National Center For Biotechnology Information Research Articles

Molecular Analysis of <i>Anapulvinaria pistaciae</i> (Bodenheimer)

This study is on the molecular evolutionary genetic analysis of Anapulvinaria pistaciae (Bodenheimer), which is a serious pest of pista. This study explored its ribosomal DNA from area 5.8S, and it now listed with the National Biotechnology Information Center (NCBI, GenBank- entry number OR074914.1). The codons involved in the coding of amino acid codons are distinguished. Tajima’s relative velocity test was used. A dendrogram of A. pistaciae has been developed using the maximum likelihood method.

B-cell epitope prediction of MPB83 protein as a candidate for serodiagnostic antigen of bovine tuberculosis in human: In silico study

Background: Bovine tuberculosis (bTB) can be transmitted to humans by inhalation or consumption of incomplete pasteurized milk and dairy products derived from infected cows. Most cases of Mycobacterium tuberculosis (M. bovis) infection are resistant to tuberculosis (TB) drugs. The risk of death during treatment for bTB has been reported to be 2.55 times higher than for TB. However, the quality of diagnostic methods for bTB remains relatively low.Objective: We aim to evaluate the potential of the B-cell epitope of the MPB83 protein as a candidate bTB serodiagnostic antigen using an in silico approach. Methods: This study was a computer-based descriptive study using secondary data from the National Center for Biotechnology Information (NCBI) protein database. The MPB83 protein sequence was obtained from M. tuberculosis variant bovis AF2122/97 from the United Kingdom. We described the characteristics of the linear epitope of the M. bovis B-cell protein MPB83 by measuring antigenicity, molecular weight, instability index, and Grand Average of Hydropathy (GRAVY) score. The tools used in this study were IBIVU PRALINE, VaxiJen v2.0, IEDB, ExPASy ProtParam, Cluspro, and the PyMOL application.Results: We found an epitope that could be used for bTB serodiagnostic antigen with low conservation, the 106KLNPDVNLVDTLN118 epitope. It has the molecular weight, instability index, and GRAVY score of 1638.76 Da, -28.44, and -0.300, respectively. Epitopes with the best criteria were simulated by docking to human major histocompatibility complex (MHC) class II. Docking results showed that the lowest binding energy was -644.8 kcal/mol. Further analysis using the PyMOL application obtained 14 hydrogen bonds with bond distances ranging from 1.7 Å to 2.2 Å, all of which showed strong hydrogen bonds.Conclusion: The B-cell epitope of MPB83 protein sequence 106KLNPDVNLVDTLN118 has a potential serodiagnostic antigen candidate for human bTB.

Signatures of Mollicutes-related endobacteria in publicly available Mucoromycota genomes.

Mucoromycota fungi and their Mollicutes-related endobacteria (MRE) are an ideal system for studying bacterial-fungal interactions and evolution due to the long-term and intimate nature of their interactions. However, methods for detecting MRE face specific challenges due to the poor representation of MRE in sequencing databases coupled with the high sequence divergence of their genomes, making traditional similarity searches unreliable. This has precluded estimations on the diversity of MRE associated with Mucoromycota. To determine the prevalence of previously undetected MRE in fungal genome sequences, we scanned 389 Mucoromycota genome assemblies available from the National Center for Biotechnology Information for the presence of MRE sequences using publicly available tools to map contigs from fungal assemblies to publicly available MRE genomes. We demonstrate a higher diversity of MRE genomes than previously described in Mucoromycota and a lack of cophylogeny between MRE and the majority of their fungal hosts. This supports the late invasion hypothesis regarding MRE acquisition across most of the examined fungal families. In contrast with other Mucoromycota lineages, MRE from the Gigasporaceae displayed some degree of cophylogeny with their hosts, which may indicate that horizontal transmission is restricted between members of this family or that transmission is strictly vertical. These results underscore the need for a refined process to capture sequencing data from potential fungal endosymbionts to discern their evolution and transmission. Screens of fungal genomes for MRE can help improve the quality of fungal genome assemblies while identifying new MRE lineages to further test hypotheses on their origin and evolution.IMPORTANCEMollicutes-related endobacteria (MRE) are obligate intracellular bacteria found within Mucoromycota fungi. Despite their frequent detection, MRE roles in host functioning are still unknown. Comparative genomic investigations can improve our understanding of the impact of MRE on their fungal hosts by identifying similarities and differences in MRE genome evolution. However, MRE genomes have only been assembled from a small fraction of Mucoromycota hosts. Here, we demonstrate that MRE can be present yet undetected in publicly available Mucoromycota genome assemblies. We use these newfound sequences to assess the broader diversity of MRE and their phylogenetic relationships with respect to their hosts. We demonstrate that publicly available tools can be used to extract novel MRE sequences from assembled fungal genomes leading to insights on MRE evolution. This work contributes to a greater understanding of the fungal microbiome, which is crucial to improving knowledge on the dynamics and impacts of fungi in microbial ecosystems.

