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The term new genomic techniques (NGTs) is an umbrella term used to describe a variety of techniques that can alter the genetic material of an organism and that have emerged or have been developed since 2001, when the existing genetically modified organism (GMO) legislation was adopted. The analytical framework used to detect GMOs in Europe is an established single harmonized procedure that is mandatory for the authorization of GM food and feed, thus generating a reliable, transparent, and effective labeling scheme for GMO products. However, NGT products can challenge the implementation and enforcement of the current regulatory system in the EU, relating in particular to the detection of NGT products that contain no foreign genetic material. Consequently, the current detection methods might fail to meet the minimum performance requirements. Although existing detection methods may be able to detect and quantify even small alterations in the genome, this does not necessarily confirm the distinction between products resulting from NGTs subject to the GMO legislation and other products. Therefore, this study provides a stepwise approach for the in silico prediction of PCR systems' specificity by testing a bioinformatics pipeline for amplicon and primer set searches in current genomic databases. In addition, it also empirically tested the PCR system evaluated during the in silico analysis. Two mutant genotypes produced by CRISPR-Cas9 in Arabidopsis thaliana were used as a case study. Overall, our results demonstrate that the single PCR system developed for identifying a nucleotide insertion in the grf1-3 genotype has multiple matches in the databases, which do not enable the discrimination of this mutated event. Empirical assays further support this demonstration. In contrast, the second mutated genotype, grf8-61, which contains a -3 bp deletion, did not yield any matches in the sequence variant database. However, the primer sequences were not efficient during the empirical assay. Our approach represents a first step in decision making for analytical methods for NGT detection, identification, and quantification in light of the European labeling regulations. [ABSTRACT FROM AUTHOR]

Simple Summary: Genetic variants explaining approximately 40% of familial breast cancer risk have been identified, thus leaving a significant fraction of the heritability of this disease still unexplained. The exact nature of this missing fraction is unknown; more extensive sequencing efforts could potentially identify new moderate-penetrance breast cancer risk alleles. The aim of this study was to perform a large-scale whole-exome sequencing study, followed by a targeted validation, in breast cancer patients and healthy women of European descent. We identified 20 novel genes with modest evidence of association (p-value < 0.05) for either overall or subtype-specific breast cancer; however, much larger studies are needed to confirm the exact role of these genes in susceptibility to breast cancer. Rare variants in at least 10 genes, including BRCA1, BRCA2, PALB2, ATM, and CHEK2, are associated with increased risk of breast cancer; however, these variants, in combination with common variants identified through genome-wide association studies, explain only a fraction of the familial aggregation of the disease. To identify further susceptibility genes, we performed a two-stage whole-exome sequencing study. In the discovery stage, samples from 1528 breast cancer cases enriched for breast cancer susceptibility and 3733 geographically matched unaffected controls were sequenced. Using five different filtering and gene prioritization strategies, 198 genes were selected for further validation. These genes, and a panel of 32 known or suspected breast cancer susceptibility genes, were assessed in a validation set of 6211 cases and 6019 controls for their association with risk of breast cancer overall, and by estrogen receptor (ER) disease subtypes, using gene burden tests applied to loss-of-function and rare missense variants. Twenty genes showed nominal evidence of association (p-value < 0.05) with either overall or subtype-specific breast cancer. Our study had the statistical power to detect susceptibility genes with effect sizes similar to ATM, CHEK2, and PALB2, however, it was underpowered to identify genes in which susceptibility variants are rarer or confer smaller effect sizes. Larger sample sizes would be required in order to identify such genes. [ABSTRACT FROM AUTHOR]

Despite over 41 million registered potential volunteer stem cell donors worldwide, many patients in need of a transplant do not find an HLA-matched unrelated donor or cord blood units, with the respective odds differing significantly between various populations. In this study, we analysed data of 2205 unsuccessful real-life donor searches sent to the DKMS Registry to identify populations in which further donor recruitment would be associated with particularly large patient benefits. For that purpose, we estimated haplotype frequencies of 67 donor populations at various sample sizes and entered them into two different mathematical models. These models assessed patient benefits from population-specific donor recruitment, operationalised by the number of originally unsuccessful searches that may become successful due to new donors. Consistently, across the different mathematical models and sample sizes, we obtained several countries from East and Southeast Asia (Thailand, Vietnam, China, and the Philippines) and the population of Asians in the USA as countries/populations where donor recruitment activities would be particularly beneficial for patients. We also identified various countries in Southeast and Central Europe as possible target regions for donor recruitment with above-average patient benefits. The results presented are registry-specific in the sense that they were obtained by optimising unsuccessful searches that had been sent to the DKMS Registry. Therefore, it would be desirable to apply the presented methods to a global data set that includes all unsuccessful stem cell donor searches worldwide and uses population-specific haplotype frequencies based on all donors available in the WMDA Search & Match Service., (© 2024 The Author(s). HLA: Immune Response Genetics published by John Wiley & Sons Ltd.)

Xanthomonas arboricola pv. corylina is the causal agent of bacterial blight of hazelnut. The bacterium has been listed as an A2 quarantine pathogen in Europe since 1978 and on the regulated non-quarantine pest list since 2019. Three isolates from various geographic regions and isolated at different times were sequenced using a hybrid approach with short- and long-read technologies to generate closed genome and plasmid sequences in order to better understand the biology of this pathogen. [ABSTRACT FROM AUTHOR]

Summary Properly and effectively managing reference datasets is an important task for many bioinformatics analyses. Refgenie is a reference asset management system that allows users to easily organize, retrieve and share such datasets. Here, we describe the integration of refgenie into the Galaxy platform. Server administrators are able to configure Galaxy to make use of reference datasets made available on a refgenie instance. In addition, a Galaxy Data Manager tool has been developed to provide a graphical interface to refgenie's remote reference retrieval functionality. A large collection of reference datasets has also been made available using the CVMFS (CernVM File System) repository from GalaxyProject.org, with mirrors across the USA, Canada, Europe and Australia, enabling easy use outside of Galaxy. Availability and implementation The ability of Galaxy to use refgenie assets was added to the core Galaxy framework in version 22.01, which is available from https://github.com/galaxyproject/galaxy under the Academic Free License version 3.0. The refgenie Data Manager tool can be installed via the Galaxy ToolShed, with source code managed at https://github.com/BlankenbergLab/galaxy-tools-blankenberg/tree/main/data%5fmanagers/data%5fmanager%5frefgenie%5fpull and released using an MIT license. Access to existing data is also available through CVMFS, with instructions at https://galaxyproject.org/admin/reference-data-repo/. No new data were generated or analyzed in support of this research. [ABSTRACT FROM AUTHOR]

In recent years, three large populations of Cyperus flavescens were found in Poland, the richest occurrence of this species in over 30 years. The goal of this research is to determine the habitat factors lead to the mass occurrence of C. flavescens and the present situation of that species and its habitat in Central Europe. Soil conditions of the three populations were studied. To determine the correlation between the occurrence and abundance of species and the chemical parameters of the soil, the DCA and CCA methods were used. TheDCAof environmental Ellenberg values was made for all relevés known from Poland. The occurrence of C. flavescens in plant communities in Central Europe was studied. The maximum entropy method was used for potential distribution analysis of C. flavescens. All analyzed traits are important for this species and none has an advantage over another, so the environmental factor affecting the occurrence of C. flavescens is different from the tested. Analysis on Ellenberg values indicate that the longest gradients are temperature, moisture and nutrients. The analysis of vegetation data involving Cyperus flavescens available from Central Europe indicates that this species occurs mainly in the company of Juncus bufonius and Plantago intermedia, whereas other species of the Isoëto-Nanojuncetea class appear rarely. In MaxEnt analysis based on bioclimatic variables, the most important variable is BIO1 (Annual Mean Temperature). The results of our observation indicate that anthropogenic factors such as grazing livestock have a positive effect on the occurrence of the species. It is also very likely that the species is promoted by very warm summers with only short periods of heavy rains. A map of the potential distribution of C. flavescens in Central Europe created according historical and future data show an extension of the range of potential habitats to the north and east. [ABSTRACT FROM AUTHOR]

