On the Analysis of Intrahost and Interhost Viral Populations: Human Cytomegalovirus as a Case Study of Pitfalls and Expectations

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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 ...

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 ...

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

Background. Respiratory syncytial virus (RSV) is associated with acute respiratory infection. We sought to identify RSV variants associated with prolonged infection. ...

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 ...

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 ...

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 ...

The arms race between viruses and their hosts shaped the evolutionary history and the genome composition of both parties. Restriction factors are the first-line antiviral effectors encoded by the host genomes and are often conserved through evolution to pr ...

We have learned from the recent COVID-19 pandemic that the emergence of a new virus can quickly become a global health burden and kill millions of lives. Antiviral drugs are essential in our fight against viral diseases, but most of them are virus-specific ...

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

Understanding how biological matter takes its shape is instrumental to biology, bioengineering, medicine, and bioinspired engineering. Gaining information on the principles of morphogenesis could enable clinicians to correct developmental abnormalities, ev ...

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

The study of insular populations was key in the development of evolutionary theory. The successful colonisation of an island depends on the geographic context, and specific characteristics of the organism and the island, but also on stochastic processes. A ...

Evolutionary diversity in species can arise in many ways, including local adaptation. Despite the global importance of tropical forest ecosystems, few studies have explored patterns of local adaptation in tropical tree species. We investigated population g ...

Contemporary genomic approaches allow us to seek answers to biological questions that were previously out of reach. Genome-wide association studies (GWAS) have identified numerous genetic polymorphisms associated with human diseases, providing new insight ...

Biofilms play pivotal roles in fluvial ecosystems, yet virtually nothing is known about viruses in these communities. Leveraging an optimized sample-to-sequence pipeline, we studied the spatiotemporal turnover of dsDNA viruses associated with stream biofil ...

The Montecristo wild goat is an endangered feral population that has been on the homonymous island in the Tuscan Archipelago since ancient times. The origins of Montecristo goats are still debated, with authors dating their introduction either back to Neol ...

Inactivation kinetics of enterovirus by disinfection is often studied using a single laboratory strain of a given genotype. Environmental variants of enterovirus are genetically distinct from the corresponding laboratory strain, yet it is poorly understood ...

Genome-wide association studies rely on the statistical inference of untyped variants, called imputation, to increase the coverage of genotyping arrays. However, the results are often suboptimal in populations underrepresented in existing reference panels ...

Set-point viral load (SPVL), a common measure of human immunodeficiency virus (HIV)-1 virulence, is partially determined by viral genotype. Epidemiological evidence suggests that this viral property has been under stabilising selection, with a typical opti ...

On the Analysis of Intrahost and Interhost Viral Populations: Human Cytomegalovirus as a Case Study of Pitfalls and Expectations

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Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Reproductive isolation arises during laboratory adaptation to a novel hot environment

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Viral Genetic Determinants of Prolonged Respiratory Syncytial Virus Infection Among Infants in a Healthy Term Birth Cohort

Impact of population size on early adaptation in rugged fitness landscapes

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

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

PSGL-1 is an evolutionarily conserved antiviral restriction factor

Ligand concentration determines antiviral efficacy of silica multivalent nanoparticles

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Development of a Robotic Microsurgeon for Embryonic Research

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Genomic consequences of colonisation, migration and genetic drift in barn owl insular populations of the eastern Mediterranean

Population structure and signals of local adaptation in Eugenia uniflora (Myrtaceae), a widely distributed species in the Atlantic Forest

The interplay between human genetic variation, chronic inflammation and persistent infection: relevance for cardiovascular morbidity

Viral diversity is linked to bacterial community composition in alpine stream biofilms

The SNP-Based Profiling of Montecristo Feral Goat Populations Reveals a History of Isolation, Bottlenecks, and the Effects of Management

Genotype-Dependent Kinetics of Enterovirus Inactivation by Free Chlorine and Ultraviolet (UV) Irradiation

Using population-specific add-on polymorphisms to improve genotype imputation in underrepresented populations

Phylogenetic estimation of the viral fitness landscape of HIV-1 set-point viral load