Two new species of Macropelopia (Diptera, Chironomidae) from Oriental China, delineated with morphology and COI sequences.

Two new species, Macropelopia (Macropelopia) excavata Xu & Fu, sp. nov. and Macropelopia (Macropelopia) quadrimacula Xu & Fu, sp. nov., are described as male adults. A key to identify the males of Macropelopia from China is provided. Furthermore, in order to ascertain the genetic distance between these species and their morphological characteristics, mitochondrial cytochrome c oxidase subunit I gene sequences were uploaded to the National Center for Biotechnology Information. These COI sequences were then utilized to infer the relationships between the species, employing the neighbor-joining method.

Vacuum aspiration biopsy: evolution of the method, prevention of hemorrhagic complications

In Russia, more than 70,000 new cases of breast cancer are registered annually. Vacuum aspiration biopsy (VAB) is a minimally invasive method for diagnosing the genesis of focal breast pathology, which is also used for therapeutic purposes for the complete removal of benign neoplasms. High efficiency and favorable clinical outcomes have allowed VAB to gain wide popularity in clinical practice, due to which the method has been widely developed. However, like any surgical intervention, the VAB procedure may be accompanied by complications, the main share of which are hemorrhagic. Generalization and systematization of information on the development of the VAB technique, prevalence and risk factors of complications, as well as methods of their prevention and timely elimination. Scientific publications cited in this literature review were selected from the Pubmed database of medical and biological publications (National Center for Biotechnology Information (NCBI), USA), the Clinical Key database (Elsevier Corporation, the Netherlands), Web of Science Citation Indexing Database (Clarivate, USA), Google Scholar (CIF), and the scientific electronic library elibrary.ru (Russia). The information presented in the article can become a theoretical basis for future research aimed at increasing safety, further development and improvement of the VAB technique.

Do Babesia microti Hosts Share a Blood Group System Gene Ortholog, Which Could Generate an Erythrocyte Antigen That Is Essential for Parasite Invasion?

The United States of America (US) has the highest annual number of human babesiosis cases caused by Babesia microti (Bm). Babesia, like malaria-causing Plasmodium, are protozoan parasites that live within red blood cells (RBCs). Both infectious diseases can be associated with hemolysis and organ damage, which can be fatal. Since babesiosis was made a nationally notifiable condition by the Centers for Disease Control and Prevention (CDC) in January 2011, human cases have increased, and drug-resistant strains have been identified. Both the Bm ligand(s) and RBC receptor(s) needed for invasion are unknown, partly because of the difficulty of developing a continuous in vitro culture system. Invasion pathways are relevant for therapies (e.g., RBC exchange) and vaccines. We hypothesize that there is at least one RBC surface antigen that is essential for Bm invasion and that all Bm hosts express this. Because most RBC surface antigens that impact Plasmodium invasion are in human blood group (hBG) systems, which are generated by 51 genes, they were the focus of this study. More than 600 animals with at least one hBG system gene ortholog were identified using the National Center for Biotechnology Information (NCBI) command-line tools. Google Scholar searches were performed to determine which of these animals are susceptible to Bm infection. The literature review revealed 28 Bm non-human hosts (NHH). For 5/51 (9.8%) hBG system genes (e.g., RhD), no NHH had orthologs. This means that RhD is unlikely to be an essential receptor for invasion. For 24/51 (47.1%) hBG system genes, NHH had 4-27 orthologs. For the ABO gene, 15/28 NHH had an ortholog, meaning that this gene is also unlikely to generate an RBC antigen, which is essential for Bm invasion. Our prior research showed that persons with blood type A, B, AB, O, RhD+, and RhD- can all be infected with Bm, supporting our current study's predictions. For 22/51 (43.1%) hBG system genes, orthologs were found in all 28 NHH. Nineteen (37.3%) of these genes encode RBC surface proteins, meaning they are good candidates for generating a receptor needed for Bm invasion. In vitro cultures of Bm, experimental Bm infection of transgenic mice (e.g., a CD44 KO strain), and analyses of Bm patients can reveal further clues as to which RBC antigens may be essential for invasion.

