Subcohort Research Articles

Representativeness of biota of the western part of Ukraine in the Data Centre ‘Biodversity of Ukraine’

This paper summarises the inventory of biota of the western region of Ukraine in the web resource Data Centre ‘Biodiversity of Ukraine’ (DCBU) (http://dc.smnh.org), a growing biodiversity platform launched on 25 May 2017 and which organises knowledge on the biodiversity of Ukraine. The main objective and originality of DCBU is to aggregate curated biodiversity data of different kinds (e.g. scientific and vernacular names, data records of species, their geotagged geographical and biotopic distribution, conservation categories, and representation in protected areas of Ukraine). The database of the resource is primarily filled with data concerning 7 oblasts (Volyn, Rivne, Lviv, Ternopil, Ivano-Frankivsk, Chernivtsi, and Zakarpattia oblasts) of the western region of Ukraine, which is discussed in this article. Currently, the following number of species of living organisms has been recorded for the mentioned oblasts of the region: Volyn Oblast—1311 species/80 protected species listed in the Red Data Book of Ukraine, Rivne Oblast—535/47, Lviv Oblast—3163/211, Ternopil Oblast—1081/164, Ivano-Frankivsk Oblast—1942/157, Chernivtsi Oblast—672/87, and Zakarpatska Oblast—2125/149. Taxonomic accounts in the DCBU cover 5 kingdoms (Chromista, Protista, Plantae, Fungi, and Animalia), 22 phyla, 81 classes, 283 orders, 1292 families, 4741 genera, and 11 763 species. DCBU enables the following operations to be accomplished: to create species lists of different taxonomic rank of separate territorial regions and water bodies of the country and also of different time intervals, to create lists of protected and endemic species and of those that are deposited in collections of scientific institutions; to find a particular specimen according to the inventory number, to create species lists according to the type of recording/collecting, collected or determined by certain specialists, to search for literature sources concerning the Ukrainian biota, and to advanced search for all mentioned parameters as well. The accumulation of information on biodiversity, the possibility of its searching and the free access would promote the development and speed-up of scientific research, the effective control of the ecological state of the environment by the public, and sustainable development.

Oncolytic Viruses, An Emerging Anti-Cancer Immunotherapy: Current Achievements and Future Directions

Oncolytic viruses (OVs) are currently influencing biological cancer therapy. It is a recently created immunotherapy that has been approved to treat cancer and can promote the death of specific cell types to promote antitumor immunological effects. Given the complicated conditions in the tumor micro environment (TME), trials involving the use of OVs demonstrated that OVs could potentially be utilized independently or in combination with other therapies like radiotherapy, chemotherapy, immune checkpoint inhibitors, as well as surgery. While immune suppression against tumors is of critical importance in OV therapy, concurrent antiviral immune responses should also be taken into consideration. Because of this, antiviral immune responses limit OV infections and replication, which also restricts the oncolytic effects of OVs. Recent studies on the operation and mechanics of OVs and how they are employed in clinics has produced results that are encouraging for the future. This review outlined the traits and biological categories of potential OVs, presented the findings of clinical trials, and discussed combinations with other forms of cancer therapy.

Integrating global microbiome data into antibiotic resistance assessment in large rivers

Rivers are important in spreading antimicrobial resistance (AMR). Assessing AMR risk in large rivers is challenged by large spatial scale and numerous contamination sources. Integrating river resistome data into a global framework may help addressing this difficulty. Here, we conducted an omics-based assessment of AMR in a large river (i.e. the Pearl River in China) with global microbiome data. Results showed that antibiotic resistome in river water and sediment was more diversified than that in other rivers, with contamination levels in some river reaches higher than global baselines. Discharge of WWTP effluent and landfill waste drove AMR prevalence in the river, and the resistome level was highly associated with human and animal sources. Detection of 54 risk rank I ARGs and emerging mobilizable mcr and tet(X) highlighted AMR risk in the river reaches with high human population density and livestock pollution. Florfenicol-resistant floR therein deserved priority concerns due to its high detection frequency, dissimilar phylogenetic distance, mobilizable potential, and presence in multiple pathogens. Co-sharing of ARGs across taxonomic ranks implied their transfer potentials in the community. By comparing with global genomic data, we found that Burkholderiaceae, Enterobacteriaceae, Moraxellaceae and Pseudomonadaceae were important potential ARG-carrying bacteria in the river, and WHO priority carbapenem-resistant Enterobacteriaceae, A. baumannii and P. aeruginosa should be included in future surveillance. Collectively, the findings from this study provide an omics-benchmarked assessment strategy for public risk associated with AMR in large rivers.

