Deciphering environmental factors influencing phytoplankton community structure in a polluted urban river

Tuojiang River Basin is a first-class tributary of the upper reaches of the Yangtze River-which is the longest river in China. As phytoplankton are sensitive indicators of trophic changes in water bodies, characterizing phytoplankton communities and their growth influencing factors in polluted urban rivers can provide new ideas for pollution control. Here, we used direct microscopic count and environmental DNA (eDNA) metabarcoding methods to investigate phytoplankton community structure in Tuojiang River Basin (Chengdu, Sichuan Province, China). The association between phytoplankton community structure and water environmental factors was evaluated by Mantel analysis. Additional environmental monitoring data were used to pinpoint major factors that influenced phytoplankton growth based on structural equation modeling. At the phylum level, the dominant phytoplankton taxa identified by the conventional microscopic method mainly belonged to Bacillariophyta, Chlorophyta, and Cyanophyta, in contrast with Chlorophyta, Dinophyceae, and Bacillariophyta identified by eDNA metabarcoding. In α-diversity analysis, eDNA metabarcoding detected greater species diversity and achieved higher precision than the microscopic method. Phytoplankton growth was largely limited by phosphorus based on the nitrogen-to-phosphorus ratios > 16:1 in all water samples. Redundancy analysis and structural equation modeling also confirmed that the nitrogen-to-phosphorus ratio was the principal factor influencing phytoplankton growth. The results could be useful for implementing comprehensive management of the river basin environment. It is recommended to control the discharge of point- and surface-source pollutants and the concentration of dissolved oxygen in areas with excessive nutrients (e.g., Jianyang-Ziyang). Algae monitoring techniques and removal strategies should be improved in 201 Hospital, Hongrihe Bridge and Colmar Town areas.

Bioenergy recovery and carbon emissions benefits of short-term bio-thermophilic pretreatment on low organic sewage sludge anaerobic digestion: A pilot-scale study

Sewage sludge in cities of Yangzi River Belt, China, generally exhibits a lower organic content and higher silt contentdue to leakage of drainage system, which caused low bioenergy recovery and carbon emission benefits in conventional anaerobic digestion (CAD). Therefore, this paper is on a pilot scale, a bio-thermophilic pretreatment anaerobic digestion (BTPAD) for low organic sludge (volatile solids (VS) of 4%) was operated with a long-term continuous flow of 200 days. The VS degradation rate and CH4 yield of BTPAD increased by 19.93% and 53.33%, respectively, compared to those of CAD. The analysis of organic compositions in sludge revealed that BTPAD mainly improved the hydrolysis of proteins in sludge. Further analysis of microbial community proportions by high-throughput sequencing revealed that the short-term bio-thermophilic pretreatment was enriched in Clostridiales, Coprothermobacter and Gelria, was capable of hydrolyzing acidified proteins, and provided more volatile fatty acid (VFA) for the subsequent reaction. Biome combined with fluorescence quantitative polymerase chain reaction (PCR) analysis showed that the number of bacteria with high methanogenic capacity in BTPAD was much higher than that in CAD during the medium temperature digestion stage, indicating that short-term bio-thermophilic pretreatment could provide better methanogenic conditions for BTPAD. Furthermore, the greenhouse gas emission footprint analysis showed that short-term bio-thermophilic pretreatment could reduce the carbon emission of sludge anaerobic digestion system by 19.18%.

Chloroplast genome evolution of Berberis (Berberidaceae): Implications for phylogeny and metabarcoding

Berberidis Radix (Sankezhen), a typical multi-origin Chinese medicinal material, originates from the dried roots of plants of the Berberis genus and is used to treat various ailments. These species have similar morphologies, potentially leading to misidentifications that can impact medicine efficacy. Therefore, developing suitable molecular markers to identify medicinal species is imperative. Furthermore, discrepancies exist in the taxonomy of the Berberis genus. In the present study, we de novo assembled the chloroplast genomes of six Berberis species (Berberis woomungensis C. Y. Wu, Berberis pruinosa Franch., Berberis thunbergii DC., Berberis chinensis Poir., Berberis wilsoniae Hemsl., and Berberis sp.) that commonly constitute Berberidis Radix and compared them with previously reported genomes. Our comparative analysis revealed similarities in genome structure, relative synonymous codon usage, amino acid frequency, repeats, and substitutions. Higher synonymous substitutions, indicative of predominant purifying selection on protein-coding genes, were observed compared to non-synonymous substitutions. However, positive selection was identified in six genes across 29 Berberis species-accD, matK, ndhD, rbcL, ycf1, and ycf2-highlighting their potential roles in adaptive responses to specific environmental conditions within the genus. Inverted repeats expansion and contraction affected the rate of mutations and were associated with the phylogenetic classification of Berberis. Our phylogenetic analysis supported the division of the Berberis complex into four genera, which corroborates previous studies involving extensive sampling. We identified the ndhD-ccsA region as the most polymorphic region and applied this region to Chinese patent medicines containing Berberidis Radix through metabarcoding. The metabarcoding analysis confirmed that five Berberis species commonly constitute Berberidis Radix in Chinese patent medicines. In conclusion, this study provides insight into the molecular evolution of the chloroplast genome and the phylogeny of the Berberis genus. In addition, metabarcoding provides insight into the species composition of Berberidis Radix in Chinese patent medicines.

Evaluation and characteristic analysis of SSRs from the transcriptomic sequences of Perilla crop (Perilla frutescens L.)

Perilla crop is a self-fertilizing annual plant, cultivated and used mainly in East Asia. Perilla frutescens var. frutescens seeds are rich in unsaturated fatty acids, which have health benefits, and Perilla frutescens var. crispa leaves are rich in anthocyanins. However, genomic analysis such as whole genome sequencing or genetic mapping has not been performed on Perilla crop. This current study confirms the abundance and diversity of 15,991 simple sequence repeats (SSRs) classified in previous studies in the Perilla genome, selects and designs 1,538 SSR primer sets, and confirms which SSR primer sets exhibit high polymorphism. Of the 15,991 SSRs classified, there were 9,910 (62%) dinucleotide repeats, 5,652 (35.3%) trinucleotide repeats, and 429 (2.7%) tetranucleotide repeats. Among these, the most identified was (CT)n with a total of 4,817. The 15,991 SSRs had 4 to 26 repeats. Four repeats were the most frequent with 11,084 (69.3%). A total of 1,538 SSR primers were selected and designed to confirm polymorphism, of which 157 showed persistent and clear polymorphism. Among these 157 SSR primer sets, 98 (62.4%) were dinucleotide repeats, 39 (24.8%) were trinucleotide repeats, and 20 (12.7%) were tetranucleotide repeats. Among 549 SSR primers that showed polymorphism, trinucleotide repeats showed persistent polymorphism at a high rate. Therefore, when developing SSR primer sets for Perilla crop in the future, it is recommended that trinucleotide repeats be selected first. These research results will be helpful in future genomic analysis and development of SSR primers in Perilla crop.

Fermentative and metabolic screening of candidate yeast strains hybridisable with Saccharomyces cerevisiae for beer production optimisation

Yeast optimisation has been crucial in improving the quality and efficiency of beer production, one of the world's most widely consumed beverages. In this context, rare mating hybridisation is a promising technique for yeast optimization to generate novel and improved non-GMO strains. The limitation of this technique is the lack of knowledge and comparable data on yeast strains hybridisable to Saccharomyces cerevisiae, probably the most important yeast species in beer production. Yeast from the genera Saccharomyces, Naumovozyma, Nakaseomyces and Kazachstania have been described to be able to form hybrids with S. cerevisiae. In the present study, 242 yeast strains were analysed under brewing conditions, including Saccharomyces species (S. cerevisiae, S. kudriavzevii, S. uvarum, S. eubayanus, S. paradoxus, S. mikatae, S. jurei and S. arboricola) and non-Saccharomyces species (Naumovozyma, Nakaseomyces and Kazaschtania), representing the full genetic variability (species and subpopulations) described up to the start of the study. The fermentation profile was analysed by monitoring weight loss during fermentation to determine kinetic parameters and CO2 production. Metabolic analysis was performed to determine the concentration of sugars (maltotriose, maltose and glucose), alcohols (ethanol, glycerol and 2,3-butanediol) and organic acids (malic acid, succinic acid and acetic acid). Maltose and maltotriose are the predominant sugars in beer wort. The ability to consume these sugars determines the characteristics of the final product. Dataset comparisons were then made at species, subpopulation and isolation source level. The results obtained in this study demonstrate the great phenotypic variability that exists within the genus Saccharomyces and within each species of this genus, which could be useful in the generation of optimised brewing hybrids. Yeasts with different fermentative capacities and fermentative behaviours can be found under brewing conditions. S. cerevisiae, S. uvarum and S. eubayanus are the species that contain strains with similar fermentation performance to commercial strains.