Gradient Boosting Prediction of Overlapping Genes From Weighted Co-expression and Differential Gene Expression Analysis of Wnt Pathway: An Artificial Intelligence-Based Bioinformatics Study.

Introduction The Wnt (wingless-related integration site) signalling pathway is crucial for bone formation and remodelling, regulating the commitment of mesenchymal stem cells (MSCs) to the osteoblastic lineage. It triggers the transcriptional activation of Wnt target genes and promotes osteoblast proliferation and survival. Weighted co-expression network analysis (WGCNA) and differential gene expression analysis help researchers understand gene roles. Gradient boosting, a machine learning technique, enhances understanding of genetic and molecular mechanisms contributing to overlap genes, improving gene regulation and functional genomics. The aim is to predict overlapping genes in the Wnt signalling pathway. Methods Differential gene expression analysis was performed using the National Center for Biotechnology Information (NCBI) geo dataset-GSE251951, focusing on the effect of Wnt signaling on treatment. The WGCNA module was analyzed using the iDEP tool to identify interconnected gene clusters. Hub genes were identified by calculating module eigengenes, correlated with external traits, and ranked based on module membership values. The study utilized gradient boosting, an ensemble learning method, to predict models, evaluate their performance using metrics like accuracy, precision, recall, and F1 score, and adjust predictions based on gradient and learning rate. Results The dendrogram uses the "Dynamic TreeCut" algorithm to analyze gene clusters, aiding researchers in understanding gene modules and biological processes, identifying co-expressed genes, and discovering new pathways. The confusion matrix displays 88 actual and predicted cases. The gradient boosting model achieves 78.9% accuracy in predicting Wnt pathway overlapping genes, with a respectable area under the curve (AUC) and classification accuracy values. It accurately predicts 73.9% of samples, with a high precision ratio and low recall. Conclusion Future research should enhance differential expression analysis and WGCNA to identify key Wnt pathway genes, improve sensitivity, specificity, hyperparameter tuning, and validation experiments, and use larger datasets.

Can We Standardize Name Reconciliaton via OpenRefine?