APOE is a well-studied gene with multiple effects on aging and longevity. The gene has three alleles: e2, e3, and e4, whose frequencies vary by ethnicity. While the e2 is associated with healthy cognitive aging, the e4 allele is associated with Alzheimer's disease and early mortality and therefore its prevalence among people with extreme longevity (EL) is low. Using the PopCluster algorithm, we identified several ethnically different clusters in which the effect of the e2 and e4 alleles on EL changed substantially. For example, PopCluster discovered a large group of 1,309 subjects enriched of Southern Italian genetic ancestry with weaker protective effect of e2 (odds ratio [OR] = 1.27, p = .14) and weaker damaging effect of e4 (OR = 0.82, p = .31) on the phenotype of EL compared to other European ethnicities. Further analysis of this cluster suggests that the odds for EL in carriers of the e4 allele with Southern Italian genetic ancestry differ depending on whether they live in the United States (OR = 0.29, p = .009) or Italy (OR = 1.21, p = .38). PopCluster also found clusters enriched of subjects with Danish ancestry with varying effect of e2 on EL. The country of residence (Denmark or United States) appears to change the odds for EL in the e2 carriers. [ABSTRACT FROM AUTHOR]

Global incidence and mortality of pancreatic cancer, comprising mostly pancreatic ductal adenocarcinoma (PDAC), is predicted to rise by almost 80% by 2040. Despite considerable investment in research, there has been no significant improvement in the mortality figures of PDAC for both men and women in Europe during the past 3 decades. One of the challenges in development of effective therapy for PDAC is the mismatch between research models and patients. The aim of this study was to utilize comparative proteomics, protein-protein interactions (PPI) and prediction of drug-target interactions (DTI) with multiple research models and patients for preclinical development of treatment for PDAC. PDAC cells, spheroids, organoids and tumors of mouse models and patients were included. Mass spectrometry-based proteomics and bioinformatics were used. The comparative proteomics showed translational potential of preclinical models and potential targets including central hub proteins, neuronal signaling, soluble N-ethylmaleimide-sensitive factor activating protein receptor (SNARE) proteins, and particularly plasma membranes in association with exocytosis/endocytosis-coupled extracellular vesicles (EVs). PPI and DTI indicated potential drug repurposing with Botulinum toxin-A and ivermectin for PDAC. Furthermore, validations using in vitro and in vivo experiments showed that treatments with Botulinum toxin-A and/or ivermectin suppressed the plasma membrane plasticity and increased crinophagy of PDAC cells, and that Botulinum toxin-A inhibited the SNARE protein complex signaling pathway, whereas ivermectin eliminated the formation of membrane microvilli and inhibited cell proliferation, and clathrin-mediated endocytic signaling. Botulinum toxin-A/ivermectin treatment inhibited the formation and release of EVs and induced down-regulations of EVinvolved signaling pathways, such as axonal guidance signaling, clathrin-medicated endocytosis signaling, neuroinflammation signaling pathway, epithelial adherents junction signaling, EIF2 signaling, and integrin signaling, and toxicities in neuro-immune, kidney, liver, and heart. Treatments with Botulinum toxin-A and ivermectin either alone or in combination enhanced the inhibitory effects of chemotherapy on the tumors and increased median survivals of PDAC tumor-bearing mice. In conclusion, arresting exocytosis/endocytosis coupling with Botulinum toxin-A and/or ivermectin increased the survival rate in PDAC mice, probably by inhibiting the formation/release of EVs and thereby suppressing the tumorigenesis/progression as well as the systemic effects of PDAC. [ABSTRACT FROM AUTHOR]

Species of Gasterophilus Leach are obligate parasites in domestic and wild equids and responsible for cosmopolitan gasterophilosis. Although with only eight species known so far, they have received considerable attention because of their significant veterinary and economic importance. Surprisingly, we found that G. flavipes (Olivier) is a valid species based on morphological characters from male, female and the egg, after spending half a century as a synonym of G. haemorrhoidalis (Linnaeus). In the present study, G. flavipes, G. haemorrhoidalis and G. inermis (Brauer), which are the three closely related species possessing a remarkable mixture of shared morphological characters, are diagnosed and comparatively redescribed; the key to separate adults and eggs are provided, together with a series of high-resolution photographs from all the body parts. COI barcodes do not allow for a separation of G. flavipes, G. haemorrhoidalis and G. inermis, but showed a closer relationship between G. flavipes and G. haemorrhoidalis than the other two combinations, which is consistent with the morphological evidence. Geographically, G. flavipes seems to be common and widespread in the warmer parts of the Palaearctic region. Thus, the epidemiology of gasterophilosis where G. flavipes is known or supposed to occur calls for a more careful veterinarian re-assessment. A decline in the populations of Gasterophilus spp. has been noticed in Europe, but all seven Palaearctic species of Gasterophilus appear to maintain stable populations in Xinjiang (China), which may be explained by a higher biodiversity of equids and less use of anti-parasitic treatments in Xinjiang than in Europe. Our study shows that morphological characters still provide the solid backbone in classification of Gasterophilus at species-level, and updated diagnoses and a key is provided to distinguish G. flavipes, G. haemorrhoidalis and G. inermis, and to facilitate studies of epidemiology, phylogeny and host-parasite co-evolution. [ABSTRACT FROM AUTHOR]

Knowledge on the trophic interactions among predators and their prey is important in order to understand ecology and behaviour of animals. Traditionally studies on the diet composition of insectivorous bats have been based on the morphological identification of prey remains, but the accuracy of the results has been hampered due to methodological limitations. Lately, the DNA metabarcoding and High Throughput Sequencing (HTS) techniques have changed the scene since they allows prey identification to the species level, ultimately giving more precision to the results. Nevertheless, the use of one single primer set to amplify faecal DNA produces biases in the assessed dietary composition. Three horseshoe bats overlap extensively in their distribution range in Europe: Rhinolophus euryale, R. hipposideros and R. ferrumequinum. In order to achieve the deepest insight on their prey list we combined two different primers. Results showed that the used primers were complementary at the order and species levels, only 22 out of 135 prey species being amplified by both. The most frequent prey of R. hipposideros belonged to Diptera and Lepidoptera, to Lepidoptera in R. euryale, and Lepidoptera, Diptera and Coleoptera in R. ferrumequinum. The three bats show significant resource partitioning, since their trophic niche overlap is not higher than 34%. Our results confirm the importance of combining complementary primers to describe the diet of generalist insectivorous bats with amplicon metabarcoding techniques. Overall, each primer set showed a subset of the prey composition, with a small portion of the total prey being identified by both of them. Therefore, each primer presented a different picture of the niche overlap among the three horseshoe bats due to their taxonomic affinity. [ABSTRACT FROM AUTHOR]

Introduction: The study presents the results of the genomic surveillance of invasive meningococcal disease (IMD) in the Czech Republic for the period of 2015–2017. Material and methods: The study set includes all available IMD isolates recovered in the Czech Republic and referred to the National Reference Laboratory for Meningococcal Infections in 2015–2017, a total of 89 Neissseria meningitidis isolates—from 2015 (n = 20), 2016 (n = 27), and from 2017 (n = 42). All isolates were studied by whole genome sequencing (WGS). Results: Serogroup B (MenB) was the most common, followed by serogroups C, W, and Y. Altogether 17 clonal complexes were identified, the most common of which was hypervirulent complex cc11, followed by complexes cc32, cc41/44, cc269, and cc865. Over the three study years, hypervirulent cc11 (MenC) showed an upward trend. The WGS method showed two clearly differentiated clusters of N. meningitidis C: P1.5,2:F3-3:ST-11 (cc11). The first cluster is represented by nine isolates, all of which are from 2017. The second cluster consisted of five isolates from 2016 and eight isolates from 2017. Their genetic discordance is illustrated by the changing nadA allele and subsequently by the variance in BAST type. Clonal complex cc269 (MenB) also increased over the time frame. WGS identified the presence of MenB vaccine antigen genes in all B and non-B isolates of N. meningitidis. Altogether 49 different Bexsero antigen sequence types (BAST) were identified and 10 combinations of these have not been previously described in the PubMLST database. Conclusions: The genomic surveillance of IMD in the Czech Republic provides data needed to update immunisation guidelines for this disease. WGS showed a higher discrimination power and provided more accurate data on molecular characteristics and genetic relationships among invasive N. meningitidis isolates. [ABSTRACT FROM AUTHOR]