Synopsis of Osmunda (royal ferns; Osmundaceae): towards reconciliation of genetic and biogeographic patterns with morphologic variation

Abstract We present an overview of the morphology, biogeography, and ecology of the fern genus Osmunda (i.e. without previously included taxa of Claytosmunda, Osmundastrum, and Plenasium), with a focus on the American O. spectabilis Willd. and Old World O. regalis L. While genetic data supports the separation of these taxa, commonly used morphologic characters to distinguish between O. regalis and O. spectabilis (maximum frond size; pinnae sessile vs. stalked; pinnules opposite vs. alternate; general pinnule proportions) are not infallible. We recorded morphometric differences among and between O. regalis and O. spectabilis and correlated these with spatio-environmental gradients. Our work provides an updated taxonomic overview with full synonymy and diagnostic key of Osmunda. We preliminarily recognize six informal subtaxa in O. regalis (‘regalis’, ‘abyssinica’, ‘huegeliana’, ‘longifolia’, ‘transvaalensis’, ‘obtusifolia’) and three in O. spectabilis (‘spectabilis’, ‘palustris’, ‘piresii’) that separate in a morphological traits-based principal component analysis. The morphotaxa appeared geographically structured and their distribution showed significant correlations with elevation, mean annual precipitation, annual mean temperature, and temperature seasonality. The taxonomic rank and validity of the proposed subtaxa has to be tested through a large-scale sampling, e.g. with comparative cp/nr genomic and cytogenetic analyses. Such future analyses may help to ascertain whether the observed morphologic peculiarities are conditioned solely by abiotic factors (which would allow addressing them as forms) or are manifested in the genome.

Diversity of Neotropical stalked-puffball: Two new species of Tulostoma with reticulated spores

Species of the genus Tulostoma are easily recognizable by the presence of a spore sac, with a mouth from which spores are released, attached to a stipe. Tulostoma is a species-diverse genus with a worldwide distribution, and some attempts were made to delimitate species and to evaluate reliable taxonomic-informative characteristics for species identification. However, there is a notable information gap regarding Neotropical species, especially for geographic distribution and DNA data, which hampers further understanding of the infrageneric diversity, evolution, and ecology of this genus. Based on morphological analysis, molecular phylogenetics and geographic distribution, we propose here two new species of Tulostoma with reticulated spores, from the two threatened Brazilian geographical areas, Atlantic Forest and “campos rupestres” (rupestrian grassland), as well as we provide notes on the taxonomic rank of Tulostoma exasperatum var. ridleyi.

IDENTIFICAREA UNOR AGENȚI PATOGENI DE TIP VIRAL PRIN TEHNICI SEROLOGICE SI MOLECULARE DE DIAGNOSTIC LA CAIS, PIERSIC ȘI MIGDAL

In order to obtain plants of the biological category Pre-basic, plants of the genotypes ꞌOlimpꞌ and ꞌDe Valuꞌ in apricot, ꞌRalucaꞌ, ꞌMonicaꞌ, ꞌTomis 1ꞌ in peach, ꞌMirelaꞌ and ꞌVeronicaꞌ in almond were evaluated for the presence of virus-type harmful organisms. Diagnosis was made by the serological DAS-ELISA method for ACLSV, ApMV, PPV, PDV, PNRSV and SLRSV and by the molecular RT-PCR test for ESFY, ApLV and PLMVd. No positive samples were found in apricot. In peach the viruses were identified in ꞌMonicaꞌ: ApLV in 57.15% of the plants tested, PNRSV in 14.29% and PLMVd in 7.15% of the plants. Two of the positive plants had mixed infections produced by PNRSV +ApLV and PNRSV +PLMVd. In peach genotype ꞌTomis 1ꞌ, 23.08 % plants were found infected with ApMV, 7.7 % with ACLSV and 7.7 % with PPV. ACLSV and PPV infections were identified in the same plant. In almond the diagnosis revealed a mixed infection with ACLSV + ApMV (7.7 % of plants from ꞌMirelaꞌ variety).