Scientific names in biodiversity represent one of the oldest identifiers used in science. As a result, a common repetitive task is being able to reconcile a list of scientific names against curated data sources. Reconciliation allows one to determine if names in a list are spelled correctly, whether they are currently accepted, and their nomenclatural status. There are several online and local resources that provide reconciliation services. We share here the potential in interoperability across reconciliation tools. Global Names Verifier (GNverifier), Catalogue of Life, Global Biodiversity Information Facility (GBIF), Taxonomic Name Resolution Service (TNRS), LifeWatch, National Center for Biotechnology Information (NCBI), World Flora Online, Global Biotic Interactions (GloBI), Nomer, Wikidata, and others provide their own tools for name reconciliation. All these tools have their scope, design decisions, input, and output formats. It is often useful to do reconciliation using several such services, because they often include complementary data. However, with all the idiosyncrasies of services and lack of standardization, it is not an easy task (Islam et al. 2024). It would be great for researchers if all existing and future tools could be standardized. Then moving from one resource to another would be as easy as changing the URL. Implementing elements of Findable, Accessible, Interoperable, and Reusable (FAIR) data management principles would help to create such standards. However, standardizing all existing and future resources to a common interface would be difficult. Some of them have no monetary or programmatic means to modify their code, while others have more urgent priorities. Some resources support a specific research path where adhering to a rigid standard might hinder their innovation. In this paper we suggest interoperability between reconciliation tools by implementing the OpenRefine Reconciliation Service. OpenRefine is a popular and powerful reconciliation and data cleaning application. It is used by many researchers for data transformation and normalization. Any service that implements the OpenRefine Service can be incorporated into data-management workflows just by providing the service's OpenRefine-compatible URL. Such compatible services can easily be discovered by providing their metadata in the OpenRefine Services Registry. In this paper we discuss our implementation of the OpenRefine Service with the Global Names Verifier (GNverifier) reconciliation tool. GNverifier is developed at the Species File Group as a part of the Global Names Architecture initiative. It offers a powerful, configurable, fast way to reconcile scientific names. GNverifier software aggregates data from more than 100 source datasets. Queries return currently accepted names when provided in a dataset. It allows finding matches for names that historically had several suffixes and can do fuzzy and partial matches. It sorts data by many factors to reliably provide the best available results. With a strong focus on software optimization and a sophisticated matching algorithm, it can process 2000 names a second, making it one of the fastest services available. OpenRefine can use GNverifier directly because it is compatible with the OpenRefine protocol. As shown in Fig. 1, switching between GNverifier and Wikidata reconciliation of scientific names requires only change of a service URL. Implementation of the OpenRefine protocol might solve many standardization problems. Some resources already have it implemented (e.g., Wikidata, GNverifier Whitmire and Mozzherin 2023, WFO Plant List, IPNI). Many people already use OpenRefine for their other reconciliation needs. For them, the incorporation of name reconciliation would be especially beneficial because it will fit into their existing data-management workflow Fig. 2. Basic reconciliation by itself is standard by design and a big step forward. Beyond the basic reconciliation (as seen in Fig. 2) there are more data that researchers are interested in. The Service Protocol allows one to add optional "extended" features. For example, for scientific names, we provide "currently accepted" names, data sources where a name was found, taxonomic classification, etc. Fig. 3. To make these fields standardized, we would need a recommendation document that describes additional fields and their format. We need interested parties to participate in its creation and agree on its usage. The same would apply to optional input filters, for example for restricting reconciliation to certain data sources or higher taxonomic entities. We think OpenRefine would be a significant step forward for standardization between name-reconciliation tools.

GMMID: genetically modified mice information database.

Genetically engineered mouse models (GEMMs) are vital for elucidating gene function and disease mechanisms. An overwhelming number of GEMM lines have been generated, but endeavors to collect and organize the information of these GEMMs are seriously lagging behind. Only a few databases are developed for the information of current GEMMs, and these databases lack biological descriptions of allele compositions, which poses a challenge for nonexperts in mouse genetics to interpret the genetic information of these mice. Moreover, these databases usually do not provide information on human diseases related to the GEMM, which hinders the dissemination of the insights the GEMM provides as a human disease model. To address these issues, we developed an algorithm to annotate all the allele compositions that have been reported with Python programming and have developed the genetically modified mice information database (GMMID; http://www.gmmid.cn), a user-friendly database that integrates information on GEMMs and related diseases from various databases, including National Center for Biotechnology Information, Mouse Genome Informatics, Online Mendelian Inheritance in Man, International Mouse Phenotyping Consortium, and Jax lab. GMMID provides comprehensive genetic information on >70 055 alleles, 65 520 allele compositions, and ∼4000 diseases, along with biologically meaningful descriptions of alleles and allele combinations. Furthermore, it provides spatiotemporal visualization of anatomical tissues mentioned in these descriptions, shown alongside the allele compositions. Compared to existing mouse databases, GMMID considers the needs of researchers across different disciplines and presents obscure genetic information in an intuitive and easy-to-understand format. It facilitates users in obtaining complete genetic information more efficiently, making it an essential resource for cross-disciplinary researchers. Database URL: http://www.gmmid.cn.

Identification of prostate cancer associated genes for diagnosis and prognosis: a modernized in silico approach.