The neurobiology of parenting and infant-evoked aggression

Parenting behavior comprises a variety of adult-infant and adult-adult interactions across multiple timescales. The state transition from nonparent to parent requires an extensive reorganization of individual priorities and physiology and is facilitated by combinatorial hormone action on specific cell types that are integrated throughout interconnected and brainwide neuronal circuits. In this review, we take a comprehensive approach to integrate historical and current literature on each of these topics across multiple species, with a focus on rodents. New and emerging molecular, circuit-based, and computational technologies have recently been used to address outstanding gaps in our current framework of knowledge on infant-directed behavior. This work is raising fundamental questions about the interplay between instinctive and learned components of parenting and the mutual regulation of affiliative versus agonistic infant-directed behaviors in health and disease. Whenever possible, we point to how these technologies have helped gain novel insights and opened new avenues of research into the neurobiology of parenting. We hope this review will serve as an introduction for those new to the field, a comprehensive resource for those already studying parenting, and a guidepost for designing future studies.

From the cauldron of conflict: Endogenous gene regulation by piRNA and other modes of adaptation enabled by selfish transposable elements

Transposable elements (TEs) provide a prime example of genetic conflict because they can proliferate in genomes and populations even if they harm the host. However, numerous studies have shown that TEs, though typically harmful, can also provide fuel for adaptation. This is because they code functional sequences that can be useful for the host in which they reside. In this review, I summarize the "how" and "why" of adaptation enabled by the genetic conflict between TEs and hosts. In addition, focusing on mechanisms of TE control by small piwi-interacting RNAs (piRNAs), I highlight an indirect form of adaptation enabled by conflict. In this case, mechanisms of host defense that regulate TEs have been redeployed for endogenous gene regulation. I propose that the genetic conflict released by meiosis in early eukaryotes may have been important because, among other reasons, it spurred evolutionary innovation on multiple interwoven trajectories - on the part of hosts and also embedded genetic parasites. This form of evolution may function as a complexity generating engine that was a critical player in eukaryotic evolution.

Impact of microbial-based biopreparations on soil quality, plant health, and fruit chemistry in raspberry cultivation

Application of microbial-based biopreparations as a pre-harvest strategy offers a method to obtain sustainable agricultural practices and could be an important approach for advancing food science, promoting sustainability, and meeting global food market demands. The impact of a bacterial-fungal biopreparation mixture on soil-plant-microbe interactions, fruit chemical composition and yield of 7 raspberry clones was investigated by examining the structural and functional profiles of microbial communities within leaves, fruits, and soil. Biopreparation addition caused the enhancement of the microbiological utilization of specific compounds, such as d-mannitol, relevant in plant-pathogen interactions and overall plant health. The biopreparation treatment positively affected the nitrogen availability in soil (9-160%). The analysis of plant stress marker enzymes combined with the evaluation of fruit quality and chemical properties highlight changes inducted by the pre-harvest biopreparation application. Chemical analyses highlight biopreparations' role in soil and fruit quality improvement, promoting sustainable agriculture. This effect was dependent on tested clones, showing increase of soluble solid content in fruits, concentration of polyphenols or the sensory quality of the fruits. The results of the next-generation sequencing indicated increase in the effective number of bacterial species after biopreparation treatment. The network analysis showed stimulating effect of biopreparation on microbial communities by enhancing microbial interactions (increasing the number of network edges up to 260%) of and affecting the proportions of mutual relationships between both bacteria and fungi. These findings show the potential of microbial-based biopreparation in enhancing raspberry production whilst promoting sustainable practices and maintaining environmental homeostasis and giving inshght in holistic understanding of microbial-based approaches for advancing food science monitoring.

Interaction between a Lactococcus lactis autochthonous starter and a raw goat milk microbial community during long-term backslopping

Traditional cheesemaking processes often involve backslopping practice. However, over successive inoculations, acidification deficiencies may arise. In such cases, adding a starter is recommended to restore the ecosystem stability. This study examines the impact of an autochthonous starter composed of three Lactococcus lactis strains on a raw goat milk microbial community during their evolution. Bacterial composition and technological features (acidification and aroma) were analyzed during communities' evolution over 800 generations. 16S rRNA gene metabarcoding showed that Lactococcus lactis strains predominated. The raw goat milk community acidification capacities varied early in the evolution and then remained stable. Adding the L. lactis starter to this community stabilized the ecosystem from the beginning of the evolution. The acetoin production was associated with the starter presence, consistent with the establishment of the diacetylatis biovar strain from the starter in the raw goat milk community throughout the evolution. Increased or decreased production of some volatile organic compounds when the starter was added revealed a specific aroma footprint due to interactions between the two communities. This study showed that adding a starter could help to achieve the maximum acidification rate from the early inoculation cycles and could significantly modify the aroma profile during long-term backslopping.

Advances in understanding the interaction between Solanaceae NLR resistance proteins and the viral effector Avr

The rising prevalence of viral-induced diseases, particularly those caused by certain strains, poses a substantial risk to the genetic diversity of Solanaceae crops and the overall safety of horticultural produce. According to the "gene-for-gene" hypothesis, resistance proteins are capable of selectively identifying nontoxic effectors produced by pathogens, as they are under purview of the host's immune defenses. The sensitivity and responsiveness of Solanaceae plants to viral attacks play a crucial role in shaping the outcomes of their interactions with viruses. Pathogenic organisms, devise an array of infection tactics aimed at circumventing or neutralizing the host's immune defenses to facilitate effective invasion. The invasion often accomplishes by suppressing or disrupting the host's defensive mechanisms or immune signals, which are integral to the infection strategies of such invading pathogens. This comprehensive review delves into the myriad approaches that pathogenic viruses employ to infiltrate and overcome the sophisticated immune system of tomatoes. Furthermore, the review explores the possibility of utilizing these viral strategies to bolster the resilience of horticultural crops, presenting a hopeful direction for forthcoming progress in plant health and agricultural stability.

The ecology of ageing in wild societies: linking age structure and social behaviour

The age of individuals has consequences not only for their fitness and behaviour but also for the functioning of the groups they form. Because social behaviour often changes with age, population age structure is expected to shape the social organization, the social environments individuals experience and the operation of social processes within populations. Although research has explored changes in individual social behaviour with age, particularly in controlled settings, there is limited understanding of how age structure governs sociality in wild populations. Here, we synthesize previous research into age-related effects on social processes in natural populations, and discuss the links between age structure, sociality and ecology, specifically focusing on how population age structure might influence social structure and functioning. We highlight the potential for using empirical data from natural populations in combination with social network approaches to uncover pathways linking individual social ageing, population age structure and societal functioning. We discuss the broader implications of these insights for understanding the social impacts of anthropogenic effects on animal population demography and for building a deeper understanding of societal ageing in general.This article is part of the discussion meeting issue 'Understanding age and society using natural populations'.

More social species live longer, have longer generation times and longer reproductive windows

The role of sociality in the demography of animals has become an intense focus of research in recent decades. However, efforts to understand the sociality-demography nexus have hitherto focused on single species or isolated taxonomic groups. Consequently, we lack generality regarding how sociality associates with demographic traits within the Animal Kingdom. Here, I propose a continuum of sociality, from solitary to tightly social, and test whether this continuum correlates with the key demographic properties of 152 species, from jellyfish to humans. After correction for body mass and phylogenetic relationships, I show that the sociality continuum is associated with key life history traits: more social species live longer, postpone maturity, have longer generation time and greater probability of achieving reproduction than solitary, gregarious, communal or colonial species. Contrary to the social buffering hypothesis, sociality does not result in more buffered populations. While more social species have a lower ability to benefit from disturbances, they display greater resistance than more solitary species. Finally, I also show that sociality does not shape reproductive or actuarial senescence rates. This cross-taxonomic examination of sociality across the demography of 13 taxonomic classes highlights key ways in which individual interactions shape most aspects of animal demography.This article is part of the discussion meeting issue 'Understanding age and society using natural populations'.

Age-dependent shaping of the social environment in a long-lived seabird: a quantitative genetic approach

Individual differences in social behaviour can result in fine-scale variation in spatial distribution and, hence, in the social environment experienced. Given the expected fitness consequences associated with differences in social environments, it is imperative to understand the factors that shape them. One potential such factor is age. Age-specific social behaviour-often referred to as 'social ageing'-has only recently attracted attention, requiring more empirical work across taxa. Here, we use 29 years of longitudinal data collected in a pedigreed population of long-lived, colonially breeding common terns (Sterna hirundo) to investigate sources of variation in, and quantitative genetic underpinnings of, an aspect of social ageing: the shaping of the social environment experienced, using the number of neighbours during breeding as a proxy. Our analyses reveal age-specific declines in the number of neighbours during breeding, as well as selective disappearance of individuals with a high number of neighbours. Moreover, we find this social trait, as well as individual variation in the slope of its age-specific decline, to be heritable. These results suggest that social ageing might underpin part of the variation in the overall multicausal ageing phenotype, as well as undergo microevolution, highlighting the potential role of social ageing as a facilitator for, or constraint of, the evolutionary potential of natural populations.This article is part of the discussion meeting issue 'Understanding age and society using natural populations'.

