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The Use of STR locus in studying the relations between siblings for the need of ethnic genetic database in Indonesia for identifying disaster victims, criminals and paternity test is not well established compared to other countries. Targeted outcomes are STR typing and profiling of the human genome for individual identification and kinship relations. The aim of this study was to analyse kinship relationships among siblings by assessing and determining a better STR locus and the level of allelic distribution among full siblings in Madurese people of Surabaya, East Java, with 3 kinship categories namely male-male, female-female and male-female. Objectives to explain the sibling relationship from a pool of 25 Madurese families in Surabaya, there were 6, 11 and 8 pairs of siblings in the male-male, female-female and male-female categories respectively. Kin relationships were analysed by using 12 STR loci technique (CSF1PO, F13B, FES, TH01, TPOX, VWA, D5S818, D7S820, D8S1179, D13S317, D16S539, and D18S51). Through the use of 12 autosomal STR loci, this study provides evidence that the strength of sharing 2 alleles can be used as a reference in that siblings have high kinship relations. Based on the results of this study, STR loci D5S818, CSF1PO, and F13 are recommended when typing male-male siblings whereas STR locus FES is recommended for female-female siblings of the Madurese population. The recommended main STR loci in male-female siblings of Madurese ethnicity are D13S317, D8S1179, FES, and CSF1PO. [ABSTRACT FROM AUTHOR]

[Display omitted] • MVAR aggregates and annotates genome variation from large-scale sequencing of different mouse strains and expertly curated variants for phenotypic alleles. • Variant annotation in MVAR includes variant type, molecular consequence, impact, and region. • Data in MVAR are accessible in both human- and machine- readable formats. • MVAR serves as both a stand-alone database of mouse genome variation and as a variant annotation service. • MVAR is a platform for facilitating genotype-phenotype associations in the laboratory mouse. • MVAR resource was implemented using a micro-services architecture, providing both interoperability and ease of software maintenance. The Mouse Variation Registry (MVAR) resource is a scalable registry of mouse single nucleotide variants and small indels and variant annotation. The resource accepts data in standard Variant Call Format (VCF) and assesses the uniqueness of the submitted variants via a canonicalization process. Novel variants are assigned a unique, persistent MVAR identifier; variants that are equivalent to an existing variant in the resource are associated with the existing identifier. Annotations for variant type, molecular consequence, impact, and genomic region in the context of specific transcripts and protein sequences are generated using Ensembl's Variant Effect Predictor (VEP) and Jannovar. Access to the data and annotations in MVAR are supported via an Application Programming Interface (API) and web application. Researchers can search the resource by gene symbol, genomic region, variant (expressed in Human Genome Variation Society syntax), refSNP identifiers, or MVAR identifiers. Tabular search results can be filtered by variant annotations (variant type, molecular consequence, impact, variant region) and viewed according to variant distribution across mouse strains. The registry currently comprises more than 99 million canonical single nucleotide variants for 581 strains of mice. MVAR is accessible from https://mvar.jax.org. [ABSTRACT FROM AUTHOR]

• HPAIVs caused the largest number of outbreaks in Japan during the winter of 2022/2023. • HA genes were divided into 3 subgroups (G2b, G2d, and G2c) of clade 2.3.4.4b. • G2c viruses, which caused the largest number of outbreaks, likely originated from H5N1 viruses in Asia and Russia. • HPAIVs were divided into 17 genotypes because of different internal genes. • Multiple genotypes were generated by reassortment with wild birds AIVs in North America as well as Eurasian countries. High pathogenicity avian influenza viruses (HPAIVs) of the H5N1 and H5N2 subtypes were responsible for 84 HPAI outbreaks on poultry premises in Japan during October 2022–April 2023. The number of outbreaks during the winter of 2022–2023 is the largest ever reported in Japan. In this study, we performed phylogenetic analyses using the full genetic sequences of HPAIVs isolated in Japan during 2022–2023 and those obtained from a public database to identify their genetic origin. Based on the hemagglutinin genes, these HPAIVs were classified into the G2 group of clade 2.3.4.4b, whose ancestors were H5 HPAIVs that circulated in Europe in late 2020, and were then further divided into three subgroups (G2b, G2d, and G2c). Approximately one-third of these viruses were classified into the G2b and G2d groups, which also included H5N1 HPAIVs detected in Japan during 2021–2022. In contrast, the remaining two-thirds were classified into the G2c group, which originated from H5N1 HPAIVs isolated in Asian countries and Russia during the winter of 2021–2022. Unlike the G2b and G2d viruses, the G2c viruses were first detected in Japan in the fall of 2022. Importantly, G2c viruses caused the largest number of outbreaks throughout Japan over the longest period during the season. Phylogenetic analyses using eight segment genes revealed that G2b, G2d, and G2c viruses were divided into 2, 4, and 11 genotypes, respectively, because they have various internal genes closely related to those of avian influenza viruses detected in wild birds in recent years in Asia, Russia, and North America, respectively. These results suggest that HPAIVs were disseminated among migratory birds, which may have generated numerous reassortant viruses with various gene constellations, resulting in a considerable number of outbreaks during the winter of 2022–2023. [ABSTRACT FROM AUTHOR]

National forensic DNA databases are a valuable investigative tool, that have the potential to increase the efficacy of criminal investigations. Their unfettered expansion in recent years raises unsettling ethical issues that require close attention. DNA database expansion threatens the rights to privacy, non-discrimination, and equality, and can undermine public trust in government. This perspective piece relies on data from an international mapping study of Forensic DNA Databases to document the expansion of these databases, highlight the ethical issues they raise, and propose key recommendations for more responsible use of this infrastructure. • The expansion of forensic DNA databases raises numerous legal issues that must be addressed by policymakers and database custodians worldwide. • While Interpol has developed Best Practice guidelines, these guidelines have yet to prescribe minimal standards towards governance and human rights. • Greater governance is needed, if tools intended to facilitate criminal investigations are not to become a source of oppression. [ABSTRACT FROM AUTHOR]

The aldo-keto reductase (AKR) superfamily is a large family of proteins found across the kingdoms of life. Shared features of the family include 1) structural similarities such as an (α/β) 8 -barrel structure, disordered loop structure, cofactor binding site, and a catalytic tetrad, and 2) the ability to catalyze the nicotinamide adenine dinucleotide (phosphate) reduced (NAD(P)H)-dependent reduction of a carbonyl group. A criteria of family membership is that the protein must have a measured function, and thus, genomic sequences suggesting the transcription of potential AKR proteins are considered pseudo-members until evidence of a functionally expressed protein is available. Currently, over 200 confirmed AKR superfamily members are reported to exist. A systematic nomenclature for the AKR superfamily exists to facilitate family and subfamily designations of the member to be communicated easily. Specifically, protein names include the root "AKR", followed by the family represented by an Arabic number, the subfamily-if one exists-represented by a letter, and finally, the individual member represented by an Arabic number. The AKR superfamily database has been dedicated to tracking and reporting the current knowledge of the AKRs since 1997, and the website was last updated in 2003. Here, we present an updated version of the website and database that were released in 2023. The database contains genetic, functional, and structural data drawn from various sources, while the website provides alignment information and family tree structure derived from bioinformatics analyses. • The AKR superfamily is a primordial class of proteins found across all life forms. • Most AKR members catalyze carbonyl reduction. • AKRs have (α/β) 8 barrel, 3 loops, a (NADP(H)) binding site, and a catalytic tetrad. • We communicate a AKR Superfamily website and database update after 20 years. • The database provides structural, genetic, and evolutionary information for AKRs. [ABSTRACT FROM AUTHOR]