Seed protein biotyping in Amaranthus species: a tool for rapid identification of weedy amaranths of concern

BackgroundThe Amaranthus genus contains at least 20 weedy and invasive species, including Amaranthus palmeri (palmer’s amaranth) and Amaranthus tuberculatus (tall waterhemp), two species of regulatory concern in North America, impacting production and yield in crops like corn, soybean and cotton. Amaranthus tuberculatus is regulated in Canada with limited establishment, while current climate models predict a range expansion of A. palmeri impacting crop growing areas in Ontario, Quebec and Manitoba. Since many Amaranthus species are similar in their morphology, especially at the seed stage, this demands the development of additional methods that can efficiently aid in the detection and identification of these species. Protein biotyping using Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS) has been traditionally used to identify microorganism species, races and pathotypes. Major protein fractions extracted from an organism, ionized and run through a biotyper using mass spectrometry, result in protein spectra that represent a fingerprint at the species or lower taxonomic rank, providing an efficient molecular diagnostics method. Here we use a modified protein biotyping protocol to extract major protein fractions from seeds of the family Brassicaceae to test our protocol, and then implemented the standardized approach in seeds from Amaranthus species. We then created a database of Amaranthus protein spectra that can be used to test blind samples for a quick identification of species of concern.ResultsWe generated a protein spectra database with 16 Amaranthus species and several accessions per species, spanning target species of regulatory concern and species which are phylogenetically related or easily confused at the seed stage due to phenotypic plasticity. Testing of two Amaranthus blind sample seed sets against this database showed accuracies of 100% and 87%, respectively.ConclusionsOur method is highly efficient in identifying Amaranthus species of regulatory concern. The mismatches between our protein biotyping approach and phenotypic identification of seeds are due to absence of the species in the database or close phylogenetic relationship between the species. While A. palmeri cannot be distinguished from A. watsonii, there is evidence these two species have the same native range and are closely related.

Applying regional climatic indicators to study plant diversity patterns in Inner Mongolia

Climate factors have a major influence on biodiversity patterns have often used their mean values to reflect the distribution of different organisms, reducing the faceted information of the study unit to point information, a situation that may affect the accuracy of the study results. However, there has been a lack of systematic and comprehensive discussion on regional climatic indicators and their selection. To address this, we evaluated plant distribution and meteorological data from 88 banners and counties in Inner Mongolia considering five regional climatic indicators that reflect the state of climate factors, heterogeneity, and total resources in each sampling unit. Additionally, we compared and analyzed the advantages of the regional climatic indicators over mean climate indicators to determine the dominant climate factors driving the diversity patterns of plant families, genera, and species. Our results showed that the regional climatic indicators were better than the mean values at reflecting the diversity patterns of plant families and genera. In Inner Mongolia, plant species diversity patterns were mainly influenced by total precipitation and temperature heterogeneity indicators; and concurrently, the correlation between plant family and genus diversity patterns and regional climatic indicators was also higher than the mean values. The extent to which climate explains the diversity patterns of plants increases with decreasing plant taxonomic rank. The results of this study expand the available selection and use of climate indicators in biodiversity research and deepen the understanding of the effects of climate on plant family diversity patterns in arid and semi-arid regions. Therefore, this study provides new perspectives for the rational selection and accurate use of climate or environmental indicators in biodiversity conservation and restoration research.

