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Genetic testing, including whole genome, whole exome, and other next‐generation sequencing technologies, has evolved vastly in the past decade. With this, the number of identified genes and genetic variants is constantly increasing. Although a variety of databases and online tools exist that summarize, categorize, and classify genes, a clear guideline of which information is needed when reporting a gene and what to do when identifying a new gene is lacking. This includes the correct nomenclature, descriptive information about genetic loci and genetic variation, aliases, and correlated phenotypes. This tutorial is meant to serve as an introduction to reporting genes in a paper and provides an overview of available databases and tools to obtain all necessary information on the genes of interest. [ABSTRACT FROM AUTHOR]

In a nuclear or radiological incident, first responders must quickly and accurately measure radiation exposure among civilians as medical countermeasures are radiation dose-dependent and time-sensitive. Although several approaches have been explored to measure absorbed radiation dose, there is an important need to develop point-of-care (POC) bioassay devices that can be used immediately to triage thousands of individuals potentially exposed to radiation. Here we present a proof-of-concept study showing the use of a paper-based vertical flow immunoassay (VFI) to detect radiation dosimetry genes. Using labeled primers during amplification and a multiplex membrane, our results showed that the nucleic acid VFI can simultaneously detect two biodosimetry genes, CDKN1A and DDB2, as well as one housekeeping gene MRPS5. The assay demonstrated good linearity and precision with an inter- and intra-assay coefficient of variance <20% and <10%, respectively. Moreover, the assay showed its ability to discriminate non-irradiated controls (0 Gy) from irradiated samples (1 + 2 Gy) with an overall sensitivity of 62.5% and specificity of 100% (AUC = 0.8672, 95% CI: 0.723–1.000; p = 0.004). Interestingly, the gene combination also showed a dose-dependent response for 0, 1, and 2 Gy, similar to data obtained by real-time PCR benchmark. These preliminary results suggest that a VFI platform can be used to detect simultaneously multiple genes that can be then quantified, thus offering a new approach for a POC biodosimetry assay that could be rapidly deployed on-site to test a large population and help triage and medical management after radiological event. [ABSTRACT FROM AUTHOR]

R.A. Fisher's 1922 paper On the dominance ratio has a strong claim to be the foundation paper for modern population genetics. It greatly influenced subsequent work by Haldane and Wright, and contributed 3 major innovations to the study of evolution at the genetic level. First, the introduction of a general model of selection at a single locus, which showed how variability could be maintained by heterozygote advantage. Second, the use of the branching process approach to show that a beneficial mutation has a substantial chance of loss from the population, even when the population size is extremely large. Third, the invention of the concept of a probability distribution of allele frequency, caused by random sampling of allele frequencies due to finite population size, and the first use of a diffusion equation to investigate the properties of such a distribution. Although Fisher was motivated by an inference that later turned out to lack strong empirical support (a substantial contribution of dominance to quantitative trait variability), and his use of a diffusion equation was marred by a technical mistake, the paper introduced concepts and methods that pervade much subsequent work in population genetics. [ABSTRACT FROM AUTHOR]

Objectives: This study aimed to elucidate the connection between osteoclastic forkhead transcription factor O1 (FoxO1) and periodontitis and explore the underlying mechanism by which FoxO1 knockdown regulates osteoclast formation. Materials and Methods: A conventional ligature‐induced periodontitis model was constructed to reveal the alterations in the proportion of osteoclastic FoxO1 in periodontitis via immunofluorescence staining. Additionally, RNA sequencing (RNA‐seq) was performed to explore the underlying mechanisms of FoxO1 knockdown‐mediated osteoclastogenesis, followed by western blotting, quantitative polymerase chain reaction, and enzyme‐linked immunosorbent assay. Results: FoxO1+ osteoclasts were enriched in the alveolar bone in experimental periodontitis. Moreover, FoxO1 knockdown led to impaired osteoclastogenesis with low expression of osteoclast differentiation‐related genes, accompanied by an insufficient osteoclast maturation phenotype. Mechanistically, RNA‐seq revealed that the nuclear factor kappa B (NF‐κB) and nucleotide‐binding oligomerization domain‐like receptor family pyrin domain containing 3 (NLRP3) inflammasome signaling pathways were inhibited in FoxO1‐knockdown osteoclasts. Consistent with this, MCC950, an effective inhibitor of the NLRP3 inflammasome, substantially attenuated osteoclast formation. Conclusions: FoxO1 knockdown contributed to the inhibition of osteoclastogenesis by effectively suppressing NF‐κB signaling and NLRP3 inflammasome activation. This prospective study reveals the role of FoxO1 in mediating osteoclastogenesis and provides a viable therapeutic target for periodontitis treatment. [ABSTRACT FROM AUTHOR]

Sepsis, a disease caused by severe infection, has a high mortality rate. At present, there is a lack of reliable algorithmic models for biomarker mining and diagnostic model construction for sepsis. Programmed cell death (PCD) has been shown to play a vital role in disease occurrence and progression, and different PCD-related genes have the potential to be targeted for the treatment of sepsis. In this paper, we analyzed PCD-related genes in sepsis. Implicated PCD processes include apoptosis, necroptosis, ferroptosis, pyroptosis, netotic cell death, entotic cell death, lysosome-dependent cell death, parthanatos, autophagy-dependent cell death, oxeiptosis, and alkaliptosis. We screened for diagnostic-related genes and constructed models for diagnosing sepsis using multiple machine-learning models. In addition, the immune landscape of sepsis was analyzed based on the diagnosis-related genes that were obtained. In this paper, 10 diagnosis-related genes were screened for using machine learning algorithms, and diagnostic models were constructed. The diagnostic model was validated in the internal and external test sets, and the Area Under Curve (AUC) reached 0.7951 in the internal test set and 0.9627 in the external test set. Furthermore, we verified the diagnostic gene via a qPCR experiment. The diagnostic-related genes and diagnostic genes obtained in this paper can be utilized as a reference for clinical sepsis diagnosis. The results of this study can act as a reference for the clinical diagnosis of sepsis and for target discovery for potential therapeutic drugs. [ABSTRACT FROM AUTHOR]