Environmental DNA (eDNA) is increasingly applied in ecological studies, including studies with the primary purpose of criminal investigation, in which eDNA from soil can be used to pair samples or reveal sample provenance. We collected soil eDNA samples as part of a large national biodiversity research project across 130 sites in Denmark. We investigated the potential for soil eDNA metabarcoding in predicting provenance in terms of environmental conditions, habitat type and geographic regions. We used linear regression for predicting environmental gradients of light, soil moisture, pH and nutrient status (represented by Ellenberg Indicator Values, EIVs) and Quadratic Discriminant Analysis (QDA) to predict habitat type and geographic region. eDNA data performed relatively well as a predictor of environmental gradients (R2 > 0.81). Its ability to discriminate between habitat types was variable, with high accuracy for certain forest types and low accuracy for heathland, which was poorly predicted. Geographic region was also less accurately predicted by eDNA. We demonstrated the application of provenance prediction in forensic science by evaluating and discussing two mock crime scenes. Here, we listed the plant species from annotated sequences, which can further aid in identifying the likely habitat or, in case of rare species, a geographic region. Predictions of environmental gradients and habitat types together give an overall accurate description of a crime scene, but care should be taken when interpreting annotated sequences, e.g. due to erroneous assignments in GenBank. Our approach demonstrates that important habitat properties can be derived from soil eDNA, and exemplifies a range of potential applications of eDNA in forensic ecology. [ABSTRACT FROM AUTHOR]

In fish, the circadian clock represents a key regulator of many aspects of biology and is controlled by combinations of abiotic and biotic factors. These environmental factors are frequently manipulated in fish farms as part of strategies designed to maximize productivity. The flatfish turbot, Scophthalmus maximus, represents one of the most important species within the aquaculture sector in Asia and Europe. Despite the strategic importance of this species, the function and regulation of the turbot circadian system remains poorly understood. Here, we have characterized the core circadian clock genes, clock1, per1, per2 and cry1 in turbot and have studied their daily expression in various tissues under a range of lighting conditions and feeding regimes. We have also explored the influence of light and feeding time on locomotor activity. Rhythmic expression of the four core clock genes was observed in all tissues studied under light dark (LD) cycle conditions. Rhythmicity of clock gene expression persisted upon transfer to artificial free running, constant conditions confirming their endogenous circadian clock control. Furthermore, turbot showed daily cycles of locomotor activity and food anticipatory activity (FAA) under LD and scheduled-feeding, with the activity phase as well as FAA coinciding with and being dependent upon exposure to light. Thus, while FAA was absent under constant dark (DD) conditions, it was still detected in constant light (LL). In contrast, general locomotor activity was arrhythmic in both constant darkness and constant light, pointing to a major contribution of light, in concert with the circadian clock, in timing locomotor activity in this species. Our data represents an important contribution to our understanding of the circadian timing system in the turbot and thereby the optimization of rearing protocols and the improvement of the well-being of turbot within fish farming environments. [ABSTRACT FROM AUTHOR]

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of a devastating pig disease present all over the world. The remarkable genetic variation of PRRSV, makes epidemiological and molecular analysis of circulating viruses highly important to review current diagnostic tools and vaccine efficacy. Monitoring PRRS viruses supports modern herd management by explaining the source of found viruses, either internally or externally from the herd. No epidemiological or molecular study has been published on circulating PRRS-viruses in the Netherlands, since the early nineties. Therefore, the objective of this study is to investigate circulating PRRS-viruses in the Netherlands in 2014, 2015 and 2016 on a molecular level by sequencing ORF2, ORF3, ORF4, ORF5, ORF6 and ORF7. The results demonstrate that the 74 PRRSV strains belong to PRRSV-1, but the diversity among strains is high, based on nucleotide identity, individual ORF length and phylogenetic trees of individual ORFs. Furthermore, the data presented here show that the phylogenetic topology of some viruses is ORF dependent and suggests recombination. The identity of the strain of interest might be misinterpreted and wrong conclusions may be drawn in a diagnostic and epidemiological perspective, when only ORF5 is analyzed, as performed in many routine sequencing procedures. [ABSTRACT FROM AUTHOR]

Genetically related highly pathogenic avian influenza viruses (HPAIVs) of H5N6 subtype caused outbreaks simultaneously in East Asia and Europe—geographically distinct regions—during winter 2017–2018. This situation prompted us to consider whether the application of phylogeographic analysis to a particular gene segment of AIVs could provide clues for understanding how AIV had been disseminated across the continent. Here, the N6 NA genes of influenza viruses isolated across the world were subjected to phylogeographic analysis to illustrate the inter- and intracontinental dissemination of AIVs. Those isolated in East Asia during winter and in Mongolia/Siberia during summer were comingled within particular clades of the phylogeographic tree. For AIVs in one clade, their dissemination in eastern Eurasia extended from Yakutia, Russia, in the north to East Asia in the south. AIVs in western Asia, Europe, and Mongolia were also comingled within other clades, indicating that Mongolia/Siberia plays an important role in the dissemination of AIVs across the Eurasian continent. Mongolia/Siberia may therefore have played a role in the simultaneous outbreaks of H5N6 HPAIVs in Europe and East Asia during the winter of 2017–2018. In addition to the long-distance intracontinental disseminations described above, intercontinental disseminations of AIVs between Eurasia and Africa and between Eurasia and North America were also observed. Integrating these results and known migration flyways suggested that the migration of wild birds and the overlap of flyways, such as that observed in Mongolia/Siberia and along the Alaskan Peninsula, contributed to the long-distance intra- and intercontinental dissemination of AIVs. These findings highlight the importance of understanding the movement of migratory birds and the dynamics of AIVs in breeding areas—especially where several migration flyways overlap—in forecasting outbreaks caused by HPAIVs. [ABSTRACT FROM AUTHOR]

In the geobotanical division of Poland, Pomerania was treated as a separate subdivision, divided into "coastal plains" and the "Pomeranian uplands" or, in the newest regionalization, the "Pomeranian division". The goal of this paper is to determine how well the distinctiveness of Pomerania is floristically justified. A total of 1,467 native species occur within the area of Pomerania, representing 57.5% of the native flora of Poland. Fifty-seven species distinguishing Pomerania were selected and their phytogeographic features were discussed and compared to the Polish vascular flora. The distribution of 32 species (56.1%) is characterized as (sub)Atlantic/oceanic. Of the taxa that characterize Pomerania, 47.45% represent the northern element of the Polish flora and 7.01% the western element; species of the eastern element do not exist in Pomerania. The maximum entropy (MaxEnt) method was used for collective distribution analysis of the 57 selected taxa. The analyzes were performed using 41 environmental variables. All the species analyzed are strictly linked to the western and the North Atlantic part of Europe. Statistical evaluation of the MaxEnt model yielded an AUC value of 0.75 for both training and test. The most important environmental variables are minimum high (min_h), temperature annual range (bio07), and mean temperature of driest quarter (bio09). The results of the MaxEnt analysis allowed us also to verify the boundaries of the region and suggest new criteria for them. The southern limit of Pomerania should run along the northern boundary of the terminal moraine belt. Also, the area east of the Vistula does not contain abundant representatives of the flora characteristic for Pomerania. The results of the present study may be used for a broader discussion on the revision of the geobotanical division of Poland, at least in its northern part. [ABSTRACT FROM AUTHOR]