Conventional net tow versus environmental DNA for metabarcoding-based analysis of plankton-environment interactions in polluted aquatic ecosystems

Human societal development has caused rapid degradation of freshwater ecosystems, resulting in significant biodiversity decline globally. The conservation of aquatic ecosystems, particularly the management of biodiversity in urban areas, has become an increasingly significant issue for ensuring the sustainability of these ecosystems. The restoration of degraded aquatic ecosystems relies on a comprehensive understanding of the interactions between biological communities and multiple stressors derived from human activities. Environmental DNA (eDNA)-based methods have emerged as effective tools for dissecting complex community-environment interactions. Nevertheless, potential causes for technical disparities and conclusions drawn from conventional sampling versus eDNA-based methods remain inadequately evaluated. In this study, we conducted a comprehensive survey of plankton communities along the environmental gradient of the North Canal River in Northern China to assess causes and consequences for any disparities between conventional plankton net tow and eDNA sampling for metabarcoding-based analysis of plankton-environment interactions. Our findings demonstrated that eDNA-metabarcoding was effective for characterizing both biodiversity and geographical distribution. Both methods exhibited general consistency in elucidating community structure and identifying the key environmental factors influencing geographical distribution of both zooplankton and phytoplankton. As we explored lower taxonomic ranks, we found inconsistent patterns at certain levels (e.g., phylum or order) within some taxa (e.g., Bacillariophyta and Rotifera), even substantial variability for several taxonomic groups (e.g., Euglenozoa and Apicomplexa). The varied environmental prevalence and persistence of eDNA, biological and ecological characteristics of diverse taxa in plankton, and sampling efficiency of both methods likely contributed to the observed disparities. Given its higher biodiversity recovery capacity, efficiency, sampling convenience, and capability to identify influential factors driving the geographical distribution of biodiversity, eDNA-based metabarcoding is recommended for studying plankton-environment interactions, particularly in studies involving a large number of samples at extended geographical scales.

Comparison of databases useful for the analysis of vaginal microbiota in Japanese women using next-generation sequencing data (QIIME 2 software).

Approximately 10% of children are born prematurely, and bacterial vaginosis during pregnancy is associated with preterm delivery. Highly accurate species-level vaginal microflora analysis helps control bacteria-induced preterm birth. Therefore, we aimed to conduct a bioinformatic analysis of gene sequences using 16S databases and compare their efficacy in comprehensively identifying potentially pathogenic vaginal microbiota in Japanese women. The 16s rRNA databases, Silva, Greengenes, and basic local alignment search tool (BLAST) were compared to determine whether the classification quality could be improved using the V3-V4 region next-generation sequencing (NGS) sequences. It was found that NGS data were aligned using the BLAST database with the QIIME 2 platform, whose classification quality was higher than that of Silva, and the combined Silva and Greengenes databases based on the mutual complementarity of the two databases. The reference database selected during the bioinformatic processing influenced the recognized sequence percentage, taxonomic rankings, and accuracy. This study showed that the BLAST database was the best choice for NGS data analysis of Japanese women's vaginal microbiota.

Arthropod associates of Kenyan buffelgrass (Cenchrus ciliaris): a field survey for biological control candidates of a globally important invasive grass

Invasive species are the second largest contributor to biodiversity loss and drivers of ecosystem change. Buffelgrass is a C4, perennial grass native to Africa and Asia that was widely introduced across tropical and subtropical rangelands as livestock forage. Buffelgrass reduces native biodiversity and ecosystem stability in its introduced range when it escapes livestock pastures. Understanding the ecology of insects associated with buffelgrass in its native range may provide an understanding of invasion processes and biological control opportunities where buffelgrass has become an invasive challenge. Here, we present the results of a six-year survey of herbivorous arthropods of a native buffelgrass population from Kenya. Buffelgrass was examined for externally and internally feeding insects of vegetative and reproductive tissues. We also categorised buffelgrass detritivores and parasitoids that may use buffelgrass herbivores as hosts. The samples were photographed and Sanger sequenced to identify them to the lowest possible taxonomic ranking. We collected information on sample abundances, phenologies, tissues consumed, and putative diet breadths. We identified 25 morphospecies representing seven orders and 16 families. The putative host plant specialisation was as high as 67% for Diptera. Phenological variation in herbivore presence correlated with seasonal rainfall and provided a guide for when to conduct follow-up biological control agent searches. The most abundant herbivore was a gall midge (Diptera: Cecidomyiidae) that inhabits buffelgrass culms. Additional research should focus on bringing this species into containment where host choice trials can be conducted to determine if it is truly monophagous and assess its impact on buffelgrass growth.