Background: Post-stroke upper limb (UL) motor improvement is associated with adaptive neuroplasticity and motor learning. Both intervention-related (including provision of intensive, variable, and task-specific practice) and individual-specific factors (including the presence of genetic polymorphisms) influence improvement. In individuals with stroke, most commonly, polymorphisms are found in Brain Derived Neurotrophic Factor (BDNF), Apolipoprotein (APOE) and Catechol-O-Methyltransferase (COMT). These involve a replacement of cystine by arginine (APOEε4) or valines by 1 or 2 methionines (BDNF:val66met, met66met; COMT:val158met; met158met). However, the implications of these polymorphisms on post-stroke UL motor improvement specifically have not yet been elucidated. Objective: Examine the influence of genetic polymorphism on post-stroke UL motor improvement. Design: Systematic Review and Meta-Analysis. Methods: We conducted a systematic search of the literature published in English language. The modified Downs and Black checklist helped assess study quality. We compared change in UL motor impairment and activity scores between individuals with and without the polymorphisms. Meta-analyses helped assess change in motor impairment (Fugl Meyer Assessment) scores based upon a minimum of 2 studies/time point. Effect sizes (ES) were quantified based upon the Rehabilitation Treatment Specification System as follows: small (0.08-0.18), medium (0.19 -0.40) and large (≥0.41). Results: We retrieved 10 (4 good and 6 fair quality) studies. Compared to those with BDNF val66met and met66met polymorphism, meta-analyses revealed lower motor impairment (large ES) in those without the polymorphism at intervention completion (0.5, 95% CI: 0.11-0.88) and at retention (0.58, 95% CI:0.06-1.11). The presence of CoMT val158met or met158met polymorphism had similar results, with lower impairment (large ES ≥1.5) and higher activity scores (large ES ranging from 0.5-0.76) in those without the polymorphism. Presence of APOEε4 form did not influence UL motor improvement. Conclusion: Polymorphisms with the presence of 1 or 2 met alleles in BDNF and COMT negatively influence UL motor improvement. Registration: https://osf.io/wk9cf/. Plain language summary: This research paper focuses on the impact of variations in DNA sequence in certain genes on improvement seen in the arms in people who have had a stroke. In this study, we studied the role of 3 genes previously identified as having variations in DNA sequence. The authors searched published research articles from 2000 onwards and selected articles that satisfied certain criteria. We then checked the quality of the selected papers. Next, we combined common data from same tests used to examine motor improvement in the arms to check if there was an overall effect. A total of 10 papers were found. The selected articles were either good or moderate in quality. Variations in DNA structure in 2 out of the 3 genes studied affected the ability to improve the use of the arms in daily life after a stroke. Such information can have important implications in the extent of recovery that is possible after a stroke. It can also be helpful to decide the best rehabilitation options that can be offered to help maximize their ability to use the arms after a stroke. [ABSTRACT FROM AUTHOR]

Background: Lung cancer is one of the cancers with the highest mortality rate in China. With the rapid development of high-throughput sequencing technology and the research and application of deep learning methods in recent years, deep neural networks based on gene expression have become a hot research direction in lung cancer diagnosis in recent years, which provide an effective way of early diagnosis for lung cancer. Thus, building a deep neural network model is of great significance for the early diagnosis of lung cancer. However, the main challenges in mining gene expression datasets are the curse of dimensionality and imbalanced data. The existing methods proposed by some researchers can't address the problems of high-dimensionality and imbalanced data, because of the overwhelming number of variables measured (genes) versus the small number of samples, which result in poor performance in early diagnosis for lung cancer. Method: Given the disadvantages of gene expression data sets with small datasets, high-dimensionality and imbalanced data, this paper proposes a gene selection method based on KL divergence, which selects some genes with higher KL divergence as model features. Then build a deep neural network model using Focal Loss as loss function, at the same time, we use k-fold cross validation method to verify and select the best model, we set the value of k is five in this paper. Result: The deep learning model method based on KL divergence gene selection proposed in this paper has an AUC of 0.99 on the validation set. The generalization performance of model is high. Conclusion: The deep neural network model based on KL divergence gene selection proposed in this paper is proved to be an accurate and effective method for lung cancer prediction. [ABSTRACT FROM AUTHOR]

Hence, the Special Issue "Tree Genetics: Molecular and Functional Characterization of Genes" aimed to collect woody species gene-centered studies, with a special emphasis on functions related to trees' tolerance and resilience to global changes. Two research papers investigate the role of specific genes in the response of trees to pathogens: the function of thaumatin-like proteins (TLP), as most of them exhibit antifungal activity, was investigated in [[4]]; four TLP genes were isolated, identified, and characterized, and their role in defense response demonstrated in I Picea likiangensis i . Indeed, six papers focus on broadleaved trees and four on conifers, including economically relevant species for a plethora of different uses, but also rare/endangered species [[3]] and ecologically important trees [[4]]. [Extracted from the article]

Simple Summary: A bibliometric analysis was carried out to know the evolution of research on genes associated with meat tenderness, of interest for the development of selection programs. Since 1993, studies have been limited to a few researchers in high-income countries due to the costs associated with the techniques. The main findings showed that the scientific production had a discontinuous growth because science experienced a significant change since approximately 2010. Marker-assisted selection was widely used, evaluating mainly CAPN (calpain) and CAST (calpastatin) genes for their contribution to meat tenderness, especially in cattle. However, the effects are small; therefore, genomic selection was implemented by genotyping thousands of single nucleotide polymorphisms (SNPs) for further explanation of genetic variation. The results shown are important for scholars to identify emerging methodologies and gaps in the literature and to know who the prolific authors and institutions in the field for possible collaborations, etc., are. Tenderness is one of the main characteristics of meat because it determines its price and acceptability. This is the first bibliometric study on the trend of research on the role of genes in meat tenderness. A total of 175 original and English-language articles published up to 2021 were retrieved from Scopus. The bibliometric analysis was carried out with VOSviewer (version 1.6.18, Eck and Waltman, Leiden, Netherlands) and complemented with the Analyze search results service from Scopus. Erroneous and duplicate data were eliminated, and incomplete information was added to standardize the results. Scientific production was evaluated by means of quantity, quality and structure indicators. As a first glance, 8.816% of authors have published more than 50% of papers mainly related to genes encoding the calpain (CAPN)-calpastatin (CAST) system and single nucleotide polymorphisms (SNPs). Among other findings, a strong link was found between the contribution of the main countries (led by the United States with) and their institutions (led by the USDA Agricultural Research Service with) to their gross domestic product. Most studies on the topic are published in the Journal of Animal Science, and other journals with high impact according to the number of citations and different metrics. Finally, when evaluating the most cited articles, the occurrence and association of the main keywords, it was confirmed that research is focused on the role of CAPN and CAST genes and of SNPs in beef tenderness. The change in science was emphasized; although marker-assisted selection is still used, genes have an infinitesimal effect on complex traits. Therefore, since about 2010, new research groups adopted genomic selection to evaluate dense panels of SNPs and better explain genetic variation in meat tenderness. [ABSTRACT FROM AUTHOR]

