National Center For Biotechnology Information Research Articles

ISOLATION AND MOLECULAR IDENTIFICATION OF INDIGENOUS BACTERIOCIN-PRODUCING WEISSELLA CIBARIA

Globally, over 6.22 million deaths are associated with antibiotic resistance. Bacteriocins, a set of antimicrobial peptides synthesized on the ribosomes, are widely viewed as a potential answer to this issue. This is due to their pore-forming ability and antimicrobial activity against antibiotic-resistant pathogens. The aim of this study is to isolate bacteriocin-producing Weissella cibaria and evaluate its antimicrobial activity against Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Salmonella typhi, Proteus mirabilis, Streptococcus sp., Candida sp. and Rhizopus stolonifer. Weissella cibaria man1 was isolated by inoculating deMan Rogosa Sharpe (MRS) broth with small pieces of ripe Mangifera indica (mango), 24-hour incubation at 370C, 10-fold serial dilution and plating on MRS agar. Molecular identification was achieved by DNA extraction, amplification of the 16S rRNA gene through polymerase chain reaction (PCR), agarose gel electrophoresis, gene sequencing, and BLASTN homology searches in the National Center for Biotechnology Information (NCBI). Antimicrobial activity of the bacteriocin was determined by agar well diffusion assay. Mangifera indica (mango) was found to harbor bacteriocin-producing Weissella cibaria man1. The bacteriocin (weissellicin man1) exhibited a broad spectrum of antimicrobial activity. Weissellicin man1 suppressed the growth of several target pathogens (Pseudomonas aeruginosa, Klebsiella pneumoniae, Salmonella typhi, Proteus mirabilis, Candida sp. and Rhizopus stolonifer) but had no inhibitory action against Escherichia coli, Streptococcus sp., Staphylococcus aureus. In conclusion, weissellicin man1 from Weissella cibaria man1 has a broad-spectrum of antimicrobial action. These findings will facilitate further evaluation of the antimicrobial potency of weissellicin man1.

Bioinformatics and machine learning-driven key genes screening for vortioxetine

Vortioxetine is a pharmacological agent that acts as a serotonin modulator and stimulant, with safety and tolerability being important health issues. This study aimed to use bioinformatic and machine learning methods to find differentially expressed genes (DEG) between rats exposed to vortioxetine and matched controls. The GSE236207 dataset (Rattus norvegicus) was obtained from the National Center for Biotechnology Information (NCBI) and analyzed with R, followed by genetic ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses, and String's protein-protein interaction network was established to identify important genes. The original datasets were preprocessed in the second step by detecting and correcting missing and noisy data and then merged. After feature selection for the cleaned dataset, machine learning algorithms such as the K-nearest neighbors' algorithm, Naive Bayes, and Support Vector Machine (SVM) were used. In addition, an accuracy of 0.90 was observed with SVM. Leveraging these techniques, the study linked IGFBP7, KLRA22, PROB1, SHQ1, NTNG1, and LOC102546359 to vortioxetine exposure. The bioinformatic analysis revealed 18 upregulated genes and 27 downregulated genes, with all approaches identifying only one common locus, LOC102546359, responsible for noncoding ribonucleic acid (ncRNA) synthesis. The crucial point is that this locus bears no connection to any disease or trigger mechanism, thereby bolstering the safety of vortioxetine.

A highly sensitive and specific real-time quantitative polymerase chain reaction assay for Perkinsus marinus detection in oysters

Oyster aquaculture is one of the fastest-growing food production industries worldwide; however, it faces a significant challenge from the protist Perkinsus marinus, particularly in the USA. Although several quantitative molecular diagnostic methodologies are available for identifying diseases caused by P. marinus, the primer pairs used therein led to non-specific identification of other Perkinsus spp. Hence, a quantitative real-time PCR (Pm-qPCR) assay specific for P. marinus was developed using a TaqMan-based probe with the internal quencher in this study. A primer pair and probe specific to P. marinus were designed from a hypothetical protein of P. marinus collected from the whole-genome shotgun sequence database of the National Center for Biotechnology Information (NCBI). In silico analysis using homologous sequences of P. olseni and P. chesapeaki confirmed the high specificity of primers designed in this study. The Pm-qPCR assay was performed using seven different strains of P. marinus, P. olseni, and P. chesapeaki, revealing high specificity and sensitivity for detecting only P. marinus strains. In conclusion, it was demonstrated that Pm-qPCR can effectively and accurately diagnose P. marinus with high specificity and sensitivity. This assay is promising for monitoring oyster health and disease management in ecosystems and aquaculture.

Cryptosporidium spp. Infection in Adult Kidney Transplant Patients: A Systematic Review and Meta-Analysis.