Comparative transcriptome analysis of two contrasting genotypes provides new insights into the drought response mechanism in pigeon pea (Cajanus cajan L. Millsp.).

Despite plant's ability to adapt and withstand challenging environments, drought poses a severe threat to their growth and development. Although pigeon peaisalready quite resistant to drought, the prolonged dehydration induced by the aberrant climate poses a serious threat to their survival and productivity. Comparative physiological and transcriptome analyses of drought-tolerant (CO5) and drought-sensitive (CO1) pigeon pea genotypes subjected to drought stress were carried out in order to understand the molecular basis of drought tolerance in pigeon pea. The transcriptomic analysis allowed us to examine how drought affects the gene expression of C. cajan. Using bioinformatics tools, the unigenes were de novo assembled, annotated, and functionally evaluated. Additionally, a homology-based sequence search against the droughtDB database was performedto identify the orthologs of the DEGs. 1102 potential drought-responsive genes werefound to be differentially expressed genes (DEGs) between drought-tolerant and drought-sensitive genotypes. These included Abscisic acid insensitive 5 (ABI5), Nuclear transcription factor Y subunit A-7 (NF-YA7), WD40 repeat-containing protein 55 (WDR55), Anthocyanidin reductase (ANR) and Zinc-finger homeodomain protein 6 (ZF-HD6) andwere highly expressed in the tolerant genotype. Further, GO analysis revealed that the most enriched classes belonged to biosynthetic and metabolic processes in the biological process category, binding and catalytic activity in the molecular function category and nucleus and protein-containing complex in the cellular component category. Results of KEGG pathway analysis revealed that the DEGs were significantly abundant in signalling pathways such as plant hormone signal transduction and MAPK signalling pathways. Consequently, in our investigation, we have identified and validated by qPCR a group of genes involved in signal reception and propagation, stress-specific TFs, and basal regulatory genes associated with drought response. In conclusion, our comprehensive transcriptome dataset enabled the discovery of candidate genes connected to pathways involved in pigeon pea drought response. Our research uncovered a number of unidentified genes and transcription factors that could be used to understand andimprove susceptibility to drought.

Cambrian explosion and Ordovician biodiversification or Cambrian biodiversification and Ordovician explosion?

In this study, we examine how metazoan biodiversity has accumulated from the late Precambrian until the Silurian at various scales of taxonomic organization using compilations of the First Appearance Data (FAD) of global marine Metazoa from the datasets available in the Paleobiology Database (PBDB) and primary literature. The results indicate that all animal phyla appear during the late Precambrian and the earlier parts of the Cambrian, which corresponds to the usual concept of the Cambrian Explosion. However, at lower taxonomic ranks, a significant increase of first appearances is observed during the Ordovician, corresponding to an Ordovician Explosion of animal orders, families and genera. The cumulative counts of metazoan FADs at these lower taxonomic ranks reveal a gradual and long-term increase of diversity, reflecting a single large-scale radiation that started in the late Precambrian and lasted at least until the Silurian. This scenario corroborates recent studies that point towards a single long-term radiation during the early Palaeozoic, without clearly distinguishable global diversity explosions during discrete intervals.

Antagonistic Activity of Streptomyces alfalfae 11F against Fusarium Wilt of Watermelon and Transcriptome Analysis Provides Insights into the Synthesis of Phenazine-1-Carboxamide.