To illustrate the results achieved by genes in premature ovarian insufficiency (POI) and collaborations in the field, and to explore key themes and future directions. Articles and reviews related to POI genes published between 1990 and 2022 were retrieved from the Web of Science core collection (WoSCC) for the total bibliometric analysis. Tools were analyzed for publication, country, institution, journal, authors, reference, keywords, subject categories, funding agencies, and research hotspots using a bibliometric online analysis platform, Bibliographic Co-occurrence Matrix Builder (BICOMB), CiteSpace V, and VOSviewer. A total of 2,232 papers were included in this study. Articles were published in 52 countries, with the United States publishing the most, followed by China. A total of 308 institutions contributed to relevant publications. Shandong University published the most papers. Qin Y's team published the most relevant papers. Human reproduction and fertility and sterility are the two journals with the most papers. X-chromosome abnormalities, transcription factor mutations, and FMR1 genes are the directions of more POI, and DNA repair is the keyword of the research frontier in recent years. This study summarizes the relevant literature on POI gene research for the first time and analyzes the current hotspots and future trends in this field. The findings can further reveal the etiology, diagnosis, and treatment of POI, which is beneficial for researchers to grasp the genetic dynamics of POI women. [ABSTRACT FROM AUTHOR]

Cluster analysis is a principal approach to discover unknown tumor subtypes. Innovative and effective cluster analysis methods are of great significance for tumor diagnosis and malignant tumor treatment. Existing studies on the cluster analysis of tumor gene data generally have defects in aspects such as unsatisfactory performance in clustering highdimensional and high-noise data, and insufficient accuracy in selecting cluster centers. To overcome these defects, this paper performed cluster analysis on tumor gene data based on an improved Density peaks clustering (DPC) algorithm. At first, this paper elaborated on the composition and storage format of tumor tissue samples used in the experiment, gave the tumor gene expression profile data in the matrix format, and introduced the preprocessing process of gene expression profile data. Then, this paper carried out feature selection of tumor gene expression profile data. At last, this paper innovatively divided the target gene density into two parts of K-nearest neighbor local density and neighborhood density, thereby completing the improvement of conventional DPC algorithm and expanding its application scenarios. Combining with experiment, the clustering results of the algorithm before and after introducing the idea of Approximate Nearest Neighbor (ANN) were given, which had verified the effectiveness of the algorithm proposed in this paper. [ABSTRACT FROM AUTHOR]

This document is a publisher's note regarding an issue with the authorship of a paper titled "Identification and characterization of GRIM-1, a cell-death-associated gene product." The journal received a complaint from Jonathan D'Cunha, who stated that he did not consent to or was contacted about the publication of the paper. The corresponding author, Dhananjaya Kalvakolanu, attempted to contact Dr. D'Cunha regarding authorship but did not receive a response. As a result, Jonathan D'Cunha has been removed as an author of the paper and its subsequent retraction notice. [Extracted from the article]

Background: With the emergence of Oxford Nanopore technology, now the on-site sequencing of 16S rRNA from environments is available. Due to the error level and structure, the analysis of such data demands some database of reference sequences. However, many taxa from complex and diverse environments, have poor representation in publicly available databases. In this paper, we propose the METASEED pipeline for the reconstruction of full-length 16S sequences from such environments, in order to improve the reference for the subsequent use of on-site sequencing. Results: We show that combining high-precision short-read sequencing of both 16S and full metagenome from the same samples allow us to reconstruct high-quality 16S sequences from the more abundant taxa. A significant novelty is the carefully designed collection of metagenome reads that matches the 16S amplicons, based on a combination of uniqueness and abundance. Compared to alternative approaches this produces superior results. Conclusion: Our pipeline will facilitate numerous studies associated with various unknown microorganisms, thus allowing the comprehension of the diverse environments. The pipeline is a potential tool in generating a full length 16S rRNA gene database for any environment. [ABSTRACT FROM AUTHOR]

Inflammatory bowel disease (IBD) is a complex disease that develops through a sequence of molecular events that are still poorly defined. This process is driven by a multitude of context-dependent genes that play different roles based on their environment. The complexity and multi-faceted nature of these genes make it difficult to study the genetic basis of IBD. The goal of this article is to review the key genes in the pathophysiology of IBD and highlight new technology that can be used in further research. This paper examines Nanostring RNA probe technology, which uses tissue analyzed without the use of enzymes, transcription, or amplification. Nanostring offers several panels of genes to test, including an inflammation panel of 234 genes. This article analyzes this panel and reviews the literature for each gene's effect in IBD for use as a framework to review the pathophysiology of the disease. The panel was narrowed to 26 genes with significant evidence of mechanistic potential in IBD, which were then categorized into specific areas of pathogenesis. These include gut barrier breakdown, inappropriate recognition of commensal bacteria, immune cell activation, proinflammatory cytokine release, and subsequent impairment of the anti-inflammatory response. The eventual goal of this paper is the creation of a customized panel of IBD genes that can be used to better understand the genetic mechanism of IBD and aid in the development of future therapies in IBD. [ABSTRACT FROM AUTHOR]

