North Pontic crossroads: Mobility in Ukraine from the Bronze Age to the early modern period.

The North Pontic region, which encompasses present-day Ukraine, was a crossroads of migration, connecting the vast Eurasian Steppe with Central Europe. We generated shotgun-sequenced genomic data for 91 individuals dating from around 7000 BCE to 1800 CE to study migration and mobility history in the region, with a particular focus on historically attested migrating groups during the Iron Age and the medieval period. We infer a high degree of temporal heterogeneity in ancestry, with fluctuating genetic affinities to different present-day Eurasian groups.

TransLeish: Identification of membrane transporters essential for survival of intracellular Leishmania parasites in a systematic gene deletion screen.

For the protozoan parasite Leishmania, completion of its life cycle requires sequential adaptation of cellular physiology and nutrient scavenging mechanisms to the different environments of a sand fly alimentary tract and the acidic mammalian host cell phagolysosome. Transmembrane transporters are the gatekeepers of intracellular environments, controlling the flux of solutes and ions across membranes. To discover which transporters are vital for survival as intracellular amastigote forms, we carried out a systematic loss-of-function screen of the L.

ThirdPeak is a flexible tool designed for the robust analysis of two- and three-dimensional tracking data.

Biological processes, though often imaged and visualized in two dimensions, inherently occur in at least three-dimensional space. As time-resolved volumetric imaging becomes increasingly accessible, there emerges a necessity for tools that empower non-specialists to process and interpret intricate datasets. We introduce ThirdPeak, an open-source tool tailored for the comprehensive analysis of two- and three-dimensional track data across various scales.

Time memory in social insects with a special focus on honey bees.

The ability to associate time and location with food sources is an evolutionary advantage for foraging animals. We find highly sophisticated time memory capabilities especially in social insects, which require efficient foraging capabilities for colony provisioning. Honey bees are perfectly suitable to study time memory mechanisms: they possess an elaborated time memory combined with a relatively simple neuronal clock network and a smaller gene set compared with the mouse model organism.

PCR analysis: a comprehensive bioinformatics tool for enhancing nucleic acid amplification assays.

Nucleic acid amplification assays represent a pivotal category of methodologies for targeted sequence detection within contemporary biological research, boasting diverse utility in diagnostics, identification, and DNA sequencing. The foundational principles of these assays have been extrapolated to various simple and intricate nucleic acid amplification technologies. Concurrently, a burgeoning trend toward computational or virtual methodologies is exemplified by PCR analysis.

Transcriptomic signatures during normothermic liver machine perfusion correspond with graft quality and predict the early graft function.

Background: A better understanding of the molecular events during liver normothermic machine perfusion (NMP) is warranted to develop a data-based approach for the identification of biomarkers representative of graft quality and posttransplant outcome. We analysed the dynamic transcriptional changes during NMP and linked them to clinical and biochemical parameters.

Methods: 50 livers subjected to NMP for up to 24 h were enrolled.

Low Genetic Impact of the Roman Occupation of Britain in Rural Communities.

The Roman period saw the empire expand across Europe and the Mediterranean, including much of what is today Great Britain. While there is written evidence of high mobility into and out of Britain for administrators, traders, and the military, the impact of imperialism on local, rural population structure, kinship, and mobility is invisible in the textual record. The extent of genetic change that occurred in Britain during the Roman military occupation remains underexplored.

A comprehensive study of SARS-CoV-2 main protease (Mpro) inhibitor-resistant mutants selected in a VSV-based system.

Nirmatrelvir was the first protease inhibitor specifically developed against the SARS-CoV-2 main protease (3CLpro/Mpro) and licensed for clinical use. As SARS-CoV-2 continues to spread, variants resistant to nirmatrelvir and other currently available treatments are likely to arise. This study aimed to identify and characterize mutations that confer resistance to nirmatrelvir.

Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO.

Acinetobacter baumannii is an opportunistic Gram-negative pathogen that infects critically ill patients. The emergence of antimicrobial resistant A. baumannii has exacerbated the need to characterize environmental adaptation, antibiotic resistance and pathogenicity and their genetic regulators to inform intervention strategies.

READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics.

The advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy.

High rate of gene family evolution in proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae.

The genomes of ectomycorrhizal (ECM) fungi have a reduced number of genes encoding Carbohydrate-Active EnZymes (CAZymes), expansions in transposable elements (TEs) and small secreted proteins (SSPs) compared with saprotrophs. Fewer genes for specific peptidases and lipases in ECM fungi are also reported. It is unclear whether these changes occur at the shift to the ECM habit or are more gradual throughout the evolution of ECM lineages.

Intermolecular Gene Conversion for the Equalization of Genome Copies in the Polyploid Haloarchaeon : Identification of Important Proteins.

The model haloarchaeon is polyploid with about 20 copies of its major chromosome. Recently it has been described that highly efficient intermolecular gene conversion operates in to equalize the chromosomal copies. In the current study, 24 genes were selected that encode proteins with orthologs involved in gene conversion or homologous recombination in archaea, bacteria, or eukaryotes.

A new Activity Monitor for Aquatic Zooplankter (AMAZE) allows the recording of swimming activity in wild-caught Antarctic krill (Euphausia superba).

Antarctic krill (Euphausia superba, hereafter krill) is a pelagic living crustacean and a key species in the Southern Ocean ecosystem. Krill builds up a huge biomass and its synchronized behavioral patterns, such as diel vertical migration (DVM), substantially impact ecosystem structure and carbon sequestration. However, the mechanistic basis of krill DVM is unknown and previous studies of krill behavior in the laboratory were challenged by complex behavior and large variability.

An In Vivo and In Silico Approach Reveals Possible Sodium Channel Nav1.2 Inhibitors from as a Novel Treatment for Epilepsy.

Epilepsy is a neurological disease that affects approximately 50 million people worldwide. Despite an existing abundance of antiepileptic drugs, lifelong disease treatment is often required but could be improved with alternative drugs that have fewer side effects. Given that epileptic seizures stem from abnormal neuronal discharges predominately modulated by the human sodium channel Nav1.

Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders.

The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry.

The release of host-derived antibodies bound to the variant surface glycoprotein (VSG) of cannot be explained by pH-dependent conformational changes of the VSG dimer.

Background: is a protozoan parasite that evades the mammalian host's adaptive immune response by antigenic variation of the highly immunogenic variant surface glycoprotein (VSG). VSGs form a dense surface coat that is constantly recycled through the endosomal system. Bound antibodies are separated in the endosome from the VSG and destroyed in the lysosome.

A clock for all seasons.

Circadian clocks play an essential role in adapting locomotor activity as well as physiological, and metabolic rhythms of organisms to the day-night cycles on Earth during the four seasons. In addition, they can serve as a time reference for measuring day length and adapt organisms in advance to annual changes in the environment, which can be particularly pronounced at higher latitudes. The physiological responses of organisms to day length are also known as photoperiodism.

Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection.

West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.

Chemo-Phosphoproteomic Profiling with ATR Inhibitors Berzosertib and Gartisertib Uncovers New Biomarkers and DNA Damage Response Regulators.

The ATR kinase protects cells against DNA damage and replication stress and represents a promising anti-cancer drug target. The ATR inhibitors (ATRi) berzosertib and gartisertib are both in clinical trials for the treatment of advanced solid tumors as monotherapy or in combination with genotoxic agents. We carried out quantitative phospho-proteomic screening for ATR biomarkers that are highly sensitive to berzosertib and gartisertib, using an optimized mass spectrometry pipeline.

Revealing the profound influence of diapause on gene expression: Insights from the annual transcriptome of the copepod Calanus finmarchicus.

Annual rhythms are observed in living organisms with numerous ecological implications. In the zooplanktonic copepod Calanus finmarchicus, such rhythms are crucial regarding its phenology, body lipid accumulation, and global carbon storage. Climate change drives annual biological rhythms out of phase with the prevailing environmental conditions with yet unknown but potentially catastrophic consequences.