Phenol is a water-soluble contaminant frequently detected in sediments, yet sediment-specific toxicity data are scarce. To address this data gap, we evaluated the use of water-based toxicity data for sediment ecological risk assessment (ERA) by combining the equilibrium partitioning method (EPM) with species sensitivity distributions (SSDs). Acute and chronic toxicity data from laboratory and artificial-stream tests using native aquatic species were compiled and converted to sediment-equivalent values for SSD construction. We quantified how species origin (native vs. foreign), habitat type (benthic vs. non-benthic), taxonomic composition, and sample size affect SSD-derived hazardous concentration for 5% of species (HC5). Inclusion of benthic taxa, including early life-stage amphibians classified as benthic, was associated with lower HC5 estimates; sensitivity differences across groups were generally < one order of magnitude. At least 8 species were needed for stable SSD performance. Applying an assessment factor to the HC5 yielded a PNECsediment of 0.81µg/g dry weight. Using this value, phenol concentrations from 23 monitoring sites indicate that 87% of locations would be categorized as moderate to high risk. As a phenol case study, the EPM-SSD framework demonstrates a pragmatic, transparent route to sediment ERA for moderately hydrophilic substances under data-limited conditions.

Almonds (Prunus dulcis) (Mill.) are an economically important crop in California, with an estimated value of $8.6 billion dollars annually. The aim of this study was to identify the hemipteran pest and beneficial species in conventionally managed almond orchards when the developing almond crop was vulnerable to feeding damage. Insects were collected in 9 orchards by multiple methods and then Hemiptera were sorted to morphospecies. The DNA barcode of the mitochondrial DNA COI gene was sequenced for each specimen. For each species, the haplotype diversity was determined. A high diversity of Hemiptera was collected, including 26 species from 12 families. Pest species included Halyomorpha halys Stål (Hemiptera: Pentatomidae), Chinavia hilaris (Say) (Hemiptera: Pentatomidae), Lygus hesperus Knight, and Leptoglossus zonatus (Dallas) (Hemiptera: Coreidae); beneficials included Brochymena quadripustulata (Fabricius) (Hemiptera: Pentatomidae), Orius spp. Wolff (Hemiptera: Anthocoridae), Nabis spp. Latreille (Hemiptera: Nabidae) and Geocoris atricolor Montandon (Hemiptera: Geocoridae). Several orchards had high species diversity (13 species), others had only one species recovered. Haplotype diversity was low in most pest species except for L. hesperus (0.6) and was high in 2 beneficial groups, Nabis spp. and Orius tristicolor (White) (0.6 to 0.76). Hemipteran pests were detected through the time when developing almonds were susceptible to feeding damage, while beneficial Hemiptera were more abundant later. Correct identification of insect species is an integral component to Integrated Pest Management (IPM) to trace the origin of invasive species, uncover cryptic species, and to develop a relationship between species and crop damage.

The influence of Amazonian rivers and landscape changes on species origin and distribution remains debated. Here, we combine sedimentary, geomorphological, and chronological evidence from Central Amazonia to show that the main Amazonian rivers constructed large tracts of land that now support present-day Amazonian upland forest (terra firme). These deposits record a sequence of landscape rearrangements driven by river processes in Central Amazonia during the Pleistocene redefined the spatial boundaries of key habitats critical for many species. Our findings reveal that Amazonian rivers have acted not only as biogeographic barriers but also as powerful agents of landscape and habitat transformation, offering a unified framework for understanding how geological and biological processes together shaped the evolution of Amazonian biodiversity.

In phylogeography, ancestral state inference methods are used to identify the geographic or host species origin of viral or bacterial lineages and reconstruct their transmission histories over time. However, differences in sampling among states can bias these inference methods. Here, we introduce sampling-aware ancestral state inference (SAASI), a method that accounts for sampling differences. We apply SAASI to the multi-host spread of the H5N1 virus in the United States in 2024 and find that the key transmission event from wild birds to cattle is estimated to occur later under lower sampling in wild birds (compared to other species) than when sampling is not accounted for. Using simulation, we find that SAASI infers past viral locations/host species considerably more accurately than standard methods when sampling bias exists, is computationally feasible for large datasets, and scales to trees with 100,000 tips.

