Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization.

Antimicrobial peptides (AMPs) emerge as a type of promising therapeutic compounds that exhibit broad spectrum antimicrobial activity with high specificity and good tolerability. Natural AMPs usually need further rational design for improving antimicrobial activity and decreasing toxicity to human cells. Although several algorithms have been developed to optimize AMPs with desired properties, they explored the variations of AMPs in a discrete amino acid sequence space, usually suffering from low efficiency, lack diversity, and local optimum.

A lineage 1 branch porcine reproductive and respiratory syndrome virus live vaccine candidate provides broad cross-protection against HP-like PRRSV in piglets.

Multiple porcine reproductive and respiratory syndrome virus (PRRSV) subtypes coinfect numerous pig farms in China, and commercial PRRSV vaccines offer limited cross-protection against heterologous strains. Our previous research confirmed that a PRRSV lineage 1 branch attenuated live vaccine (SD-R) provides cross-protection against HP-PRRSV, NADC30-like PRRSV and NADC34-like PRRSV. HP-PRRSV has undergone significant genetic variation following nearly two decades of evolution and has transformed into a subtype referred to as HP-like PRRSV, which also exhibits high pathogenicity.

The Bacterial and pathogenic landscape of African buffalo (Syncerus caffer) whole blood and serum from Kenya.

Background: African buffalo (Syncerus caffer) is a significant reservoir host for many zoonotic and parasitic infections in Africa. These include a range of viruses and pathogenic bacteria, such as tick-borne rickettsial organisms. Despite the considerations of mammalian blood as a sterile environment, blood microbiome sequencing could become crucial for agnostic biosurveillance.

A broadly neutralizing antibody against the SARS-CoV-2 Omicron sub-variants BA.1, BA.2, BA.2.12.1, BA.4, and BA.5.

The global spread of Severe Acute Respiratory Syndrome Coronavirus 2. (SARS-CoV-2) and its variant strains, including Alpha, Beta, Gamma, Delta, and now Omicron, pose a significant challenge. With the constant evolution of the virus, Omicron and its subtypes BA.

The Calicophoron daubneyi genome provides new insight into mechanisms of feeding, eggshell synthesis and parasite-microbe interactions.

Background: The rumen fluke, Calicophoron daubneyi, is the major paramphistome species infecting ruminants within Europe. Adult flukes reside within the rumen where they are in direct contact with a unique collection of microorganisms. Here, we report a 1.

The world's most venomous spider is a species complex: systematics of the Sydney funnel-web spider (Atracidae: Atrax robustus).

The Sydney funnel-web spider Atrax robustus O. Pickard-Cambridge, 1877 is an iconic Australian species and considered among the most dangerously venomous spiders for humans. Originally described in 1877 from a single specimen collected in "New Holland", this spider has a complex taxonomic history.

Adaptive evolution of stress response genes in parasites aligns with host niche diversity.

Background: Stress responses are key the survival of parasites and, consequently, also the evolutionary success of these organisms. Despite this importance, our understanding of the evolution of molecular pathways dealing with environmental stressors in parasitic animals remains limited. Here, we tested the link between adaptive evolution of parasite stress response genes and their ecological diversity and species richness.

Long-term outcome of oesophageal atresia in adolescence (TransEAsome): a national French cohort study protocol.

Introduction: The project, funded by the Agence Nationale de la Recherche, aims to evaluate the long-term outcomes of patients with oesophageal atresia (OA) between 13 and 14 years old and establish multiomics profiles using data from the world's biggest OA registry.

Methods And Analysis: is a national multicentre population-based cohort study recruiting participants from all qualified French centres for OA surgery at birth. The primary objective is to assess the prevalence of gastro-oesophageal reflux disease in adolescence among patients with OA, with several secondary objectives including the identification of risk factors and multiomic profiles from oesophageal biopsies and blood samples collected between 13 and 14 years old, compared with a control group.

Evolution and effectiveness of bilateral and multilateral development assistance for health: a mixed-methods review of trends and strategic shifts (1990-2022).