Streptomyces alfalfa strain 11F has inhibitory effects on many phytopathogenic fungi and improves the establishment and biomass yield of switchgrass. However, the antagonistic effects of strain 11F on Fusarium wilt of watermelon and its secondary metabolites that contribute to its biocontrol activity are poorly understood. We evaluated the antagonistic and growth-promoting effects of strain 11F and conducted a transcriptome analysis to identify the metabolites contributing to antifungal activity. Strain 11F had marked inhibitory effects on six fungal pathogens. The incidence of Fusarium wilt of watermelon seedlings was decreased by 46.02%, while watermelon seedling growth was promoted, as indicated by plant height (8.7%), fresh weight (23.1%), and dry weight (60.0%). Clean RNA-sequencing data were annotated with 7553 functional genes. The 2582 differentially expressed genes (DEGs) detected in the Control vs. Case 2 comparison were divided into 42 subcategories of the biological process, cellular component, and molecular function Gene Ontology categories. Seven hundred and forty functional genes (55.47% of the DEGs) were assigned to Kyoto Encyclopedia of Genes and Genomes metabolic pathways, reflecting the complexity of the strain 11F metabolic regulatory system. The expression level of the gene phzF, which encodes an enzyme essential for phenazine-1-carboxylic acid (PCA) synthesis, was downregulated 3.7-fold between the 24 h and 48 h fermentation time points, suggesting that strain 11F can produce phenazine compounds. A phenazine compound from 11F was isolated and identified as phenazine-1-carboxamide (PCN), which contributed to the antagonistic activity against Fusarium oxysporum f. sp. niveum. PCA was speculated to be the synthetic precursor of PCN. The downregulation in phzF expression might be associated with the decrease in PCA accumulation and the increase in PCN synthesis in strain 11F from 24 to 48 h. Streptomyces alfalfae 11F protects watermelon seedlings from Fusarium wilt of watermelon and promotes seedling growth. The transcriptome analysis of strain 11F provides insights into the synthesis of PCN, which has antifungal activity against F. oxysporum f. sp. niveum of watermelon.

The Identification of a Quantative Trait Loci-Allele System of Antixenosis against the Common Cutworm (Spodoptera litura Fabricius) at the Seedling Stage in the Chinese Soybean Landrace Population.

Common cutworm (CCW) is an omnivorous insect causing severe yield losses in soybean crops. The seedling-stage mini-tray identification system with the damaged leaf percentage (DLP) as an indicator was used to evaluate antixenosis against CCW in the Chinese soybean landrace population (CSLRP) under three environments. Using the innovative restricted two-stage multi-locus genome-wide association study procedure (RTM-GWAS), 86 DLP QTLs with 243 alleles (2-11/QTL) were identified, including 66 main-effect loci with 203 alleles and 57 QTL-environment interaction loci with 172 alleles. Among the main-effect loci, 12 large-contribution loci (R2 ≥ 1%) explained 25.45% of the phenotypic variation (PV), and 54 small-contribution loci (R2 < 1%) explained 16.55% of the PV. This indicates that the CSLRP can be characterized with a DLP QTL-allele system complex that has not been found before, except for a few individual QTLs without alleles involved. From the DLP QTL-allele matrix, the recombination potentials expressed in the 25th percentile of the DLP of all possible crosses were predicted to be reduced by 41.5% as the maximum improvement and 14.2% as the maximum transgression, indicating great breeding potential in the antixenosis of the CSLRP. From the QTLs, 62 candidate genes were annotated, which were involved in eight biological function categories as a gene network of the DLP. Changing from susceptible to moderate plus resistant varieties in the CSLRP, 26 QTLs had 32 alleles involved, in which 19 genes were annotated from 25 QTL-alleles, including eight increased negative alleles on seven loci and 11 decreased positive alleles on 11 loci, showing the major genetic constitution changes for the antixenosis enhancement at the seedling stage in the CSLRP.

Name game conundrum: identical specific epithets in Microgastrinae (Hymenoptera, Braconidae).

