SORTEZ: a relational translator for NCBI's ASN.1 database.

Cyanobacteria play a key role in many ecosystems. Cell-environment interaction has been attributed to their metabolite production, allowing cyanobacteria to adapt and survive under extreme conditions. A strain of cyanobacteria (Chlorogloeopsis sp. ULAP01) isolated from a copper mine tailing site in Ampucao, Benguet, the Philippines, was examined in this study. It aimed to construct the whole genome sequence of the cyanobacterium, characterize it, and compare the assembled genome with the sequences available in the National Center for Biotechnology Information (NCBI) database. The whole genome of Chlorogloeopsis sp. ULAP01 was assembled, constructed, and functionally analyzed. Sequence analysis of the Chlorogloeopsis sp. ULAP01 with the C. fritschii genomes available in the NCBI database was also performed. The assembled genome had a total length of 7.9 Mb, 45 contigs, and 41% GC content. The isolate was identified as putatively Chlorogloeopsis sp. ULAP01 by morphological and molecular characterization through GTDB-Tk results and evolutionary analysis. It forms a separate node from the two known clusters of Chlorogloeopsis, indicating that it may be a separate strain or a new, previously uncharacterized strain or species. Chlorogloeopsis sp. ULAP01 shared 2,019 core genes with the other C. fritschii assemblies in the NCBI database but also possessed a total of 4,449 unique genes, 65.24% of its total annotated genes. It was noted that the strain shared the same core genes, but the accessory genes of Chlorogloeopsis sp. ULAP01 varied widely with the other Chlorogloeopsis sp. in the database. Chlorogloeopsis sp. ULAP01 is the first isolate to be added to NCBI that came from a tropical freshwater ecosystem. The unique specialized genes such as copB, entS, yfeA, and ftsP are involved in cellular processes for survival in a metal-stressed condition that may be responsible for its survival in an extreme environment.

BackgroundThe fidelity of DNA replication serves as the nidus for both genetic evolution and genomic instability fostering disease. Single nucleotide polymorphisms (SNPs) constitute greater than 80% of the genetic variation between individuals. A new theory regarding DNA replication fidelity has emerged in which selectivity is governed by base-pair geometry through interactions between the selected nucleotide, the complementary strand, and the polymerase active site. We hypothesize that specific nucleotide combinations in the flanking regions of SNP fragments are associated with mutation.ResultsWe modeled the relationship between DNA sequence and observed polymorphisms using the novel multifactor dimensionality reduction (MDR) approach. MDR was originally developed to detect synergistic interactions between multiple SNPs that are predictive of disease susceptibility. We initially assembled data from the Broad Institute as a pilot test for the hypothesis that flanking region patterns associate with mutagenesis (n = 2194). We then confirmed and expanded our inquiry with human SNPs within coding regions and their flanking sequences collected from the National Center for Biotechnology Information (NCBI) database (n = 29967) and a control set of sequences (coding region) not associated with SNP sites randomly selected from the NCBI database (n = 29967). We discovered seven flanking region pattern associations in the Broad dataset which reached a minimum significance level of p ≤ 0.05. Significant models (p << 0.001) were detected for each SNP type examined in the larger NCBI dataset. Importantly, the flanking region models were elongated or truncated depending on the nucleotide change. Additionally, nucleotide distributions differed significantly at motif sites relative to the type of variation observed. The MDR approach effectively discerned specific sites within the flanking regions of observed SNPs and their respective identities, supporting the collective contribution of these sites to SNP genesis.ConclusionThe present study represents the first use of this computational methodology for modeling nonlinear patterns in molecular genetics. MDR was able to identify distinct nucleotide patterning around sites of mutations dependent upon the observed nucleotide change. We discovered one flanking region set that included five nucleotides clustered around a specific type of SNP site. Based on the strongly associated patterns identified in this study, it may become possible to scan genomic databases for such clustering of nucleotides in order to predict likely sites of future SNPs, and even the type of polymorphism most likely to occur.