The Forensic Databases Advisory Board (FDAB), an independent board that assists the International Society for Forensic Genetics (ISFG), has presented a First Report on ethical aspects of the following Forensic Genetic Frequency Databases (FGFD): EMPOP, STRidER and YHRD. The FDAB designed an ethical framework to evaluate the content of these FGFD, and the factors to be considered for retention and acceptance of submissions. The FDAB framework proposes to categorize submissions according to the risk of having contravened the universal ethical principles outlined by international organizations, and the guidelines adopted by the ISFG. The report has been open to discussion by the scientific community since 2023. Herein we present the conception and development of the First Report along with a summary of its content, with consideration of the feedback received. • Presentation of the Forensic Databases Advisory Board work since its establishment in 2021. • Rationale behind the ethical framework to evaluate the content of the FGFD. • Design of risk categories of submissions to FGFD. • Suggested actions on risk submissions. • Continued debate on emerging challenges is needed. [ABSTRACT FROM AUTHOR]

Single Nucleotide Polymorphisms (SNPs), as the most prevalent type of variation in the human genome, play a pivotal role in influencing human traits. They are extensively utilized in diverse fields such as population genetics, forensic science, and genetic medicine. This study focuses on the 'Rita' BeadChip, a custom SNP microarray panel developed using Illumina Infinium HTS technology. Designed for high-throughput genotyping, the panel facilitates the analysis of over 4000 markers efficiently and cost-effectively. After careful clustering performed on a set of 1000 samples, an evaluation of the Rita panel was undertaken, assessing its sensitivity, repeatability, reproducibility, precision, accuracy, and resistance to contamination. The panel's performance was evaluated in various scenarios, including sex estimation and parental relationship assessment, using GenomeStudio data analysis software. Findings show that over 95 % of the custom BeadChip assay markers were successful, with better performance of transitions over other mutations, and a considerably lower success rate for Y chromosome loci. An exceptional call rate exceeding 99 % was demonstrated for control samples, even with DNA input as low as 0.781 ng. Call rates above 80 % were still obtained with DNA quantities under 0.1 ng, indicating high sensitivity and suitability for forensic applications where DNA quantity is often limited. Repeatability, reproducibility, and precision studies revealed consistency of the panel's performance across different batches and operators, with no significant deviations in call rates or genotyping results. Accuracy assessments, involving comparison with multiple available genetic databases, including the 1000 Genome Project and HapMap, denoted over 99 % concordance, establishing the Rita panel's reliability in genotyping. The contamination study revealed insights into background noise and allowed the definition of thresholds for sample quality evaluation. Multiple metrics for differentiating between negative controls and true samples were highlighted, increasing the reliability of the obtained results. The sex estimation tool in GenomeStudio proved highly effective, correctly assigning sex in all samples with autosomal loci call rates above 97 %. The parental relationship assessment of family trios highlighted the utility of GenomeStudio in identifying genotyping errors or potential Mendelian inconsistencies, promoting the application of arrays such as Rita in kinship testing. Overall, this evaluation confirms the Rita microarray as a robust, high-throughput genotyping tool, underscoring its potential in genetic research and forensic applications. With its custom content and adaptable design, it not only meets current genotyping demands but also opens avenues for further research and application expansion in the field of genetic analysis. • Illumina custom microarray 'Rita' delivers high-quality results for human samples. • Call rate exceeds 90 % with a DNA input as low as 0.195 ng. • Consistently high call rate with a 200 ng input (>99 %), with accuracy beyond 99 %. • High repeatability, reproducibility, and precision across batches and operators. • Rita confirmed as robust method for human genotyping and potential forensic use. [ABSTRACT FROM AUTHOR]

• Digital Sequence Information (DSI) caused new discursive struggles. • Biodiversity and access and benefit-sharing discourses structured DSI negotiations. • Actors mobilized discourses to define DSI and reframe access and benefit-sharing. • Discourses enabled actors to form coalitions and push for certain policy options. • Some discourses were institutionalized and others marginalized in decisions on DSI. In 2016, negotiations of the Convention on Biological Diversity on access and benefit-sharing policies were shaken up by the emergence of digital sequence information (DSI) as policy issue. Open access to DSI on genetic resources in genetic databases is standard practice in data-driven biological research, but such access was argued to bypass access and benefit-sharing policies of the Convention. As Parties and observers had to take a position on governing DSI, this research investigated the influence of discourses on the negotiations through argumentative discourse analysis. Actors in international environmental negotiations mobilize 'background' discourses – both consciously and unconsciously – to define and 'foreground' issues, which in turn shape negotiation and decision-making processes. The analysis shows that existing discourses on access and benefit-sharing and biodiversity structured actors' statements aimed at defining DSI, thus applying and redefining access and benefit-sharing principles in the context of DSI. Actors with similar and slightly varying interests formed discourse-coalitions on the basis of shared storylines. Developing countries formed a separate discourse-coalition to push for DSI regulation wherein ideas about sustainable development and environmental justice were integrated, and to a lesser extent about biopiracy (the notion that open access to DSI enables the misappropriation of genetic resources and associated traditional knowledge). In response, developed countries adopted narratives put forward by industry and research, advocating that open access to DSI is essential for science, biodiversity conservation and sustainable development. A third coalition, consisting of Indigenous peoples and local communities and civil society, also mobilized environmental justice and biopiracy discourses, but more prominently a unique holistic discourse on nature. Finally, holistic and biopiracy discourses were marginalized in official negotiation documents, while scientific and sustainable development discourses were adopted in official negotiation documents. The research provides a novel understanding of the DSI-negotiations as discursive politics, and highlights how different positionalities in discourses structure and are structured by statements in this political arena. [ABSTRACT FROM AUTHOR]

Background: Although many pathological mechanisms and etiological hypotheses of acute unilateral vestibulopathy (AUVP) have been reported, but the actual etiology remains to be elucidated. Objective: This study was based on comprehensive bioinformatics to identify the critical genes of AUVP and explore its pathological mechanism. Methods: Gene expression profiles of AUVP and normal samples were collected from GSE146230 datasets of the Gene Expression Omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was constructed, and the WGCNA R-package extracted significant modules. The limma R-package was applied to identify differentially expressed genes (DEGs). The common genes of practical modules and DEGs were screened for GO and KEGG pathways analysis. The protein--protein interaction (PPI) layout and hub genes validation was created by Cytoscape software using the link from the STRING database. The functions of hub genes were predicted through the CTD (comparative genetics database). Results: A total of 332 common genes were screened from practical modules and DEGs. Functional enrichment analysis revealed that these genes were predominantly associated with inflammation and infection. After construction of PPI, expressions of hub genes, and drawing ROC curves, LILRB2, FPR1, AQP9, and LILRA1 are highly expressed in AUVP (p < 0.05) and have a certain diagnostic efficacy for AUVP (AUC > 0.7), so they were selected as hub genes. The functions of hub genes suggested that the occurrence of AUVP may be related to inflammation, necrosis, hepatomegaly, and other conditions in CTD. Conclusion: LILRB2, FPR1, AQP9, and LILRA1 may play essential roles in developing AUVP, providing new ideas for diagnosing and treating AUVP. [ABSTRACT FROM AUTHOR]