Understanding age and society using natural populations

Ageing affects almost all aspects of life and therefore is an important process across societies, human and non-human animal alike. This article introduces new research exploring the complex interplay between individual-level ageing and demography, and the consequences this interplay holds for the structure and functioning of societies across various natural populations. We discuss how this Special Issue provides a foundation for integrating perspectives from evolutionary biology, behavioural ecology and demography to provide new insights into how ageing shapes individuals' social behaviour and social associations, and how this in turn impacts social networks, social processes (such as disease or information transfer) and fitness. Through examining these topics across taxa, from invertebrates to birds and mammals, we outline how contemporary studies are using natural populations to advance our understanding of the relationship between age and society in innovative ways. We highlight key emerging research themes from this Special Issue, such as how sociality affects lifespan and health, the genetic and ecological underpinnings of social ageing and the adaptive strategies employed by different species. We conclude that this Special Issue underscores the importance of studying social ageing using diverse systems and interdisciplinary approaches for advancing evolutionary and ecological insights into both ageing and sociality more generally.This article is part of the discussion meeting issue 'Understanding age and society using natural populations '.

Wild capuchin monkeys as a model system for investigating the social and ecological determinants of ageing

Studying biological ageing in animal models can circumvent some of the confounds exhibited by studies of human ageing. Ageing research in non-human primates has provided invaluable insights into human lifespan and healthspan. Yet data on patterns of ageing from wild primates remain relatively scarce, centred around a few populations of catarrhine species. Here, we introduce the white-faced capuchin, a long-lived platyrrhine primate, as a promising new model system for ageing research. Like humans, capuchins are highly social, omnivorous generalists, whose healthspan and lifespan relative to body size exceed that of other non-human primate model species. We review recent insights from capuchin ageing biology and outline our expanding, integrative research programme that combines metrics of the social and physical environments with physical, physiological and molecular hallmarks of ageing across the natural life courses of multiple longitudinally tracked individuals. By increasing the taxonomic breadth of well-studied primate ageing models, we generate new insights, increase the comparative value of existing datasets to geroscience and work towards the collective goal of developing accurate, non-invasive and reliable biomarkers with high potential for standardization across field sites and species, enhancing the translatability of primate studies.This article is part of the discussion meeting issue 'Understanding age and society using natural populations'.

A comparative study of population structure and genetic diversity of commercial and indigenous chickens from different agro-ecological zones in Ghana using SilicoDArT and SNP markers

Chicken production, both in the local and commercial sectors, contributes significantly to human livelihood and food security. Precise use of diverse genetic resources is primary in breeding programs. The study analyzed the genetic diversity and population structure of commercial chickens and indigenous chicken ecotypes from three different agro-ecological zones (Semi-Deciduous Rainforest Zone, Guinea Savannah, and Coastal Savannah) using SilicoDArT and SNP markers, utilizing whole-genome sequencing and phenotypic data. Phenotypic data were collected from 72 indigenous chicken ecotypes across the three AEZs, and 32 commercial birds kept at the Kwame Nkrumah University of Science and Technology (KNUST). DNA samples used for sequencing were obtained from 88 chickens (62 indigenous chicken ecotypes and 26 commercial chickens). A total of 54,995 SilicoDArT and 85,396 SNPs markers were generated from DArTseq genotyping. After filtering, 44,784 SilicoDArT and 58,353 SNP were used for genetic diversity and population structure analysis. Both markers showed high reproducibility and call rate. Polymorphic information content (PIC) values ranged from 0.00 to 0.50, while ≥ 50 % showed PIC values more than the median. Furthermore, we obtained FST values, Nei's genetic distance, dendrogram analysis, and principal component analysis (PCA) of commercial and indigenous chickens. The FST and Nei's genetic distance showed that there is high genetic diversity between the commercial chickens and the indigenous chicken ecotypes. However, there was low genetic diversity among the indigenous chicken ecotypes. The PCA analysis indicated a clear separation between the commercial and indigenous chicken ecotypes, while no clear separation was observed between the indigenous chicken ecotypes. The phenotypic data and the dendrogram indicated that naked and frizzle genes do not markedly alter the genetics of indigenous and commercial birds, and their influence on economic traits may be solely determined by the prevailing environmental conditions. The results indicate that there is high genetic differentiation between commercial and indigenous chickens based on SilicoDArT and SNP markers. The indigenous chickens from the agro-ecological zones have low genetic diversity and might have a common origin. Naked neck and frizzle genes do not markedly alter the genetic performance of birds in terms of economic traits. Therefore, the superiority of birds carrying these genes in economic traits may be solely due to environmental variation.

Into the Blue: Exploring genetic mechanisms behind the evolution of baleen whales

Marine ecosystems are ideal for studying evolutionary adaptations involved in lineage diversification due to few physical barriers and reduced opportunities for strict allopatry compared to terrestrial ecosystems. Cetaceans (whales, dolphins, and porpoises) are a diverse group of mammals that successfully adapted to various habitats within the aquatic environment around 50 million years ago. While the overall adaptive transition from terrestrial to fully aquatic species is relatively well understood, the radiation of modern whales is still unclear. Here high-quality genomes derived from previously published data were used to identify genomic regions that potentially underpinned the diversification of baleen whales (Balaenopteridae). A robust molecular phylogeny was reconstructed based on 10,159 single copy and complete genes for eight mysticetes, seven odontocetes and two cetacean outgroups. Analysis of positive selection across 3,150 genes revealed that balaenopterids have undergone numerous idiosyncratic and convergent genomic variations that may explain their diversification. Genes associated with aging, survival and homeostasis were enriched in all species. Additionally, positive selection on genes involved in the immune system were disclosed for the two largest species, blue and fin whales. Such genes can potentially be ascribed to their morphological evolution, allowing them to attain greater length and increased cell number. Further evidence is presented about gene regions that might have contributed to the extensive anatomical changes shown by cetaceans, including adaptation to distinct environments and diets. This study contributes to our understanding of the genomic basis of diversification in baleen whales and the molecular changes linked to their adaptive radiation, thereby enhancing our understanding of cetacean evolution.

New gel from a water-soluble Carboxymethyl chitosan-Cinnamaldehyde Schiff base derivative as an effective preservative against soft rot in ginger

Ginger, valued for its culinary and medicinal properties, suffers substantial production loss-up to 90 %-due to fungal soft rot. To combat this, we have developed an environmentally sustainable antifungal polysaccharide gel derived from a water-soluble Schiff base of O-carboxymethyl chitosan (CMC) and cinnamaldehyde (CIN). Terpene incorporation was confirmed via various characterization techniques, including Fourier transform infrared (FT-IR), pH-dependent release, solubility, thermogravimetric analysis, and UV-vis spectra. Results showed successful grafting of CIN onto the polysaccharide, at a CIN:CMC ratio of 120 mg/g. In vitro evaluation demonstrated significant antifungal activity against F. oxysporum, with a MIC value of 159.25 μg/mL. Application of the CMC=CIN gel to ginger rhizomes inhibited spore germination in all evaluated wounds, enhancing gloss and appearance. These findings validate the efficacy of this novel, environmentally friendly gel in preventing ginger loss caused by fungal infections.

Analysis of wheat fungal community succession in traditional storage structures using Illumina MiSeq sequencing technology

The diversity of fungi in wheat with different deoxynivalenol (DON) content at various periods post-harvest and in the environment of storage were investigated. The changes in DON content were measured with ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS), and an amplicon sequence analysis of fungi was performed in traditional storage structures using high-throughput sequencing. The changes in temperature, humidity, and CO2 concentration were collected by sensors. In addition, we analyzed principal component analysis, species composition, species differences, and community differences of fungi. There was an obvious separation of the fungal communities under different storage conditions and times. Many fungal genera were gradually decreasing during storage and were eventually undetectable, and many fungal genera that were undetectable at first gradually increased during storage and even became dominant fungal genera. The competition between fungi was fierce. The competition between fungi were affected by the presence of DON. As the initial DON content increased, the contribution of inter-group differences became more obvious. The temperature, humidity, and CO2 concentration of wheat in the silo's environment changed with extended storage time. The content of DON decreased with extended storage time. We had investigated the changes in DON content and their correlation with the changes in fungal communities and environmental factors, which showed a high degree of correlation. This study offers theoretical justification for optimizing safe wheat grain in traditional storage conditions.