Prostate cancer (PCa) ranks as the second leading cause of cancer-related deaths in men. Diagnosing PCa relies on molecular markers known as diagnostic biomarkers, while prognostic biomarkers are used to identify key proteins involved in PCa treatments. This study aims to gather PCa-associated genes and assess their potential as either diagnostic or prognostic biomarkers for PCa. A corpus of 152,064 PCa-related data from PubMed, spanning from May 1936 to December 2020, was compiled. Additionally, 4199 genes associated with PCa terms were collected from the National Center of Biotechnology Information (NCBI) database. The PubMed corpus data was extracted using pubmed.mineR to identify PCa-associated genes. Network and pathway analyses were conducted using various tools, such as STRING, DAVID, KEGG, MCODE 2.0, cytoHubba app, CluePedia, and ClueGO app. Significant marker genes were identified using Random Forest, Support Vector Machines, Neural Network algorithms, and the Cox Proportional Hazard model. This study reports 3062 unique PCa-associated genes along with 2518 corresponding unique PMIDs. Diagnostic markers such as IL6, MAPK3, JUN, FOS, ACTB, MYC, and TGFB1 were identified, while prognostic markers like ACTB and HDAC1 were highlighted in PubMed. This suggests that the potential target genes provided by PubMed data outweigh those in the NCBI database.

A response to: Evaluating the reliability of DNA Barcoding for Central American Pacific shallow water echinoderms identification

Introduction: Chacón-Monge et al. (2024) sought to test the accuracy of DNA barcoding for species identification in Pacific Central American shallow water echinoderms. They used cytochrome c oxidase I (COI) sequences derived from new material collected as part of the BioMar-ACG project in Costa Rica. Using their set of 348 echinoderm sequences, they compared species identification results from two online platforms: the National Center for Biotechnology Information (NCBI) GenBank using the nucleotide Basic Local Alignment Search Tool (BLASTn), and the Barcode of Life Data Systems (BOLD) Identification Engine. Objective: The present article is a response to their results and conclusions. Methods: We reinterpreted the results from the authors’ Appendix 2 to enable an objective comparison between the BOLD Identification Engine and BLASTn in GenBank. Results: While the authors found that both platforms were limited by the number of reference sequences available in their respective databases, they concluded that GenBank outperformed BOLD for identification; however, we identify several methodological flaws in their analysis. These include pseudoreplication amongst query sequences, contaminated sequences stemming from sampling errors, and a lack of standardization when interpreting results from the two platforms. Their assessment of the BOLD Identification Engine was also limited by improper selection of a reference database. Conclusion: Addressing these errors, we reinterpret their results and demonstrate that there is no difference in performance between the two platforms.

Genome mining for ribosomally synthesized and post-translationally modified peptides (RiPPs) in Streptomyces bacteria

Ribosomally synthesized post-translationally modified peptides (RiPPs) are a novel category of bioactive natural products (NPs). Streptomyces bacteria are a potential source of many bioactive NPs. Limited opportunities are available to characterize all the bioactive NP gene clusters. In this study, 410 sequences of Streptomyces were analyzed for RiPPs through genome mining using the National Center for Biotechnology Information (NCBI), by combining BAGEL and anti-SMASH. A total of 4098 RiPPs were found; including both classified (lanthipeptide, RiPP-like, bacteriocin, LAPs, lassopeptide, thiopeptides) and nonclassified RiPPs. Soil was identified as a rich habitat for RiPPs. These data may offer alternative future remedies for various health issues.

Glycoscience data content in the NCBI Glycans and PubChem.