A career in pursuit of the origin of species: celebrating Roger Butlin's contributions to the advancement of knowledge and growth of our scientific community.

Accurate species identification is essential for conserving and managing plants that provide important ecosystem services and have ethnobotanical value. The Greyia tree genus (G. sutherlandii, G. radlkoferi and G. flanaganii) is endemic to South Africa and Eswatini, and certain genotypes have medicinal value for treating skin hyper-pigmentation. However, distinguishing among species is difficult because of overlapping phenotypes and the limited resolution of standard DNA barcodes. To overcome these limitations, a robust molecular identification assay was developed using a two-phase strategy. First, de novo SNP discovery using 3RAD sequencing identified 47,726 genome-wide SNPs from two to three plants sampled from each species' core geographic range: G. radlkoferi in northern Limpopo, G. sutherlandii in eastern KwaZulu-Natal, and G. flanaganii in the south-eastern Eastern Cape. Principal component analysis and coancestry matrices revealed three discrete genetic clusters, supporting the recognition of the three species. Selecting a set of 200 SNPs with intermediate Fst values (0.2-0.5) resulted in optimal separation of the three clusters. This led to the final selection of a 23-SNP panel that included five informative barcoding loci (ITS, trnL-F, matK). Second, the 23 SNPs were converted into allele-specific fluorescent PCR assays (SNP Type) for genotyping on the BioMark HD platform. The panel was validated using genomic DNA from 17 individuals from the 3RAD population groups and successfully differentiated all three species. It was then applied to 73 trees sampled across a 1000-km transect from the Eastern Cape to Limpopo. Genetic clustering (PCA, UPGMA and ADMIXTURE) assigned each tree to one of three species-level groups matching their expected ranges. In a practical case study, the assay also identified the species origin of 33 Greyia trees of unknown provenance from production orchards. This study provides an efficient SNP-based tool for accurate species identification, supporting conservation planning and the sustainable management of Greyia populations.

Milk fat globule membrane from cow, goat, and human differentially modulate Lacticaseibacillus rhamnosus GG: Proteomic insights from human MFGM.

Functional and protein interaction analysis of Nop7 in trypanosomatid parasites.

Testicular steroidogenesis is fundamental to male reproductive health, but its disruption by environmental and emerging chemicals remains insufficiently characterized due to limitations in existing test systems. Traditional animal models pose ethical and logistical challenges, while the validated H295R assay-based on a female adrenal carcinoma cell line-fails to reflect male gonadal steroidogenesis. This review uses a semi-systematic approach to evaluate over 1500 studies employing in vitro models, including primary Leydig cells, Leydig cell lines, stem cell-derived Leydig-like cells, and advanced 3D testicular systems. We assess species origin, developmental relevance, culture conditions, and the extent to which these models replicate key steroidogenic pathways. Most models rely on rodent-derived, cancerous cell lines cultured in two-dimensional monolayers, with limited representation of human and immature Leydig cells. A targeted full-text analysis examined the effects of 23 reference chemicals on testosterone, progesterone, androstenedione, and estrogen levels across the H295R assay and eight testicular in vitro models. Forskolin, genistein, prochloraz, and ketoconazole showed consistent effects and may serve as promising reference compounds. However, data for most chemicals in testicular models are scarce or inconsistent-particularly for androstenedione and progesterone-underscoring the need for improved model standardization. We propose future directions to enhance predictive power, including the development of hormone-responsive, species- and stage-specific models cultured under hormone-controlled conditions. Such advances are essential to improve chemical safety assessment and facilitate regulatory acceptance of alternative test methods.