Biogeographic patterns of meio- and micro-eukaryotic communities in dam-induced river-reservoir systems

Although the Three Gorges Dam (TGD) is the world's largest hydroelectric dam, little is known about the spatial-temporal patterns and community assembly mechanisms of meio- and micro-eukaryotes and its two subtaxa (zooplankton and zoobenthos). This knowledge gap is particularly evident across various habitats and during different water-level periods, primarily arising from the annual regular dam regulation. To address this inquiry, we employed mitochondrial cytochrome c oxidase I (COI) gene-based environmental DNA (eDNA) metabarcoding technology to systematically analyze the biogeographic pattern of the three communities within the Three Gorges Reservoir (TGR). Our findings reveal distinct spatiotemporal characteristics and complementary patterns in the distribution of meio- and micro-eukaryotes. The three communities showed similar biogeographic patterns and assembly processes. Notably, the diversity of these three taxa gradually decreased along the river. Their communities were less shaped by stochastic processes, which gradually decreased along the longitudinal riverine-transition-lacustrine gradient. Hence, deterministic factors, such as seasonality, environmental, and spatial variables, along with species interactions, likely play a pivotal role in shaping these communities. Environmental factors primarily drive seasonal variations in these communities, while hydrological conditions, represented as spatial distance, predominantly influence spatial variations. These three communities followed the distance-decay pattern. In winter, compared to summer, both the decay and species interrelationships are more pronounced. Taken together, this study offers fresh insights into the composition and diversity patterns of meio- and micro-eukaryotes at the spatial-temporal level. It also uncovers the mechanisms behind community assembly in various environmental niches within the dam-induced river-reservoir systems. KEY POINTS: • Distribution and diversity of meio- and micro-eukaryotes exhibit distinct spatiotemporal patterns in the TGR. • Contribution of stochastic processes in community assembly gradually decreases along the river. • Deterministic factors and species interactions shape meio- and micro-eukaryotic community.

Prion forensics: a multidisciplinary approach to investigate CWD at an illegal deer carcass disposal site

Infectious prions are resistant to degradation and remain infectious in the environment for several years. Chronic wasting disease (CWD) has been detected in cervids inhabiting North America, the Nordic countries, and South Korea. CWD-prion spread is partially attributed to carcass transport and disposal. We employed a forensic approach to investigate an illegal carcass dump site connected with a CWD-positive herd. We integrated anatomic, genetic, and prion amplification methods to discover CWD-positive remains from six white-tailed deer (Odocoileus virginianus) and, using microsatellite markers, confirmed a portion originated from the CWD-infected herd. This approach provides a foundation for future studies of carcass prion transmission risk.

"Active carbon" is more advantageous to the bacterial community in the rice rhizosphere than "stable carbon"

Carbon materials are commonly used for soil carbon sequestration and fertilization, which can also affect crop growth by manipulating the rhizosphere bacterial community. However, the comparison of the differences between active carbon (e.g., organic fertilizers) and stable carbon (e.g., biochar) on rhizosphere microdomains is still unclear. Hence, a trial was implemented to explore the influence of control (CK, no fertilizer; NPK, chemical fertilizer), organic fertilizer (CF-O, organic fertilizer; CF-BO, biochar-based organic fertilizer) and biochar material (CF-B, perishable garbage biochar; CF-PMB, pig manure biochar) on the diversity, composition, and interaction of rice rhizosphere bacterial community through 16 S rRNA gene high-throughput sequencing. Our results demonstrate that organic fertilizer increases bacterial alpha-diversity compared to no-carbon supply treatment to the extend, whereas biochar has the opposite effect. The rhizosphere bacterial community composition showed pronounced variations among the various fertilization treatments. The relative abundance in Firmicutes decreased with organic fertilizer application, whereas that in Chloroflexi and Actinobacteria decreased with biochar application. Bacterial network analysis demonstrate that organic fertilizer enhances the complexity and key taxa of bacterial interactions, while biochar exhibits an opposing trend. The findings of our study indicate that organic fertilizer may contribute to a positive and advantageous impact on bacterial diversity and interaction in rice rhizosphere, whereas the influence of biochar is not as favorable and constructive. This study lays the foundation for elucidating the fate of the rhizosphere bacterial community following different carbon material inputs in the context of sustainable agricultural development.

Molecular epidemiological studies of Leucocytozoon caulleryi in commercial layer flocks in Southern peninsular India reveal the presence of new subclusters

The Leucocytozoon parasites are one of the important protozoa species affecting domestic poultry and wild birds. Though there are frequent reports about the incidence of Leucocytozoon in wild birds, the information regarding the occurrence of commercial poultry is underestimated. From October 2015 to August 2022, ailing and dead birds from 39 commercial layer flocks were submitted to the Poultry Disease Diagnosis and Surveillance Laboratory, Namakkal, with a history of brief illness, followed by mortality with oozing of blood from oro-nasal orifice. The presence of Leucocytozoon caulleryi was confirmed in all the flocks by laboratory examination and PCR. All the Leucocytozoon-positive cases were reported after heavy rainfall and the affected farms were inhabited with Culicoides flies. The infected birds were dull and depressed, exhibited labored breathing, and blood-tinted ropy mucous from the oro-nasal cavity. Necropsy examination revealed pale-anaemic comb and wattles, massive haemorrhagic clot over the surface of the kidney, peritoneum, and trachea, and scattering of greyish-white/reddish military megaloschizonts throughout the serosa of viscera and skeletal muscles. Histopathological examination revealed many spherical cysts or megaloschizonts in the intestine, pancreas, gizzard, spleen, liver, kidney, heart, and breast muscles. The cysts were deeply seated within the above organ's parenchyma or embedded in the serosa. There was extensive connective tissue proliferation with mononuclear cell infiltration around the cyst. Leucocytozoon-specific DNA was detected in all the flocks by PCR. Phylogenetic analysis of the cytochrome b gene of L. caulleryi reported from various parts of the world revealed that L. caulleryi is grouped into two major clusters (Cluster I & II). Further, Indian L. caulleryi sequences fall under sub-cluster I and II along with L. caulleryi reported from Taiwan, Egypt, China, Myanmar, Japan, South Korea, and Thailand.

Synthesis of sexual selection: a systematic map of meta-analyses with bibliometric analysis

Sexual selection has been a popular subject within evolutionary biology because of its central role in explaining odd and counterintuitive traits observed in nature. Consequently, the literature associated with this field of study became vast. Meta-analytical studies attempting to draw inferences from this literature have now accumulated, varying in scope and quality, thus calling for a synthesis of these syntheses. We conducted a systematic literature search to create a systematic map with a report appraisal of meta-analyses on topics associated with sexual selection, aiming to identify the conceptual and methodological gaps in this secondary literature. We also conducted bibliometric analyses to explore whether these gaps are associated with the gender and origin of the authors of these meta-analyses. We included 152 meta-analytical studies in our systematic map. We found that most meta-analyses focused on males and on certain animal groups (e.g. birds), indicating severe sex and taxonomic biases. The topics in these studies varied greatly, from proximate (e.g. relationship of ornaments with other traits) to ultimate questions (e.g. formal estimates of sexual selection strength), although the former were more common. We also observed several common methodological issues in these studies, such as lack of detailed information regarding searches, screening, and analyses, which ultimately impairs the reliability of many of these meta-analyses. In addition, most of the meta-analyses' authors were men affiliated to institutions from developed countries, pointing to both gender and geographical authorship biases. Most importantly, we found that certain authorship aspects were associated with conceptual and methodological issues in meta-analytical studies. Many of our findings might simply reflect patterns in the current state of the primary literature and academia, suggesting that our study can serve as an indicator of issues within the field of sexual selection at large. Based on our findings, we provide both conceptual and analytical recommendations to improve future studies in the field of sexual selection.

Patterns of feather mite (Acariformes: Astigmata) prevalence and load in a promiscuous bird during the breeding season

The effects of ectosymbiotic feather mites on avian host fitness and factors driving the variation in mite infestation levels, such as host mating and brood care system, are poorly understood. We investigated patterns of feather mite prevalence and abundance, and relationships between infestation and body condition in breeding Aquatic Warblers Acrocephalus paludicola, a promiscuous songbird with female-only parental care. In plumage, the dominant mite species was Trouessartia bifurcata, whose prevalence more than doubled during the breeding season, to reach 95% (95% confidence limits 71-99) during the second-brood period. Approximately 5% of birds were co-infested with Proctophyllodes cf. clavatus. While mite prevalence did not differ between sexes, mite abundance was significantly greater in Aquatic Warbler females than in males, and it increased between the first- and the second-brood period irrespective of sex. No significant relationship was found between mite prevalence or abundance and host condition expressed as mass scaled to size. However, in breeding females, this relationship could be confounded by the effects of nest-dwelling ectoparasites present in some nests but only sporadically if at all detected on adult birds; 2% of adult birds were heavily infested with the hematophagous mite Dermanyssus hirundinis (Mesostigmata). Our findings indicate that the mating system may affect symbiont variability between and within host species. The high prevalence of feather mites on adult birds at the late stage of the breeding season supports the hypothesis that promiscuous species have high infestation levels. Greater mite loads on Aquatic Warbler females than males reveal a different pattern from previously studied birds. However, we did not identify any consequences of mite infestation for the female body condition or current breeding success; hence, the apparently commensal relationship does not imply costs of female promiscuity.