Background: Diarrhea frequently occurs after vascular organ transplantation, including kidney transplants. This may result from non-infectious factors, adverse effects of immunosuppressive medications, or infections caused by various pathogens, including viruses, bacteria, fungi, or parasites, for example, intestinal protozoan parasites such as Cryptosporidium spp., which are particularly dangerous for immunocompromised patients. Methods: This review is based on scientific articles sourced from validated databases such as PubMed, the National Center for Biotechnology Information (NCBI), ScienceDirect, and Google Scholar. The primary search was conducted on 12-13 July 2024, using the keywords 'Cryptosporidium' AND 'cryptosporidiosis' AND 'kidney' AND 'transplant' AND 'adult'. Inclusion criteria encompassed human studies, case reports, peer-reviewed journal publications, review articles, and research articles in English. Exclusion criteria included studies not in English, gray literature (e.g., conference proceedings and abstracts), and data related to pediatric patients (under 18 years old) and HIV patients. Results: This systematic review and meta-analysis have highlighted an often-overlooked connection between Cryptosporidium spp. infections in adult kidney transplant recipients (KTR). Furthermore, it includes an analysis of the clinical presentation, diagnosis, and treatment of Cryptosporidium spp. infection in these patients, based on available case reports. Our study demonstrates that adult kidney transplant patients are at a significantly higher risk of acquiring Cryptosporidium spp. compared to healthy participants. Conclusions:Cryptosporidium spp. infections can be asymptomatic, making it essential to screen both symptomatic and asymptomatic kidney transplant recipients. The clinical presentation of cryptosporidiosis typically involves digestive symptoms and can be complicated by biliary tract involvement. In KTR patients presenting with diarrhea, it is crucial to not only test for Cryptosporidium spp. but also to rule out bacterial and viral etiologies, including infections such as C. difficile, C. colitis, Clostridium spp., and rotavirus. The diagnosis of Cryptosporidium spp. infections primarily relies on microscopic methods, which are known for their low sensitivity. Therefore, diagnostic approaches should include both direct methods and, where possible, molecular techniques. Based on the analyzed cases, the most effective treatment results were achieved with reduction in immunosuppression if possible (strong, very low) and nitazoxanide at a dose of 500 mg twice daily for 14 days. Considering the public health implications of our findings, the current epidemiological data underscore the need for further research to develop effective prevention and intervention strategies against cryptosporidiosis. Preventive measures, regular screening programs, and the treatment of Cryptosporidium spp. infections should be integrated into the clinical care of transplant patients. It is also important that patients are informed about environmental risk factors.

Cholangiocarcinoma: A Comprehensive Review and Update Guideline

Cholangiocarcinoma is a rare cancer of the gastrointestinal system. However, the prognosis for people with this disease has not improved in the last decade. CCA has a poor prognosis because most cases are diagnosed at an advanced stage and the availability of treatment options is limited. This literature review aims to provide information regarding the current understanding and guidelines for cholangiocarcinoma. In this literature review, we searched the National Center for Biotechnology Information (NCBI) and Google Scholar using the search keywords "Cholangiocarcinoma", "cholangiocarcinoma management", "cholangiocarcinoma guidelines" taken ScienceDirect, Researchgate, National Comprehensive Cancer Network, and PubMed published in the last 10 years. From various databases, the literature used and according to the selection criteria amounted to 50 articles In the latest articles and the Cancers NCCN Guidelines for Biliary Tract Cancer in 2023, CCA treatment is carried out based on the patient's profile. Targeted therapy is an additional treatment option today by targeting the molecular profile involved in the pathogenesis of CCA. The diagnosis of cholangiocarcinoma is made through histology, radiography, and laboratory examination. Based on the Cancers NCCN Guidelines for Biliary Tract Cancer in 2023, the treatment carried out consists of determining cancer staging, surgery, radiation therapy, and systemic therapy.

Understanding rhizospheric microbial dynamics in gladiolus corms through quorum sensing and quorum quenching for disease control and growth promotion

Gladiolus, a widely cultivated cut flower known for its aesthetically pleasing multicoloured spikes, has earned significant commercial popularity. A comprehensive understanding of the rhizosphere bacterial community associated with gladiolus is imperative for revealing its potential benefits. Molecular characterization is considered an effective method to gain insights into the structural and functional aspects of microbial populations. The soil characteristics and bacterial communities in the rhizosphere are typically influenced by quorum sensing (QS) and quorum quenching (QQ) mechanisms. This study aims to explore the niceties and diversity of rhizospheric bacterial populations linked with gladiolus corms, with a specific focus on understanding the dynamics of QS and QQ mechanisms in their complex interactions. The isolation of bacterial strains was achieved through the serial dilution method on nutrient agar (NA) media. The identification of the isolates was accomplished by amplifying 16 S rRNA gene sequences via polymerase chain reaction (PCR) via the use of universal primers. Sequence analysis was conducted via BLAST on the National Center for Biotechnology Information (NCBI) database. The characteristics of the isolated bacteria were elucidated via biosensors. This study identified three QS strains and five QQ strains. A consortium of quenchers was formulated utilizing five strains that demonstrated efficacy in mitigating the impact of disease on gladiolus and fostering growth. Among the three treatments—Scale, Descale, and Descale and Cut Half (DSC)—the DSC treatment emerged as the most effective. This treatment exhibited a broader range of variation in biological parameters over time, aligning with prevailing trends in the local market.