Phylogenetic inference of polyploid species is the first step towards understanding their patterns of diversification. In this paper, we review the challenges and limitations of inferring species relationships of polyploid plants using traditional phylogenetic sequencing approaches, as well as the mischaracterization of the species tree from single or multiple gene trees. We provide a roadmap to infer interspecific relationships among polyploid lineages by comparing and evaluating the application of current phylogenetic, phylogenomic, transcriptomic, and whole‐genome approaches using different sequencing platforms. For polyploid species tree reconstruction, we assess the following criteria: (1) the amount of prior information or tools required to capture the genetic region(s) of interest; (2) the probability of recovering homeologs for polyploid species; and (3) the time efficiency of downstream data analysis. Moreover, we discuss bioinformatic pipelines that can reconstruct networks of polyploid species relationships. In summary, although current phylogenomic approaches have improved our understanding of reticulate species relationships in polyploid‐rich genera, the difficulties of recovering reliable orthologous genes and sorting all homeologous copies for allopolyploids remain a challenge. In the future, assembled long‐read sequencing data will assist the recovery and identification of multiple gene copies, which can be particularly useful for reconstructing the multiple independent origins of polyploids. [ABSTRACT FROM AUTHOR]

Soursop (Annona muricata L.) is a tropical fruit highly valued for its unique flavor, nutritional value, and health-promoting properties. The ripening process of soursop involves complex changes in gene expression and metabolite accumulation, which have been studied using various omics technologies. Transcriptome analysis has provided insights into the regulation of key genes involved in ripening, while metabolic compound analysis has revealed the presence of numerous bioactive compounds with potential health benefits. However, the integration of transcriptome and metabolite compound data has not been extensively explored in soursop. Therefore, in this paper, we present a comprehensive analysis of the transcriptome and phenolic compound profiles of soursop during ripening. The integration analysis showed that the genes and phenolic compounds were mainly involved in the starch and sucrose metabolism pathways during soursop ripening. Further, the phenolic compounds Kaempferol 3-Q-galactoside, Procyanidin C1, Procyanidin trimmer C1, and m-Coumaric, as well as the genes Ubiquitin-like protein 5 (UBL5_ARATH), ATP-dependent zinc metalloprotease FTSH8 (FTSH8_ORYSJ), Zinc transporter 4 (ZIP4_ARATH), Thioredoxin-like 3-1 (TRL31_ORYSJ), Mitogen-activated protein kinase YODA (YODA_ARATH), R-mandelonitrile lyase-like (MGL_ARATH), 26s protease regulatory subunit 6A homolog (PRS6_SOLLC), Cytochrome P450 72A13 (C7A13ARATH), Cytochrome P450 84A1 (C84A1_ARATH) and Homoserine O-trans-acetylase (MET2-ORYSJ) were correlated and differentially accumulated and expressed, respectively. Our study provides new insights into the molecular mechanisms underlying soursop ripening and may contribute to the development of strategies for improving the nutritional quality and shelf life of this important fruit. [ABSTRACT FROM AUTHOR]

The nonconventional yeast Kluyveromyces marxianus has potential for industrial production, but the lack of advanced synthetic biology tools for precise engineering hinders its rapid development. Here, we introduce a CRISPR-Cas9-mediated multilocus integration method for assembling multiple exogenous genes. Using SlugCas9-HF, a high-fidelity Cas9 nuclease, we enhance gene editing precision. Specific genomic loci predisposed to efficient integration and expression of heterologous genes are identified and combined with a set of paired CRISPR-Cas9 expression plasmids and donor plasmids to establish a CRISPR-based biosynthesis toolkit. This toolkit enables genome integration of large gene modules over 12 kb and achieves simultaneous quadruple-locus integration in a single step with 20% efficiency. As a proof-of-concept, we apply the toolkit to screen for gene combinations that promote heme production, revealing the importance of HEM4Km and HEM12Sc. This CRISPR-based toolkit simplifies the reconstruction of complex pathways in K. marxianus, broadening its application in synthetic biology. Fungi has been widely used as protein and drug production factories, in which efficient heterologous gene expression is fundamental. This paper provides a genome editing tool kit for heterologous gene expression in Kluyveromyces marxianus. [ABSTRACT FROM AUTHOR]

Main conclusion: Genome-wide identification revealed 79 BpNAC genes belonging to 16 subfamilies, and their gene structures and evolutionary relationships were characterized. Expression analysis highlighted their importance in plant selenium stress responses. Paper mulberry (Broussonetia papyrifera), a deciduous arboreal plant of the Moraceae family, is distinguished by its leaves, which are abundant in proteins, polysaccharides, and flavonoids, positioning it as a novel feedstock. NAC transcription factors, exclusive to plant species, are crucial in regulating growth, development, and response to biotic and abiotic stress. However, extensive characterization of the NAC family within paper mulberry is lacking. In this study, 79 BpNAC genes were identified from the paper mulberry genome, with an uneven distribution across 13 chromosomes. A comprehensive, genome-wide analysis of BpNACs was performed, including investigating gene structures, promoter regions, and chromosomal locations. Phylogenetic tree analysis, alongside comparisons with Arabidopsis thaliana NACs, allowed for categorizing these genes into 16 subfamilies in alignment with gene structure and motif conservation. Collinearity analysis suggested a significant homologous relationship between the NAC genes of paper mulberry and those in Morus notabilis, Ficus hispida, Antiaris toxicaria, and Cannabis sativa. Integrating transcriptome data and Se content revealed that 12 BpNAC genes were associated with selenium biosynthesis. Subsequent RT-qPCR analysis corroborated the correlation between BpNAC59, BpNAC62 with sodium selenate, and BpNAC55 with sodium selenite. Subcellular localization experiments revealed the nuclear functions of BpNAC59 and BpNAC62. This study highlights the potential BpNAC transcription factors involved in selenium metabolism, providing a foundation for strategically breeding selenium-fortified paper mulberry. [ABSTRACT FROM AUTHOR]

de Magalhães has shown recently that most human genes have several papers in PubMed mentioning cancer, leading the author to suggest that every gene is associated with cancer, a conclusion that contradicts the widely held view that cancer is driven by a limited number of cancer genes, whereas the majority of genes are just bystanders in carcinogenesis. We have analyzed PubMed to decide whether publication metrics supports the distinction of bystander genes and cancer genes. The dynamics of publications on known cancer genes followed a similar pattern: seminal discoveries triggered a burst of cancer-related publications that validated and expanded the discovery, resulting in a rise both in the number and proportion of cancer-related publications on that gene. The dynamics of publications on bystander genes was markedly different. Although there is a slow but continuous time-dependent rise in the proportion of papers mentioning cancer, this phenomenon just reflects the increasing publication bias that favors cancer research. Despite this bias, the proportion of cancer papers on bystander genes remains low. Here, we show that the distinctive publication dynamics of cancer genes and bystander genes may be used for the identification of cancer genes. [ABSTRACT FROM AUTHOR]