Background: Development assistance for health (DAH) plays a vital role in supporting health programmes in low- and middle-income countries. While DAH has historically focused on infectious diseases and maternal and child health, there is a lack of comprehensive analysis of DAH trends, strategic shifts and their impact on health systems and outcomes. This study aims to provide a comprehensive review of DAH from 1990 to 2022, examining its evolution and funding allocation shifts.

Exploring DiPP (Diisopentyl Phthalate) Neurotoxicity and the Detoxification Process in Zebrafish Larvae - A Silent Contaminant?

Diisopentyl phthalate (DiPP) is present in many consumer goods, but can be absorbed into the human body, and can disrupt the endocrine system affecting reproductive health and fetal development. Studies revealed that biological samples of pregnant women in Brazil contained DiPP, raising even more the concerns about its usage. This study investigated how DiPP concentrations (12.

Effects of periodontal disease on the proteomic profile of the periodontal ligament.

Periodontal disease affects over 1 billion people globally. This study investigated how periodontitis affects the protein profile of the periodontal ligament (PDL) in rats. Eight Holtzman rats were divided into the control and experimental periodontitis groups.

A thorny tale: The origin and diversification of Cirsium (Compositae).

Widely distributed plant genera offer insights into biogeographic processes and biodiversity. The Carduus-Cirsium group, with over 600 species in eight genera, is diverse across the Holarctic regions, especially in the Mediterranean Basin, Southwest Asia, Japan, and North America. Despite this diversity, evolutionary and biogeographic processes within the group, particularly for the genus Cirsium, remain underexplored.

Symptom Evolution in Individuals with Ongoing Symptomatic COVID-19 and Post COVID-19 Syndrome After SARS-CoV-2 Vaccination Versus Influenza Vaccination.

Background: COVID-19 symptoms may persist beyond acute SARS-CoV-2 infection, as ongoing symptomatic COVID-19 [OSC] (symptom duration 4-12 weeks) and post-COVID syndrome [PCS] (symptom duration ≥12 weeks). Vaccination against SARS-CoV-2 decreases OSC/PCS in individuals subsequently infected with SARS-CoV-2 post-vaccination. Whether vaccination against SARS-CoV-2, or any other vaccinations (such as against influenza) affects symptoms in individuals already experiencing OSC/PCS, more than natural symptom evolution, is unknown.

The incidence trends of papillary thyroid carcinoma in Belarus during the post-Chernobyl epoch.

Background: The increase of papillary thyroid cancer (PTC) rate among children who were exposed to post-Chernobyl 131-I release was reported only four years after the accident, first in Belarus where the heaviest fallout happened. The evolution of the occurrence of thyroid carcinoma based on the age-period-cohort analysis and the effects of age, period, and birth cohort on time trends aimed to reveal if post-Chernobyl follicular cells irradiation still has been impacting on incidence rate of papillary thyroid carcinoma nowadays.

Methods: The Belarusian Cancer Registry was used to identify patients with PTC diagnosed during the years 1980-2019.

Comparison of optimization algorithms for automated method development of gradient profiles.

Optimization algorithms play an important role in method development workflows for gradient elution liquid chromatography. Their effectiveness has not been evaluated for chromatographic method development using standardized comparisons across factors such as sample complexity, chromatographic response functions (CRFs), gradient complexity, and application type. This study compares six optimization algorithms - Bayesian optimization (BO), differential evolution (DE), a genetic algorithm (GA), covariance-matrix adaptation evolution strategy (CMA-ES), random search, and grid search - for the development of gradient elution LC methods.

Differences in gut microbial diversity and composition between growth phenotypes of farmed juvenile sandfish, Holothuria scabra.

Background: The observed growth variability of different aquaculture species in captivity hinders its large-scale production. For the sandfish Holothuria scabra, a tropical sea cucumber species, there is a scarcity of information on its intestinal microbiota in relation to host growth, which could provide insights into the processes that affect growth and identify microorganisms with probiotic or biochemical potential that could improve current production strategies. To address this gap, this study used 16 S rRNA amplicon sequencing to characterize differences in gut and fecal microbiota among large and small juveniles reared in floating ocean nurseries.

Development of a mitochondrial mini-barcode and its application in metabarcoding for identification of leech in traditional Chinese medicine.