ConspectusThe direct oxidation of methane, which is the main component of natural gas, shale gas, methane clathrates, and biogas, to value-added products is an economically attractive and environmentally friendly alternative to strongly endothermic methane steam reforming to synthesis gas (CO/H2). Among the different routes, the oxidative coupling of methane (OCM) to ethylene/ethane (C2-hydrocarbons) is the most promising one. A key limiting factor is insufficiently high selectivity to C2-hydrocarbons due to their overoxidation to carbon oxides (COx) at industrially relevant degrees of methane conversion. Although it is generally agreed that both selective and unselective reactions are initiated by oxygen species on the surface of catalysts, the kind, role, and origin of these species remain elusive, which hampers the tailored design of catalysts.In this Account, we summarize our recent progress in understanding how product selectivity in the OCM reaction can be tuned by controlling the type of oxygen species through catalyst composition or reaction conditions. The combination of in situ time- and temperature-resolved catalyst characterization with transient kinetic methods, i.e., temporal analysis of products (TAP) and steady-state isotopic transient kinetic analysis (SSITKA), has been proven to be effective for understanding the origin and role of oxygen species involved in selective and unselective pathways. We also present strategies for regulating the concentrations of selective and unselective oxygen species. For the Mn-M(M = Na, K, Rb, or Cs)2WO4 system, the electronegativity of the alkali metal was found to influence the ability of the catalysts to form selective oxygen species from gas-phase oxygen. The binding strength of atomic oxygen species is a key parameter for hindering the oxidation of methane to COx over Gd2O3-based catalysts. This property can be adjusted by using a metal oxide promoter. The nature and concentration of different oxygen species can also be controlled through the use of steam or an alternative oxidizing agent, N2O, and by performing the OCM reaction in a chemical looping mode, i.e., by alternating between CH4- and air-containing feeds. Using steam in the latter option enabled us to largely enhance the productivity of C2-hydrocarbons, thus making this technology more attractive for large-scale applications. The knowledge summarized in this Account is expected to present insights for further studies in the development of selective catalysts for various alkane oxidation reactions and in the optimization of reactor operation.

A hybridization assay based on the microfluidic biochip was developed to identify the origin of the Atlantic salmon species. Among the 215 single nucleotide polymorphic (SNP) sites found in the mtDNA of Salmo salar, we located five sites in devising our assay method. We found two sites that worked, while the others generated either insufficient signals or specificity. We have successfully identified the North American origin of the three samples, as confirmed by Sanger sequencing.

Abstract Background Tamarillo or tree tomato ( Solanum betaceum Cav.) is a fruit tree species of Andean origin with cultural and economic relevance in Colombia. The high incidence of complex viral diseases termed “virosis” in all tamarillo-growing regions of the country leads to huge production losses and seriously threatens its cultivation. Methods RNA-seq libraries were constructed for symptomatic samples from eight tamarillo-growing locations across the Department of Nariño (Colombia). Their virus diversity was characterized using the Genome Detective software. The identified PVY isolate was subsequently subjected to RT-PCR validation and phylogenetic analysis. Results Several virus species belonging to the genera Torradovirus , Potyvirus and Polerovirus were identified in mixed infections in tamarillo. Full- or nearly full-length genomes were generated for tomato torrado virus (ToTV), physalis torrado virus (PhyTV), potato leafroll virus (PLRV), and a novel isolate of potato virus Y-Tamarillo (PVY-Tam). When present, PVY-Tam seems to synergistically boost the accumulation of unrelated viruses, therefore contributing to the severity of the infections. Nucleotide sequence analysis suggests that the PVY-Tam from Nariño originated in South America by a recent divergence of the PVY N lineage, and possibly by the recombination of geographically close isolates. Moreover, P3N-PIPO, a frameshift product from the potyviral P3 gene, shows variations in protein lenght between PVY isolates that might be involved with host-specific adaptations. Conclusions We provide evidence of a novel PVY-Tam isolate in the Andean region that might promote the severity of unrelated virus partners in field-grown tamarillo. Our findings contribute to understanding tamarillo virosis for the development of effective diagnostic and control strategies.