The security issues with mobile devices have received more attention as a result of the development of mobile Internet technology and the adoption of mobile intelligent terminal devices. It is becoming more crucial to quickly and effectively identify and remove harmful applications from systems in order to protect user data and personal devices. The Dalvik bytecode, permission applications, and system calls of Android apps are the main targets of the current Android malware analysis approaches. However, in recent years, an increasing amount of Android malware conceals harmful code in native code. The method for using program gene technology to identify malware on the Android platform is presented in this research. This method extracts executable library files from the Native layer binary executable files of Android programs and disassembles the library files to obtain program genes. Then, the programs' genes perform feature screening by the information gain method and next use Word2Vec to express the semantic abstraction of the screened features. Finally, the screened features were used in deep neural network models for training and detection. The experimental results demonstrate that compared with KNN, SVM, and other machine learning algorithms, the deep neural network model is more effective and the detection accuracy reaches up to 97.51%. Thus, it confirmed the feasibility of the Android malicious program detection method based on program genes in this paper. [ABSTRACT FROM AUTHOR]

Social insects are very successful invasive species, and the continued increase of global trade and transportation has exacerbated this problem. The yellow-legged hornet, Vespa velutina nigrithorax (henceforth Asian hornet), is drastically expanding its range in Western Europe. As an apex insect predator, this hornet poses a serious threat to the honey bee industry and endemic pollinators. Current suppression methods have proven too inefficient and expensive to limit its spread. Gene drives might be an effective tool to control this species, but their use has not yet been thoroughly investigated in social insects. Here, we built a model that matches the hornet's life history and modelled the effect of different gene drive scenarios on an established invasive population. To test the broader applicability and sensitivity of the model, we also incorporated the invasive European paper wasp Polistes dominula. We find that, due to the haplodiploidy of social hymenopterans, only a gene drive targeting female fertility is promising for population control. Our results show that although a gene drive can suppress a social wasp population, it can only do so under fairly stringent gene drive-specific conditions. This is due to a combination of two factors: first, the large number of surviving offspring that social wasp colonies produce make it possible that, even with very limited formation of resistance alleles, such alleles can quickly spread and rescue the population. Second, due to social wasp life history, infertile individuals do not compete with fertile ones, allowing fertile individuals to maintain a large population size even when drive alleles are widespread. Nevertheless, continued improvements in gene drive technology may make it a promising method for the control of invasive social insects in the future. [ABSTRACT FROM AUTHOR]

Plant genomics plays a pivotal role in enhancing global food security and sustainability by offering innovative solutions for improving crop yield, disease resistance, and stress tolerance. As the number of sequenced genomes grows and the accuracy and contiguity of genome assemblies improve, structural annotation of plant genomes continues to be a significant challenge due to their large size, polyploidy, and rich repeat content. In this paper, we present an overview of the current landscape in crop genomics research, highlighting the diversity of genomic characteristics across various crop species. We also assessed the accuracy of popular gene prediction tools in identifying genes within crop genomes and examined the factors that impact their performance. Our findings highlight the strengths and limitations of BRAKER2 and Helixer as leading structural genome annotation tools and underscore the impact of genome complexity, fragmentation, and repeat content on their performance. Furthermore, we evaluated the suitability of the predicted proteins as a reliable search space in proteomics studies using mass spectrometry data. Our results provide valuable insights for future efforts to refine and advance the field of structural genome annotation. [ABSTRACT FROM AUTHOR]

Background: Currently, no evidence exists on the expression of apoptosis (CASP3), autophagy (BECN1), and mitophagy (BNIP3) genes in the CA3 area after ischemia with long-term survival. Objective: The goal of the paper was to study changes in above genes expression in CA3 area after ischemia in the period of 6–24 months. Methods: In this study, using quantitative RT-PCR, we present the expression of genes associated with neuronal death in a rat ischemic model of Alzheimer's disease. Results: First time, we demonstrated overexpression of the CASP3 gene in CA3 area after ischemia with survival ranging from 0.5 to 2 years. Overexpression of the CASP3 gene was accompanied by a decrease in the activity level of the BECN1 and BNIP3 genes over a period of 0.5 year. Then, during 1-2 years, BNIP3 gene expression increased significantly and coincided with an increase in CASP3 gene expression. However, BECN1 gene expression was variable, increased significantly at 1 and 2 years and was below control values 1.5 years post-ischemia. Conclusions: Our observations suggest that ischemia with long-term survival induces neuronal death in CA3 through activation of caspase 3 in cooperation with the pro-apoptotic gene BNIP3. This study also suggests that the BNIP3 gene regulates caspase-independent pyramidal neuronal death post-ischemia. Thus, caspase-dependent and -independent death of neuronal cells occur post-ischemia in the CA3 area. Our data suggest new role of the BNIP3 gene in the regulation of post-ischemic neuronal death in CA3. This suggests the involvement of the BNIP3 together with the CASP3 in the CA3 in neuronal death post-ischemia. [ABSTRACT FROM AUTHOR]