In Traditional Chinese Medicine (TCM), the medicinal leech is vital for treatments to promote blood circulation and eliminate blood stasis. However, the prevalence of counterfeit leech products in the market undermines the quality and efficacy of these remedies. Traditional DNA barcoding techniques, such as the COI barcode, have been limited in their application due to amplification challenges.

Two-component system GrpP/GrpQ promotes pathogenicity of uropathogenic Escherichia coli CFT073 by upregulating type 1 fimbria.

Uropathogenic Escherichia coli (UPEC) is a major cause of urinary tract infections (UTIs). Invasion into bladder epithelial cells (BECs) on the bladder luminal surface via type 1 fimbria is the first critical step in UPEC infection. Although type 1 fimbria expression increases during UPEC invasion of BECs, the underlying regulatory mechanisms remain poorly understood.

Chromosome-level genome assembly, annotation, and population genomic resource of argali (Ovis ammon).

Argali stands as the largest species among wild sheep in Central and East Asia, with a concerning rate of decline estimated at 30%. The intraspecific taxonomy of argali remains contentious due to limited genomic data and unclear geographic separation. In this study, we constructed a chromosome-level genome assembly and annotation for the Tibetan argali (O.

Chromosome-scale genome assembly of three-spotted seahorse (Hippocampus trimaculatus) with a unique karyotype.

Three-spotted seahorse (Hippocampi trimaculata) is a unique fish with important economic and medicinal values, and its total chromosome number is potentially quite different from other seahorse species. Herein, we constructed a chromosome-level genome assembly for this special seahorse by integration of MGI short-read, PacBio HiFi long-read and Hi-C sequencing techniques. A 416.

Evolution of Omicron lineage towards increased fitness in the upper respiratory tract in the absence of severe lung pathology.

The emergence of the Omicron lineage represented a major genetic drift in SARS-CoV-2 evolution. This was associated with phenotypic changes including evasion of pre-existing immunity and decreased disease severity. Continuous evolution within the Omicron lineage raised concerns of potential increased transmissibility and/or disease severity.

CRISPR-Hybrid: A CRISPR-Mediated Intracellular Directed Evolution Platform for RNA Aptamers.

Recent advances in gene editing and precise regulation of gene expression based on CRISPR technologies have provided powerful tools for the understanding and manipulation of gene functions. Fusing RNA aptamers to the sgRNA of CRISPR can recruit cognate RNA-binding protein (RBP) effectors to target genomic sites, and the expression of sgRNA containing different RNA aptamers permit simultaneous multiplexed and multifunctional gene regulations. Here, we report an intracellular directed evolution platform for RNA aptamers against intracellularly expressed RBPs.

The North American Repository for Archaeological Isotopes.

Here, we present the North American Repository for Archaeological Isotopes (NARIA), the largest open-access compilation of previously reported isotopic measurements (n = 28,374) from bioarchaeological samples in North America (i.e., Canada, Greenland, Mexico, and the United States of America) covering a time-frame of more than 12,000 years.

Rolling schedule design for the ESP rolling process based on NSGA-II-DE.

Multiple processes connected closely during the endless strip production (ESP) rolling, it is difficult to obtain the global optimal solution by multi-objective modelling of a single process, and the parameters to be optimized coupled with each other. To obtain the optimal solution, a multi-objective optimization model combining the power consumption, product quality, and loading balance was proposed for the design of an ESP rolling schedule. The thickness and heating temperature were simultaneously taken as the decision variables for coupling the temperature and loading in the rolling process, and the non-dominated sorting genetic algorithm-II (NSGA-II) based on differential evolution (NSGA-II-DE) was applied to obtain the Pareto solutions.

DNA-binding affinity and specificity determine the phenotypic diversity in BCL11B-related disorders.

BCL11B is a Cys2-His2 zinc-finger (C2H2-ZnF) domain-containing, DNA-binding, transcription factor with established roles in the development of various organs and tissues, primarily the immune and nervous systems. BCL11B germline variants have been associated with a variety of developmental syndromes. However, genotype-phenotype correlations along with pathophysiologic mechanisms of selected variants mostly remain elusive.