similar results were obtained with models assuming recombination-suppressing mechanisms other than chromosomal inversions and for supergenes other than sex chromosomes, including those without XY-like asymmetry, such as fungal mating-type chromosomes. However, inversions capturing a permanently heterozygous allele were found to be less likely to spread when the mutation load segregating in populations was lower (e.g., under large effective population sizes or low mutation rates). This may explain why sex chromosomes remain homomorphic in some organisms but are highly divergent in others. Here, we model a simple and testable hypothesis explaining the stepwise extensions of recombination suppression on sex chromosomes, mating-type chromosomes, and supergenes in general.
Journal Article
HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle
The deacetylase enzyme HDAC8 is identified as a crucial regulator of cohesin in humans, and loss-of-function mutations in the
HDAC8
gene are found in patients with Cornelia de Lange syndrome.
HDAC defects in Cornelia de Lange syndrome
The cohesin complex is important for sister-chromatid cohesion and chromosome segregation, as well as for other chromosomal processes such as gene expression and DNA repair. Cornelia de Lange syndrome (CdLS) is a human developmental disorder associated with significant cognitive deficits and structural birth defects. It is caused by mutations in genes that encode subunits of the cohesin complex or the cohesin regulator NIPL. Here, a deacetylase enzyme, HDAC8, is shown to be a critical regulator of cohesin in human cells, and loss-of-function
HDAC8
mutations are found in six patients with CdLS from different families.
Cornelia de Lange syndrome (CdLS) is a dominantly inherited congenital malformation disorder, caused by mutations in the cohesin-loading protein NIPBL
1
,
2
for nearly 60% of individuals with classical CdLS
3
,
4
,
5
, and by mutations in the core cohesin components SMC1A (∼5%) and SMC3 (<1%) for a smaller fraction of probands
6
,
7
. In humans, the multisubunit complex cohesin is made up of SMC1, SMC3, RAD21 and a STAG protein. These form a ring structure that is proposed to encircle sister chromatids to mediate sister chromatid cohesion
8
and also has key roles in gene regulation
9
. SMC3 is acetylated during S-phase to establish cohesiveness of chromatin-loaded cohesin
10
,
11
,
12
,
13
, and in yeast, the class I histone deacetylase Hos1 deacetylates SMC3 during anaphase
14
,
15
,
16
. Here we identify HDAC8 as the vertebrate SMC3 deacetylase, as well as loss-of-function
HDAC8
mutations in six CdLS probands. Loss of HDAC8 activity results in increased SMC3 acetylation and inefficient dissolution of the ‘used’ cohesin complex released from chromatin in both prophase and anaphase. SMC3 with retained acetylation is loaded onto chromatin, and chromatin immunoprecipitation sequencing analysis demonstrates decreased occupancy of cohesin localization sites that results in a consistent pattern of altered transcription seen in CdLS cell lines with either
NIPBL
or
HDAC8
mutations.
Journal Article