Studying glycans and their functions in the body aids in the understanding of disease mechanisms and developing new treatments. This necessitates resources that provide comprehensive glycan data integrated with relevant information from other scientific fields such as genomics, genetics, proteomics, metabolomics, and chemistry. The present paper describes two resources at the U.S. National Center for Biotechnology Information (NCBI), the NCBI Glycans and PubChem, which provide glycan-related information useful for the glycoscience research community. The NCBI Glycans ( https://www.ncbi.nlm.nih.gov/glycans/ ) is a dedicated website for glycobiology data content at NCBI and provides quick access to glycan-related information scattered across multiple NCBI databases as well as other information resources external to NCBI. Importantly, the NCBI Glycans hosts the official web page for the symbol nomenclature for glycans (SNFG), which is the standard graphical representation of glycan structures recommended for scientific publication. On the other hand, PubChem ( https://pubchem.ncbi.nlm.nih.gov ) is a research-focused, large-scale public chemical database, containing a substantial number of glycan-containing records and is integrated with important glycoscience resources like GlyTouCan, GlyCosmos, and GlyGen. PubChem organizes glycan-related information within multiple data collections (i.e., Substance, Compound, Protein, Gene, Pathway, and Taxonomy) and provides various tools and services that allow users to access them both interactively through a web browser and programmatically through a REST-ful interface, including PUG-View. The NCBI Glycans and PubChem highlight glycan-related data and improve their accessibility, helping scientists exploit these data in their research.

The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop.

The automatic recognition of biomedical relationships is an important step in the semantic understanding of the information contained in the unstructured text of the published literature. The BioRED track at BioCreative VIII aimed to foster the development of such methods by providing the participants the BioRED-BC8 corpus, a collection of 1000 PubMed documents manually curated for diseases, gene/proteins, chemicals, cell lines, gene variants, and species, as well as pairwise relationships between them which are disease-gene, chemical-gene, disease-variant, gene-gene, chemical-disease, chemical-chemical, chemical-variant, and variant-variant. Furthermore, relationships are categorized into the following semantic categories: positive correlation, negative correlation, binding, conversion, drug interaction, comparison, cotreatment, and association. Unlike most of the previous publicly available corpora, all relationships are expressed at the document level as opposed to the sentence level, and as such, the entities are normalized to the corresponding concept identifiers of the standardized vocabularies, namely, diseases and chemicals are normalized to MeSH, genes (and proteins) to National Center for Biotechnology Information (NCBI) Gene, species to NCBI Taxonomy, cell lines to Cellosaurus, and gene/protein variants to Single Nucleotide Polymorphism Database. Finally, each annotated relationship is categorized as 'novel' depending on whether it is a novel finding or experimental verification in the publication it is expressed in. This distinction helps differentiate novel findings from other relationships in the same text that provides known facts and/or background knowledge. The BioRED-BC8 corpus uses the previous BioRED corpus of 600 PubMed articles as the training dataset and includes a set of newly published 400 articles to serve as the test data for the challenge. All test articles were manually annotated for the BioCreative VIII challenge by expert biocurators at the National Library of Medicine, using the original annotation guidelines, where each article is doubly annotated in a three-round annotation process until full agreement is reached between all curators. This manuscript details the characteristics of the BioRED-BC8 corpus as a critical resource for biomedical named entity recognition and relation extraction. Using this new resource, we have demonstrated advancements in biomedical text-mining algorithm development. Database URL: https://codalab.lisn.upsaclay.fr/competitions/16381.

Expansion of MALDI-TOF MS database as a strategy for identification of Haemophilus species other than H. influenzae

ABSTRACT Objectives This study aimed to evaluate an expanded matrix-assisted laser desorption-ionization-time of flight mass spectrometry (MALDI-TOF MS) database for the identification of Haemophilus species other than H. influenzae (Hi). Methods A total of 144 Haemophilus species, cultured from respiratory samples from people (living) with cystic fibrosis, were identified with MALDI-TOF MS and 16S rRNA sequencing. Of these, 99 Haemophilus strains showed >99% similarity with the best matching strain in the National Center for Biotechnology Information (NCBI) database and were assigned to a single Haemophilus subspecies using both MALDI-TOF MS and 16S rRNA sequencing. The MS profiles of a subset of strains (n = 58/99) were added to the Bruker MALDI-TOF MS database. Subsequently, 270 different strains that were analyzed previously in a routine setting were re-analyzed. Results 16S rRNA sequencing reliably identified 99/144 Haemophilus strains (>99% similarity). H. haemolyticus 16S rRNA identification was suboptimal since only 3/21 H. haemolyticus strains attained a similarity of >99% with H. haemolyticus 16S rRNA sequence in the NCBI database. Expansion of the MALDI-TOF MS database improved the number of reliable identifications only moderately for H. haemolyticus, H. influenzae and H. paraphrohaemolyticus (<10%). By contrast, improved identification was more outspoken for H. parahaemolyticus, H. parainfluenzae, H. sputorum and H. pittmaniae (>85%). Conclusion 16S rRNA sequencing is a valuable method for the identification of Haemophilus sp. other than Hi. Expansion of the MALDI-TOF MS database, based on 16S rRNA sequencing results, increased the proportion of reliable identifications and in this study resulted in an increase of 10% of Haemophilus sp. other than Hi strain identifications.