Gene Sequencing Study of Mitochondrial Cytochrome Oxidase Subunit I (COI) in Aedes aegypti Mosquito

Aedes aegypti is an important vector from the public health point of view. It transmits pathogens of Dengue and various other diseases. Controlling vector populations is key to reducing disease transmission and it is possible by understanding the taxonomic characteristics of the vectors and their genetic analysis helps in the identification of the genetic variations in species of different geographical areas. The main aim of the present study is the screening of the Aedes mosquito genome of local species as genetic studies give some insights into the vaccine for the treatment of the diseases caused by mosquito species. In the present study, the adult Ae. aegypti collected from Suryapet town where Dengue fever is endemic, used for the mitochondrial Cytochrome Oxidase subunit I (COI) gene sequencing using the techniques of polymerase chain reaction, Electrophoretic separation, spectrophotometric analysis, and BLAST. The mitochondrial COI sequence of 583 bps is published in the National Centre for Biotechnology Information (NCBI) with accession number ON413769. The sequence data was matched with the database available in the NCBI to identify variation in the gene as this gene keeps changing in the organisms and may contribute to the species establishing itself in a particular region due to congenial environmental conditions. One match with the protein called haem copper oxidase subunit I. The transmission of different pathogens in different areas can be ascertained by comparing similar sequence studies documented. Genomic studies involving genetic markers are of immense help in developing the vaccine. The mitochondrial COI gene is the marker often used for evolutionary research. The single nucleotide polymorphisms (SNP) or Restricted fragment length polymorphisms (RFLPs) that occur in DNA also contribute to the vector's adaptability to the different geographical areas and also the survival benefit which are the basis for understanding the vectors thoroughly and their role in disease transmission.

Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae.

Interpreting the phenotypes of bla SHV alleles in Klebsiella pneumoniae genomes is complex. Whilst all strains are expected to carry a chromosomal copy conferring resistance to ampicillin, they may also carry mutations in chromosomal bla SHV alleles or additional plasmid-borne bla SHV alleles that have extended-spectrum β-lactamase (ESBL) activity and/or β-lactamase inhibitor (BLI) resistance activity. In addition, the role of individual mutations/a changes is not completely documented or understood. This has led to confusion in the literature and in antimicrobial resistance (AMR) gene databases [e.g. the National Center for Biotechnology Information (NCBI) Reference Gene Catalog and the β-lactamase database (BLDB)] over the specific functionality of individual sulfhydryl variable (SHV) protein variants. Therefore, the identification of ESBL-producing strains from K. pneumoniae genome data is complicated. Here, we reviewed the experimental evidence for the expansion of SHV enzyme function associated with specific aa substitutions. We then systematically assigned SHV alleles to functional classes (WT, ESBL and BLI resistant) based on the presence of these mutations. This resulted in the re-classification of 37 SHV alleles compared with the current assignments in the NCBI's Reference Gene Catalog and/or BLDB (21 to WT, 12 to ESBL and 4 to BLI resistant). Phylogenetic and comparative genomic analyses support that (i) SHV-1 (encoded by bla SHV-1) is the ancestral chromosomal variant, (ii) ESBL- and BLI-resistant variants have evolved multiple times through parallel substitution mutations, (iii) ESBL variants are mostly mobilized to plasmids and (iv) BLI-resistant variants mostly result from mutations in chromosomal bla SHV. We used matched genome-phenotype data from the KlebNET-GSP AMR Genotype-Phenotype Group to identify 3999 K. pneumoniae isolates carrying one or more bla SHV alleles but no other acquired β-lactamases to assess genotype-phenotype relationships for bla SHV. This collection includes human, animal and environmental isolates collected between 2001 and 2021 from 24 countries. Our analysis supports that mutations at Ambler sites 238 and 179 confer ESBL activity, whilst most omega-loop substitutions do not. Our data also provide support for the WT assignment of 67 protein variants, including 8 that were noted in public databases as ESBL. These eight variants were reclassified as WT because they lack ESBL-associated mutations, and our phenotype data support susceptibility to third-generation cephalosporins (SHV-27, SHV-38, SHV-40, SHV-41, SHV-42, SHV-65, SHV-164 and SHV-187). The approach and results outlined here have been implemented in Kleborate v2.4.1 (a software tool for genotyping K. pneumoniae), whereby known and novel bla SHV alleles are classified based on causative mutations. Kleborate v2.4.1 was updated to include ten novel protein variants from the KlebNET-GSP dataset and all alleles in public databases as of November 2023. This study demonstrates the power of sharing AMR phenotypes alongside genome data to improve the understanding of resistance mechanisms.