Trichoderma spp. is a common soil fungus that penetrates plant roots and engages with various microorganisms and plants. The present study aimed to determine the phylogenetic relationships of rhizosphere isolates of Trichoderma spp. obtained from the local soil in Mosul in the north of Iraq utilizing the sequence of the internal transcribed spacer-1 (ITS-1) region of the ribosomal DNA of eight Trichoderma spp.. Approximately 192 samples were collected between March and October 2023 from the rhizospheric soil of Potato )Solanum tuberosum), Tomato (Solanum lycopersicum), Wheat (Triticum aestivum), Barley (Hordeum vulgare), Eucalyptus (Eucalyptus globulus) and Citrus (Citrus limon (. Only 5.8% of the rhizosphere samples belonged to Trichoderma spp. The samples were identified based on morphological characteristics and molecular techniques. All the selected isolates amplified a similar band (660 bp). The nucleotide sequences were then analyzed, and a phylogenetic tree was constructed to compare the present isolates with the closest isolates submitted to the National Center for Biotechnology Information (NCBI). Isolates were submitted to NCBI as new strains under the accession numbers: Trichoderma harzianum (PP968131), T. longibrachiatum (PP977534), T. harzianum (PP977576), T. longibrachiatum (PP989798), Trichoderma longibrachiatum (PP989800), T. longibrachiatum (PP989803), T. longibrachiatum (PP989804), and T. harzianum (PP989805). This study expands the NCBI database with novel Trichoderma strains, enhancing fungal genetic resources globally. These new entries provide unique genomic data, potentially revealing valuable traits, resolving taxonomic ambiguities within Trichoderma, and improving the reliability of the NCBI database for future studies.

Cattle is one of the largest livestock products in Indonesia. The purpose of this study was to determine the diversity of the myostatin (MSTN) gene found in several cattle in Indonesia. This research was a descriptive analysis research based on several literature studies. Gene data was taken from the National Center for Biotechnology Information (NCBI). The gene data taken were from several species such as Bos indicus, Bos indicus×Bos taurus, and Bos taurus. Meanwhile, Bubalus bubalis, Capra hircus, and Cervis sp. were selected as outgroups. DNA sequence data analysis was aligned using MEGA XI software. MSTN gene parameters showed results between the kinship of several cattle in Indonesia. From these results it can be found that there were still several species of cattle in Indonesia that were not yet found in the NCBI database on the MSTN gene. For example, Madura cattle (Bos javanicus), PO Kebumen, PO Aceh, and several livestock products that do not yet have the MSTN gene characterization database. Therefore, to improve the quality of beef in Indonesia, it is necessary to characterize the MSTN gene in several species that are not yet in the database as a benchmark for the quality level of cattle in Indonesia.

MPT64 protein is an effective marker for detecting Mycobacterium tuberculosis (MTB) in liquid culture and clinical tissue samples. However, some MTB clinical isolates test negative for this antigen because of varied mutation types across different regions. DNA samples of MPT64 antigen assay-negative MTB strains were collected from a tertiary hospital from January 2016 to January 2024, and mpt64 gene mutations were detected by sequencing. Clinical records of patients with negative MPT64 antigen results were collected and compared with those of patients with positive results. The global distribution of mpt64 gene mutations was analyzed using MTB genome sequences from the National Center for Biotechnology Information (NCBI) database. Among 821 mycobacterial specimens with negative MPT64 antigen assay results, 77 MTB strains were collected from 73 patients. Compared with MPT64-positive patients (n = 301), a higher percentage of MPT64-negative patients had a history of anti-tuberculosis therapy (n = 7, 11.1%; P = 0.01). Moreover, MPT64-negative patients demonstrated a lower percentage of positive Gene Xpert results than MPT64-positive patients (73.8% vs 95.1%, P < 0.001). Several gene mutations were detected in the MPT64-negative MTB strains, including 63 bp deletion, single nucleotide mutations, and IS6110 insertion. Among 7,324 MTB genomes from the NCBI database, 87 strains had mutations in the mpt64 gene sequence, with four common mutation sites causing single amino acid changes, including G34A (8.0%), A103G (27.6%), T128A (9.2%), and C477A (24.1%). A negative MPT64 antigen result in MTB cultures can be attributed to mutations in the mpt64 gene, and infections caused by these strains are more likely to be misdiagnosed.