Ancient DNA technology directly retrieves genetic information from preserved biological materials, thereby offering significant advantages for elucidating species origins and evolution. In recent years, ancient DNA studies have yielded significant advances in our understanding of human evolution and the origins and dispersal of animals. With the rapid development of ancient DNA extraction, library construction, and sequencing techniques, ancient DNA technology is increasingly contributing to plant research and is gradually developing into a standardized and systematic research area. These studies have not only deepened our understanding of the origins, dispersal routes, and evolutionary history of crop domestication, but have also provided novel perspectives for interpreting the interactive evolution among humans, plants, and the environment. In this review, we introduce the workflow of ancient plant DNA research and review the progress of ancient plant DNA technology in the fields of crop domestication, plant diseases, environmental reconstruction, and utilization of plant resources to provide a reference for the in-depth development of this field.

Evolution as a driving force in the universe: The evoluton Dr Peter Verheyen from the Sola Society &amp; Academy at Vienna University highlights key scientific advancements regarding evolution and the Universe. On 24 November 1859, Charles Darwin turned the world upside down with his publication “On the Origin of Species. By Means of Natural Selection or the Preservation of Favoured Races in the Struggle for Life”. Until that time, there was a general consensus reality and the world around us being static: all Earth life, even the whole Universe, was in a ‘steady state’. The arguments and proofs Darwin delivered were convincing: life changes over time. Life proved to be an ever-evolving organisation in its attempt to adapt to its Earth environment.

Self-fertilization reduces genetic diversity compared to outcrossing and hypothetically decreases the ability to adapt to diverse environments. Among Caenorhabditis nematodes, self-fertilization evolved three times independently in Caenorhabditis elegans, Caenorhabditis briggsae, and the more recently discovered Caenorhabditis tropicalis. To survey C. tropicalis genetic relatedness, the influence of geography and niche on species-wide variation, and the signatures of selection, we collected 785 wild strains, sequenced their genomes, and identified 622 distinct genotypes (isotypes). In contrast to C. elegans and C. briggsae, C. tropicalis relatedness shows substantial association with geography and no transcontinental selective sweeps or broadly sampled isotypes. Populations from the Hawaiian Islands or Taiwan harbor more genetic variation than populations from the Caribbean or Americas, suggesting a Pacific species origin similar to other members of the Elegans subclade. Punctuated genomic regions of extreme genetic variation pervade the genome. These hyper-divergent regions (HDRs) comprise less than 6% of the reference genome in any given strain despite harboring 73% of all variant sites and are enriched for genes likely involved in environmental adaptation. HDRs represent a shared genomic feature of self-fertilizing Caenorhabditis nematodes despite their independent evolutionary origins and suggest a mechanism to explain worldwide distributions despite low species-wide levels of genetic variation.

Propolis from Apis mellifera and cerumen from Tetragonula carbonaria are complex mixtures of beeswax, plant resins, and bee secretions whose composition varies with geography and species. Understanding these differences is important for exploring their bioactive potential. This study employs untargeted quantitative 1H NMR metabolomics to characterize A. mellifera propolis from Scandinavia (Denmark and Norway) and Australia, as well as cerumen from T. carbonaria in Australia. Hydrophilic and hydrophobic extracts were analyzed to assess compositional differences across geographical origin and bee species, and to link specific metabolites to radical scavenging activity (RSA). Principal component analysis (PCA) of the 1H NMR spectra showed a marked separation between Scandinavian and Australian propolis. Hydrophilic extracts showed that Scandinavian propolis contains higher levels of aromatic compounds, whereas Australian propolis is richer in carbohydrates. In contrast, cerumen from T. carbonaria exhibits higher amounts of terpenoids. Hydrophobic extracts revealed that Australian propolis has the highest wax content, with shorter chains and more free fatty acids, while Scandinavian propolis samples display uniform wax structures and the highest aromatic content. Multivariate regression using recursive weighted partial least squares (rPLS) to RSA prediction highlighted signals attributable to ferulic acid and p-coumaric acid, which were confirmed by statistical total correlation spectroscopy (STOCSY). These findings demonstrate the utility of quantitative 1H NMR metabolomics for distinguishing botanical and geographic chemotypes of propolis and cerumen. The findings further show that Scandinavian propolis is more consistent with respect to metabolite composition compared to Australian samples, presumably reflecting differences in resin sources for foraging.