The use of Phasmarhabditis nematodes and metabolites of Xenorhabdus bacteria in slug control

Many species of slugs are considered serious pests in agriculture and horticulture around the world. In Europe, slugs of the genera Arion and Deroceras are the most harmful pests in agriculture. Therefore, the main goal of this study was to evaluate the effect of the whole-cell metabolites of 10 strains of five Xenorhabdus and three slug-parasitic nematodes (Phasmarhabditis hermaphrodita, Phasmarhabditis bohemica, and Phasmarhabditis apuliae) on the feeding behaviour and repellent effect on target slugs and evaluate a new possible means of biocontrol of these pests. The repellent and anti-feedant effects of nematode-killed insects, metabolites, slug-parasitic nematodes and a combination of metabolites and nematodes were studied through experimental designs: sand-filled plastic boxes divided into two parts in several modifications: with dead Galleria mellonella killed by nematodes, lettuce treated with bacterial metabolites and lettuce placed on the treated sand. We found that slugs avoid eating G. mellonella killed by nematodes, while they eat freeze-killed G. mellonella. Similarly, they avoid the consumption of lettuce in areas treated with bacterial metabolites (the most effective strains being Xenorhabus bovienii NFUST, Xenorhabdus kozodoii SLOV and JEGOR) with zero feeding in the treated side. All three Phasmarhabditis species also provided a significant anti-feedant/repellent effect. Our study is the first to show the repellent and anti-feedant effects of metabolites of Xenorhabdus bacteria against Arion vulgaris, and the results suggest that these substances have great potential for biocontrol. Our study is also the first to demonstrate the repellent effect of P. apuliae and P. bohemica. KEY POINTS: • Slugs avoid eating G. mellonella killed by entomopathogenic nematodes. • Bacterial metabolites have a strong repellent and antifeedant effect on slugs. • Presence of slug parasitic nematodes increases the repellent effect of metabolites.

Weak association of Usutu virus and haemosporidian infection in birds collected in Germany

The Usutu Virus (USUV) is a mosquito-borne flavivirus originated in Africa. The virus circulates in Germany since 2010. It is primarily transmitted and maintained in the natural cycle by Culex mosquitoes and primarily affects birds, particularly Eurasian blackbird (Turdus merula), leading to significant mortality. Several studies have reported a high co-infection rate of European birds with both USUV and haemosporidians. Haemosporidians are blood parasites which maintain an enzootic life cycle with birds via different arthropod vectors. This study conducted screenings of birds from Germany received through a citizen's science project for both, USUV and haemosporidians between 2016 and 2021. The prevalence of USUV reached its peak in 2018, when it was first detected throughout most parts of Germany rather than being limited to localised hotspots. Subsequently, USUV prevalence consistently declined. On the other hand, the prevalence of haemosporidians initially declined between 2016 and 2019, but experienced a subsequent increase in the following years, exhibiting a more or less inverse pattern compared to the prevalence of USUV. In 2020, a statistically significant positive association between both pathogens was found, which was also detected across all years combined, indicating if at all a weak relationship between these pathogens.

Sex-specific modulating role of social support in the associations between oxidative stress, inflammation, and telomere length in older adults

Telomere length, a biomarker of human aging, is related to adverse health outcomes. Growing evidence indicates that oxidative stress and inflammation contributes to telomere shortening, whereas social support may protect from telomere shortening. Despite sex differences in telomere length and social support, little is known about whether there are sex differences in the relationship between oxidative stress/inflammation and telomere length, and sex-specific moderating roles of social support in older adults. Using data from the National Health and Nutrition Examination Survey (NHANES) 1999-2002, this study assessed whether the associations between oxidative stress/inflammation and telomere length vary with sex and explored social support as a moderator in these associations among 2289 older adults. Oxidative stress was measured based on serum Gamma-glutamyl transferase (GGT), and inflammation was measured based on C-reactive protein (CRP). After adjusting for the covariates, GGT was significantly associated with telomere length in females only (β =  - 0.037, 95% CI =  - 0.070, - 0.005), while CRP was associated with telomere length in males only (β =  - 0.019, 95% CI =  - 0.035, - 0.002). Moreover, high social support mitigated the negative association between GGT and telomere length, which was more evident in females. Furthermore, social support moderated the association between CRP and telomere length in males aged 70 and above. Our findings indicated that biological mechanisms related to telomere length may vary with sex, while social support plays a sex-specific moderating role.

Metabolic rate does not scale with body size or activity in some tick species

Respiration in ticks is highly efficient and exceptionally low. Ticks can survive years between bloodmeals by having low activity and respiration to conserve energetic resources. Our objective was to compare metabolic (VCO2) and activity rates across 6 tick species. We predicted that VCO2 would be different among species and scale linearly with activity and body mass. Activity and CO2 production were measured for 32 h in 6 tick species: Dermacentor andersoni, D. variabilis, Haemaphysalis longicornis, Rhipicephalus appendiculatus, R. microplus, and R. sanguineus. Individual ticks were measured for 30 min three times to ensure breathing occurred. Absolute and mass-specific VCO2, total activity, body mass, and ventilation patterns were compared among species. As expected, ticks did not always breathe during the 30-minute measurements, especially R. sanguineus. Ventilation patterns differed among species with R. microplus having primarily cyclic patterns and R. appendiculatus having discontinuous gas exchange. VCO2 did not scale with body mass in most species. Haemaphysalis longicornis and R. sanguineus had the lowest VCO2; however, H. longicornis was the second most active species. Life history, including questing behavior and range expansion, could be contributing to differences between species. For instance, H. longicornis had exceptionally low metabolic rates despite above average activity levels, suggesting an energetic advantage which may underlie recently documented range expansions in North America. Our results demonstrate how ticks utilize energetic resources to maximize longevity. Future research describing questing behavior and distribution modeling may help explain differences in metabolic rates and activity and impacts on life history traits.

Adaptive evolution of Salmonella Typhimurium LT2 exposed to carvacrol lacks a uniform pattern

Emergence of genetic variants with increased resistance/tolerance to natural antimicrobials, such as essential oils, has been previously evidenced; however, it is unknown whether mutagenesis follows a general or a specific pattern. For this purpose, we carried out four adaptive laboratory evolutions (ALE) in parallel of Salmonella enterica Typhimurium with carvacrol. After 10 evolution steps, we selected and characterized one colony from each lineage (SeCarA, SeCarB, SeCarC, and SeCarD). Phenotypic characterization of the four evolved strains revealed enhanced survival to lethal treatments; two of them (SeCarA and SeCarB) showed an increase of minimum inhibitory concentration of carvacrol and a better growth fitness in the presence of carvacrol compared to wild-type strain. Whole genome sequencing revealed 10 mutations, of which four (rrsH, sseG, wbaV, and flhA) were present in more than one strain, whereas six (nirC, fliH, lon, rob, upstream yfhP, and upstream argR) were unique to individual strains. Single-mutation genetic constructs in SeWT confirmed lon and rob as responsible for the increased resistance to carvacrol as well as to antibiotics (ampicillin, ciprofloxacin, chloramphenicol, nalidixic acid, rifampicin, tetracycline, and trimethoprim). wbaV played an important role in increased tolerance against carvacrol and chloramphenicol, and flhA in cross-tolerance to heat treatments. As a conclusion, no common phenotypical or genotypical pattern was observed in the isolated resistant variants of Salmonella Typhimurium emerged under carvacrol stress. Furthermore, the demonstration of cross-resistance against heat and antibiotics exhibited by resistant variants raises concerns regarding food safety. KEY POINTS: • Stable resistant variants of Salmonella Typhimurium emerged under carvacrol stress • No common pattern of mutagenesis after cyclic exposures to carvacrol was observed • Resistant variants to carvacrol showed cross-resistance to heat and to antibiotics.