Emerging blaNDM-positive Salmonella enterica in Chinese pediatric infections.

Non-typhoidal Salmonella (NTS) is a common zoonotic foodborne pathogen, whose rising antimicrobial resistance has been an urgent threat to global public health. Here, we reported two carbapenem-resistant Salmonella enterica (CRSE) strains (NBFE-049 and NBFE-164) carrying the blaNDM genes, which were recovered from two Chinese children, belonged to Salmonella enterica serovar Typhimurium (S. Typhimurium) monophasic variant (S. 1,4,[5],12:i:-) ST34 (a sequence type) and S. Typhimurium ST19, respectively. Genes blaNDM-5 and blaNDM-13 were detected in NBFE-049 and NBFE-164, respectively. The blaNDM-5 in NBFE-049 was located in an IncHI2-type plasmid, named pNBFE-049. In NBFE-164, the blaNDM-13 was located in an IncI1-type plasmid, named pNBFE-164. The plasmid pNBFE-164 successfully transferred its resistance phenotype into the recipient strain Escherichia coli J53 with a high efficiency of 1.1 × 10-2, while no transconjugants were obtained in pNBFE-049 conjugation assays. We further elucidated the genetic relationships of globally occurring New Delhi Metallo-β-lactamase (NDM)-positive strains and locally distributed clinical strains within the same serovar. The closest relative of NBFE-049 was clinical Salmonella strain 1722, which was recovered in 2020 and differed by only three Single Nucleotide Polymorphisms (SNPs). No NDM-positive ST19 could be found in the National Center for Biotechnology Information (NCBI) database, and NBFE-164 showed a close genetic relationship with the other ST19 in this area. To sum up, we suggested the potential contributions of clonal spread and plasmid-mediated blaNDM transfer in CRSE dissemination. This study reported the complete genome of two blaNDM-carrying S. Typhimurium isolates, shedding new insights into the antimicrobial resistance mechanisms and dissemination patterns of the emerging CRSE.IMPORTANCENTS is one of the most common zoonotic pathogens that causes foodborne illnesses, while S. Typhimurium is one of the most common serovars. With the rising prevalence of multi-resistant Salmonella worldwide, carbapenems have emerged as the last-line antibiotics for treating severe bacterial infections. In this study, we reported the genomic characteristics of two carbapenem-resistant S. Typhimurium strains, which were recovered from two pediatric patients, carrying blaNDM-5 and blaNDM-13, providing new insights into the antimicrobial resistance deteriminants and transmission risk of blaNDM-positive NTS in China. We suggested the potential contributions of clonal spread and plasmid-mediated blaNDM transfer in CRSE dissemination. Future enhanced surveillance policy should mitigate CRSE spreading, and more importantly, clinical antimicrobial therapeutic regimens should be adjusted accordingly.

Physicochemical and Structural Validation of Myxovirus Resistance 1 (Mx1) Protein of Three Strains of the Nigerian Indigenous (<i>Gallus Gallus domesticus</i>) and Exotic Chickens

This research was conducted on three strains of Nigerian Indigenous (<i>gallus gallus domesticus</i>) and Noiler (exotic) chickens. It examined the physicochemical and structural validation of Myxovirus resistance 1 (Mx1) protein on the three strains of Nigerian indigenous (naked neck, frizzle feather, normal feather) and noiler (exotic) chickens and also the prediction of the Physicochemical Analysis of protein. Nucleotide sequence were retrieved from National Center for Bio-Technology Information (NCBI) database and subjected to multiple sequence alignment, prediction of the physicochemical analysis of protein was done in the ProtParam web server. Modeling of 3D structural validation, Swiss modeling and Statistical analysis were all carried out. Software was used to align the sequences to find any Single Nucleotide Polymorphism (SNPS). The result of physicochemical analysis showed that the properties of the Mx1 protein fell within accepted threshold and predicted that the proteins were generally related. To validate the structure obtained from modeling, the obtained PDB files were ran on the Pro-check validation server and obtained Errat and Ramachandran plots. The study elucidates the unique features and potential functional implications of Mx1 protein across different strains of Nigerian indigenous and exotic chickens. This knowledge can inform the development of strategies to improve disease resistance in local chicken populations through selective breeding or genetic manipulation. Comparing the Mx1 protein among different strains of Nigerian indigenous chickens can reveal evolutionary adaptations and provide valuable information for understanding the molecular basis of immune defense mechanisms in poultry. Understanding the physicochemical properties and structural dynamics of Mx1 protein contributes to the broader understanding of innate immune responses in indigenous chicken breeds, offering insights into their disease resistance and adaptation mechanisms.