ABSTRACT Background The Himalayas emerged from a semi‐aquatic landscape into the tallest mountain system on Earth, driving major environmental changes. Yet, how mammalian communities responded to this transition remains poorly understood. Addressing this gap is critical for understanding the resilience of mammalian assemblages under ongoing environmental changes. Aim We summarize the history of the Himalayas, highlighting key landscape and environmental transformations, and use mammals to exemplify the Himalayas' role in community assembly. Findings Our review highlights that initial uplift due to the northward movement of the Indian Plate towards the Eurasian Plate resulted in a shallow sea and surrounding semi‐aquatic environments, supporting earliest ancestors of modern cetaceans. As uplift progressed, it served as a biological corridor between two plates, facilitating mammalian dispersal in both directions, with subsequent radiations. Continued uplift gave rise to differential climate zones, establishing diverse mammalian communities across elevational gradients. With further increase, it transitioned into a significant biogeographic barrier, driving desertification to the north, intensifying monsoon systems in the south, and shaping river systems and valleys, all impacting the biogeographic complexity of the region. During Quaternary glaciations, river valleys acted as climatic refugia, enabling the persistence of many mammalian lineages. Throughout, precipitation remained higher in the Eastern Himalayas than in the west, leading to additional longitudinal variation in mammalian assemblages. Today, Himalayan mammals span multiple biogeographic realms, with strongest mammalian community similarities to Southeast Asia. Future Direction Much of the material presented reflects evidence from the fossil record, spatial mapping, and recent but sparse genomic work on megafauna, which alone cannot fully explain mammalian responses to changes in the Himalayas. Modern genomic studies and broader sampling, mainly of highly diverse but underrepresented small taxa (rodents, bats, and shrews) are needed to update species origins, diversification, and community assembly to advance knowledge on Himalayan biodiversity dynamics.

The aim of our research is to explore the multifaceted and escalating impact of mold proliferation within urban environments, critically examining its implications for both microbial and macroscopic biodiversity, ecosystem function, and human well-being. As urbanization intensifies, the complex interplay between anthropogenically altered landscapes and indoor environments has precipitated a significant shift in fungal communities. This analysis moves beyond the traditional focus on merely identifying pathogenic mold to understanding its broader ecological ramifications. Specifically, we discuss how the documented increase in indoor fungal biomass and richness correlates directly with elevated water availability—a condition exacerbated by common urban infrastructure issues such as aging plumbing, poor ventilation, and the increasing frequency of extreme weather events. We investigate the hypothesis that this shift in urban mycobiomes is characterized by a proliferation of larger-spored, potentially pathogenic taxa that significantly contribute to adverse human health outcomes, including respiratory ailments and allergies. However, the scope of this research extends to the broader ecological impact on urban biodiversity. We analyze how these altered fungal communities disrupt delicate urban ecosystem services by influencing the diversity and function of other microbial and macro-organisms. Recent findings indicate a substantial reduction in both aerial and soil fungal diversity within urban areas compared to natural habitats, suggesting a profound ecological imbalance. This involves a nearly twofold reduction in species richness and a fivefold decrease in fungal DNA abundance even at small scales, underscoring a critical loss of ecological functionality necessary for urban regeneration. The prevailing indoor microbiome often comprises airborne species of outdoor origin that passively collect on surfaces rather than arising from endogenous growth. This challenges traditional views of indoor microbial sources and highlights the limitations of relying solely on mechanical systems such as heating, ventilation, and air conditioning (HVAC) to manage indoor air quality. Instead, we advocate for a holistic approach that incorporates sustainable building materials and responsive architectural design to foster resilient, diverse microbial communities. A major limitation in elucidating these complex interactions is the current reliance on 18S rRNA gene sequencing, which often lacks the taxonomic resolution required for genus-level identification. We propose that future research should employ shotgun metagenomic sequencing and RNA-based methods to distinguish viable organisms from dead cells, thereby providing a more comprehensive view of microbial diversity and metabolic pathways. Furthermore, integrating advanced "omic" approaches, ecological modeling, and machine learning will allow for the development of predictive frameworks. These frameworks are essential for understanding how urban development influences fungal successions and for informing interventions that promote beneficial microbial communities. Finally, this presentation addresses the potential of fungal bioremediation, or mycoremediation, as a sustainable solution for environmental contaminants. While current limitations in scaling exist due to knowledge gaps regarding fungal potential, biotechnological innovations offer promising avenues. We explore how genetic engineering can enhance fungal capabilities by constructing novel fungi with improved metabolic pathways for utilizing emerging contaminants. Additionally, the integration of nanotechnology with mycoremediation could significantly enhance the specificity and efficiency of contaminant degradation. By combining fungal biology with nanotechnological advancements, we can develop potent strategies for addressing persistent organic pollutants. Ultimately, this research aims to move beyond simplistic pathogen identification to embrace a functional ecological perspective, crucial for designing healthier, more resilient urban environments that balance human health needs with long-term ecosystem stability.