Efficacy of genotype-matched vaccine against re-emerging genotype V Japanese encephalitis virus

Japanese encephalitis (JE), caused by the Japanese encephalitis virus (JEV), is a highly threatening disease with no specific treatment. Fortunately, the development of vaccines has enabled effective defense against JE. However, re-emerging genotype V (GV) JEV poses a challenge as current vaccines are genotype III (GIII)-based and provide suboptimal protection. Given the isolation of GV JEVs from Malaysia, China, and the Republic of Korea, there is a concern about the potential for a broader outbreak. Under the hypothesis that a GV-based vaccine is necessary for effective defense against GV JEV, we developed a pentameric recombinant antigen using cholera toxin B as a scaffold and mucosal adjuvant, which was conjugated with the E protein domain III of GV by genetic fusion. This GV-based vaccine antigen induced a more effective immune response in mice against GV JEV isolates compared to GIII-based antigen and efficiently protected animals from lethal challenges. Furthermore, a bivalent vaccine approach, inoculating simultaneously with GIII- and GV-based antigens, showed protective efficacy against both GIII and GV JEVs. This strategy presents a promising avenue for comprehensive protection in regions facing the threat of diverse JEV genotypes, including both prevalent GIII and GI as well as emerging GV strains.

"It's been a Process": A Multiple Case Study of Biology Instructor Efforts to Reform their Sex and Gender Curriculum to be More Inclusive of Students with Queer Genders and Intersex Students

Inaccurate sex and gender narratives have saturated the political landscape, resulting in legal restrictions for people with queer genders. Biology educators can correct these false narratives by teaching scientifically accurate and queer gender and intersex inclusive sex and gender curriculum. Here, we interviewed four undergraduate biology instructors who were working to reform their sex and gender curriculum. Using their reformed curriculum to promote conversation in the interviews, we asked participants about their curriculum, their reform process, and the obstacles they faced in implementing their reformed curriculum. We noticed the instructors' journeys to reforming involved intense personal work and education, both at the beginning and iteratively throughout implementation. We found instructors focused on changing language and using a variety of inclusive activities in their undergraduate biology classroom, ranging from highlighting scientists with queer genders to assigning students to research the experiences of people with queer genders with adolescent hormone therapy. Instructors mentioned obstacles to implementing reformed curriculum, including fear of potentially isolating students and concern about the instructor's own positionality. Removing obstacles and supporting the process of unlearning exclusive ways of teaching sex and gender topics may bolster instructor efforts to provide more accurate and inclusive biology education.

Transcriptomic landscapes reveal development-related physiological processes in the two-spotted spider mite, Tetranychus urticae

The two-spotted spider mite (Tetranychus urticae Koch, TSSM) is recognized as one of the most problematic spider mite pests. However, the precise gene expression patterns across its key developmental stages remain elusive. Here, we performed a comprehensive transcriptome analysis of TSSM eggs, nymphs and adult females using publicly available RNA sequencing (RNA-seq) data to elucidate the overarching transcriptomic differences between these developmental stages. Principal component analysis and hierarchical clustering analysis unveiled distinct separations among samples across different developmental stages, regardless of their Wolbachia infection status. Differential expression analysis revealed 4,089,2,762, and 1,282 core genes specifically enriched in eggs, nymphs, and adults, respectively. KEGG and GO enrichment analyses showed upregulation of genes in eggs are associated with proteolysis, Wnt signaling pathway, DNA transcription, RNA biosynthetic and metabolic processes, as well as protein folding, sorting, and degradation pathways. Meanwhile, nymphs exhibited increased abundance of genes related to chitin/amino sugar metabolic processes, G protein-coupled receptor signaling pathways, monoatomic ion transport, and neurotransmitter transport pathways. Pathways involving sphingolipid and carbohydrate metabolic processes, proteolysis, lipid transport, and localization were particularly enriched in older females. Altogether, our findings suggest that the egg stage exhibits higher activity in cell differentiation processes, the nymph stage is more involved in chitin development, and the adult stage shows increased metabolic and reproductive activity. This study enhances our understanding of the molecular mechanisms underlying TSSM development and paves the way for further research into the intricate physiological processes of TSSM.

Drivers of genomic diversity and phenotypic development in early phases of domestication in Hermetia illucens

The black soldier fly (BSF), Hermetia illucens, has the ability to efficiently bioremediate organic waste into usable bio-compounds. Understanding the impact of domestication and mass rearing on fitness and production traits is therefore important for sustainable production. This study aimed to assess patterns of genomic diversity and its association to phenotypic development across early generations of mass rearing under two selection strategies: selection for greater larval mass (SEL lines) and no direct artificial selection (NS lines). Genome-wide single nucleotide polymorphism (SNP) data were generated using 2bRAD sequencing, while phenotypic traits relating to production and population fitness were measured. Declining patterns of genomic diversity were observed across three generations of captive breeding, with the lowest diversity recorded for the F3 generation of both selection lines, most likely due to founder effects. The SEL cohort displayed statistically significantly greater larval weight com the NS lines with pronounced genetic and phenotypic directional changes across generations. Furthermore, lower genetic and phenotypic diversity, particularly for fitness traits, were evident for SEL lines, illustrating the trade-off between selecting for mass and the resulting decline in population fitness. SNP-based heritability was significant for growth, but was low or non-significant for fitness traits. Genotype-phenotype correlations were observed for traits, but individual locus effect sizes where small and very few of these loci demonstrated a signature for selection. Pronounced genetic drift, due to small effective population sizes, is likely overshadowing the impacts of selection on genomic diversity and consequently phenotypic development. The results hold particular relevance for genetic management and selective breeding for BSF in future.

The genomics and physiology of abiotic stressors associated with global elevational gradients in Arabidopsis thaliana

Phenotypic and genomic diversity in Arabidopsis thaliana may be associated with adaptation along its wide elevational range, but it is unclear whether elevational clines are consistent among different mountain ranges. We took a multi-regional view of selection associated with elevation. In a diverse panel of ecotypes, we measured plant traits under alpine stressors (low CO2 partial pressure, high light, and night freezing) and conducted genome-wide association studies. We found evidence of contrasting locally adaptive regional clines. Western Mediterranean ecotypes showed low water use efficiency (WUE)/early flowering at low elevations to high WUE/late flowering at high elevations. Central Asian ecotypes showed the opposite pattern. We mapped different candidate genes for each region, and some quantitative trait loci (QTL) showed elevational and climatic clines likely maintained by selection. Consistent with regional heterogeneity, trait and QTL clines were evident at regional scales (c. 2000 km) but disappeared globally. Antioxidants and pigmentation rarely showed elevational clines. High elevation east African ecotypes might have higher antioxidant activity under night freezing. Physiological and genomic elevational clines in different regions can be unique, underlining the complexity of local adaptation in widely distributed species, while hindering global trait-environment or genome-environment associations. To tackle the mechanisms of range-wide local adaptation, regional approaches are thus warranted.

Genome-wide analysis for root and leaf architecture traits associated with drought tolerance at the seedling stage in a highly ecologically diverse wheat population

Drought stress occurred at early growth stages in wheat affecting the following growth stages. Therefore, selecting promising drought-tolerant genotypes with highly adapted traits at the seedling stage is an important task for wheat breeders and geneticists. Few research efforts were conducted on the genetic control for drought-adaptive traits at the seedling stage in wheat. In this study, a set of 146 highly diverse spring wheat core collections representing 28 different countries was evaluated under drought stress at the seedling stage. All genotypes were exposed to drought stress for 13 days by water withholding. Leaf traits including seedling length, leaf wilting, days to wilting, leaf area, and leaf rolling were scored. Moreover, root traits such as root length, maximum width, emergence angle, tip angle, and number of roots were scored. Considerable significant genetic variation was found among all genotypes tested in these experiments. The heritability estimates ranged from 0.74 (leaf witling) to 0.99 (root tip angle). A set of nine genotypes were selected and considered drought-tolerant genotypes. Among all leaf traits, shoot length had significant correlations with all root traits under drought stress. The 146 genotypes were genotyped using the Infinium Wheat 15 K single nucleotide polymorphism (SNP) array and diversity arrays technology (DArT) marker platform. The result of genotyping revealed 12,999 SNPs and 2150 DArT markers which were used to run a genome-wide association study (GWAS). The results of GWAS revealed 169 markers associated with leaf and root traits under drought stress. Out of the 169 markers, 82 were considered major quantitative trait loci (QTL). The GWAS revealed 95 candidate genes were identified with 53 genes showing evidence for drought tolerance in wheat, while the remaining candidate genes were considered novel. No shared markers were found between leaf and root traits. The results of the study provided mapping novel markers associated with new root traits at the seedling stage. Also, the selected genotypes from different countries could be employed in future wheat breeding programs not only for improving adaptive drought-tolerant traits but also for expanding genetic diversity.