Background: Although, several studies have assessed the association of the phospholipase A2 receptor (PLA2R) and HLA-DQA1 SNPs with primary membranous nephropathy (PMN), results were inconsistent and between-studies heterogeneity needs to be investigated. Objectives: The aim of this review was to summarize existing data on the contribution of 10 SNPs in the PLA2R and HLA-DQA1 genes to PMN susceptibility and to investigate the between-studies heterogeneity by subgroup analyses and meta-regressions. Design: This study was performed according to the PRISMA guidelines for systematic reviews and meta-analyses. Data sources and methods: An electronic literature search for eligible studies among all papers published prior to January 10, 2024, was conducted through PubMed, EMBASE, Web of science and Scopus databases. Meta-analyses together with subgroup analyses and meta-regressions were performed for the 10 following SNPs: rs4664308, rs3749117, rs3749119, rs35771982, rs3828323, rs16844715, rs1511223, rs6757188, rs2715918, and rs2187668. Results: Combined analyses revealed a significant increase in PMN risk conferred by the following alleles: rs4664308*A, rs3749117*T, rs3749119*C, rs35771982*G, rs3828323*C, rs16844715*C, rs1511223*A, rs2715918*A, and rs2187668*A, all P -values <.001. Moreover, the PLA2R-rs4664308/HLA-DQA1-rs2187668 interaction was significantly associated with an increased PMN risk, P <.001. However, there was a substantial between-studies heterogeneity for some SNPs. Subgroup analyses by ethnicity for the 9 PLA2R SNPs did not show any cross-ethnic disparity. Inversely, the risk conferred by the HLA-DQA1 rs2187668*A allele was significantly higher in Caucasians (OR [95% CI] = 3.929 [3.251–4.748]) than in Asians (OR [95% CI] = 2.537 [1.94–3.318], P =.007. Besides, meta-regressions revealed for the majority of investigated SNPs significant correlations of the effect size with albumin, 24-hours proteinuria, serum creatinine, and eGFR levels. Hence, the influence on PMN risk conferred by the PLA2R and HLA-DQA1 SNPs was rather noted in patients with a severe disease. Conclusion: This meta-analysis showed that 9 out of the 10 investigated SNPs in PLA2R and HLA-DQA1 genes were associated with increased PMN risk. Heterogeneity could be due to disparate patient groups in terms of disease presentation for almost all SNPs, and ethnicity for the HLA-DQA1 rs2187668 SNP. Registration: This review has been registered on PROSPERO: CRD42024506729. Available from: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42024506729 Plain language summary: Genetic factors in primary membranous nephritis Why was the study done? Primary membranous nephritis (PMN) is the most common etiology of adult-onset nephrotic syndrome. Understanding risk factors, particularly genetic ones, would provide a better understanding of its pathophysiological mechanisms in order to prevent and treat patients more effectively. What did the researchers do? The research team summarized published data on genetic factors associated with PMN including phospholipase A2 receptor (PLA2R) and HLA-DQA1 genes. What did the researchers find? The total number of included studies was 27. Nine out of ten genetic factors were found to be associated with PMN risk. Moreover, we noted significant interaction between PLA2R and HLA-DQA1 in potentializing PMN risk. Nevertheless, there was a significant between-studies heterogeneity which was found to be explained in part by disease severity. What do the findings mean? This study has identified some important some genetic factors associated with PMN together with confounding factors that could influence the aforementioned association. [ABSTRACT FROM AUTHOR]

Wheat (Triticum aestivum L.) is a fundamental crop essential for both human and animal consumption. Addressing the challenge of enhancing wheat yield involves sophisticated applications of molecular genetics and genomic techniques. This review synthesizes current research identifying and characterizing pivotal genes that impact traits such as grain size, number, and weight, critical factors influencing overall yield. Key genes including TaSPL17, ABP7, TaGNI, TaCKX6, TaGS5, TaDA1, WAPO1, TaRht1, TaTGW-7A, TaGW2, TaGS5-3A, TaSus2-2A, TaSus2-2B, TaSus1-7A, and TaSus1-7B are examined for their roles in these traits. The review also explores genes responsive to environmental changes, which are increasingly significant under current climate variability. Multi-trait regulatory genes and quantitative trait loci (QTLs) that contribute to these traits are discussed, highlighting their dual influences on grain size and yield. Furthermore, the paper underscores the utility of emerging technologies such as CRISPR/Cas9, Case13, and multi-omics approaches. These innovations are instrumental for future discoveries and are poised to revolutionize wheat breeding by enabling precise genetic enhancements. Facing unprecedented challenges from climate change, the identification and utilization of these candidates is crucial. This review aims to be a comprehensive resource for researchers, providing an integrative understanding of complex traits in wheat and proposing new avenues for research and crop improvement strategies. [ABSTRACT FROM AUTHOR]

Maize Ustilago maydis is a disease that severely affects maize yield and quality. In this paper, we employed transcriptome sequencing and GWAS analysis to identify candidate genes and reveal disease-resistant germplasm resources, thereby laying the foundation for further analysis of the molecular mechanism of maize Ustilago maydis resistance and genetic improvement. The results of transcriptome sequencing revealed that a considerable number of receptor kinase genes, signal-transduction-related protein genes, redox-response-related genes, WRKYs, and P450s genes were significantly upregulated. There was a wide range of mutations of Ustilago maydis in maize inbred lines. Thirty-two high-resistance maize inbred lines were selected, and 16 SNPs were significantly associated with the disease index. By integrating the results of GWAS and RNA-seq, five genes related to disease resistance were identified, encoding the chitinase 1 protein, fatty acid elongase (FAE), IAA9, GATA TF8, and EREB94, respectively. It provides a certain reference for the cloning of maize anti-tumor smut genes and the breeding of new varieties. [ABSTRACT FROM AUTHOR]

Increasing yield is an important goal of barley breeding. In this study, 54 papers published from 2001–2022 on QTL mapping for yield and yield-related traits in barley were collected, which contained 1080 QTLs mapped to the barley high-density consensus map for QTL meta-analysis. These initial QTLs were integrated into 85 meta-QTLs (MQTL) with a mean confidence interval (CI) of 2.76 cM, which was 7.86-fold narrower than the CI of the initial QTL. Among these 85 MQTLs, 68 MQTLs were validated in GWAS studies, and 25 breeder's MQTLs were screened from them. Seventeen barley orthologs of yield-related genes in rice and maize were identified within the hcMQTL region based on comparative genomics strategy and were presumed to be reliable candidates for controlling yield-related traits. The results of this study provide useful information for molecular marker-assisted breeding and candidate gene mining of yield-related traits in barley. [ABSTRACT FROM AUTHOR]