The topology of animal transport networks contributes substantially to how fast and to what extent a disease can transmit between animal holdings. Therefore, public authorities in many countries mandate livestock holdings to report all movements of animals. However, the reported data often does not contain information about the exact sequence of transports, making it impossible to assess the effect of truck sharing and truck contamination on disease transmission. The aim of this study was to analyze the topology of the Swiss pig transport network by means of social network analysis and to assess the implications for disease transmission between animal holdings. In particular, we studied how additional information about transport sequences changes the topology of the contact network. The study is based on the official animal movement database in Switzerland and a sample of transport data from one transport company. The results show that the Swiss pig transport network is highly fragmented, which mitigates the risk of a large-scale disease outbreak. By considering the time sequence of transports, we found that even in the worst case, only 0.34% of all farm-pairs were connected within one month. However, both network connectivity and individual connectedness of farms increased if truck sharing and especially truck contamination were considered. Therefore, the extent to which a disease may be transmitted between animal holdings may be underestimated if we only consider data from the official animal movement database. Our results highlight the need for a comprehensive analysis of contacts between farms that includes indirect contacts due to truck sharing and contamination. As the nature of animal transport networks is inherently temporal, we strongly suggest the use of temporal network measures in order to evaluate individual and overall risk of disease transmission through animal transportation. [ABSTRACT FROM AUTHOR]

HIV-1 strain diversity in Bulgaria is extensive and includes contributions from nearly all major subtypes and the Circulating Recombinant Forms (CRF): 01_AE, 02_AG, and 05_DF. Prior to this study, HIV-1 sequence information from Bulgaria has been based solely on the pro-RT gene, which represent less than 15% of the viral genome. To further characterize HIV-1 in Bulgaria, assess participant risk behaviors, and strengthen knowledge of circulating strains in the region, the study “Genetic Subtypes of HIV-1 in Bulgaria (RV240)” was conducted. This study employed the real time-PCR based Multi-region Hybridization Assay (MHA) B/non-B and HIV-1 sequencing to survey 215 of the approximately 1100 known HIV-1 infected Bulgarian adults (2008–2009) and determine if they were infected with subtype B HIV-1. The results indicated a subtype B prevalence of 40% and demonstrate the application of the MHA B/non-B in an area containing broad HIV-1 strain diversity. Within the assessed risk behaviors, the proportion of subtype B infection was greatest in men who have sex with men and lowest among those with drug use risk factors. During this study, 15 near full-length genomes and 22 envelope sequences were isolated from study participants. Phylogenetic analysis shows the presence of subtypes A1, B, C, F1, and G, CRF01_AE, CRF02_AG, CRF05_DF, and one unique recombinant form (URF). These sequences also show the presence of two strain groups containing participants with similar risk factors. Previous studies in African and Asian cohorts have shown that co-circulation of multiple subtypes can lead to viral recombination within super-infected individuals and the emergence of new URFs. The low prevalence of URFs in the presence of high subtype diversity in this study, may be the result of successful infection prevention and control programs. Continued epidemiological monitoring and support of infection prevention programs will help maintain control of the HIV-1 epidemic in Bulgaria. [ABSTRACT FROM AUTHOR]

Taxonomic identifications in some groups of lichen-forming fungi have been challenge largely due to the scarcity of taxonomically relevant features and limitations of morphological and chemical characters traditionally used to distinguish closely related taxa. Delineating species boundaries in closely related species or species complexes often requires a range of multisource data sets and comprehensive analytical methods. Here we aim to examine species boundaries in a group of saxicolous lichen forming fungi, the Aspiciliella intermutans complex (Megasporaceae), widespread mainly in the Mediterranean. We gathered DNA sequences of the nuclear ribosomal internal transcribed spacer (nuITS), the nuclear large subunit (nuLSU), the mitochondrial small subunit (mtSSU) ribosomal DNA, and the DNA replication licensing factor MCM7 from 80 samples mostly from Iran, Caucasia, Greece and eastern Europe. We used a combination of phylogenetic strategies and a variety of empirical, sequence-based species delimitation approaches to infer species boundaries in this group. The latter included: the automatic barcode gap discovery (ABGD), the multispecies coalescent approach *BEAST and Bayesian Phylogenetics and Phylogeography (BPP) program. Different species delimitation scenarios were compared using Bayes factors species delimitation analysis. Furthermore, morphological, chemical, ecological and geographical features of the sampled specimens were examined. Our study uncovered cryptic species diversity in A. intermutans and showed that morphology-based taxonomy may be unreliable, underestimating species diversity in this group of lichens. We identified a total of six species-level lineages in the A. intermutans complex using inferences from multiple empirical operational criteria. We found little corroboration between morphological and ecological features with our proposed candidate species, while secondary metabolite data do not corroborate tree topology. The present study on the A. intermutans species-complex indicates that the genus Aspiciliella, as currently circumscribed, is more diverse in Eurasia than previously expected. [ABSTRACT FROM AUTHOR]

The tetraploid wheat species Triticum turgidum and Triticum timopheevii are morphologically similar, and misidentification of material collected from the wild is possible. We compared published sequences for the Ppd-A1, Ppd-B1 and Ppd-G1 genes from multiple accessions of T. turgidum and T. timopheevii and devised a set of four polymerase chain reactions (PCRs), two specific for Ppd-B1 and two for Ppd-G1. We used these PCRs with 51 accessions of T. timopheevii and 20 of T. turgidum. Sixty of these accessions gave PCR products consistent with their taxon identifications, but the other eleven accessions gave anomalous results: ten accessions that were classified as T. turgidum were identified as T. timopheevii by the PCRs, and one T. timopheevii accession was typed as T. turgidum. We believe that these anomalies are not due to errors in the PCR tests because the results agree with a more comprehensive analysis of genome-wide single nucleotide polymorphisms, which similarly suggest that these eleven accessions have been misclassified. Our results therefore show that the accepted morphological tests for discrimination between T. turgidum and T. timopheevii might not be entirely robust, but that species identification can be made cheaply and quickly by PCRs directed at the Ppd-1 gene. [ABSTRACT FROM AUTHOR]

Objectives: Previous studies in food-producing animals have shown associations between antimicrobial use (AMU) and resistance (AMR) in specifically isolated bacterial species. Multi-country data are scarce and only describe between-country differences. Here we investigate associations between the pig faecal mobile resistome and characteristics at the farm-level across Europe.Methods: A cross-sectional study was conducted among 176 conventional pig farms from nine European countries. Twenty-five faecal samples from fattening pigs were pooled per farm and acquired resistomes were determined using shotgun metagenomics and the Resfinder reference database, i.e. the full collection of horizontally acquired AMR genes (ARGs). Normalized fragments resistance genes per kilobase reference per million bacterial fragments (FPKM) were calculated. Specific farm-level data (AMU, biosecurity) were collected. Random-effects meta-analyses were performed by country, relating farm-level data to relative ARG abundances (FPKM).Results: Total AMU during fattening was positively associated with total ARG (total FPKM). Positive associations were particularly observed between widely used macrolides and tetracyclines, and ARGs corresponding to the respective antimicrobial classes. Significant AMU-ARG associations were not found for β-lactams and only few colistin ARGs were found, despite high use of these antimicrobial classes in younger pigs. Increased internal biosecurity was directly related to higher abundances of ARGs mainly encoding macrolide resistance. These effects of biosecurity were independent of AMU in mutually adjusted models.Conclusions: Using resistome data in association studies is unprecedented and adds accuracy and new insights to previously observed AMU-AMR associations. Major components of the pig resistome are positively and independently associated with on-farm AMU and biosecurity conditions. [ABSTRACT FROM AUTHOR]

The pathogenic fungus Sclerotinia sclerotiorum infects over 600 species of plant. It is present in numerous environments throughout the world and causes significant damage to many agricultural crops. Fragmentation and lack of gene flow between populations may lead to population sub-structure. Within discrete recombining populations, positive selection may lead to a ‘selective sweep’. This is characterised by an increase in frequency of a favourable allele leading to reduction in genotypic diversity in a localised genomic region due to the phenomenon of genetic hitchhiking. We aimed to assess whether isolates of S. sclerotiorum from around the world formed genotypic clusters associated with geographical origin and to determine whether signatures of population-specific positive selection could be detected. To do this, we sequenced the genomes of 25 isolates of S. sclerotiorum collected from four different continents–Australia, Africa (north and south), Europe and North America (Canada and the northen United States) and conducted SNP based analyses of population structure and selective sweeps. Among the 25 isolates, there was evidence for two major population clusters. One of these consisted of 11 isolates from Canada, the USA and France (population 1), and the other consisted of nine isolates from Australia and one from Morocco (population 2). The rest of the isolates were genotypic outliers. We found that there was evidence of outcrossing in these two populations based on linkage disequilibrium decay. However, only a single candidate selective sweep was observed, and it was present in population 2. This sweep was close to a Major Facilitator Superfamily transporter gene, and we speculate that this gene may have a role in nutrient uptake from the host. The low abundance of selective sweeps in the S. sclerotiorum genome contrasts the numerous examples in the genomes of other fungal pathogens. This may be a result of its slow rate of evolution and low effective recombination rate due to self-fertilisation and vegetative reproduction. [ABSTRACT FROM AUTHOR]