Exploring fatty acids from royal jelly as a source of histone deacetylase inhibitors: from the hive to applications in human well-being and health

A differential diet with royal jelly (RJ) during early larval development in honeybees shapes the phenotype, which is probably mediated by epigenetic regulation of gene expression. Evidence indicates that small molecules in RJ can modulate gene expression in mammalian cells, such as the fatty acid 10-hydroxy-2-decenoic acid (10-HDA), previously associated with the inhibition of histone deacetylase enzymes (HDACs). Therefore, we combined computational (molecular docking simulations) and experimental approaches for the screening of potential HDAC inhibitors (HDACi) among 32 RJ-derived fatty acids. Biochemical assays and gene expression analyses (Reverse Transcriptase - quantitative Polymerase Chain Reaction) were performed to evaluate the functional effects of the major RJ fatty acids, 10-HDA and 10-HDAA (10-hydroxy-decanoic acid), in two human cancer cell lines (HCT116 and MDA-MB-231). The molecular docking simulations indicate that these fatty acids might interact with class I HDACs, specifically with the catalytic domain of human HDAC2, likewise well-known HDAC inhibitors (HDACi) such as SAHA (suberoylanilide hydroxamic acid) and TSA (Trichostatin A). In addition, the combined treatment with 10-HDA and 10-HDAA inhibits the activity of human nuclear HDACs and leads to a slight increase in the expression of HDAC-coding genes in cancer cells. Our findings indicate that royal jelly fatty acids collectively contribute to HDAC inhibition and that 10-HDA and 10-HDAA are weak HDACi that facilitate the acetylation of lysine residues of chromatin, triggering an increase in gene expression levels in cancer cells.

Insights from homozygous signatures of cervus nippon revealed genetic architecture for components of fitness

This study investigates the genomic landscape of Sika deer populations, emphasizing the detection and characterization of runs of homozygosity (ROH) and their contribution towards components of fitness. Using 85,001 high-confidence SNPs, the investigation into ROH distribution unveiled nuanced patterns of autozygosity across individuals especially in 2 out of the 8 farms, exhibiting elevated ROH levels and mean genome coverage under ROH segments. The prevalence of shorter ROH segments (0.5-4 Mb) suggests historical relatedness and potential selective pressures within these populations. Intriguingly, despite observed variations in ROH profiles, the overall genomic inbreeding coefficient (FROH) remained relatively low across all farms, indicating a discernible degree of genetic exchange and effective mitigation of inbreeding within the studied Sika deer populations. Consensus ROH (cROH) were found to harbor genes for important functions viz., EGFLAM gene which is involved in the vision function of the eye, SKP2 gene which regulates cell cycle, CAPSL involved in adipogenesis, SPEF2 which is essential for sperm flagellar assembly, DCLK3 involved in the heat stress. This first ever study on ROH in Sika deer, to shed light on the adaptive role of genes in these homozygous regions. The insights garnered from this study have broader implications in the management of genetic diversity in this vulnerable species.

Intra-species quantification reveals differences in activity and sleep levels in the yellow fever mosquito, Aedes aegypti

Aedes aegypti is an important mosquito vector of human disease with a wide distribution across the globe. Climatic conditions and ecological pressure drive differences in the biology of several populations of this mosquito species, including blood-feeding behaviour and vector competence. However, no study has compared activity and/or sleep among different populations/lineages of Ae. aegypti. Having recently established sleep-like states in three mosquito species with observable differences in timing and amount of sleep among species, we investigated differences in activity and sleep levels among 17 Ae. aegypti lines drawn from both its native range in Africa and its invasive range across the global tropics. Activity monitoring indicates that all the lines show consistent diurnal activity, but significant differences in activity level, sleep amount, number of sleep bouts and bout duration were observed among the lines. The variation in day activity was associated with differences in host preference and ancestry for the lineages collected in Africa. This study provides evidence that the diurnal sleep and activity profiles for Ae. aegypti are consistent, but there are significant population differences for Ae. aegypti sleep and activity levels and interactions with host species may significantly impact mosquito activity.

Evolution of parasites in the Anthropocene: new pressures, new adaptive directions

The Anthropocene is seeing the human footprint rapidly spreading to all of Earth's ecosystems. The fast-changing biotic and abiotic conditions experienced by all organisms are exerting new and strong selective pressures, and there is a growing list of examples of human-induced evolution in response to anthropogenic impacts. No organism is exempt from these novel selective pressures. Here, we synthesise current knowledge on human-induced evolution in eukaryotic parasites of animals, and present a multidisciplinary framework for its study and monitoring. Parasites generally have short generation times and huge fecundity, features that predispose them for rapid evolution. We begin by reviewing evidence that parasites often have substantial standing genetic variation, and examples of their rapid evolution both under conditions of livestock production and in serial passage experiments. We then present a two-step conceptual overview of the causal chain linking anthropogenic impacts to parasite evolution. First, we review the major anthropogenic factors impacting parasites, and identify the selective pressures they exert on parasites through increased mortality of either infective stages or adult parasites, or through changes in host density, quality or immunity. Second, we discuss what new phenotypic traits are likely to be favoured by the new selective pressures resulting from altered parasite mortality or host changes; we focus mostly on parasite virulence and basic life-history traits, as these most directly influence the transmission success of parasites and the pathology they induce. To illustrate the kinds of evolutionary changes in parasites anticipated in the Anthropocene, we present a few scenarios, either already documented or hypothetical but plausible, involving parasite taxa in livestock, aquaculture and natural systems. Finally, we offer several approaches for investigations and real-time monitoring of rapid, human-induced evolution in parasites, ranging from controlled experiments to the use of state-of-the-art genomic tools. The implications of fast-evolving parasites in the Anthropocene for disease emergence and the dynamics of infections in domestic animals and wildlife are concerning. Broader recognition that it is not only the conditions for parasite transmission that are changing, but the parasites themselves, is needed to meet better the challenges ahead.

Progress and persistence of diseases of high consequence to livestock in the United States

The USDA/ARS-National Disease Center (NADC) will celebrate its 65th anniversary of existence in November 2026. NADC continues as one of the world's premier animal health research centers conducting basic and applied research on endemic diseases with economic impact on U.S. livestock and wildlife. This research center also supports a program studying important food safety pathogens such as Salmonella, E. coli and Campylobacter. NADC has contributed significantly to the elimination of a few diseases, notably hog cholera and milk fever, and made progress in reducing the impact of many other animal diseases through vaccines, therapies and managerial recommendations. Despite nearly 65 years of targeted research on these diseases and much progress, some of these continue to persist. The reasons for such persistence varies for each disease condition and they are often multifactorial involving host susceptibility, virulence and even environmental conditions. Individually and in aggregate, these disease conditions have a massive economic impact and can be devasting to animal producers, owners and individuals that become infected through zoonotic disease agents such as tuberculosis, leptospirosis and avian influenza. They also diminish the health, well-being and welfare of affected animals, which directly affects the food supply. The NADC is using all available technologies including genomic, biochemical, reverse genetics, and vaccine trials in the target host to combat these significant diseases. We review the progress and reasons for persistence of selected diseases and food safety pathogens as well as the progress and potential outcomes should research and programmatic plans to eliminate these disease conditions cease.

On-host flea phenology and flea-borne pathogen surveillance among mammalian wildlife of the pineywoods of East Texas

Flea-borne diseases are endemic in Texas, U.S.A., with an increasing incidence of flea-borne typhus and cat scratch disease. Knowledge of flea natural history could provide information to protect public health, yet many knowledge gaps remain outside of plague-endemic regions. Our objective was to characterize seasonal activity patterns of fleas on common mammalian wildlife species and test fleas and wildlife for Rickettsia and Bartonella pathogens. We performed one year of monthly trapping for rodents and medium-sized mammals in a national forest with high recreational use and urban encroachment in East Texas. From 90 mammal captures representing seven species, 101 fleas were collected representing Polygenis spp., Ctenocephalides felis, and Orchopeas species. Virginia opossums (Didelphis virginianus) hosted 99% of the collected fleas (100 fleas) and a single flea was on an eastern woodrat (Neotoma floridana). Flea infestation prevalence of opossums was 79% (23/29). Mean flea abundance was 4.39 fleas, with intensity peaking in spring. One cat flea removed from an opossum was positive for Bartonella henselae. Furthermore, we identified tissue or blood of four raccoons (Procyon lotor) and one golden mouse (Ochrotomys nuttalli) positive for Rickettsia amblyommatis. These findings provide an ecological basis for the maintenance of vectors and pathogens from sylvatic settings.