Taxonomic Data Objects for Communicating the Meaning of Species Names

A central problem in biodiversity data science remains the inability to precisely aggregate observations that originate from the same species. Current approaches still rely heavily on the ‘Genus species’ pair of Linnaean taxonomy to label and group data. However, such binomial species names do not alone contain enough information to distinguish variation in a name’s conceptual usage (i.e., meaning) across time, place, or investigator. This “species name-to-meaning” problem is well known, but no robust and scalable solutions yet exist (Berendsohn 1995Bisby 2000, Sutherland et al. 2000, Page 2007, Franz and Sterner 2018, Upham et al. 2021, Sterner et al. 2023, Sterner et al. 2020, Beach et al. 1993). The problem is widespread especially for well-studied groups like mammals, for which 45% more species are now recognized than 30 years ago, including many species splits and rearrangements (Burgin et al. 2018, Mammal Diversity Database 2024). To address this problem, we here propose to digitally package and sign the relevant taxonomic data associated with a given species name usage to form a ‘Taxonomic Data Object’ (TDO). These TDOs are conceptually similar to 'secundus' references (i.e., species name sec. author, Berendsohn 1995) but differ in being machine readable and thus operational from the perspective of high-throughput data science. TDOs aim to move from analog secundus references, which require a human to track meaning by reading the cited article, to a digital and machine-actionable taxonomic reference. Versioned TDOs that are digitally signed using hash algorithms (e.g., md5 or sha256, see Elliott et al. 2023) will allow for precisely communicating, with verified data provenance from sender to receiver, certain aspects of what a species name means according to a given authority at a given time. Example TDO contents include DarwinCore terms (e.g., scientificName, namePublishedIn, nameAccordingTo, nomenclaturalStatus (Darwin Core Maintenance Group 2021)) as well as meaning-rich digital assets like geographic range maps (e.g., GeoJSON format), exemplar DNA sequences (e.g., FASTA format or National Center for Biotechnology Information (NCBI) accession number), holotype specimen information (e.g., catalog number, type locality coordinates), and taxonomic treatment texts (including material citations, e.g., as digitized and extracted by Plazi TreatmentBank, Agosti and Egloff 2009; see Fig. 1). We discuss pilot examples comparing global bat species according to the v1.2 vs. v1.11 taxonomies of the Mammal Diversity Database (Sep 2020 vs. Apr 2023), showing how TDOs enable the reliable tracking of taxonomic meaning for the 63 bat species affected by splits during this period. We posit that widespread use of TDOs will enable the traceable exchange of taxonomic information across a variety of existing platforms, providing a path for accurate species-level data aggregation at global scales, at least for well-studied taxa.

Taxonomy Identifiers (TaxId) for Biodiversity Genomics: a guide to getting TaxId for submission of data to public databases.

Biodiversity genomics critically depends on correct taxonomic identification of the sample from which data are derived. Tracking of that taxonomic information through systems that archive data and report on genome sequencing efforts. For submission of data to the International Nucleotide Sequence Database Collaboration (INSDC) databases (DNA DataBank of Japan [DDBJ], European Nucleotide Archive [ENA] and National Center for Biotechnology Information [NCBI]), samples and data derived from them must be assigned a species-level NCBI Taxonomy taxonomic identifier (TaxId, sometimes referred to as taxId or txid). We thus need to be able to identify the TaxId for a target species efficiently. Because the NCBI Taxonomy does not include all known species and cannot preemptively represent unknown taxa, we also need an efficient process for generating new TaxIds for species not yet listed. This document provides workflows for different kinds of TaxId acquisition scenarios and was created to guide users in these processes. Although developed for European projects such as Darwin Tree of Life and the European Reference Genome Atlas, the workflows are universally applicable and describe the use of ENA in resolving taxonomic issues. Too Long: Didn't Read (TL;DR): Use the ENA REST API programmatically to retrieve TaxIds for target species and confirm that sequence data can be submitted to those TaxIds.Use the NCBI Web interface to NCBI Taxonomy to identify potential homotypic synonyms.Request a new TaxId from ENA for a species not yet in NCBI Taxonomy, and for species-like entries for which the full Linnaean binomen is not determined (see https://ena-docs.readthedocs.io/en/latest/faq/taxonomy_requests.html#creating-taxon-requests).Discuss directly with the NCBI Taxonomy curators or the curators at ENA and NCBI whenever you think there is an opportunity to improve their database.

Surgical Management of Secondary Complex Microsurgical Reconstructions after Amputation and Severe Trauma Injuries: A Case Series.

Secondary complex microsurgical reconstructions after amputation and severe trauma injuries are often necessary to optimize functional outcomes. We reviewed eight patients who underwent extensive reconstruction after severe trauma. The details of secondary procedures are further described in the article. A literature search was performed using the National Center for Biotechnology Information (NCBI) database for studies evaluating secondary procedures after complex reconstructions. To date, the order and the need for performing secondary procedures have yet to be fully defined. The tissues encountered include skin, soft tissue, bone, nerve, joint, and tendon. We described the use of a decision-theoretic approach to the secondary reconstruction. Treatment of a complex trauma should be measured by functional outcome.