It is a privilege to recognize a new species and immortalize it with a name. Taxonomists may use etymologies recalling the sampling locality, habitat, species morphology, people (actor, writer, singer, politician, scientist), culture (customs, beliefs), fictional characters (gods, demons, cartoons), brands, ancient names, and others. Naming a species is a creative act that allows scientists to express their love for nature. By drawing on personal and cultural associations, species names are often imbued with far greater meaning than one might initially assume. Unconventional names for species can be an effective way to capture the imagination of the public and make the species memorable. In other words, species names can be both meaningful and whimsical. The central focus of this study was to pinpoint species in the subfamily Microgastrinae that share the same specific epithet that often creates confusion regarding which species is being referred to. The findings showed that 153 specific epithets were repeated representing 340 species in 52 genera, while the remaining 2,823 species have unique epithets. Three of the five categories proposed accommodate the majority of the etymologies: people (42%), morphology (27%), and geography (15%) whereas the categories of other (9%) and biology (7%) achieve the least representation. Approximately 95% of the same specific epithets had a single clear meaning, while for the remaining 5%, it was not possible to trace etymology. The study revealed that the average length of specific epithets was 9.01 letters, the longest contains 18 (eliethcantillanoae) while the shortest four (eros and erro). Additionally, most identical specific epithets were repeated two times (85.25% of the occurrences), although three (12.82%), five, six, and even nine (each one with 0.64%) repetitions were also found. Finally, a list of recommendations for taxonomists when faced with the task of naming a new species is provided.

Machine Learning Suggests That Small Size Helps Broaden Plasmid Host Range.

Plasmids mediate gene exchange across taxonomic barriers through conjugation, shaping bacterial evolution for billions of years. While plasmid mobility can be harnessed for genetic engineering and drug-delivery applications, rapid plasmid-mediated spread of resistance genes has rendered most clinical antibiotics useless. To solve this urgent and growing problem, we must understand how plasmids spread across bacterial communities. Here, we applied machine-learning models to identify features that are important for extending the plasmid host range. We assembled an up-to-date dataset of more than thirty thousand bacterial plasmids, separated them into 1125 clusters, and assigned each cluster a distribution possibility score, taking into account the host distribution of each taxonomic rank and the sampling bias of the existing sequencing data. Using this score and an optimized plasmid feature pool, we built a model stack consisting of DecisionTreeRegressor, EvoTreeRegressor, and LGBMRegressor as base models and LinearRegressor as a meta-learner. Our mathematical modeling revealed that sequence brevity is the most important determinant for plasmid spread, followed by P-loop NTPases, mobility factors, and β-lactamases. Ours and other recent results suggest that small plasmids may broaden their range by evading host defenses and using alternative modes of transfer instead of autonomous conjugation.

Evaluating the academic scientific laboratories' safety by applying failure mode and effect analysis (FMEA) at the public university in Lebanon

Workers at scientific academic laboratories are at risk of potential exposure to different types of hazards. The study's purpose was to assess the potential failure modes (FMs) of hazards facing them through the application of the Failure Mode and Effect Analysis (FMEA) method to propose corrective actions preventive actions (CAPA) to mitigate them and to improve the safety outcomes in these workplaces (WP) at the Lebanese public University (PbU). The potential FMs leading to accident occurrence in biological and chemical labs were identified and prioritized, their causes and effects were determined by applying two surveys, and the risk priority number (RPN) for each failure was calculated. A total of 24 FMs were identified. The most alarming FM having the highest RPN scores (80) was found in the workplace ‘category requiring an emergency for corrective actions (CA), it is related to the unavailability of a hazard pictogram plot and the lack of labeling of chemicals and waste containers according to their categories. The FMs having RPN scores (75-60) requiring an urgent CA were assigned to other hazards of the WP, chemical, biological, and failure of the educational system. The need to program for the remaining FMs (RPN scores 20–48) is related to the safety, biological, physical, and radioactive categories ‘hazards. It is recommended to apply continuously FMEA and implement the CA proposed for each detected FM in the scientific laboratories of the PbU in order to support the decision-makers to improve laboratory safety.