Anoa is an endemic ungulate in Sulawesi and its status now is endangered because the population continues to decline. Conservation genetics is one of the crucial issues in the anoa conservation strategy and action plan 2013-2022 document, but this genetic data is not yet available. To investigate and provide valuable information for conservation genetics measures, thirteen polymorphic microsatellites were used to analyze 20 adult anoa. Anoa has relatively low genetic diversity within populations (HO = 0.58), and high genetic differentiation among populations (FST = 0157). Although the anoa population has a bottleneck signal (T.P.M: 0.019; P0.05), the bottleneck simulation results show that the loss of genetic diversity is being slow over the next 100 years (9.5%). We provide some recommendations for conservation genetics based on the findings in this paper, including monitoring and genetically mapping for other anoa populations due to bottleneck signals, establishing the founder of the ex-situ population by examining their genetic diversity status, maintaining and increasing the number of individuals in the ex-situ population to genetically safe population size, and managing anoa populations by avoiding inbreeding. In-situ and ex-situ conservation programs should be combined to maintain the genetic diversity of anoa. [ABSTRACT FROM AUTHOR]

Despite efforts to collect genomics and phenomics ('omics') and environmental data, spatiotemporal availability and access to digital resources still limit our ability to predict plants' response to changes in climate. Our goal is to quantify the improvement in the predictability of maize yields by enhancing climate data. Large-scale experiments such as the Genomes to Fields (G2F) are an opportunity to provide access to 'omics' and climate data. Here, the objectives are to: (i) improve the G2F 'omics' and environmental database by reducing the gaps of climate data using deep neural networks; (ii) estimate the contribution of climate and genetic database enhancement to the predictability of maize yields via environmental covariance structures in genotype by environment (G×E) modeling; and (iii) quantify the predictability of yields resulting from the enhancement of climate data, the implementation of the G×E model, and the application of three trial selection schemes (i.e. randomization, ranking, and precipitation gradient). The results show a 12.1% increase in predictability due to climate and 'omics' database enhancement. The consequent enhancement of covariance structures evidenced in all train–test schemes indicated an increase in maize yield predictability. The largest improvement is observed in the 'random-based' approach, which adds environmental variability to the model. [ABSTRACT FROM AUTHOR]

Even in the era of information "prosperity" in the form of databases and registries that compile a wealth of data, information about ASD and ADHD remains scattered and disconnected. These data systems are powerful tools that can inform decision-making and policy creation, as well as advancing and disseminating knowledge. Here, we review three types of data systems (patient registries, clinical trial registries and genetic databases) that are concerned with ASD or ADHD and discuss their features, advantages and limitations. We noticed the lack of ethnic diversity in the data, as the majority of their content is curated from European and (to a lesser extent) Asian populations. Acutely aware of this knowledge gap, we introduce here the framework of the Neurodevelopmental Disorders Database (NDDB). This registry was designed to serve as a model for the national repository for collecting data from Saudi Arabia on neurodevelopmental disorders, particularly ASD and ADHD, across diverse domains. [ABSTRACT FROM AUTHOR]

Inhibin subunit beta B (INHBB) is a potential prognostic biomarker for a variety of cancers. However, its role in gastric cancer (GC) remains elusive. The differential expression data of INHBB in tumor and normal tissues were extracted from several databases and genetic alterations of INHBB were assessed by cBioPortal. Kaplan-Meier analysis was used to evaluate the survival rate of patients with GC with INHBB and association with clinical features in GC. Cox regression analysis was used to explore the prognostic value of clinical indicators and INHBB in GC, and a nomogram prognostic model was established. In addition, the predictive validity of the nomogram model was assessed by time-depended receiver operating characteristic (ROC) and calibration curves. Functional enrichment analyses were conducted to functionally annotate INHBB. Notably, we found that the quantitative assessment of immune cell subpopulation infiltration correlated with INHBB expression. INHBB expression is upregulated in GC and is correlated with several clinical features including prognostic indicators and a histological type. Genetic alterations were observed in INHBB, its DNA methylation level was negatively correlated with INHBB expression. High INHBB expression is associated with a poor prognosis and is an independent risk factor for prognosis in GC, along with age and residual tumor. The nomogram model showed a good prediction ability and was validated by time-depended ROC and calibration curves. Functional enrichment analysis indicated that INHBBassociated genes were enriched in tumor microenvironment Gene Ontology (GO) terms and were correlated with tumor-associated pathways. INHBB has a regulatory function in immune cell infiltration, especially macrophage infiltration in GC. Specifically, patients with GC with high INHBB expression and high macrophage infiltration have a worse prognosis. INHBB expression was negatively correlated with the expression of chemokines/chemokine receptors and plays a regulatory role in immunoinhibitor/immunostimulatorinvolved pathways. INHBB is a potential prognostic biomarker for GC and may drive the abnormal activity of critical cancer-associated pathways, potentially contributing to immune cell infiltration to promote GC development. [ABSTRACT FROM AUTHOR]

Objective. To describe the relevance and some tools of genome mining to explore genetic and molecular determinants encoded in bacterial genomes to address agronomic problems. Design/Methodology/Approach. Literature review of the importance of bacteria as a reservoir of biosynthetic gene clusters (BGC), involved in the production of metabolites with biological activity as antipathogens; and of genome mining as a tool to reveal this potential. Results. Bioinformatic tools are useful for the exploration of bacterial genomes and have the potential to contribute to the resolution of agronomy problems. For example, the use of bacteria, their genes and metabolites for the control of phytopathogens that attack crops of global importance. Likewise, the limitations of the genome mining and their coupling with other experimental approaches to achieve bioprospecting of BGC or their related metabolites are summarized. Limitations of the study/implications: Although the use of genome mining to explore the potential of bacteria is a very powerful approach, it will always be necessary the experimental corroboration at the laboratory level, to confirm the hypotheses generated by bioinformatics tools. Findings/conclusions: Genome mining allows to take advantage of the large number of bacterial genomes currently sequenced, that are available in public databases to understand the genetic bases of their biological activities. As well as for the heterologous expression of biosynthetic genes, or the identification and purification of new metabolites. The foregoing with the objective of contributing with more effective and environmentally friendly solutions that address agronomic problems. [ABSTRACT FROM AUTHOR]

Background: Insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) controls the cytoplasmic fate of certain mRNAs and is hypothesized to predict a poor patient prognosis in several malignant tumors. However, the prognostic relevance of IGF2BP1 in breast cancer remains debatable. Methods: We interrogated large publicly available datasets from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA), and cBioportal databases to analyze the genetic alterations in the expression levels of IGF2BP1 in patients with invasive breast carcinoma (BRCA), and to discern the prognostic value of IGF2BP1 in BRCA. We applied Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genome (KEGG), and gene set enrichment analysis (GSEA) to uncover a functional association between IGF2BP1 and BRCA using differentially expressed genes (DEGs), and we screened genes and proteins related to BRCA. Results: We determined that both genetic alterations in IGF2BP1 (approximately 10%) and an increase in IGF2BP1 mRNA levels were related to certain cancer subtypes and an unfavorable prognosis in BRCA patients, and we then established an OS nomogram upon our multivariate regression model. The DEGs and IGF2BP1-correlated genes/proteins that implied the involvement of cornification, keratinization, drug/xenobiotic metabolism by cytochrome P450, chemical carcinogenesis, cell interactions, and cell adhesion to the extracellular matrix (ECM) pathways with respect to the prognostic relevance of IGF2BP1. Conclusion: In summary, our results indicated that both genetic alterations in IGF2BP1 and increased levels of IGF2BP1 mRNA and protein predict a poor patient prognosis in BRCA patients. [ABSTRACT FROM AUTHOR]