Whey acidic protein (WAP) has been identified as a major whey protein in milk of a wide range of species and reportedly plays important roles in regulating the proliferation of mammary epithelial cells. However, in some species including humans, WAP is not synthesized in the mammary gland. The presence of WAP in carnivore species has not been reported. We searched the National Center for Biotechnology Information (NCBI) database for the dog WAP gene and tried biochemically to identify WAP in dog milk. The nucleotide sequence of the examined dog genomic DNA was completely identical to that in the NCBI database and showed that the dog WAP gene, like other known functional WAP genes, has four exons. Biochemical analysis of milk protein by reverse-phase HPLC and Western blotting demonstrated the presence of WAP in dog milk.

ObjectivesThis study aimed to analyze chromosomal arm-level copy number variations (CNVs) in benign diseases, cervical intraepithelial neoplasia (CIN), and cervical cancer (CC) using low-coverage whole genome sequencing (LC-WGS) and evaluate the efficacy of the ultrasensitive chromosomal aneuploidy detector (UCAD) model in distinguishing CC from CIN and benign diseases.MethodsCervical exfoliated cell specimens from 50 patients were collected for high-risk human papillomavirus(hr-HPV) testing, ThinPrep Cytologic Test (TCT), and CNV detection via LC-WGS. UCAD was employed to analyze chromosomal changes, with validation using WGS data from the National Center for Biotechnology Information(NCBI) database.ResultsAmong 50 patients, 8 had benign disease, 3 CIN1, 15 CIN2, 6 CIN2-3, 13 CIN3, and 5 CC. Chromosomal instability was detected in 9 patients (18%): all 5 CC cases, 3 CIN3 cases, and 1 CIN1 case. Gains in 3q were observed in all CC and CIN3 cases with CNVs. UCAD achieved 100% sensitivity and 91.11% specificity in differentiating CC from CIN and benign diseases, outperforming hr-HPV and TCT. The UCAD model was also applied to 5 CC and 1 high-grade squamous intraepithelial lesion (HSIL) cases obtained from the NCBI database, and the findings validated its ability to detect chromosomal aberrations in all cases.ConclusionsCNV analysis of cervical exfoliated cells shows promise for CC detection, with UCAD demonstrating high accuracy. Further validation in larger cohorts is needed to confirm its clinical utility.

To establish an improved ribosomal gene sequence database as part of the Ribosomal Differentiation of Microorganisms (RIDOM) project and to overcome the drawbacks of phenotypic identification systems and publicly accessible sequence databases, both strands of the 5' end of the 16S ribosomal DNA (rDNA) of 81 type and reference strains comprising all validly described staphylococcal (sub)species were sequenced. Assuming a normal distribution for pairwise distances of all unique staphylococcal sequences and choosing a reporting criterion of > or =98.7% similarity for a "distinct species," a statistical error probability of 1.0% was calculated. To evaluate this database, a 16S rDNA fragment (corresponding to Escherichia coli positions 54 to 510) of 55 clinical Staphylococcus isolates (including those of the small-colony variant phenotype) were sequenced and analyzed by the RIDOM approach. Of these isolates, 54 (98.2%) had a similarity score above the proposed threshold using RIDOM; 48 (87.3%) of the sequences gave a perfect match, whereas 83.6% were found by searching National Center for Biotechnology Information (NCBI) database entries. In contrast to RIDOM, which showed four ambiguities at the species level (mainly concerning Staphylococcus intermedius versus Staphylococcus delphini), the NCBI database search yielded 18 taxon-related ambiguities and showed numerous matches exhibiting redundant or unspecified entries. Comparing molecular results with those of biochemical procedures, ID 32 Staph (bioMerieux, Marcy I'Etoile, France) and VITEK 2 (bioMerieux) failed to identify 13 (23.6%) and 19 (34.5%) isolates, respectively, due to incorrect identification and/or categorization below acceptable values. In contrast to phenotypic methods and the NCBI database, the novel high-quality RIDOM sequence database provides excellent identification of staphylococci, including rarely isolated species and phenotypic variants.