Symposium 02: Current Directions in Women’s Neuropsychology Research

Summary Abstract:A longstanding trend of underrepresentation of women in pre-clinical and clinical research limits our understanding of women’s issues across several scientific fields, including neuropsychology and related disciplines. Highlighting this trend is the fact that only 2-6% of studies across major neuroscience journals over the last decade were conducted exclusively in women/females. This pattern of research limits our understanding of how women’s unique physiological, hormonal, psychiatric, and psychosocial presentations contribute to their brain health. Inclusion efforts aimed at increasing the study of more diverse populations have resulted in a nascent understanding of sex differences across several neuropsychological conditions, with implications for identification, prevention, and intervention efforts unique to women.In this seminar, we highlight current efforts by neuropsychologists to expand research of women in order to enhance our understanding and clinical care of this population. Of note, we use the standardized term “women” to describe a biological category (females) and/or a self-identified gender trait, which varies depending on the scope of the research and data availability. We highlight five lines of women’s-focused research spanning epilepsy/seizure disorders, traumatic brain injury (TBI), Alzheimer’s Disease (AD), and neurotoxicant exposure. In Dr. Sullivan-Baca’s presentation, ongoing lines of research into the clinical presentations of women with epilepsy are discussed. Findings highlight substantial psychiatric burden and unique medical factors to consider in women within this population. Dr. Jak’s presentation expands on concussion outcomes in women using the national FITBIR database and highlights a sex difference in postconcussive outcomes, with increased cognitive and somatic symptoms in women compared to men. Dr. Rapport and colleagues focus on the experience of menopause after TBI and discuss validation of a menopause symptom survey for TBI survivors. Dr. Sundermann’s presentation covers findings on women’s unique preclinical Alzheimer’s Disease trajectories. Dr. Krengel focuses on health trajectories for women Veterans exposed to neurotoxicants during the Gulf War and underlines sex differences in neuropsychological test performance. Through these presentations, our goal is both to inform and to inspire. Overall, we seek to orient members of our field to current directions in women’s research so they can better understand how women are differentially affected by neurological conditions. Clinically, we hope this knowledge will encourage neuropsychologists to understand how their women patients’ unique experiences of sex and gender contribute to their brain health. For researchers, we hope that attending this symposium will encourage pursuit of women’s-focused lines of inquiry. Furthermore, we hope to inspire training institutions to integrate this type of research more systematically into graduate student didactics and training, particularly for those students in neuropsychology-focused training.

Assessing plant trait diversity as an indicators of species α‐ and β‐diversity in a subalpine grassland of the Italian Alps

AbstractAs the need for ecosystem biodiversity assessment increases within the climate crisis framework, more and more studies using spectral variation hypothesis (SVH) are proposed to assess biodiversity at various scales. The SVH implies optical diversity (also called spectral diversity) is driven by light absorption dynamics associated with plant traits (PTs) variability (which is an indicator of functional diversity) which is, in turn, determined by biodiversity. In this study, we examined the relationship between PTs variability, optical diversity and α‐ and β‐diversity at different taxonomic ranks at the Monte Bondone grasslands, Trentino province, Italy. The results of the study showed that the PTs variability, at the α scale, was not correlated with biodiversity. On the other hand, the results observed at the community scale (β‐diversity) showed that the variation of some of the investigated biochemical and biophysical PTs was associated with the β‐diversity. We used the Mantel test to analyse the relationship between the PTs variability and species β‐diversity. The results showed a correlation coefficient of up to 0.50 between PTs variability and species β‐diversity. For higher taxonomic ranks such as family and functional groups, a slightly higher Spearman's correlation coefficient of up to 0.64 and 0.61 was observed, respectively. The SVH approach was also tested to estimate β‐diversity and we found that spectral diversity calculated by Spectral Angle Mapper showed to be a better proxy of biodiversity in the same ecosystem where the spectral diversity approach failed to estimate α‐diversity. These findings suggest that optical and PTs diversity approaches can be used to predict species diversity in the grasslands ecosystem where the species turnover is high.