Background: Mutations in PRKAR1A gene can lead to Carney complex (CNC), and most CNC patients develop cardiac and cutaneous myxomas. In particular, cardiac myxomas are a common cause of mortality in CNC patients. Cutaneous myxomas of the external ear are extremely rare, and do not have any specific clinical features. Methods: In this retrospective study, we analyzed the clinical and genetic data of the proband and his family and fifty whole blood control samples selected from the molecular genetic database of our hospital. Whole exome DNA sequencing analysis was used to detect the mutation in the peripheral blood samples. Results: The results of the clinical analysis showed the presence of spotty skin pigmentation and external auditory canal myxoma in the proband as well as in his sister and mother. Whole-exome DNA sequencing showed a novel heterozygous mutation in the PRKAR1A gene i.e., c.824_825delAG (p.Gln275Leufs*2), in the proband and his sister and mother. Conclusion: In conclusion, the family members had the same autosomal dominant PRKAR1A mutation. DNA sequencing revealed a novel c.824_825delAG in exon 9 of PRKAR1A. This pathogenic mutation has not been reported previously, and may be related to the occurrence of external auditory canal myxomas and spotty pigmentation. This study broadens the genotypic spectrum of PRKAR1A mutations in CNC. [ABSTRACT FROM AUTHOR]

In commercial fruit production, synchronized ripening and stable shelf life are important properties. The loosely clustered or non-bunching muscadine grape has unrealized potential as a disease-resistant cash crop, but requires repeated hand harvesting due to its unsynchronized or long or heterogeneous maturation period. Genomic research can be used to identify the developmental and environmental factors that control fruit ripening and postharvest quality. This study coupled the morphological, biochemical, and genetic variations between "Carlos" and "Noble" muscadine grape cultivars with RNA-sequencing analysis during berry maturation. The levels of antioxidants, anthocyanins, and titratable acids varied between the two cultivars during the ripening process. We also identified new genes, pathways, and regulatory networks that modulated berry ripening in muscadine grape. These findings may help develop a large-scale database of the genetic factors of muscadine grape ripening and postharvest profiles and allow the discovery of the factors underlying the ripeness heterogeneity at harvest. These genetic resources may allow us to combine applied and basic research methods in breeding to improve table and wine grape ripening uniformity, quality, stress tolerance, and postharvest handling and storage. [ABSTRACT FROM AUTHOR]

Tea (Camellia sinensis) is both a plant and a foodstuff. Many bioactive compounds, which are present in the final tea product and related to its quality or functional properties, are produced during the tea manufacturing process. However, the characteristic secondary metabolites, which give tea its unique qualities and are beneficial to human health, are produced mainly in the leaves during the process of plant growth. Therefore, it is important to understand how tea leaves produce these specialized metabolites. In this review, we first compare the common metabolites and specialized metabolites in tea, coffee, cocoa, and grape and discuss the occurrence of characteristic secondary metabolites in tea. Progress in research into the formation of these characteristic secondary metabolites in tea is summarized, including establishing a biological database and genetic transformation system, and the biosynthesis of characteristic secondary metabolites. Finally, speculation on future research into the characteristic secondary metabolites of tea is provided from the viewpoints of the origin, resources, cultivation, and processing of tea. This review provides an important reference for future research on the specialized metabolites of tea in terms of its characteristics. [ABSTRACT FROM AUTHOR]

Many metagenomic and environmental DNA studies require the taxonomic assignment of individual reads or sequences by aligning reads to a reference database, known as taxonomic binning. When a read aligns to more than one reference sequence, it is often classified based on sequence similarity. This step can assign reads to incorrect taxa, at a rate which depends both on the assignment algorithm and on underlying population genetic and database parameters. In particular, as we move towards using environmental DNA to study eukaryotic taxa subject to regular recombination, we must take into account issues concerning gene tree discordance. Though accuracy is often compared across algorithms using a fixed data set, the relative impact of these population genetic and database parameters on accuracy has not yet been quantified. Here, we develop both a theoretical and simulation framework in the simplified case of two reference species, and compute binning accuracy over a wide range of parameters, including sequence length, species–query divergence time, divergence times of the reference species, reference database completeness, sample age and effective population size. We consider two assignment methods and contextualize our results using parameters from a recent ancient environmental DNA study, comparing them to the commonly used discriminative k‐mer‐based method Clark (Current Biology, 31, 2021, 2728; BMC Genomics, 16, 2015, 1). Our results quantify the degradation in assignment accuracy as the samples diverge from their closest reference sequence, and with incompleteness of reference sequences. We also provide a framework in which others can compute expected accuracy for their particular method or parameter set. Code is available at https://github.com/bdesanctis/binning‐accuracy. [ABSTRACT FROM AUTHOR]

As more sporadic cases of chloroquine resistance occur (CQR) in Plasmodium vivax (P. vivax) malaria, molecular markers have become an important tool to monitor the introduction and spread of drug resistance. P. vivax multidrug resistance-associated protein 1 (PvMRP1), as one of the members of the ATP-binding cassette (ABC) transporters, may modulate this phenotype. In this study, we investigated the gene mutations and copy number variations (CNVs) in the pvmrp1 in 102 P. vivax isolates from China, the Republic of Korea (ROK), Myanmar, Papua New Guinea (PNG), Pakistan, the Democratic People's Republic of Korea (PRK), and Cambodia. And we also obtained 72 available global pvmrp1 sequences deposited in the PlasmoDB database to investigate the genetic diversity, haplotype diversity, natural selection, and population structure of pvmrp1. In total, 29 single nucleotide polymorphisms reflected in 23 non-synonymous, five synonymous mutations and one gene deletion were identified, and CNVs were found in 2.9% of the isolates. Combined with the antimalarial drug susceptibility observed in the previous in vitro assays, except the prevalence of S354N between the two CQ sensitivity categories revealed a significant difference, no genetic mutations or CNVs associated with drug sensitivity were found. The genetic polymorphism analysis of 166 isolates worldwide found that the overall nucleotide diversity (π) of pvmrp1 was 0.0011, with 46 haplotypes identified (Hd = 0.9290). The ratio of non-synonymous to synonymous mutations (dn/ds = 0.5536) and the neutrality tests statistic Fu and Li's D* test (Fu and Li's D* = −3.9871, p < 0.02) suggests that pvmrp1 had evolved under a purifying selection. Due to geographical differences, genetic differentiation levels of pvmrp1 in different regions were different to some extent. Overall, this study provides a new idea for finding CQR molecular monitoring of P. vivax and provides more sequences of pvmrp1 in Asia for subsequent research. However, further validation is still needed through laboratory and epidemiological field studies of P. vivax samples from more regions. [ABSTRACT FROM AUTHOR]