Indo-Pacific bottlenose dolphins (Tursiops aduncus) are a coastal species found in Thai waters off the coasts of the Andaman Sea and the Gulf of Thailand. This species was recently re-listed as near-threatened by the IUCN Red List, though the population status in Thai seas is not known. Here, we investigated genetic diversity, population structure, maternal lineage, and demographics by analyzing skin tissue samples (n = 30) of T. aduncus stranded along the Andaman coastline of Thailand between 1990 and 2019. This study was based on 11 microsatellite loci and 265 bp mtDNA control regions compared to data available through the National Center for Biotechnology Information (NCBI). From microsatellites, the observed heterozygosity (Ho) ranged from 0.46 to 0.85. The mean fixation index (F) value for all loci was 0.10 ± 0.04, which suggests some degree of inbreeding. Two genetic clusters (the most likely K at K = 2) were observed in T. aduncus through the population structure analysis using multiple criteria. For the mtDNA control region, a total of 17 haplotypes were found for dolphins in Thai seas (14 haplotypes from our samples; three haplotypes from the NCBI database) with high levels of haplotype diversity (h) at 0.926 ± 0.027 and nucleotide diversity (π) at 0.045 ± 0.002. A decline in the effective population size from 0.05 million years ago also was observed in Thai T. aduncus through Bayesian Skyline Plots analysis. A unique set of haplotypes was identified in our samples, which may have originated from the Australian and Indian Oceans rather than the Western Pacific Ocean. These results improve our understanding of the maternal lineage of the Indo-Pacific bottlenose dolphin, which can be used for monitoring population status and establishing better conservation plans for this species in the Thai Andaman Sea.

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

The partial sequence of <i>trn</i>L-<i>ndh</i>J of chloroplast genome ofthe new species of the genus Yulania Spach of Magnoliaceae, Yulania baotaina D. L. Fu, Q. Zhang et M. Xu, collected from Baotai Mountain of Yongping County of Yunnan province of China, and the similar species, Y. campbellii (Hook. f. et Thoms.) D. L. Fu, collected from Yongping and Gongshan county of Yunnan, and Yadong county of Xizang, were amplified and sequenced respectively, which were compared with 39 samples of the chloroplast complete genomes of Magnoliaceae in the NCBI (National Center for Biotechnology Information, USA) database. The results indicated that Y. baotaina has two PEL (particularly evolutionary loci): <i>trn</i>L-<i>ndh</i>J (...TTTCATTTC<u>G</u>GAATTTC<u>C</u>TATTTTCTT...) not possessed by others, and the oppositely evolutionary loci of transversions <i>trn</i>L-<i>ndh</i>J (...TTTCATTTC<u>T</u>GAATTTC<u>A</u>TATTTTCTT...) is possessed by all contrasted experimental materials and most simples of Magnoliaceae in NCBI. So the new species was described and illustrated. Its floral buds cylindrical, ovaries subcordiform, and peduncles of flower and fruits obviously elongate are particular, which can be easily distinguished to the similar species and all other ones in the genus. The new species is distributed in Hengduan Mountain of west Yunnan province and south Xizang Autonomous Region at an altitude of 1900~3000 m, a colloquial name is Mulianhua, just as the similar species Y. campbellii. The designated type of the new species was collected from Baotai Mountain of Yongping County at altitude of 2600 m and kept at the Chinese Academy of Forestry. This paper will provide a new research method that can be easily verified for the evolutionary taxonomy and the new science of evolutionomy.

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 37 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include iCn3D, MutaBind, and the Antimicrobial Resistance Gene Reference Database; and resources that were updated in the past year include My Bibliography, SciENcv, the Pathogen Detection Project, Assembly, Genome, the Genome Data Viewer, BLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.

BackgroundEvidence implicates the role of gut microbiota in colorectal cancer (CRC). Veillonella parvula (V. parvula), an anaerobic bacterium that metabolizes lactic acid, is positively related to the development of CRC....

Objective: This study examined susceptibility of the clinical isolate Streptococcus sanguinis, isolated from an infected root canal to various antibiotics, and tested its capacity to form a slime layer. Method: PCR and gel electrophoresis both confirmed it as bacterial identification. The 16S rRNA gene sequence of S. sanguinis was determined and compared to previously determined sequences in the NCBI (National Center for Biotechnology Information) database. Growth of the isolate was determined to consist of a strong ability to form a slime layer when grown on Congo red-modified Schaedler agar medium. Results: GenBank records for the resulting sequences are under the accession numbers PQ654829 and PQ654911. The antibiotic susceptibility profile was high to levofloxacin, moderate to gentamicin, tobramycin and vancomycin, and complete resistance to cefixime. Novelty: The results of this study provide important information about the bacterium's virulence and antibiotic resistance.