The co-occurrence of plant species is a fundamental aspect of plant ecology that contributes to understanding ecological processes, including the establishment of ecological communities and its applications in biological conservation. A priori algorithms can be used to measure the co-occurrence of species in a spatial distribution given by coordinates. We used 17 species of the genus Brachypodium, downloaded from the Global Biodiversity Information Facility data repository or obtained from bibliographical sources, to test an algorithm with the spatial points process technique used by Silva et al. (2016), generating association rules for co-occurrence analysis. Brachypodium spp. has emerged as an effective model for monocot species, growing in different environments, latitudes, and elevations; thereby, representing a wide range of biotic and abiotic conditions that may be associated with adaptive natural genetic variation. We created seven datasets of two, three, four, six, seven, 15, and 17 species in order to test the algorithm with four different distances (1, 5, 10, and 20 km). Several measurements (support, confidence, lift, Chi-square, and p-value) were used to evaluate the quality of the results generated by the algorithm. No negative association rules were created in the datasets, while 95 positive co-occurrences rules were found for datasets with six, seven, 15, and 17 species. Using 20 km in the dataset with 17 species, we found 16 positive co-occurrences involving five species, suggesting that these species are coexisting. These findings are corroborated by the results obtained in the dataset with 15 species, where two species with broad range distributions present in the previous dataset are eliminated, obtaining seven positive co-occurrences. We found that B. sylvaticum has co-occurrence relations with several species, such as B. pinnatum, B. rupestre, B. retusum, and B. phoenicoides, due to its wide distribution in Europe, Asia, and north of Africa. We demonstrate the utility of the algorithm implemented for the analysis of co-occurrence of 17 species of the genus Brachypodium, agreeing with distributions existing in nature. Data mining has been applied in the field of biological sciences, where a great amount of complex and noisy data of unseen proportion has been generated in recent years. Particularly, ecological data analysis represents an opportunity to explore and comprehend biological systems with data mining and bioinformatics tools. [ABSTRACT FROM AUTHOR]

Oil bodies are the unique feature of most liverworts. Their shape, color and distribution pattern in leaf and underleaf cells are important taxonomic features of the genus Calypogeia. Most species of the genus Calypogeia have pellucid and colorless oil bodies, whereas colored, including gray to pale brown, purple-brown or blue oil bodies, are rare. To date, C. azurea was the only species with blue oil bodies to have been considered as a species of the Holarctic range. This species has been noted in various parts of the northern hemisphere–from North America, through Europe to the Far East. The aim of this study was to determine the genetic diversity of C. azurea from different parts of its distribution range and to ascertain whether blue oil bodies appeared once or several times in the evolution of the genus Calypogeia. The phylogenetic analyses based on four plastid regions (rbcL, trnG, trnL, trnH-psbA) and one nuclear region (ITS2) revealed that C. azurea is presently a paraphyletic taxon, with other Calypogeia species nested among C. azurea accessions that were clustered into four different clades. Based on the level of genetic divergence (1.03–2.17%) and the observed morphological, ecological and geographical differences, the evaluated clades could be regarded as previously unrecognized species. Four species were identified: C. azurea Stotler & Crotz (a European species corresponding to the holotype), two new species from Pacific Asia—C. orientalis Buczkowska & Bakalin and C. sinensis Bakalin & Buczkowska, and a North American species which, due to the lack of identifiable morphological features, must be regarded as the cryptic species of C. azurea with a provisional name of C. azurea species NA. [ABSTRACT FROM AUTHOR]

Objectives: We present the results of two European external quality assessments (EQAs) conducted in 2014 and 2016 under the auspices of the Study Group on Staphylococci and Staphylococcal Infections of ESCMID. The objective was to assess the performance of participating centres in characterizing Staphylococcus aureus using their standard in-house phenotypic and genotypic protocols.Methods: A total of 11 well-characterized blindly coded S. aureus (n = 9), Staphylococcus argenteus (n = 1) and Staphylococcus capitis (n = 1) strains were distributed to participants for analysis. Species identification, MIC determination, antimicrobial susceptibility testing, antimicrobial resistance and toxin gene detection and molecular typing including spa typing, SCCmec typing and MLST were performed.Results: Thirteen laboratories from 12 European countries participated in one EQA or both EQAs. Despite considerable diversity in the methods employed, good concordance (90%-100%) with expected results was obtained. Discrepancies were observed for: (i) identification of the S. argenteus strain; (ii) phenotypic detection of low-level resistance to oxacillin in the mecC-positive strain; (iii) phenotypic detection of the inducible MLSB strain; and (iv) WGS-based detection of some resistance and toxin genes.Conclusions: Overall, good concordance (90%-100%) with expected results was observed. In some instances, the accurate detection of resistance and toxin genes from WGS data proved problematic, highlighting the need for validated and internationally agreed-on bioinformatics pipelines before such techniques are implemented routinely by microbiology laboratories. We strongly recommend all national reference laboratories and laboratories acting as referral centres to participate in such EQA initiatives. [ABSTRACT FROM AUTHOR]

In this study, we report 21 ancient shotgun genomes from present-day Western Hungary, from previously understudied Late Copper Age Baden, and Bronze Age Somogyvár-Vinkovci, Kisapostag, and Encrusted Pottery archeological cultures (3,530-1,620 cal Bce). Our results indicate the presence of high steppe ancestry in the Somogyvár-Vinkovci culture. They were then replaced by the Kisapostag group, who exhibit an outstandingly high (up to ∼47%) Mesolithic hunter-gatherer ancestry, despite this component being thought to be highly diluted by the time of the Early Bronze Age. The Kisapostag population contributed the genetic basis for the succeeding community of the Encrusted Pottery culture. We also found an elevated hunter-gatherer component in a local Baden culture-associated individual, but no connections were proven to the Bronze Age individuals. The hunter-gatherer ancestry in Kisapostag is likely derived from two main sources, one from a Funnelbeaker or Globular Amphora culture-related population and one from a previously unrecognized source in Eastern Europe. We show that this ancestry not only appeared in various groups in Bronze Age Central Europe but also made contributions to Baltic populations. The social structure of Kisapostag and Encrusted Pottery cultures is patrilocal, similarly to most contemporaneous groups. Furthermore, we developed new methods and method standards for computational analyses of ancient DNA, implemented to our newly developed and freely available bioinformatic package. By analyzing clinical traits, we found carriers of aneuploidy and inheritable genetic diseases. Finally, based on genetic and anthropological data, we present here the first female facial reconstruction from the Bronze Age Carpathian Basin., (© The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Rivers are a vital resource for human wellbeing. To reduce human impact on water bodies, the European Union has established an essential regulatory framework for protection and sustainable management (WFD; 2000/60/EC). In this strategy, reliable and economic bioindicators are a fundamental component. Benthic macroinvertebrates are the group most commonly used as bioindicators through all European countries. However, their conventional assessment currently entails serious cost-efficiency limitations. In this study, we have tested the reliability of metabarcoding as a tool to record river macroinvertebrates using samples from a mock community (in vitro validation) and eDNA extracted for field validation from water from six sites within a north Iberian river (River Nalón, Asturias, Spain). Two markers (V4 region within the nuclear 18S rDNA and a fragment of the mitochondrial COI gene) were amplified and sequenced using an Illumina platform. The molecular technique has proven to be more sensitive than the visual one. A cost-benefit analysis shows that the metabarcoding approach is more expensive than conventional techniques for determining macroinvertebrate communities but requires fewer sampling and identification efforts. Our results suggest metabarcoding is a useful tool for alternative assessment of freshwater quality. [ABSTRACT FROM AUTHOR]