CaliPopGen is a database of population genetic data for native and naturalized eukaryotic species in California, USA. It summarizes the published literature (1985–2020) for 5,453 unique populations with genetic data from more than 187,394 individuals and 448 species (513 species plus subspecies) across molecular markers including allozymes, RFLPs, mtDNA, microsatellites, nDNA, and SNPs. Terrestrial habitats accounted for the majority (46.4%) of the genetic data. Taxonomic groups with the greatest representation were Magnoliophyta (20.31%), Insecta (13.4%), and Actinopterygii (12.85%). CaliPopGen also reports life-history data for most included species to enable analyses of the drivers of genetic diversity across the state. The large number of populations and wide taxonomic breadth will facilitate explorations of ecological patterns and processes across the varied geography of California. CaliPopGen covers all terrestrial and marine ecoregions of California and has a greater density of species and georeferenced populations than any previously published population genetic database. It is thus uniquely suited to inform conservation management at the regional and state levels across taxonomic groups. Measurement(s) genetic variation Technology Type(s) DNA sequencing Factor Type(s) Kingdom • Phylum • TaxonGroup • MarkerType • SampleSize • GeneTarget • NumMarkers • YearStart • YearEnd • PopName • LongitudeDD • LatitudeDD • CoordError • HabitatType • Lifespan • Fecundity • LifetimeReprodOutput • AgeSexMat • NumBreedingEvents • ReprodMode • BodyLength • AdultMass • CANativeStatus • CESAStatus • SSCStatus • ESAStatus • LifeCycle • AdultHeight • SelfCompatibility • MonoeciousDioecious • Asexual • PollinationMode • SeedDispMode • MassPerSeed • CAEndemicStatus Sample Characteristic - Organism eukaryota Sample Characteristic - Location California [ABSTRACT FROM AUTHOR]

The article seeks to assess whether constitutional protections for genetic data could be judicially crafted by adapting the Fourth Amendment expectation of privacy or extending the larger constitutional right to privacy to the realm of genetic data. It mentions assesses European privacy laws and state-based initiatives or viable alternatives to the present situation and a federal law should be crafted that protects consumer's genetic privacy under Fourth Amendment.

This study represents a first reference database of genetic diversity of macroinvertebrates for a barcoding marker for Lake Maggiore, focusing on the two dominant groups of the littoral benthic fauna (chironomids and oligochaetes), commonly used for biological monitoring of freshwater lakes. Sediment samples were sorted at the stereomicroscope and single animals were cut in two pieces, one piece to be used for morphological identification and one piece for DNA extraction. This study allowed us to collect and identify 427 organisms: 309 oligochaetes belonging to 27 identifiable taxa and 118 chironomid larvae belonging to 26 identifiable taxa. Four families of oligochaetes: Naididae, Lumbricidae, Lumbriculidae, and Enchytraeidae and five subfamilies of Chironomidae: Chironominae, Tanypodinae, Orthocladiinae, Diamesinae, and Prodiamesinae were found. The extraction and amplification of the DNA covered a total of 10 oligochaete taxa. For 7 of them (Ophidonais serpentina, Uncinais uncinata, Vejdovskyella intermedia, Psammoryctides barbatus, Limnodrilus hoffmeisteri, Tubifex tubifex, and Bothrioneurum vejdovskyanum), we found other sequences in GenBank to compare genetic similarities with available data. For the other taxa (Lumbriculidae, and Enchytraeidae, and Nais sp.) no best hits were found in GenBank. The extraction and amplification of the DNA covered a total of 21 chironomid taxa. For ten species (Cladotanytarsus mancus, Cladotanytarsus atridorsum, Polypedilum scalaenum, Polypedilum nubeculosum, Benthalia carbonaria, Phaenopsectra flavipes, Clinotanypus nervosus, Paracladopelma laminatum, Cryptochironomus rostratus and Parakiefferiella finnmarkica) sequences were available in GenBank to compare genetic similarities. For the other taxa (Cryptochironomus sp., Demicryptochironomus vulneratus, Chironomus sp., Stictochironomus sp., Orthocladius sp., Cricotopus sp., Eukiefferiella sp., Procladius sp., Diamesa sp., Potthastia sp., and Monodiamesa bathyphila) no best hits were found in GenBank. For chironomids, DNA taxonomy revealed the existence of several species complexes. Covering more populations and more genetic markers for those taxa within a rationale of integrative taxonomy could solve the taxonomic problems and provide a reliable description of diversity. [ABSTRACT FROM AUTHOR]

Simple Summary: The aim of our study was to address the research gap in the molecular taxonomy of Sri Lankan bats. The accurate identification of animals plays a major role in observing them in their natural environments and hence understanding possible disease-transmitting pathways from animals to humans. Being a tropical country, Sri Lanka has a high density of animals. There are 30 different species of bats described in Sri Lanka. Until now, the animals have been identified by observing their physical features. However, the visual identification of animals is not accurate because closely related animal groups may show similar physical features. During our study, we accurately differentiated five bat groups living in one of the largest caves in Sri Lanka by using a more sophisticated laboratory technique. Using molecular techniques, we were able to provide more accurate results than by the visual identification of the bats. The results from our study are stored in the NCBI database as a baseline for a repository of Sri Lankan bats. With the new sequence data provided here, we filled the gap concerning the molecular taxonomy of bat species of the entire region and we contributed to the future conservation and systematic studies of these mammals. This is the first report on the molecular identification and phylogeny of the Rousettus leschenaultii Desmarest, 1810, Rhinolophus rouxii Temminck, 1835, Hipposideros speoris Schneider, 1800, Hipposideros lankadiva Kelaart, 1850, and Miniopterus fuliginosus Kuhl, 1817, bat species in Sri Lanka, inferred from analyses by mitochondrially encoded cytochrome b gene sequences. Recent research has indicated that bats show enormous cryptic genetic diversity. Moreover, even within the same species, the acoustic properties of echolocation calls and morphological features such as fur color could vary in different populations. Therefore, we have used molecular taxonomy for the accurate identification of five bat species recorded in one of the largest cave populations in Sri Lanka. The bats were caught using a hand net, and saliva samples were collected non-invasively from each bat by using a sterile oral swab. Nucleic acids were extracted from the oral swab samples, and mitochondrial DNA was amplified by using primers targeting the mitochondrially encoded cytochrome b gene. This study reports the first molecular evidence for the identification of five bat species in Sri Lanka. Our findings will contribute to future conservation and systematic studies of bats in Sri Lanka. This study will also provide the basis for a genetic database of Sri Lankan bats which will contribute significantly to the investigation of potentially zoonotic bat viruses. [ABSTRACT FROM AUTHOR]

The goal of this research was to establish a new genetic database of faba bean SSR primers and categories them according to their target genes and biological processes. Twenty-seven SSR PCR primers were synthesized to 12 Egyptian faba bean genotypes. Approximately 11 SSR provided one to two PCR bands, whereas other SSRs provided only one sharp band with polymorphic band size. There were 13 polymorphic primers. The polymorphism information content was 0.3, which implied moderate informativeness. The principle component analysis (PCA) was used to infer the genetic structure of the studied faba accessions using the data of applied SSR primers. The PCA analysis revealed 24.3% and 22.1% explanation of the genetic variation on both axes. The heatmap conducted using SSR data and clustered the faba beans into three groups, where Noubaria 1, Noubaria 2, Sakha 1 and Giza 3 were differentiated by their high genetic variation compared to other accessions. [ABSTRACT FROM AUTHOR]