Transcriptome Profile and Gene Expression During Different Ovarian Maturation Stages of Macrobrachium rosenbergii (De Man, 1879).

Macrobrachium rosenbergii, or giant river prawn, is the most economically crucial cultured freshwater crustacean. A predominant challenge in developing crustacean aquaculture is reproduction management, particularly ovary maturation, where identifying regulative mechanisms at the molecular level is critical. Ovary is the primary tissue for studying gene and protein expressions involved in crustacean growth and reproduction. Despite significant interest in M. rosenbergii, its gene discovery has been at a relatively small scale compared to other genera. In this study, comprehensive transcriptomic sequencing data for different maturation stages of the ovary of M. rosenbergii were observed. The 20 female M. rosenbergii samples evaluated were categorised into four maturation stages, 1 to 4. A total of 817,793,14, 841,670,70, 914,248,78 and 878,085,88 raw reads were obtained from stages 1, 2, 3 and 4, respectively. The assembled unique sequences (unigenes) post-clustering (n = 98013) was 131,093,546 bp with an average size of 1,338 bp. The BLASTX unigene search against National Centre for Biotechnology Information (NCBI), non-redundant (NR), nucleotide sequence (NT), Kyoto Encyclopaedia of Genes and Genomes Orthology (KO), Swiss-Prot, Protein Family (PFAM), Gene Ontology (GO), and euKaryotic Orthologous Groups (KOG) databases yielded 27,680 (28.24%), 7,449 (7.59%), 13,026 (13.29%), 22,606 (23.06%), 29,907 (30.51%), 30,025 (30.63%) and 14,368 (14.65%) significant matches, respectively, totalling to 37,338 annotated unigenes (38.09%). The differentially expressed genes (DEG) analysis conducted in this study led to identifying cyclin B, insulin receptor (IR), oestrogen sulfotransferase (ESULT) and vitellogenin (Vg), which are critical in ovarian maturation. Nevertheless, some M. rosenbergii ovarian maturation-related genes, such as small ubiquitin-like modifier (SUMO)-activating enzyme subunit 1, E3 ubiquitin-protein ligase RNF25, and neuroparsin, were first identified in this study. The data obtained in the present study could considerably contribute to understanding the gene expression and genome structure in M. rosenbergii ovaries throughout its developmental stage.

DDBJ update in 2024: the DDBJ Group Cloud service for sharing pre-publication data.

The Bioinformation and DNA Data Bank of Japan Center (DDBJ Center, https://www.ddbj.nig.ac.jp) provides public databases that cover a wide range of fields in life sciences. As a founding member of the International Nucleotide Sequence Database Collaboration (INSDC), the DDBJ Center accepts and distributes nucleotide sequence data ranging from raw reads to assembled and annotated sequences with the National Center for Biotechnology Information and the European Bioinformatics Institute. Besides INSDC databases, the DDBJ Center provides databases for functional genomics (Genomic Expression Archive), metabolomics (MetaboBank), human genetic variations (TogoVar-repository) and human genetic and phenotypic data (Japanese Genotype-phenotype Archive). These database systems have been built on the National Institute of Genetics supercomputer, which is also a platform for the DDBJ Group Cloud (DGC) services for sharing and analysis of pre-publication data among research groups. This paper reports recent updates on the databases and the services of the DDBJ Center, highlighting the DGC service.

A molecular approach to identify parrotfish (Sparisoma) species during early ontogeny.

Sparisoma species (parrotfish) comprise an important functional group contributing to coral-reef resilience. The morphological diagnostic characteristics for species identification are clearly described for adult forms but not for the early stages. Consequently, many taxonomical listings of Sparisoma larvae are restricted to the genus level. The aims of this study are to determine whether the morphological and molecular identification techniques are useful to assign the species taxonomic level to Sparisoma larvae occurring in the Gulf of Mexico and whether there is a set of diagnostic features that could be used to discriminate between species in larvae of different developmental stages. Morphological assignment of Sparisoma was performed based on morphological and meristic features for 30 larvae collected in the Gulf of Mexico from late August to mid-September 2015. To corroborate and complement the morphological assignments, molecular identification was carried out using DNA sequences from regions of two mitochondrial genes, mitochondrial cytochrome oxidase I (mtDNA COI) and mitochondrial 16S rRNA (mtDNA 16S rRNA). COI and 16S gene trees for Sparisoma and related fish taxa were constructed using sequences available in the NCBI (National Center for Biotechnology Information) GenBank and BOLD (Barcode of Life Data) databases. Two morphotypes were identified based on morphology, but no diagnostic characteristics for species discrimination were found. Molecular identification, in contrast, successfully discriminated four early development stages of Sparisoma atomarium, three stages of Sparisoma radians, and two stages of Sparisoma chrysopterum and Sparisoma aurofrenatum, therefore demonstrating the successful and necessary application of molecular taxonomic approaches for species-level identifications of Sparisoma larvae.