Tuna fisheries and processing represent economic activities of paramount importance around the world. Most of these products are traded for human consumption and in general are highly demanded commodities. However, not all tuna products achieve the same market price, some consumers are willing to pay a huge amount of money for certain species (i.e. Japanese market for Bluefin tuna) while other species are rather affordable (i.e. Skipjack tuna), therefore mislabelling has been observed frequently. We collected and analysed 545 tuna samples in six European countries, including fresh, frozen and canned products, and we have investigated whether or not these products were correctly labelled under European and national legislations. We found an overall mislabelling rate of 6.79%; in particular, 6.70% of the fresh and frozen tuna products and 7.84% of canned tuna were mislabelled, and only in the case of fresh and frozen tuna samples significant differences among countries were found. Mislabelling rates for Atlantic Bluefin tuna labelled products were very high, ranging from 50 up to 100%. In general, mislabelling was higher when specific names were included in the labels. The “tuna” umbrella term is a very popular one with consumers, but also one that remains vulnerable to ambiguity, hampering efforts towards market transparency and with potential negative consequences to the adequate management of tuna species stocks. [ABSTRACT FROM AUTHOR]

Background: Thousands of clinically relevant variations in BRCA1 and BRCA2 have been discovered and this poses a significant challenge with respect to the accurate detection, analysis turn-around time, characterisation and interpretation of these sequence variants.Methods: We evaluated the performance of different BRCA1/2 gene testing practices in routine diagnostic use in 20 European laboratories, with a focus on next-generation sequencing-based strategies as this is the technical approach implemented by or under adoption by most European clinical laboratories. Participant laboratories, selected on expertise and diagnostic service quality, tested 10 identical DNA samples containing a range of challenging pathogenic variants.Results: A small number of errors in the detection of pathogenic and significant variants were identified (2.6% diagnostic error rate). There was a high degree of concordance (>97%) across all laboratories for all variants detected. No systematic technical flaw was identified in the strategies employed across the participating laboratories.Conclusions: The discrepancies identified are most likely due to human error or the way the methodology has been implemented locally, for example, next-generation sequencing bioinformatics pipelines, rather than technical limitations of the methods. The choice of BRCA1/2 testing method will therefore depend on multiple factors including required throughput and turn-around times, access to equipment, expertise and budget. [ABSTRACT FROM AUTHOR]

The agricultural revolution in Eastern Europe began in the Eneolithic with the Cucuteni-Trypillia culture complex. In Ukraine, the Trypillian culture (TC) existed for over two millennia (ca. 5,400–2,700 BCE) and left a wealth of artifacts. Yet, their burial rituals remain a mystery and to date almost nothing is known about the genetic composition of the TC population. One of the very few TC sites where human remains can be found is a cave called Verteba in western Ukraine. This report presents four partial and four complete mitochondrial genomes from nine TC individuals uncovered in the cave. The results of this analysis, combined with the data from previous reports, indicate that the Trypillian population at Verteba carried, for the most part, a typical Neolithic farmer package of mitochondrial DNA (mtDNA) lineages traced to Anatolian farmers and Neolithic farming groups of central Europe. At the same time, the find of two specimens belonging to haplogroup U8b1 at Verteba can be viewed as a connection of TC with the Upper Paleolithic European populations. At the level of mtDNA haplogroup frequencies, the TC population from Verteba demonstrates a close genetic relationship with population groups of the Funnel Beaker/ Trichterbecker cultural complex from central and northern Europe (ca. 3,950–2,500 BCE). [ABSTRACT FROM AUTHOR]

The inferred phylogenetic relationships between organisms often depend on the molecular marker studied due to the diverse evolutionary mode and unlike evolutionary histories of different parts of the genome. Previous studies have shown conflicting patterns of differentiation of mtDNA and several nuclear markers in chamois (genus Rupicapra) that indicate a complex evolutionary picture. Chamois are mountain caprine that inhabit most of the medium to high altitude mountain ranges of southern Eurasia. The most accepted taxonomical classification considers two species, R. pyrenaica (with the subspecies parva, pyrenaica and ornata) from southwestern Europe and R. rupicapra (with the subspecies cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica) from northeastern Europe. Phylogenies of mtDNA revealed three very old clades (from the early Pleistocene, 1.9 Mya) with a clear geographical signal. Here we analyze a set of 23 autosomal introns, comprising 15,411 nucleotides, in 14 individuals covering the 10 chamois subspecies. Introns offered an evolutionary scenario that contrasts with mtDNA. The nucleotidic diversity was 0.0013± 0.0002, at the low range of what is found in other mammals even if a single species is considered. A coalescent multilocus analysis with *BEAST indicated that introns diversified 88 Kya, in the late Pleistocene, and the effective population size at the root was lower than 10,000 individuals. The dispersal of some few migrant males should have rapidly spread trough the populations of chamois, given the homogeneity of intron sequences. The striking differences between mitochondrial and nuclear markers can be attributed to strong female philopatry and extensive male dispersal. Our results highlight the need of analyzing multiple and varied genome components to capture the complex evolutionary history of organisms. [ABSTRACT FROM AUTHOR]

To gain an overview of crocodile species held in zoos, the number of individuals kept, and the number of keeping institutions, we analyzed collection information from the Zoological Information Management System (ZIMS) database. Our analysis performed from June to July 2016 revealed that there were 24 species of crocodiles kept globally in 451 zoos, with 22 species kept in 185 European zoos. Two globally-kept species were lacking in European zoo holdings according to ZIMS. Of the 27 currently recognized species of crocodiles, one ( Mecistops sp.) is not held in zoos at present. In addition we have opposed ZIMS data with information available from European studbooks and, based on literature evaluation, analyzed the development of crocodile collections in Europe during the last 40 years. Although ZIMS data is not complete, there is a trend discernible that only a few species are widely kept by the zoo community, whereas most species are represented in smaller numbers. We further discuss the importance of “Regional Collection Plans”, viz. long-term crocodile collection planning, and provide recommendations for population management such as considering a shift from very commonly kept species towards species that are in greater need of conservation support through zoo husbandry efforts. [ABSTRACT FROM AUTHOR]

BACKGROUND: Humans are exposed to thousands of man-made chemicals in the environment. Some chemicals mimic natural endocrine hormones and, thus, have the potential to be endocrine disruptors. Most of these chemicals have never been tested for their ability to interact with the estrogen receptor (ER). Risk assessors need tools to prioritize chemicals for evaluation in costly in vivo tests, for instance, within the U.S. EPA Endocrine Disruptor Screening Program. OBJECTIVES: We describe a large-scale modeling project called CERAPP (Collaborative Estrogen Receptor Activity Prediction Project) and demonstrate the efficacy of using predictive computational models trained on high-throughput screening data to evaluate thousands of chemicals for ER-related activity and prioritize them for further testing. METHODS: CERAPP combined multiple models developed in collaboration with 17 groups in the United States and Europe to predict ER activity of a common set of 32,464 chemical structures. Quantitative structure--activity relationship models and docking approaches were employed, mostly using a common training set of 1,677 chemical structures provided by the U.S. EPA, to build a total of 40 categorical and 8 continuous models for binding, agonist, and antagonist ER activity. All predictions were evaluated on a set of 7,522 chemicals curated from the literature. To overcome the limitations of single models, a consensus was built by weighting models on scores based on their evaluated accuracies. RESULTS: Individual model scores ranged from 0.69 to 0.85, showing high prediction reliabilities. Out of the 32,464 chemicals, the consensus model predicted 4,001 chemicals (12.3%) as high priority actives and 6,742 potential actives (20.8%) to be considered for further testing. CONCLUSION: This project demonstrated the possibility to screen large libraries of chemicals using a consensus of different in silico approaches. This concept will be applied in future projects related to other end points. [ABSTRACT FROM AUTHOR]