We report five cases of tri-allelic patterns observed during establishment of genetic fingerprint database for 354 individual from Iraqi security forces volunteers. These individuals had been typed by using the PowerPlex® Fusion System for the following 22 autosomal STRs: D3S1358, D1S1656, D2S441, D10S1248, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, TH01, vWA, D21S11, D7S820, D5S818, TPOX, D8S1179, D12S391, D19S433, FGA and D22S1045. All five tri-allelic patterns were observed at the Penta D locus and had the genotype 9/11/13, 9.4/13/14, 9/10/11, 7/9/11 and 9/10/14 respectively. All cases belonged to the Type 2 tri-allelic pattern; involve a fairly balanced set of three alleles. Five cases in 354 typed individuals is a frequency for tri-allelic patterns in autosomal STRs of 1.41%. [ABSTRACT FROM AUTHOR]

Significant disparities in the clinical usefulness of genomic information across diverse groups are due to underrepresentation in genetic databases and inequitable access to genetic services. Remedying disparities is immediately needed to ensure that genomic medicine is more equitable but will take a long-term commitment and active engagement of diverse communities. [ABSTRACT FROM AUTHOR]

Austria is inhabited by more than 80 species of native and non-native freshwater fishes. Despite considerable knowledge about Austrian fish species, the latest Red List of threatened species dates back 15 years and a systematic genetic inventory of Austria's fish species does not exist. To fulfill this deficit, we employed DNA barcoding to generate an up-to-date and comprehensive genetic reference database for Austrian fish species. In total, 639 newly generated cytochrome c oxidase subunit 1 (COI) sequences were added to the 377 existing records from the BOLD data base, to compile a near complete reference dataset. Standard sequence similarity analyses resulted in 83 distinct clusters almost perfectly reflecting the expected number of species in Austria. Mean intraspecific distances of 0.22% were significantly lower than distances to closest relatives, resulting in a pronounced barcoding gap and unique Barcode Index Numbers (BINs) for most of the species. Four cases of BIN sharing were detected, pointing to hybridization and/or recent divergence, whereas in Phoxinus spp., Gobio spp. and Barbatula barbatula intraspecific splits, multiple BINs and consequently cryptic diversity were observed. The overall high identification success and clear genetic separation of most of the species confirms the applicability and accuracy of genetic methods for bio-surveillance. Furthermore, the new DNA barcoding data pinpoints cases of taxonomic uncertainty, which need to be addressed in further detail, to more precisely assort genetic lineages and their local distribution ranges in a new National Red-List. [ABSTRACT FROM AUTHOR]

Through the network pharmacology thought, the action target of the active ingredients of Drynariae Rhizoma was predicted, and the mapping was combined with the related targets of ONFH, and the key nodes of interaction were identified for enrichment analysis, so as to comprehensively explore the pharmacological mechanism of Drynariae Rhizoma against ONFH. The main active ingredients of Drynariae Rhizoma were screened based on pharmacokinetic characteristics in pharmacokinetic database and analysis platform of TCM system (TCMSP). We used the organic small molecule bioactivity database (PubChem) and Swiss target prediction database to predict related targets based on 2D or 3D structural similarity and then mined the known ONFH therapeutic targets through the Human Mendelian Genetic Database (OMIM) and Pubmed texts. Combined with the predicted targets, String database was imported to construct the OP target interaction network diagram of bone fracture therapy. CytoNCA software was used to topology the key nodes of interaction according to relevant node parameters, and String was imported again to construct the protein interaction network diagram. Finally, biological functions and metabolic pathways of key nodes were analyzed through DAVID database. It was revealed that Drynariae Rhizoma may regulate stem cells, osteoblasts, osteoclasts, and immune cells through multiple pathways, including proliferation, differentiation, immunity, and oxidative stress. Conclusion: Pharmacological studies based on network indicate that Drynariae Rhizoma may participate in the regulation of several major signaling pathways through direct or indirect action targets and affect the proliferation and differentiation of multiple types of cells, thus playing an anti-ONFH role, which provides a scientific basis for explaining the material basis and mechanism of its anti- ONFH. [ABSTRACT FROM AUTHOR]

Pantothenate kinase associated neurodegeneration (PKAN) is a severe autosomal recessive rare disease and characterized by iron accumulation in the basal ganglia. To investigate the pathogenesis of this disease in two sibling patients with PANK in a Chinese family, whole-exome variant detection and functional analysis were performed. Clinical and radiographic investigations were performed in the two brother patients. Whole exome sequencing (WES) was used in mutation detection, and the mutations were confirmed by Sanger sequencing. A longevity cohort genetic database was applied as Chinese urban controls. Bioinformatic analysis was performed to predict the pathogenicity. Compound heterozygous mutations of PANK2 were detected in two sibling brothers with PKAN in a Chinese family: c.510_522del (p.A170fs) and c.1319G > C (p.R440P) in the transcript NM_153638. PANK2: c.510_522del (p.A170fs) was absent in public data and the Chinese urban controls. Bioinformatics analysis showed that the above two variants were pathogenicity. We identified a rare compound heterozygous combination of PANK2 mutations found in a Chinese family in which two sibling brothers suffered from PKAN. PANK2 c.510_522del (p.A170fs) was the first reported to be a PKAN pathogenic variant. [ABSTRACT FROM AUTHOR]

The reefs at Palmyra Atoll, a small outlying atoll in the equatorial Pacific, have been undergoing a phase shift from scleractinian corals to a corallimorph-dominated benthos. It has been unclear whether there has been cryptic speciation or morphological plasticity leading to different ecotypes of Rhodactis howesii. Here, we use mitochondrial genomic analysis to assess species validation and underlying cause of morphological variation across the atoll. We mapped sequenced reads to Rhodactis indosinensis, R. howesii's closest recorded genomic taxon. In addition to one individual from American Sāmoa, we assessed phylogenetic relationships of published corallimorph genomes with those from Palmyra. There was no identifiable population structure within Palmyra, and available dinoflagellate symbiont communities were consistent among the sequenced individuals. There were noticeable differences in symbiont communities between Palmyra and American Sāmoa individuals, as well as six fixed nucleotide differences. We conclude that the lack of taxonomically validated genetic reference material together with vague species descriptions, morphological plasticity and overlap among morphological characters, combine to raise doubts about the validity of the currently accepted species name, R. howesii. Comparison of our results to all currently available genetic data for corallimorpharians suggests that the species at Palmyra is most closely related to an unidentified species of Rhodactis from Okinawa. However, taxonomically confirmed R. howesii is absent from genetic databases, so no firm conclusions about species identification can yet be drawn. It seems clear that this group is in need of additional taxonomic work and a broad phylogenetic survey of taxa with geographic distribution would further our understanding of marine biodiversity, conservation, and invasion dynamics of this understudied group. [ABSTRACT FROM AUTHOR]

With the development of society and economy, the rural financial institution system mainly includes cooperatives and political and commercial rural financial institutions, and they are supplemented by agricultural insurance, guarantee, securities and other nonfinancial organizations to improve their own functions. Rural credit cooperatives have higher investment and operation risks than other financial institutions. New-type rural financial institutions are more sensitive to the market environment, asset quality and profitability, and risk-taking ability. Internal and external risks continue to accumulate, and their potential is low. These risks pose serious obstacles to the development and growth of financial institutions such as rural banks and microfinance companies, and pose major challenges to the security and stability of rural areas and agriculture. Using database and genetic algorithm to study rural credit risk, profitability, and liquidity, in order to track the impact of each explanatory variable in the system on the explained variable, the impulse response function is used to analyze the impact of nonperforming loan ratio on asset profitability. The data are all close to 0, indicating that the influence between the two is more obvious. The intelligent decision-making system support system evaluates the market risk, credit risk, liquidity risk, and risk management and risk acceptance of rural financial institutions and explores effective countermeasures for their sustainable development. [ABSTRACT FROM AUTHOR]