HPV16 Genomes: In Silico Analysis of E6 and E7 Oncoproteins in 20 South American Variants.

Human papillomavirus (HPV) is the main risk factor for the development of squamous cell cervical cancer, and E6 oncoprotein and E7 oncoprotein are important components of the viral genome and its oncogenic potential. It is known that different viral variants of HPV16 have different pathology and impact on the development of neoplasia, although few studies have been performed on South American variants. Therefore, the present study aimed to analyze in silico the genomic diversity of HPV16 in 20 complete genome variants of South America in the National Center for Biotechnology Information (NCBI) database. We performed a descriptive study to characterize the polymorphic regions of the E6 and E7 genes in HPV16 variants, using software for genomic data and single nucleotide polymorphism (SNP) analysis and others for phylogenetic analysis. The variants analyzed included six SNPs linked to cancer (A131G, G145T, C335T, T350G, C712A, and T732C) and significant variation (798 nucleotide substitutions). Despite this, the variants showed low genetic diversity. Eighteen variants of unclear significance (VUS) were identified, 10 of which were in the coding E6 regions and 8 in the coding E7 regions. The prevalence of lineage D variants is of concern due to their pathology in cervical cancer and requires more research and epidemiological vigilance regarding their prevalence in the population. The data obtained in this study may contribute to future research on South American variants of HPV16, their pathogenicity, and the development of treatments.

The anti-neoplastic impact of thymoquinone from Nigella sativa on small cell lung cancer: In vitro and in vivo investigations.

Malignant and aggressive, small cell lung cancer (SCLC) constitutes about 15% of all diagnosed lung cancer cases. With primary therapeutic options such as chemotherapy accompanied by debilitating side effects, interest has been soaring in the therapeutic competencies of herbs. The pharmacological driving force behind the beneficial properties of Nigella sativa is the quinone, thymoquinone (TQ). The anti-cancer effects of TQ on different cancers have been extensively studied. Nonetheless, only one paper in the entire National Center for Biotechnology Information (NCBI) database describes its effects on SCLC. A more detailed investigation is required. The current study examined the impact of TQ in vitro on five SCLC cell lines and in vivo in a nude mouse xenograft model. The following in vitro effects of TQ on SCLC were evaluated: (a) cell viability; (b) apoptosis; (c) cell cycle arrest; (d) intracellular reactive oxygen species (ROS) levels, and (e) protein expression in concomitant signaling pathways. For the in vivo effects of TQ on SCLC, (a) tumor volume was measured, and (b) selected protein expression in selected concomitant signaling pathways was determined by Western blotting. In general, TQ reduced cell viability, induced apoptosis and cell cycle arrest, depleted ROS, and altered protein expression in associated signaling pathways. Furthermore, TQ exhibited a tumor-suppressive effect in an H446 SCLC xenograft model. The cytotoxic impact of TQ arising from anti-cancer mechanisms was elucidated. The positive results obtained in this study warrant further investigation.

Toxin-antitoxin system gene mutations driving Mycobacterium tuberculosis transmission revealed by whole genome sequencing.

