The fitness landscape of the codon space across environments

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Lung cancer is the leading cause of cancer-related deaths worldwide and the most common lung cancer subtype is lung adenocarcinoma (LUAD). Frequently mutated genes involve activating mutations in KRAS and loss of function mutations in TP53. LUADs primarily ...

Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations ...

Background: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpre ...

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

Owing to stochastic fluctuations arising from finite population size, known as genetic drift, the ability of a population to explore a rugged fitness landscape depends on its size. In the weak mutation regime, while the mean steady-state fitness increases ...

nvestigation of potential hosts of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is crucial to understanding future risks of spillover and spillback. SARS-CoV-2 has been reported to be transmitted from humans to various animals after req ...

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative motor disorder, which results in death within a few years of diagnosis. While the cause of most cases of ALS is unknown, 10% of cases are familial (fALS), and associated with mutations in one of ov ...

The resilience of the mitochondrial genome (mtDNA) to a high mutational pressure depends, in part, on negative purifying selection in the germline. A paradigm in the field has been that such selection, at least in part, takes place in primordial germ cells ...

At present, there is no general standard automated method for engineering metalloenzymes, industrially-relevant systems able to catalyze environmentally friendly reactions. One of the most studied natural metalloenzymes is the second isoform of human carbo ...

We introduce a reconfigurable medium for the manipulation of elastic propagation properties of Lamb waves. It is based on a shape memory polymer (SMP) with temperature-dependent Young's modulus. Waves are excited by a laser pulse and detected by a laser vi ...

Background: Cancer genome sequencing enables accurate classification of tumours and tumour subtypes. However, prediction performance is still limited using exome-only sequencing and for tumour types with low somatic mutation burden such as many paediatri ...

Organocatalysis has evolved significantly over the last decades, becoming a pillar of synthetic chemistry, but traditional theoretical approaches based on quantum mechanical computations to investigate reaction mechanisms and provide rationalizations of ca ...

Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes o ...

In this account, we discuss the use of genetic algorithms in the inverse design process of homogeneous catalysts for chemical transformations. We describe the main components of evolutionary experiments, specifically the nature of the fitness function to o ...

The A-to-G point mutation at position 3243 in the human mitochondrial genome (m.3243A > G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A > G levels decrease in blood with age, and an age c ...

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...

Protein synthesis is an energy consuming process characterised as a pivotal and highly regulated step in gene expression. The net protein output is dictated by a combination of translation initiation, elongation and termination rates that have remained dif ...

The mutational spectrum of the mitochondrial DNA (mtDNA) does not resemble any of the known mutational signatures of the nuclear genome and variation in mtDNA mutational spectra between different organisms is still incomprehensible. Since mitochondria are ...

Significant increases in sedimentation rate accompany the evolution of multicellularity. These increases should lead to rapid changes in ecological distribution, thereby affecting the costs and benefits of multicellularity and its likelihood to evolve. How ...

Type I CRISPR-Cas systems typically rely on a two-step process to degrade DNA. First, an RNA-guided complex named Cascade identifies the complementary DNA target. The helicase-nuclease fusion enzyme Cas3 is then recruited in trans for processive DNA degrad ...

The fitness landscape of the codon space across environments

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The role of LRRK2 in lung adenocarcinoma

Reproductive isolation arises during laboratory adaptation to a novel hot environment

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Impact of population size on early adaptation in rugged fitness landscapes

Cryo-EM structures and binding of mouse and human ACE2 to SARS-CoV-2 variants of concern indicate that mutations enabling immune escape could expand host range

The role of the NF-kappaB pathway in Amyotrophic lateral sclerosis pathogenesis

Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive

Computational Studies for the Design of Metalloenzyme Mimics

Optimization of elastic wave propagation in a reconfigurable medium by genetic algorithms with adaptive mutation probability

Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping

Enriching the Computational Toolbox for Organocatalysis

DNA modifications impact natural transformation of Acinetobacter baumannii

Genetic Algorithms for the Discovery of Homogeneous Catalysts

Dynamics of the most common pathogenic mtDNA variant m.3243A > G demonstrate frequency-dependency in blood and positive selection in the germline

Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter

Ribo-DT: An automated pipeline for inferring codon dwell times from ribosome profiling data

A mitochondria-specific mutational signature of aging: increased rate of A > G substitutions on the heavy strand

Regulation of sedimentation rate shapes the evolution of multicellularity in a close unicellular relative of animals

Allosteric control of type I-A CRISPR-Cas3 complexes and establishment as effective nucleic acid detection and human genome editing tools