Aims: Despite major improvements in pharmacological and device treatments, heart failure remains a syndrome with high morbidity and mortality, poor quality of life, and high health-care costs. Given the extensive heterogeneity among patients with heart failure, substantial differences in the response to therapy can be expected. We hypothesize that individualized therapy is an essential next step to improve outcomes in patients with heart failure.Methods: The BIOlogy Study to TAilored Treatment in Chronic Heart Failure (BIOSTAT-CHF) included 2516 patients with worsening signs and/or symptoms of heart failure from 11 European countries, who were considered to be on suboptimal medical treatment. Another 1738 patients from Scotland were included in a validation cohort. Overall, both patient cohorts were well matched. The majority of patients were hospitalized for acute heart failure, and the remainder presented with worsening signs and/or symptoms of heart failure at outpatient clinics. Approximately half of the patients were in New York Heart Association class III, and 7% vs 34% of patients of the index vs validation cohort had heart failure with preserved ejection fraction. According to study design, all patients used diuretics, but owing to the inclusion criteria of both cohorts, patients were not on optimal, evidence-based medical therapy. In the follow-up phase, uptitration to guideline-recommended doses was encouraged.Conclusion: By using a novel systems biology approach, incorporating demographics, biomarkers, genome-wide analysis, and proteomics, a model that predicts response to therapy will be developed, which should be instrumental in developing alternative therapies for patients with suboptimal response to currently recommended therapies and thus further improve care for patients with heart failure. [ABSTRACT FROM AUTHOR]

Background: An improved understanding of the contribution of the diet to health and disease risks requires accurate assessments of dietary exposure in nutritional epidemiologic studies. The use of dietary biomarkers may improve the accuracy of estimates. Objective: We applied a metabolomic approach in a large cohort study to identify novel biomarkers of intake for a selection of polyphenolcontaining foods. The large chemical diversity of polyphenols and their wide distribution over many foods make them ideal biomarker candidates for such foods. Design: Metabolic profiles were measured with the use of highresolution mass spectrometry in 24-h urine samples from 481 subjects from the large European Prospective Investigation on Cancer and Nutrition cohort. Peak intensities were correlated to acute and habitual dietary intakes of 6 polyphenol-rich foods (coffee, tea, red wine, citrus fruit, apples and pears, and chocolate products) measured with the use of 24-h dietary recalls and food-frequency questionnaires, respectively. Results: Correlation (r . 0.3, P , 0.01 after correction for multiple testing) and discriminant [pcorr (1) . 0.3, VIP . 1.5] analyses showed that .2000 mass spectral features from urine metabolic profiles were significantly associated with the consumption of the 6 selected foods. More than 80 polyphenol metabolites associated with the consumption of the selected foods could be identified, and large differences in their concentrations reflecting individual food intakes were observed within and between 4 European countries. Receiver operating characteristic curves showed that 5 polyphenol metabolites, which are characteristic of 5 of the 6 selected foods, had a high predicting ability of food intake. Conclusion: Highly diverse food-derived metabolites (the so-called food metabolome) can be characterized in human biospecimens through this powerful metabolomic approach and screened to identify novel biomarkers for dietary exposures, which are ultimately essential to better understand the role of the diet in the cause of chronic diseases. [ABSTRACT FROM AUTHOR]

Background: Hepatitis B virus (HBV) genotypes have a distinct geographical distribution and influence disease progression and treatment outcomes. The purpose of this study was to investigate the distribution of HBV genotypes in Europe, the impact of mutation of different genotypes on HBV gene abnormalities, the features of CpG islands in each genotype and their potential role in epigenetic regulation. Results: Of 383 HBV isolates from European patients, HBV genotypes A-G were identified, with the most frequent being genotype D (51.96%) in 12 countries, followed by A (39.16%) in 7 countries, and then E (3.66%), G (2.87%), B (1.57%), F (0.52%) and C (0.26%). A higher rate of mutant isolates were identified in those with genotype D (46.7%) followed by G (45.5%), and mutations were associated with structural and functional abnormalities of HBV genes. Conventional CpG island I was observed in genotypes A, B, C, D and E. Conventional islands II and III were detected in all A-G genotypes. A novel CpG island IV was found in genotypes A, D and E, and island V was only observed in genotype F. The A-G genotypes lacked the novel CpG island VI. "Split" CpG island I in genotypes D and E and "split" island II in genotypes A, D, E, F and G were observed. Two mutant isolates from genotype D and one from E were found to lack both CpG islands I and III. Conclusions: HBV genotypes A-G were identified in European patients. Structural and functional abnormalities of HBV genes were caused by mutations leading to the association of genotypes D and G with increased severity of liver disease. The distribution, length and genetic traits of CpG islands were different between genotypes and their biological and clinical significances warrant further study, which will help us better understand the potential role of CpG islands in epigenetic regulation of the HBV genome. [ABSTRACT FROM AUTHOR]

The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe-KB; pdbekb.org), we provide data, data-access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling., (© 2022 The Authors. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)

Abstract: Ethnopharmacological relevance: Herbal medicine value chains have generally been overlooked compared with food commodities. Not surprisingly, revenue generation tends to be weighted towards the end of the chain and consequently the farmers and producers are the lowest paid beneficiaries. Value chains have an impact both on the livelihood of producers and on the composition and quality of products commonly sold locally and globally and consequently on the consumers. In order to understand the impact of value chains on the composition of products, we studied the production conditions for turmeric (Curcuma longa) and the metabolomic composition of products derived from it. We aimed at integrating these two components in order to gain a better understanding of the effect of different value chains on the livelihoods of some producers. Materials and methods: This interdisciplinary project uses a mixed methods approach. Case studies were undertaken on two separate sites in India. Data was initially gathered on herbal medicine value chains by means of semi-structured interviews and non-participant observations. Samples were collected from locations in India, Europe and the USA and analysed using 1H NMR spectroscopy coupled with multivariate analysis software and with high performance thin layer chromatography (HPTLC). Results: We investigate medicinal plant value chains and interpret the impact different value chains have on some aspects of the livelihoods of producers in India and, for the first time, analytically assess the chemical variability and quality implications that different value chains may have on the products available to end users in Europe. There are benefits to farmers that belonged to an integrated chain and the resulting products were subject to a higher standard of processing and storage. By using analytical methods, including HPTLC and 1H NMR spectroscopy, it has been possible to correlate some variations in product composition for selected producers and identify strengths and weaknesses of some types of value chains. The two analytical techniques provide different and complementary data and together they can be used to effectively differentiate between a wide variety of crude drug powders and herbal medicinal products. Conclusions: This project demonstrates that there is a need to study the links between producers and consumers of commodities produced in so-called ‘provider countries’ and that metabolomics offer a novel way of assessing the chemical variability along a value chain. This also has implications for understanding the impact this has on the livelihood of those along the value chain. [Copyright &y& Elsevier]

Different programs of The European Science Foundation (ESF) have contributed significantly to connect researchers in Europe and beyond through several initiatives. This support was particularly relevant for the development of the areas related with extracting information from papers (text-mining) because it supported the field in its early phases long before it was recognized by the community. We review the historical development of text mining research and how it was introduced in bioinformatics. Specific applications in (functional) genomics are described like it''s integration in genome annotation pipelines and the support to the analysis of high-throughput genomics experimental data, and we highlight the activities of evaluation of methods and benchmarking for which the ESF programme support was instrumental. [Copyright &y& Elsevier]

H1N1 influenza A virus is a respiratory pathogen that undergoes antigenic shift and antigenic drift to improve viral fitness. Tracking the evolutionary trends of H1N1 aids with the current detection and the future response to new viral strains as they emerge. Here, we characterize antigenic drift events observed in the hemagglutinin (HA) sequence of the pandemic H1N1 lineage from 2015-2019. We observed the substitutions S200P, K147N, and P154S, together with other mutations in structural, functional, and/or epitope regions in 2015-2019 HA protein sequences from the Mountain West region of the United States, the larger United States, Europe, and other Northern Hemisphere countries. We reconstructed multiple phylogenetic trees to track the relationships and spread of these mutations and tested for evidence of selection pressure on HA. We found that the prevalence of amino acid substitutions at positions 147, 154, 159, 200, and 233 significantly changed throughout the studied geographical regions between 2015 and 2019. We also found evidence of coevolution among a subset of these amino acid substitutions. The results from this study could be relevant for future epidemiological tracking and vaccine prediction efforts. Similar analyses in the future could identify additional sequence changes that could affect the pathogenicity and/or infectivity of this virus in its human host.