Relationship between Sleep Quality and Vertigo Incidence in College Students

One-third of adults are affected by poor sleep quality. Sleep problems are not only experienced by adults. Knowing the relationship between sleep quality and the incidence of vertigo is very important and urgent because of its very broad impact on health, understanding pathophysiology, clinical development, improving quality of life, as well as education and awareness in the community, especially students. In Indonesia, the prevalence of sleep disorders in adolescents is 62.9%. This study aims to determine the relationship between sleep quality and the incidence of vertigo in students. Literature review using Google Scholar, National Center for Biotechnology Information (NCBI) & Research Science found 9 journals based on inclusion & exclusion criteria. The results of the research is the relationship between sleep quality and vertigo involves a complex interaction between physiological and psychological factors. Physiological effects include disorientation and instability, motor coordination, and physiological stress responses such as cortisol. The psychological effects that can occur are anxiety, depression, decreased concentration, decreased cognitive function, and increased psychological discomfort. Lack of sleep in students makes vertigo symptoms worse. Lack of sleep will make vertigo symptoms worse. It is best to arrange the right sleeping position so that symptoms of vertigo do not occur, because vertigo can occur even in people who have never experienced it. The conclusion is there is a relationship between sleep quality and the incidence of vertigo in students.

Bioinformatics analysis of the antigenic epitopes of L7/L12 protein in the B- and T-cells active against Brucella melitensis

Abstract The objective is to analyse the physicochemical properties, spatial structure and protein–protein interactions (PPIs) of L7/L12 protein using bioinformatics methods and predict their B- and T-cell epitopes to lay a theoretical foundation for developing a novel multiepitope vaccine (MEV). The National Center for Biotechnology Information (NCBI) database was searched for the amino acid sequences of L7/L12 from Brucella melitensis. In addition, the online softwares, ProtParam and ProtScale, were used to predict the physicochemical properties: NetPhos3.1 and CD-search to predict the phosphorylation sites and conserved domains; SOMPA and SWISS-MODEL to predict the secondary and tertiary structures; the STRING database to analyse the PPIs; and the IEDB, ABCpred, SVMTrip and SYFPEITHI databases to predict the B- and T-cell epitopes. L7/L12 was docked to Toll-like receptor 4 (TLR4), B-cell receptor (BCR), Major histocompatibility complex I-T cell receptor (MHC I-TCR) and MHC II-TCR complexes, respectively, and the binding ability of L7/L12 to the targeted receptors was tested. L7/L12, consisting of 124 amino acids, was determined to be a stable, intracellular, hydrophilic protein containing 6 phosphorylation sites and ribosomal protein-related conserved domains. α-helices accounted for 70.16 %, β-turns for 2.42 %, extended strands for 8.87 % and irregular coils for 18.55 % of the secondary structure. The PPIs indicated that L7/L12 was involved in the constitution of ribosomes and regulating the accuracy of the translation process. Three B-cells, two cytotoxic T lymphocytes and three helper T lymphocyte epitopes were finally screened by comparing multiple databases. L7/L12 binds to TLR4, BCR, MHC I-TCR and MHC II-TCR complexes and forms stable hydrogen bonds, respectively. L7/L12, which governs the translation curate of proteins, possesses several potentially advantageous epitopes, laying a theoretical foundation for designing MEVs.

Research on the Regulatory Mechanism of Ginseng on the Tumor Microenvironment of Colorectal Cancer based on Network Pharmacology and Bioinformatics Validation.