Freshwaters are a very valuable resource in arid areas, such as Mediterranean countries. Freshwater systems are vulnerable ecological habitats, significantly disturbed globally and especially in arid areas. The Sea of Galilee is the largest surface freshwater body in the Middle East. It is an isolated habitat supporting unique fish populations, including endemic species and populations on the edge of their distribution range. Using the Sea of Galilee for water supply, fishing and recreation has been placing pressure on these fish populations. Therefore, efficient monitoring and effective actions can make a difference in the conservation of these unique fish populations. To set a baseline and develop molecular tools to do so, in this study, DNA barcoding was used to establish a database of molecular species identification based on sequences of Cytochrome C Oxidase subunit I gene. DNA barcodes for 22 species were obtained and deposited in Barcode of Life Database. Among these, 12 barcodes for 10 species were new to the database and different from those already there. Barcode sequences were queried against the database and similar barcodes from the same and closely related species were obtained. Disagreements between morphological and molecular species identification were identified for five species, which were further studied by phylogenetic and genetic distances analyses. These analyses suggested the Sea of Galilee contained hybrid fish of some species and other species for which the species definition should be reconsidered. Notably, the cyprinid fish defined as Garra rufa, should be considered as Garra jordanica. Taken together, along with data supporting reconsideration of species definition, this study sets the basis for further using molecular tools for monitoring fish populations, understanding their ecology, and effectively managing their conservation in this unique and important habitat and in the region. [ABSTRACT FROM AUTHOR]

Mutant-specific inhibitors of KRASG12C, such as AMG510 (sotorasib) and MRTX849 (adagrasib), offer the unprecedented opportunity to inhibit KRAS, the most frequently mutated and heretofore undruggable oncoprotein. While clinical data are still limited, on-target mutations in KRASG12C at position 12 and other sites are emerging as major drivers of clinical relapse. We identified additional mutations in KRASG12C that impact inhibitor sensitivity through a saturation mutagenesis screen in the KRASG12C NCIH358 non–small-cell lung cancer (NSCLC) cell line. We also identified individuals in population genetic databases harboring these resistance mutations in their germline and in tumors, including a subset that co-occur with KRASG12C, indicating that these mutations may preexist in patients treated with KRASG12C inhibitors. Notably, through structural modeling, we found that one such mutation (R68L) interferes with the critical protein–drug interface, conferring resistance to both inhibitors. Finally, we uncovered a mutant (S17E) that demonstrated a strong sensitizing phenotype to both inhibitors. Functional studies suggest that S17E sensitizes KRASG12C cells to KRASG12C inhibition by impacting signaling through PI3K/AKT/mTOR but not the MAPK signaling pathway. Our studies highlight the utility of unbiased mutation profiling to understand the functional consequences of all variants of a disease-causing genetic mutant and predict acquired resistant mutations in the targeted therapeutics. [ABSTRACT FROM AUTHOR]

Although Slavic populations account for over 4.5% of world inhabitants, no centralised, open-source reference database of genetic variation of any Slavic population exists to date. Such data are crucial for clinical genetics, biomedical research, as well as archeological and historical studies. The Polish population, which is homogenous and sedentary in its nature but influenced by many migrations of the past, is unique and could serve as a genetic reference for the Slavic nations. In this study, we analysed whole genomes of 1222 Poles to identify and genotype a wide spectrum of genomic variation, such as small and structural variants, runs of homozygosity, mitochondrial haplogroups, and de novo variants. Common variant analyses showed that the Polish cohort is highly homogenous and shares ancestry with other European populations. In rare variant analyses, we identified 32 autosomal-recessive genes with significantly different frequencies of pathogenic alleles in the Polish population as compared to the non-Finish Europeans, including C2, TGM5, NUP93, C19orf12, and PROP1. The allele frequencies for small and structural variants, calculated for 1076 unrelated individuals, are released publicly as The Thousand Polish Genomes database, and will contribute to the worldwide genomic resources available to researchers and clinicians. [ABSTRACT FROM AUTHOR]

Primary ciliary dyskinesia (PCD) is a motile ciliopathy characterised by otosinopulmonary infections. Inheritance is commonly autosomal recessive, with extensive locus and allelic heterogeneity. The prevalence is uncertain. Most genetic studies have been done in North America or Europe. The aim of the study was to estimate the worldwide prevalence and ethnic heterogeneity of PCD. We calculated the allele frequency of disease-causing variants in 29 PCD genes associated with autosomal recessive inheritance in 182 681 unique individuals to estimate the global prevalence of PCD in seven ethnicities (African or African American, Latino, Ashkenazi Jewish, Finnish, non-Finnish European, east Asian, and south Asian). We began by aggregating variants that had been interpreted by Invitae, San Francisco, CA, USA, a genetics laboratory with PCD expertise. We then determined the allele frequency of each variant (pathogenic, likely pathogenic, or variant of uncertain significance [VUS]) in the Genome Aggregation Database (gnomAD), a publicly available next-generation sequencing database that aggregates exome and genome sequencing information from a wide variety of large-scale projects and stratifies allele counts by ethnicity. Using the Hardy–Weinberg equilibrium equation, we were able to calculate a lower-end prevalence of PCD for each ethnicity by including only pathogenic and likely pathogenic variants; and upper-end prevalence by also including VUS. This approach was similar to previous work on Li-Fraumeni (TP53 variants) prevalence. We were not diagnosing PCD, but rather estimating prevalence based on known variants. The overall minimum global prevalence of PCD is calculated to be at least one in 7554 individuals, although this is likely to be an underestimate because some variants currently classified as VUS might be disease-causing and some pathogenic variants might not be detected by our methods. In the overall cohort, Invitae data could be included for variants without gnomAD data for a primary ethnicity. When using only gnomAD allele frequencies to calculate prevalence in individual ethnicities, the estimated prevalence of PCD was lower in each ethnicity compared with the overall cohort. This is because the overall cohort includes additional data from the Invitae database such as copy number variants and other variants not present in gnomAD. With gnomAD we found the expected PCD frequency to be higher in individuals of African ancestry than in most other populations (excluding VUS: 1 in 9906 in African or African American vs 1 in 10 388 in non-Finnish European vs 1 in 14 606 in east Asian vs 1 in 16 309 in Latino; including VUS: 1 in 106 in African or African American vs 1 in 178 in non-Finnish European vs 1 in 196 in Latino vs 1 in 188 in east Asian). In addition, we found that the top 5 genes most commonly implicated in PCD differed across ethnic ancestries and contrasted commonly published findings. PCD appears to be more common than has been recognised, particularly in individuals of African ancestry. We identified gene distributions that differ from those in previous European and North American studies. These results could have an international impact on case identification. Our analytic approach can be expanded as more PCD loci are identified, and could be adapted to study the prevalence of other inherited diseases. None. [ABSTRACT FROM AUTHOR]