The toxin-antitoxin (TA) system plays a vital role in the virulence and pathogenicity of Mycobacterium tuberculosis (M. tuberculosis). However, the regulatory mechanisms and the impact of gene mutations on M. tuberculosis transmission remain poorly understood. To investigate the influence of gene mutations in the toxin-antitoxin system on M. tuberculosis transmission dynamics. We performed whole-genome sequencing on the analyzed strains of M. tuberculosis. The genes associated with the toxin-antitoxin system were obtained from the National Center for Biotechnology Information (NCBI) Gene database. Mutations correlating with enhanced transmission within the genes were identified by using random forest, gradient boosting decision tree, and generalized linear mixed models. A total of 13,518 M. tuberculosis isolates were analyzed, with 42.29% (n = 5,717) found to be part of genomic clusters. Lineage 4 accounted for the majority of isolates (n = 6488, 48%), followed by lineage 2 (n = 5133, 37.97%). 23 single nucleotide polymorphisms (SNPs) showed a positive correlation with clustering, including vapB1 G34A, vapB24 A76C, vapB2 T171C, mazF2 C85T, mazE2 G104A, vapB31 T112C, relB T226A, vapB11 C54T, mazE5 T344C, vapB14 A29G, parE1 (C103T, C88T), and parD1 C134T. Six SNPs, including vapB6 A29C, vapB31 T112C, parD1 C134T, vapB37 G205C, Rv2653c A80C, and vapB22 C167T, were associated with transmission clades across different countries. Notably, our findings highlighted the positive association of vapB6 A29C, vapB31 T112C, parD1 C134T, vapB37 G205C, vapB19 C188T, and Rv2653c A80C with transmission clades across diverse regions. Furthermore, our analysis identified 32 SNPs that exhibited significant associations with clade size. Our study presents potential associations between mutations in genes related to the toxin-antitoxin system and the transmission dynamics of M. tuberculosis. However, it is important to acknowledge the presence of confounding factors and limitations in our study. Further research is required to establish causation and assess the functional significance of these mutations. These findings provide a foundation for future investigations and the formulation of strategies aimed at controlling TB transmission.

Morphological and Molecular Identification of Oryctes (Coleoptera: Scarabaeidae) Collected from Date Palm Plantations in Algeria1

Abstract Light traps operated from May 2022 to August 2023 collected Oryctes beetles (Coleoptera: Scarabaeidae) in date palm (Phoenix dactylifera L.) plantations in El Oued, Algeria. Morphological examination of 105 adult Oryctes specimens collected from the plantations revealed them to be Oryctes agamemnon arabicus (Fairmaire). Molecular identification, using the cytochrome oxidase c subunit I (COI) marker, confirmed those identifications. Notably, MASH analysis revealed differing degrees of genetic similarity, suggesting nuanced genetic diversity within the population. Utilizing Kraken2 software and the COI database from the National Center for Biotechnology Information, we also determined a high classification rate of approximately 99% of reads for all samples, reinforcing the identity of the specimens as O. agamemnon. These results help advance taxonomic knowledge of the insect fauna of the region as well as supporting environmental conservation initiatives.

Designing primer-probe sets for Escherichia coli and E. coli O157 detection: Comparative genomic approach and food interference assessment

This study aimed to develop novel primer-probe sets specifically optimized for detecting E. coli and E. coli O157 through comparative genomic analysis. Genomic data from 2396 E. coli strains, including 228 strains of E. coli O157, were retrieved from the National Center for Biotechnology Information (NCBI). From the analysis, yegR and GDP-mannose mannosyl hydrolase (GDPMH) genes were selected as primer targets for E. coli and E. coli O157:H7, respectively. The sensitivity and specificity of the designed primer-probe sets were evaluated in 48 E. coli strains (including 30 E. coli O157) and 17 non-E. coli strains, totaling 65 strains, and the results indicated high sensitivity and specificity. Tryptic soy broth (TSB), carrots, chicken, milk, potatoes, apple juice, and orange juice did not significantly interfere with detecting E. coli and E. coli O157; however, 50% potato samples did. The efficacy of the designed primers was compared among ground pork, lettuce, and potato samples. Reduced detection efficiency was noted in the lettuce and potato samples. Wavelength interference with components of the lettuce homogenate may have reduced detection efficiency. For potato samples, the high affinity of chlorogenic acid, a compound found in potatoes, for Taq DNA polymerase, a component of the mastermix, contributed to the reduced detection efficiency. The primer and probe sets described in this study, coupled with an understanding of possible interference from food components, will aid in detecting E. coli O157 in the food industry.