Abstract: Forest age structure is an important factor for understanding the history of forests, their current functioning and their future development. It is, for instance, crucial information to be able to assess sustainable harvesting potentials. Furthermore, since the development of growing stock and increment, and thus the patterns of net carbon exchange, are strongly affected by the age of the forest, information about the age structure is needed to understand the temporal variability of the greenhouse gas budgets and potential contributions of forest management (i.e. their additionality) to long-term removal of carbon from the atmosphere. European forests have changed drastically in recent decades, but to date no European level compilation of historical forest age structure data is available. In this study, country level historical age-class data was combined with a backcasting method to reconstruct the age-class structure for 25 European countries from 1950 to 2010 (total forest area in 2010: 118.3million ha). Based on the results, dynamic maps of forest age-class distributions on 0.25°×0.25° grid were generated, and the change in the forest age structure was analysed. Results show that the share of old forests (>100years) has decreased from 26% in 1950 to 17% in 2010, and the mean age over the studied area decreased from 67 to 60years. However, when looking at the change of the mean age from 1950 to 2010 at country level, there is a large variation between the countries. We discuss implications of the results and argue that the development of forest age structure contributed less than previously thought to the carbon sink in European forests from 1950 onwards. [Copyright &y& Elsevier]

The human immunodeficiency virus (HIV) has a high rate of evolution generated by mutations and recombinations in association with the high replication rate of this virus into the susceptible cells. The diversity of HIV can be easily observed in HIV-1 group M which comprises 9 subtypes, more that 50 inter-subtype circulating recombinant forms (CRFs) and several unique recombinant forms (URFs). Subtype distribution in Europe is geographically influenced; subtype B is highly prevalent in the Western part of the continent and subtype A is mainly responsible for the infections in the Eastern countries. From the beginning of the epidemic in Romania, a particular subtype has been reported as being highly prevalent, the F1subtype. Previous data suggested that the HIV-1 epidemiology in Romania has changed over time, other subtypes than F1 (subtype B, C and A1) being more and more encountered. 32 of 2132 sequences corresponding to HIV-1 strains isolated during 2003 and 2011 in the reference laboratory from the National Institute for Infectious Diseases 'Matei Bals' were unassigned for the HIV-1 subtype. We have analysed these sequences using four different recombination algorithms. Half of them were classified as being CRFs (7 were CRF14_BG and 8 were CRF02_AG) and subtype F1 (1 sequence). The other 16 sequences were recombinants with more complex patterns of recombination. Therefore, we have improved the figure of HIV-1 subtype distribution in Romania, showing how using of more different bioinformatic tools can improve the subtype assignment. [ABSTRACT FROM AUTHOR]

This study combines Web usage mining, Web link analysis, and bibliometric methods for analyzing research activities in research organizations. It uses visits to the Expert Protein Analysis System ( ExPASy) server-a virtual research infrastructure for bioinformatics-as a proxy for measuring bioinformatic research activity. The study finds that in the United Kingdom ( UK), Germany, and Spain the number of visits to the ExPASy Web server made by research organizations is significantly positively correlated with research output in the field of biochemistry, molecular biology, and genetics. Only in the UK do we find a significant positive correlation between ExPASy visits per publication and the normalized impact of an organization's publications. The type of indicator developed in this study can be used to measure research activity in fields in which e-research has become important. In addition, it can be used for the evaluation of e-research infrastructures. [ABSTRACT FROM AUTHOR]

The article discusses the challenges facing the Protein Data Bank in Europe (PDBe) and its guardians. Previously known as the European Macromolecular Structure Database, PDBe is the worldwide archive of biomacromolecular structures which was established at the European Bioinformatics Institute in 1995. It expects PDB to involve growth in the number of entries and experimental techniques used in determining the structures of biologically relevant molecules. Recommendations on the way in which the structural archive is organized are outlined.

The cancer Biomedical Informatics Grid (caBIG) was launched in 2003 by the US National Cancer Institute with the aim of connecting research teams through the use of shared infrastructure and software to collect, analyse and share data. It was an ambitious project, and the issue it aimed to address was huge and far-reaching. With such developments as the mapping of the human genome and the advancement of new technologies for the analysis of genes and proteins, cancer researchers have never produced so much complex data, nor have they understood so much about cancer on a molecular level. This new 'molecular understanding' of cancer, according to the caBIG 2007 'Pilot Report'[1], leads to molecular or 'personalised' medicine being the way forward in cancer research and treatment, and connects basic research to clinical care in an unprecedented way. But the former 'silo-like' nature of research does not lend itself to this brave new world of molecular medicine—individual labs and institutes working in isolation, "in effect, as cottage industries, each collecting and interpreting data using a unique language of their own"[2] will not advance cancer research as it should be advanced. The solution proposed by the NCI in caBIG was to produce an integrated informatics grid ('caGrid') to incorporate open source, open access tools to collect, analyse and share data, enabling everyone to use the same methods and language for these tasks. caBIG is primarily a US-based endeavour, and though the tools are openly available for users worldwide, it is in US NCI-funded cancer centres that they have been actively introduced and promoted with the eventual hope, according to the pilot report, of being able to do the same worldwide. caBIG also has a collaboration in place with the UK organisation NCRI to exchange technologies and research data. The European Association for Cancer Research, a member association for cancer researchers, conducted an online survey in January 2011 to identify the penetration of the ambitious caBIG project into European laboratories. The survey was sent to 6396 researchers based in Europe, with 764 respondents, a total response rate of 11.94%. [ABSTRACT FROM AUTHOR]

The oceans are the Earth's largest ecosystem, covering 70% of our planet and providing goods and services for the majority of the world's population. Understanding the complex abiotic and biotic processes on the micro- to macroscale is the key to protect and sustain the marine ecosystem. Marine microorganisms are the ‘gatekeepers’ of the biotic processes that control the global cycles of energy and organic matter. A multinational, multidisciplinary approach, bringing together research on oceanography, biodiversity and genomics, is now needed to understand and finally predict the complex responses of the marine ecosystem to ongoing global changes. Such an integrative approach will not only bring better understanding of the complex interplay of the organisms with their environment, but will reveal a wealth of new metabolic processes and functions, which have a high potential for biotechnological applications. This potential has already been recognized by the European commission which funded a series of workshops and projects on marine genomics in the sixth and seventh framework programme. Nevertheless, there remain many obstacles to achieving the goal – such as a lack of bioinformatics tailored for the marine field, consistent data acquisition and exchange, as well as continuous monitoring programmes and a lack of relevant marine bacterial models. Marine ecosystems research is complex and challenging, but it also harbours the opportunity to cross the borders between disciplines and countries to finally create a rewarding marine research era that is more than the sum of its parts. [ABSTRACT FROM AUTHOR]

A. halleri is a psuedometallophyte with a patchy distribution in Europe and is often spread by human activity. To determine the population history and whether this history is consistent with potential human effects, we surveyed nucleotide variation using 24 loci from 12 individuals in a large A. halleri population. The means of total and silent nucleotide variation (θW) are within the range expected for the species. The population genetic neutrality tests Tajima’s D and Wall’s B had significant composite results rejecting panmixia, and Approximate Bayesian Computation analysis revealed that a subdivision model better explained the variation than the standard neutral model, refugia (or admixture), bottleneck or change of population size models. A categorical regression analysis further supports the subdivision model, and under the subdivision model, the neutrality tests are no longer significant. The best support was for two source populations, a situation consistent with the mixing of two populations possibly mediated by human activity. This scenario might limit the genetic diversity and adaptive potential of the population. The non-neutral population variation described here should be considered in bioinformatic searches for adaptation. [ABSTRACT FROM AUTHOR]

Over recent years, five European PhD programmes have organized a series of 'Bioinformatics Research and Education Workshops'. These workshops address the needs of first-year PhD students and have been designed to combine a maximum of educational impact and scientific stimulation with a minimum of financial and administrative effort. We describe the BREW experience and argue that this type of event constitutes an attractive component of PhD education in computational biology and beyond. [ABSTRACT FROM AUTHOR]