Osteogenesis Imperfecta (OI) is a complex disease caused by genetic alterations in production of collagen type I, and collagen-related proteins. Bone fragility is the most common patient issue, but extraskeletal complications also present an adverse factor in the quality of life and prognosis of patients with OI. However, still little is known about the morbidity and mortality of these patients. The objective of this paper is to determine and describe to what extent OI impacts patients' life in terms of hospitalization and complications describing the incidence and prevalence of the Dutch cohort of OI patients and the characteristics of their hospital admissions. Information regarding OI patients and their hospital admission was extracted from the Statistics Netherlands Database and matched to the OI Genetics Database of Amsterdam UMC. Hospital admission data was available for 674 OI patients. This OI nationwide registry study shows that the life expectancy of OI patients is adversely affected by the disease. The median annual incidence risk of OI between 1992 and 2019 was 6.5 per 100,000 live births. Furthermore, patients with OI had a 2.9 times higher hospitalization rate compared to the general Dutch population. The highest hospitalization rate ratio of 8.4 was reported in the patient group between 0 and 19 years old. OI type and severity had impact on extraskeletal manifestations, which play a key role in the numerous hospital admissions. More awareness about the impact of OI on patients' life is needed to improve and implement prevention and follow-up guidelines. [ABSTRACT FROM AUTHOR]

Keywords: biobank data analysis; GWAS; integrative analysis; personalized medicine; statistical genetics EN biobank data analysis GWAS integrative analysis personalized medicine statistical genetics 1 4 4 04/19/22 20220414 NES 220414 Global health care systems are severely strained under the burden of aging populations, which are prone to enhanced incidence of chronic diseases. Association Test Using Copy Number Profile Curves (CONCUR) Enhances Power in Rare Copy Number Variant Analysis. Single nucleotide polymorphism (SNP) genotyping arrays allow genome-wide association studies (GWASs) and polygenic risk score (PRS) development ([15]) or phenome-wide association studies (PheWASs) ([17]). GWAS, integrative analysis, personalized medicine, biobank data analysis, statistical genetics. [Extracted from the article]

The Psyra Walker, 1860, is a typical Sino-Himalayan genus of the subfamily Ennominae, currently known by 18 species/4 subspecies globally and 9 species from India. This study aims to revise the taxonomy and ecology of Indian Psyra by providing a morphology-based diagnostic key, highlighting their altitudinal, habitat and seasonal preferences, and modelling their distribution based on current and future climatic scenarios. Here, we describe a new species, P. variabilissp. nov. and document 4 species and 1 subspecies as new to India, viz. P. gracilis, P. szetschwana, P. dsagara, P. falcipennis and P. debilis debilis, thus updating the global species count to 19 with 14 species/1 subspecies from India. We also submitted partial mitochondrial COI sequences of P. crypta, P. similaria, P. spurcataria and P. gracilis as novel to the global genetic database and calculated the overall genetic divergence was 5.17% within the genus, suggesting strong monophyly. Being a typical montane genus, most of the species of Psyra were active within 2000–2280 m altitude, 10.55–15.7°C annual mean temperature, 1200–2300 mm annual precipitation and 168–179 NDVI. Psyra species were predominant in wet temperate, mixed coniferous and moist temperate deciduous forests, their abundance and richness being at peak during post-monsoon months of October–November. The major bioclimatic variables influencing the overall distribution of the genus were mean temperature of warmest quarter, temperature seasonality and precipitation of coldest/driest quarter. While two of the modelled species were predicted to lose area occupancy under future climatic scenarios, the narrow-specialist, Trans-Himalayan species P. debilis debilis was projected to gain up to 75% additional area in the years 2041–60. The results of this study will be helpful to identify sites with maximum area loss projection in ecologically fragile Indian Himalaya and initiating conservation management for such climatically vulnerable insect species groups. [ABSTRACT FROM AUTHOR]

With the rapid development of modern science technology and Internet technology, the establishment of a unified and standardized bibliographic summary database to realize the exchange and resource sharing of ancient Chinese medicine bibliography, is the inevitable trend of ancient Chinese medicine bibliography digital service. Firstly, this paper formulates the bibliographic metadata specification of traditional Chinese medicine ancient books (TCMAB), extracts each cataloging file into an XML document in line with the bibliographic metadata specification of TCMAB. Secondly, this paper realizes the unified description of ancient book resources in the database system of TCMAB, uses the native XML database eXist to store and manage the XML documents of all traditional Chinese medicine ancient book resources, and integrates the multimedia data with XML data. Finally, genetic algorithm and BP neural network are used for knowledge mining and discovery, the overall model design of TCMAB bibliographic abstracts database system is proposed based on the construction process of knowledge map. The system platform adopts B/S mode, eXist database management system, PowerSSP streaming media and video server for audio video processing. [ABSTRACT FROM AUTHOR]

The last 2 decades have seen the collection of increasingly rich bodies of genetic data, opening up a multitude of new research avenues. These data have made undeniable contributions to health research, but have they equally contributed to the population sciences? This article critically surveys the assumptions underlying sociogenomics, a new field that explores the links between genetics and human behaviour. While sociogenomics as such is new, these links have long been debated, as seen for example in the writings of Alfred Jacquard and Daniel Courgeau. [ABSTRACT FROM AUTHOR]

The aim of the paper is to present the results of the VNTR gene polymorphism genetic variants molecular typing for endothelial nitric oxide synthase (eNOS) in human population of Tuzla Canton. Based on the analysis of the distribution of eNOS gene genotypes in the total sample of respondents, the highest frequency was recorded for the (b/b) genotype, which was 73.0%. For the heterozygous (a/b) genotype of the eNOS gene, a frequency of 24.0% was determined, and a frequency of 3.0% was recorded for the (a/a) genotype. The research resulted in a database of local and global significance, namely, the incorporation of these data into the existing regional and European genetic database. [ABSTRACT FROM AUTHOR]

BACKGROUND & OBJECTIVE: Leukocyte adhesion deficiency (LAD1) is an autosomal recessive type of inherited disorder caused by total or partial deficiency of CD18 expression. LAD1 is characterized by recurrent bacterial and fungal infections, in some cases delayed umbilical cord separation, delayed wound healing due to blockade in leukocyte migration to site of inflammation and infection. The present study involves genetic analysis of two unrelated families suffering from LAD1. METHODOLOGY: In the present study, two separated and unrelated Pakistani families are included suffering from Leukocyte Adhesion Deficiency type -1 (PAD1). After detailed clinical evaluation, whole blood samples were collected from patients, parents and available healthy siblings. Genomic DNA was extracted from all the blood samples, and using a specific primer all the coding ITGB2 gene exons were PCR amplified. RESULTS: The amplified products were sanger sequenced. DNA sequencing analysis revealed a nonsense mutation c.186C > A, p.(Cys62*) in exon four and a missense mutation c.382G>T, p.(Asp128Tyr) in exon five of the gene. The mutation is segregating in autosomal recessive pattern in the family. CONCLUSION: Recurrent mutations on a specific locus (gene) changes the allele frequency from a healthy allele to a disease allele and hence play role in new genotype. This research study demonstrates the allelic heterogeneity of the ITGB2 gene in Pakistani patients diagnosed with LAD1. The research findings in the present study suggest that every population should develop national registry of patients suffering from primary immune deficiencies and a mutation database for rare genetic disorders. This will facilitate early diagnosis and genetic counseling to the patient family. [ABSTRACT FROM AUTHOR]