Simple Summary: The role of neurogenic locus notch homolog protein 1 (NOTCH1)- and nuclear factor erythroid 2-related factor 2 (NRF2)-related pathways is highly heterogeneous in small cell lung cancer (SCLC) and, when they are both abnormally activated, they can synergistically cause neoplastic proliferation. In this paper, we investigate the possible role of KEAP1 silencing in NRF2 and NOTCH axis deregulation in SCLC by evaluating its impact on the modulation of cellular defense systems, cell growth, and differentiation. We also investigate the impact of these systems' impairment in response to conventional chemotherapies and NOTCH inhibitors in silenced SCLC cell lines with different Kelch-like ECH-associated protein 1 (KEAP1) alterations. The KEAP1/NRF2 pathway is a master regulator of several redox-sensitive genes implicated in the resistance of tumor cells against therapeutic drugs. The dysfunction of the KEAP1/NRF2 system has been correlated with neoplastic patients' outcomes and responses to conventional therapies. In lung tumors, the growth and the progression of cancer cells may also involve the intersection between the molecular NRF2/KEAP1 axis and other pathways, including NOTCH, with implications for antioxidant protection, survival of cancer cells, and drug resistance to therapies. At present, the data concerning the mechanism of aberrant NRF2/NOTCH crosstalk as well as its genetic and epigenetic basis in SCLC are incomplete. To better clarify this point and elucidate the contribution of NRF2/NOTCH crosstalk deregulation in tumorigenesis of SCLC, we investigated genetic and epigenetic dysfunctions of the KEAP1 gene in a subset of SCLC cell lines. Moreover, we assessed its impact on SCLC cells' response to conventional chemotherapies (etoposide, cisplatin, and their combination) and NOTCH inhibitor treatments using DAPT, a γ-secretase inhibitor (GSI). We demonstrated that the KEAP1/NRF2 axis is epigenetically controlled in SCLC cell lines and that silencing of KEAP1 by siRNA induced the upregulation of NRF2 with a consequent increase in SCLC cells' chemoresistance under cisplatin and etoposide treatment. Moreover, KEAP1 modulation also interfered with NOTCH1, HES1, and DLL3 transcription. Our preliminary data provide new insights about the downstream effects of KEAP1 dysfunction on NRF2 and NOTCH deregulation in this type of tumor and corroborate the hypothesis of a cooperation of these two pathways in the tumorigenesis of SCLC. [ABSTRACT FROM AUTHOR]

Purpose: Atherosclerosis (AS) is a chronic inflammatory vascular disease and the predominant cause of ischemic stroke (IS). AS is a potential pathogenetic factor in IS. However, the processes by which they interact remain unknown. The purpose of this paper was to investigate the shared gene signatures and putative molecular processes in AS and IS. Methods: Gene Expression Omnibus (GEO) data for AS and IS microarrays were retrieved. The co-expression modules associated with AS and IS were identified using the Weighted Gene Co-Expression Network Analysis (WGCNA). We constructed an interaction network of shared differentially expressed genes in AS and IS and conducted an enrichment analysis using ClueGO software. We validated the results in a separate cohort through differential gene analysis. Additionally, we retrieved AS and IS-related miRNAs from the Human microRNA Disease Database (HMDD) and predicted their target genes using miRWalk. We then built a network of miRNAs-mRNAs-KEGG pathways using the shared genes. Results: Through WGCNA, we identified five modules and six modules as significant in AS and IS, respectively. A ClueGO enrichment analysis of common genes showed that highly active CCR1 chemokine receptor binding is critical to AS and IS pathogenesis. The differential analysis expression results in another cohort closely matched these findings. The miRNA-mRNA network suggested that hsa-miR-330-5p, hsa-miR-143-3p, hsa-miR-16-5p, hsa-miR-152-3p might regulate the shared gene KRAS, which could be a key player in AS and IS. Conclusion: We integrated ischemic stroke and carotid atherosclerosis public database data and found that ATF3, CCL3, CCL4, JUNB, KRAS, and ZC3H12A may affect both, making them novel biomarkers or therapeutic target genes. Clinical samples and expression trends supported our analyses of pivotal genes. [ABSTRACT FROM AUTHOR]

Functional genes encode various biological functions required for the life activities of organisms. By analyzing the functional genes of edible and medicinal fungi, varieties of edible and medicinal fungi can be improved to enhance their agronomic traits, growth rates, and ability to withstand adversity, thereby increasing yield and quality and promoting industrial development. With the rapid development of functional gene research technology and the publication of many whole-genome sequences of edible and medicinal fungi, genes related to important biological traits have been mined, located, and functionally analyzed. This paper summarizes the advantages and disadvantages of different functional gene research techniques and application examples for edible and medicinal fungi; systematically reviews the research progress of functional genes of edible and medicinal fungi in biological processes such as mating type, mycelium and fruit growth and development, substrate utilization and nutrient transport, environmental response, and the synthesis and regulation of important active substances; and proposes future research directions for functional gene research for edible and medicinal fungi. The overall aim of this study was to provide a valuable reference for further promoting the molecular breeding of edible and medicinal fungi with high yield and quality and to promote the wide application of edible and medicinal fungi products in food, medicine, and industry. [ABSTRACT FROM AUTHOR]