A network pharmacology study on the biological action of ginseng in the treatment of colorectal cancer (CRC) by regulating the tumor microenvironment (TME). To investigate the potential mechanism of action of ginseng in the treatment of CRC by regulating TME. This research employed network pharmacology, molecular docking techniques, and bioinformatics validation. Firstly, the active ingredients and the corresponding targets of ginseng were retrieved using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), the Traditional Chinese Medicine Integrated Database (TCMID), and the Traditional Chinese Medicine Database@Taiwan (TCM Database@Taiwan). Secondly, the targets related to CRC were retrieved using Genecards, Therapeutic Target Database (TTD), and Online Mendelian Inheritance in Man (OMIM). Tertiary, the targets related to TME were derived from screening the GeneCards and National Center for Biotechnology Information (NCBI)-Gene. Then the common targets of ginseng, CRC, and TME were obtained by Venn diagram. Afterward, the Protein-protein interaction (PPI) network was constructed in the STRING 11.5 database, intersecting targets identified by PPI analysis were introduced into Cytoscape 3.8.2 software cytoHubba plugin, and the final determination of core targets was based on degree value. The OmicShare Tools platform was used to analyze the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the core targets. Autodock and PyMOL were used for molecular docking verification and visual data analysis of docking results. Finally, we verified the core targets by Gene Expression Profiling Interactive Analysis (GEPIA) and Human Protein Atlas (HPA) databases in bioinformatics. A total of 22 active ingredients and 202 targets were identified to be closely related to the TME of CRC. PPI network mapping identified SRC, STAT3, PIK3R1, HSP90AA1, and AKT1 as possible core targets. Go enrichment analysis showed that it was mainly involved in T cell co-stimulation, lymphocyte co-stimulation, growth hormone response, protein input, and other biological processes; KEGG pathway analysis found 123 related signal pathways, including EGFR tyrosine kinase inhibitor resistance, chemokine signaling pathway, VEGF signaling pathway, ErbB signaling pathway, PD-L1 expression and PD-1 checkpoint pathway in cancer, etc. The molecular docking results showed that the main chemical components of ginseng have a stable binding activity to the core targets. The results of the GEPIA database showed that the mRNA levels of PIK3R1 were significantly lowly expressed and HSP90AA1 was significantly highly expressed in CRC tissues. Analysis of the relationship between core target mRNA levels and the pathological stage of CRC showed that the levels of SRC changed significantly with the pathological stage. The HPA database results showed that the expression levels of SRC were increased in CRC tissues, while the expression of STAT3, PIK3R1, HSP90AA1, and AKT1 were decreased in CRC tissues. Ginseng may act on SRC, STAT3, PIK3R1, HSP90AA1, and AKT1 to regulate T cell costimulation, lymphocyte costimulation, growth hormone response, protein input as a molecular mechanism regulating TME for CRC. It reflects the multi-target and multi-pathway role of ginseng in modulating TME for CRC, which provides new ideas to further reveal its pharmacological basis, mechanism of action and new drug design and development.

Designing a multi-epitope construct using immuno-informatic tools to prepare a messenger RNA vaccine against Rhipicephalus microplus ticks

Background and Aim: Ticks are blood-feeding ectoparasites that transmit pathogens to animals and humans. One of the most important hard ticks in animals is Rhipicephalus microplus, which transmits Babesia and Anaplasma spp. Although many potential tick vaccine candidates have been identified, no effective vaccine that can provide sterile immunity against R. microplus tick infestations has been developed. This study aimed to design a construct using different computational tools to identify and predict immunogenic epitopes within protein sequences and to prepare a messenger RNA (mRNA) vaccine against R. microplus based on lipid nanoparticles (LNPs). Materials and Methods: The R. microplus proteins (Bm86, Subolesin, and ATAQ) were selected and their consensus sequence was obtained from the National Center for Biotechnology Information in FASTA format. The Immune Epitope Database and Analysis Resource (IEBD) server was used for the prediction of helper T-cell epitopes, the NetCTL 1.2 server was used to predict cytotoxic T-cell epitopes, and the ABCpred server was used for B-cell epitope prediction. Antigenicity testing, allergenicity assessment, and toxicity screening were immuno-informatic techniques used to identify potent epitopes within protein sequences. The multi-epitope construct was prepared and cloned into the pVAX1 plasmid. Plasmids were transformed in compatible competent cells, and restriction analysis was performed. After restriction analysis of the transformed plasmid, in vitro transcription was performed to prepare mRNA. The mRNA was purified, quantified, and converted into complementary DNA, and gene-specific primers were used to confirm the in vitro transcription of mRNA. A mixture of four lipids containing 1,2-dioleoyl-3-dimethylammonium-propane (DODAP), Distearoylphosphatidylcholine (DSPC, cholesterol, and 1,2-Dimyristoyl-sn-glycero-3-methoxypolyethylene glycol-2000 (DMG PEG-2000 was used to prepare LNPs. LNPs were characterized using a scanning electron microscope, Zeta potential, and Zeta Sizer tests. Results: More than 1000 epitopes were predicted, from which only nine helper T-lymphocytes, 18 cytotoxic T-lymphocytes, and nine B-cell epitopes of all three proteins were selected with high antigenic scores of 0.958 for Bm86, 0.752 for Subolesin, and 0.964 for ATAQ, respectively. An adjuvant was used to enhance immune responses, all of which were linked to one another using GPGPG, AAY, and KK linkers, respectively. The physiochemical properties predicted that the instability index of the construct would be <40%, indicating that the construct is stable. Plasmids were transformed in compatible competent cells, and white-transformed colonies were observed. Restriction analysis was performed, DNA was transcribed into mRNA, and LNPs were prepared and characterized. Conclusion: More than 1000 epitopes were predicted using immune informatic tools, and only high-scoring epitopes were selected. A multi-epitope construct was designed using bio-informatic tools, and its physicochemical properties were predicted. The design construct was inserted into the pVAX1 plasmid, and in vitro transcription was performed to prepare the mRNA. LNPs of mRNA were prepared and characterized to be used as vaccines. It was found that LNPs were stable and nanometer-sized. Keywords: immuno-informatic tools, lipid nanoparticles, multiepitope construct, Rhipicephalus microplus.