Baxiaga (བ་ཤ་ཀ) is a typical Tibetan medicinal species of multiple origin. These plants have been used in traditional Tibetan medicine for centuries and are currently used to treat various types of fever, such as Chiba fever, liver fever, reduce inflammation, relieve pain, and heal other diseases. This review aims to provide a comprehensive analysis of the traditional uses of the baxiaga series of plants (Justicia adhatoda L., Veronica ciliata Fisch., Veronica eriogyne H.J.P. WinkI., Corydalis impatiens (Pall.) Fisch. ex DC., and Corydalis crispa Prain) as well as their phytochemical and pharmacological studies; it also provides a scientific basis for the clinical application of Baxiaga and promotes the development of its pharmaceutical preparations. This review performed an extensive database search to collect detailed information about baxiaga and the literature was systematically interpreted, analyzed, and documented. This review summarizes the traditional usage of five plants in Tibetan medicine baxiaga, which includes 195 chemical constituents such as alkaloids, flavonoids, terpenoids, and iridoid glycosides. This research elaborates on the pharmacological activities and mechanisms of these medicinal plants, along with discussions on multi-origin and quality control issues, while also proposing future research directions. This study presents a comprehensive analysis of the five medicinal plants commonly used in baxiaga. Our analysis highlights the significant value of baxiaga as an ethnomedicinal resource and reveals that its pharmacological activity is mainly attributed to its alkaloid. These alkaloids demonstrate anti-inflammatory, antioxidant and hepatoprotective, activities. However, current studies on the medicinal effects, active ingredient content, quality control, and clinical applications of baxiaga have limitations.

Catfishes of the subfamily Trichomycterinae comprise the most diverse fish group with species adapted to live in Neotropical caves, but past evolutionary scenarios that have driven the origin of these troglobitic species remain unknown. We herein investigate the phylogenetic position of the cave-restricted Trichomycterus rubbioli, endemic to the semi-arid Caatinga of northeastern Brazil, through a time-calibrated molecular phylogenetic analysis of a broad sample of trichomycterine taxa (84 spp), using two nuclear and two mitochondrial genes (3030 bp). The analysis supported T. rubbioli as a member of the Trichomycterus s.s. clade endemic to eastern South America and an early Miocene origin for the T. rubbioli lineage. The combination of available data suggests that the T. rubbioli lineage adapted to the troglobitic lifestyle between the Middle and Late Miocene, a period when the semi-arid conditions of the Caatinga biome became established and consequently streams of the region became seasonal. This past scenario would be responsible for extinction of epigean trichomycterines while preserving the lineage within the cave system. Morphological characters of the troglobitic 'Trichomycterus' itacarambiensis from the transition area between the Cerrado and the Caatinga indicate distant relationships with T. rubbioli, suggesting an independent evolutionary event of cave colonization.