In the early 1900s, mutation breeding to select varieties with desirable traits using spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.25. Although this low mutation rate was a major problem for breeding in those days, in the modern era with the development of next-generation sequencing (NGS) technology, it was conversely considered to be an advantage for efficient gene identification. In this paper, we proposed an in silico approach using NGS to compare the whole genome sequence of a spontaneous mutant with that of a closely related strain with a nearly identical genome, to find polymorphisms that differ between them, and to identify the causal gene by predicting the functional variation of the gene caused by the polymorphism. Using this approach, we found four causal genes for the dwarf mutation, the round shape grain mutation and the awnless mutation. Three of these genes were the same as those previously reported, but one was a novel gene involved in awn formation. The novel gene was isolated from Bozu-Aikoku, a mutant of Aikoku with the awnless trait, in which nine polymorphisms were predicted to alter gene function by their whole-genome comparison. Based on the information on gene function and tissue-specific expression patterns of these candidate genes, Os03g0115700/LOC_Os03g02460, annotated as a shortchain dehydrogenase/reductase SDR family protein, is most likely to be involved in the awnless mutation. Indeed, complementation tests by transformation showed that it is involved in awn formation. Thus, this method is an effective way to accelerate genome breeding of various crop species by enabling the identification of useful genes that can be used for crop breeding with minimal effort for NGS analysis. [ABSTRACT FROM AUTHOR]

Background: In the precision medicine era, identifying predictive factors to select patients most likely to benefit from treatment with immunological agents is a crucial and open challenge in oncology. Methods: This paper presents a pan-cancer analysis of Tumor Mutational Burden (TMB). We developed a novel computational pipeline, TMBcalc, to calculate the TMB. Our methodology can identify small and reliable gene signatures to estimate TMB from custom targeted-sequencing panels. For this purpose, our pipeline has been trained on top of 17 cancer types data obtained from TCGA. Results: Our results show that TMB, computed through the identified signature, strongly correlates with TMB obtained from whole-exome sequencing (WES). Conclusion: We have rigorously analyzed the effectiveness of our methodology on top of several independent datasets. In particular we conducted a comprehensive testing on: (i) 126 samples sourced from the TCGA database; few independent whole-exome sequencing (WES) datasets linked to colon, breast, and liver cancers, all acquired from the EGA and the ICGC Data Portal. This rigorous evaluation clearly highlights the robustness and practicality of our approach, positioning it as a promising avenue for driving substantial progress within the realm of clinical practice. [ABSTRACT FROM AUTHOR]

This paper focuses on the creation of an in vitro collection of grapevine hybrids from the breeding program of the Kazakh Scientific Research Institute of Fruit Growing and Viticulture and investigates the presence of Plasmopara viticola resistance mediated by Rpv3 and Rpv12 loci. We looked at the optimization of in vitro establishment using either shoots taken directly from field-grown plants or from budwood cuttings forced indoors. We further screened for the presence of endophyte contamination in the initiated explants and optimized the multiplication stage. Finally, the presence of the resistance loci against P. viticola was studied. The shoots initiated from the field-sourced explants were the more effective method of providing plant sources for in vitro initiation once all plant accessions met the goal of in vitro establishment. The concentration of phytohormones and the acidity of the culture medium have a great effect on the multiplication rate and the quality of in vitro stock cultures. Out of 17 grapevine accessions, 16 showed the presence of single or combined resistance loci against P. viticola. The grapevine accessions identified as carrying Rpv3 and Rpv12 alleles represent important genetic resources for disease resistance breeding programs. These accessions may further contribute to the creation of new elite cultivars of economic interest. [ABSTRACT FROM AUTHOR]

Clostridioides difficile infections (CDIs) continue to be a persistent healthcare concern despite newer antibiotic treatments, enhanced infection control practices, and preventive strategies focused on restoring the protective intestinal microbial barrier. Recent strides in gene sequencing research have identified many genes regulating diverse virulence factors for CDIs. These genes may be over- or under-expressed when triggered by various environmental and nutritional factors. The aims of this paper are to review the important genes involved in C. difficile pathogenesis and to identify modifiable environmental, nutritional, and other factors that may trigger the expression of these genes and thus offer new strategies to prevent CDIs. [ABSTRACT FROM AUTHOR]

• Inheritance of organisms is introduced into innovation design. • Computer digital coding technology is introduced into intelligent innovative design process. • Histogram similarity algorithm intelligently identifies functional genes. The inheritance and variation of functional knowledge is an important way to achieve product innovation. Analogous biological genetic inheritance can solve the problems with the inheritance and variation of functional knowledge. However, the different expressions of functional knowledge in different domains lead designers to consuming a lot of time for functional knowledge characterization and identification, which reduces the efficiency of functional knowledge application. Therefore, in order to solve the problem of inefficient application of functional knowledge in the genetic process caused by irregular expression of functional knowledge, the paper proposes a digital characterization and identification process model of functional genes for product intelligent innovative design. The process model enables product intelligent innovative design through digital characterization of functional genes and rapid identification of functional genes using computer assistance. The process model consists of four following steps. First, extract functional knowledge from patents and perform preliminary functional gene characterization. Second, characterize functional genes digitally by using computerized digital coding techniques. Third, identify the required functional genes by using image similarity matching algorithm. It assists designers to quickly identify the functional genes required for the target system. Fourth, obtain the target product design scheme. By "transcribing" and "translating" the required functional genes and using TRIZ tools to solve the translated scheme, the product innovative design scheme is finally obtained. The feasibility and effectiveness of the model are verified by the intelligent innovative design of shared bicycle parking management device. [ABSTRACT FROM AUTHOR]

Neural tube defects (NTDs) are congenital abnormalities in the central nervous system. The exact etiology of NTDs is still not determined, but several genetic and epigenetic factors have been studied. Folate supplementation during gestation is recommended to reduce the risk of NTDs. In this review we examine single nucleotide polymorphisms (SNPs) of the genes in the folate pathway associated with NTD. We reviewed the literature for all papers discussing both NTDs and SNPs in the folate pathway. Data were represented through five different genetic models. Quality assessment was performed using the Newcastle–Ottawa Scale (NOS) and Cohen's Kappa inter-rater coefficient assessed author agreement. Fifty-nine papers were included. SNPs in MTHFR, MTRR, RFC genes were found to be highly associated with NTD risk. NOS showed that high quality papers were selected, and Kappa Q-test was 0.86. Our combined results support the notion that SNPs significantly influence NTDs across the population, particularly in Asian ethnicity. Additional high-quality research from diverse ethnicities is needed and meta-regression analysis based on a range of criteria may provide a more complete understanding of the role of folate metabolism in NTDs. [ABSTRACT FROM AUTHOR]