Transcriptomics reveals the regulation of the immune system of the mushroom-forming fungus Schizophyllum commune during interaction with four competitors

Mushroom-forming fungi frequently encounter competitors during their lifecycle, but their defense mechanisms remain largely unexplored. We studied the response of the mushroom-forming fungus Schizophyllum commune during interaction with the fungal competitors Trichoderma harzianum, Trichoderma aggressivum and Purpureocillium lilacinum and the bacterial competitor Serratia quinivorans. Transcriptomics revealed 632 up-regulated genes in the direct interaction zone, which were enriched in small secreted proteins and transporters. A set of 26 genes were up-regulated during all interactions, indicating a core transcriptomic defense response. In the non-interacting edge of the mycelium of S. commune, there were 154 up-regulated genes, suggesting that there is a systemic response due to a signal that reaches unaffected areas. The GATA zinc finger transcription factor gene gat1 was up-regulated during interaction and a Δgat1 strain displayed increased colonization by T. harzianum. Previously linked to mushroom development, this transcription factor apparently has a dual role. Moreover, 138 genes were up-regulated during both interaction and mushroom development, indicating priming of the defense response during development to prepare the fruiting body for future interactions. Overall, we unveiled a defensive response of S. commune during interaction with fungal and bacterial competitors and identified a regulator of this response.

Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms

Organic farming utilizes farmyard manure, compost, and organic wastes as sources of nutrients and organic matter. Soil under organic farming exhibits increased microbial diversity, and thus, becomes naturally suppressive to the development of soil-borne pathogens due to the latter's competition with resident microbial communities. Such soils that exhibit resistance to soil-borne phytopathogens are called disease-suppressive soils. Based on the phytopathogen suppression range, soil disease suppressiveness is categorised as specific- or general- disease suppression. Disease suppressiveness can either occur naturally or can be induced by manipulating soil properties, including the microbiome responsible for conferring protection against soil-borne pathogens. While the induction of general disease suppression in agricultural soils is important for limiting pathogenic attacks on crops, the factors responsible for the phenomenon are yet to be identified. Limited efforts have been made to understand the systemic mechanisms involved in developing disease suppression in organically farmed soils. Identifying the critical factors could be useful for inducing disease suppressiveness in conducive soils as a cost-effective alternative to the application of pesticides and fungicides. Therefore, this review examines the soil properties, including microbiota, and assesses indicators related to disease suppression, for the process to be employed as a tactical option to reduce pesticide use in agriculture.

Heat waves induce milkweed resistance to a specialist herbivore via increased toxicity and reduced nutrient content

Over the last decade, a large effort has been made to understand how extreme climate events disrupt species interactions. Yet, it is unclear how these events affect plants and herbivores directly, via metabolic changes, and indirectly, via their subsequent altered interaction. We exposed common milkweed (Asclepias syriaca) and monarch caterpillars (Danaus plexippus) to control (26:14°C, day:night) or heat wave (HW) conditions (36:24°C, day:night) for 4 days and then moved each organism to a new control or HW partner to disentangle the direct and indirect effects of heat exposure on each organism. We found that the HW directly benefited plants in terms of growth and defence expression (increased latex exudation and total cardenolides) and insect her'bivores through faster larval development. Conversely, indirect HW effects caused both plant latex and total cardenolides to decrease after subsequent herbivory. Nonetheless, increasing trends of more toxic cardenolides and lower leaf nutritional quality after herbivory by HW caterpillars likely led to reduced plant damage compared to controls. Our findings reveal that indirect impacts of HWs may play a greater role in shaping plant-herbivore interactions via changes in key physiological traits, providing valuable understanding of how ecological interactions may proceed in a changing world.

Manipulating hormones to mitigate trade-offs in crops

Addressing trait coupling due to gene pleiotropy presents challenges in conventional breeding system. However, targeted hormonal manipulation and precise genetic engineering designs hold promise to alleviate trade‐offs and unlock the potential of crops for multiple desirable traits.

Stress-induced epigenetic effects driven by maternal lactation in dairy cattle: a comethylation network approach

Epigenetic marks do not follow the Mendelian laws of inheritance. The environment can alter the epigenotype of an individual when exposed to different external stressors. In lactating cows, the first stages of gestation overlap with the lactation peak, creating a negative energy balance that is difficult to overcome with diet. This negative energy balance could affect early embryo development that must compete with the mammary tissue for nutrients. We hypothesize that the methylation profiles of calves born to nonlactating heifers are different from those of calves born to lactating cows. We found 50,277 differentially methylated cytosines and 2,281 differentially methylated regions between these two groups of animals. A comethylation network was constructed to study the correlation between the phenotypes of the mothers and the epigenome of the calves, revealing 265 regions associated with the phenotypes. Our study revealed the presence of DMCs and DMRs in calves gestated by heifers and lactating cows, which were linked to the dam's lactation and the calves' ICAP and milk EBV. Gene-specific analysis highlighted associations with vasculature and organ morphogenesis and cell communication and signalling. These finding support the hypothesis that calves gestated by nonlactating mothers have a different methylation profile than those gestated by lactating cows.

Generational stability of epigenetic transgenerational inheritance facilitates adaptation and evolution

The epigenome and epigenetic inheritance were not included in the original modern synthesis theory or more recent extended evolutionary synthesis of evolution. In a broad range of species, the environment has been shown to play a significant role in natural selection, which more recently has been shown to occur through epigenetic alterations and epigenetic inheritance. However, even with this evidence, the field of epigenetics and epigenetic inheritance has been left out of modern evolutionary synthesis, as well as other current evolutionary models. Epigenetic mechanisms can direct the regulation of genetic processes (e.g. gene expression) and also can be directly changed by the environment. In contrast, DNA sequence cannot be directly altered by the environment. The goal of this review is to present the evidence of how epigenetics and epigenetic inheritance can alter phenotypic variation in numerous species. This can occur at a significantly higher frequency than genetic change, so correlates with the frequency of evolutionary change. In addition, the concept and importance of generational stability of transgenerational inheritance is incorporated into evolutionary theory. For there to be a better understanding of evolutionary biology, we must incorporate all aspects of molecular (e.g. genetics and epigenetics) and biological sciences (e.g. environment and adaptation).

Genome-wide expanding of genetic evolution and potential pathogenicity in Vibrio alginolyticus

Vibrio alginolyticus, an emergent species of Vibrio genus, exists in aquatic and marine environments. It has undergone genetic diversification, but its detailed genomic diversity is still unclear. Here, we performed a multi-dimensional comparative genomic analysis to explore the population phylogeny, virulence-related genes and potential drug resistance genes of 184 V. alginolyticus isolates. Although genetic diversity is complex, we analysed the population structure using three sub-datasets, including the subdivision for three lineages into sublineages and the distribution of strains in the marine ecological niche. Accessory genes, most of which reclassified V. alginolyticus genomes as different but with relatively close affinities, were nonuniformly distributed among these isolates. We demonstrated that the spread of some post-evolutionary isolates (mainly L3 strains isolated from Chinese territorial seas) was likely to be closely related to human activities, whereas other more ancestral strains (strains in the L1 and L2) tended to be locally endemic and formed clonal complex groups. In terms of pathogenicity, the potential virulence factors were mainly associated with toxin, adherence, motility, chemotaxis, and the type III secretion system (T3SS). We also found five types of antibacterial drug resistance genes. The prevalence of β-lactam resistance genes was 100%, which indicated that there may be a potential risk of natural resistance to β-lactam drugs. Our study reveals insights into genomic characteristics, evolution and potential virulence-associated gene profiles of V. alginolyticus.

Polychromophilus (Haemosporida: Plasmodiidae): A review of association with bats (Mammalia, Chiroptera) and the first record in the Neotropical bat, Myotis albescens (Chiroptera, Vespertilionidae) from Colombia

Some species within the family Plasmodiidae (Haemosporida) have been extensively studied due to their implications for human health. However, for other haemosporidians that infect wild animals the knowledge is limited. Species within the genus Polychromophilus have thus far been documented exclusively as hemoparasites of bats. Records of Polychromophilus are primarily from Africa, Europe, and Southeast Asia, with limited information available for the Americas. Here, we assessed the state of knowledge on Polychromophilus species infecting bats worldwide and searched for the presence of Polychromophilus in blood samples of neotropical bats from Colombia. We found a total of 65 records of Polychromophilus in 46 bat species belonging to the families Emballonuridae, Hipposideridae, Miniopteridae, Rhinolophidae, Rhinonycteridae, and Vespertilionidae worldwide, except for Antarctica. In the Americas, records of the genus Polychromophilus are exclusively from Vespertilionidae bats in Brazil, Colombia, the United States, and Panama. The morphological and molecular analyses of blood from 125 bats, belonging to 39 species and captured in seven localities within the departments of Arauca and Caldas (Colombia), confirmed the presence of Polychromophilus deanei in a silver-tipped myotis, Myotis albescens (Vespertilionidae). This finding represents the first morphological and molecular confirmation of P. deanei in the Americas. Additionally, it expands the knowledge on the diversity and distribution of Polychromophilus in Neotropical bats.