NCBI Tools Research Articles

Teaching research skills to the undergraduate bioscience students through COVID-19 studies

Objective: To describe experience of teaching research skills to the undergraduate bioscience students through COVID-19 studies.Methodology: Undergraduate students taking physiology, microbiology or biomanufacturing at a public college in Kansas City Kansas, during spring 2020 to fall 2023 were encouraged and mentored to 1) do literature survey on COVID-19 2) read the COVID-19 related clinical case study 3) read the COVID-19 related review article 4) learn basic bioinformatics tools 4) prepare and present poster in scientific conference 5) prepare review article.Results: This exercise allowed the students to learn using search engines like PubMed to find reliable information about the disease such as COVID-19. In the fall semester of 2020, students prepared a research paper about the coronavirus, COVID-19 disease, its symptoms and transmission. In the fall semester of 2022, students performed literature survey using PubMed, prepare presentations on various aspects of COVID-19 and wrote a review article. Students read review article about COVID-19 in the Spring semester of 2023 and responded to the questions related to the article. In the fall of 2021, students learned about the clinical aspects of COVID-19 by reading a clinical case study. This also helped students to understand molecular techniques like polymerase chain reaction (PCR), serology tests and how they are used to diagnose the disease. Similarly, in spring of 2022 students learned using NCBI tools to find the genomic and protein sequence of SARS-CoV-2 and its spike protein respectively. They also learned to design primers for PCR for the detection of coronavirus. Finally, students prepared and presented the poster on COVID-19 in a scientific conference.Conclusion: The methodology adopted enabled training the students to learn many research skills like literature survey, write review article, thoroughly read articles, understand the mechanism behind PCR, learn basic bioinformatics, prepare research poster and give scientific presentations. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Isolation and molecular characterization of Acanthamoeba spp. from Iraqi patients with Keratitis

Isolation and molecular characterization of Acanthamoeba spp. related corneal infections in Iraqi Patients. A total of 96 samples from corneal scraps and contact lenses were gathered from corneal patients for the current trial, which runs from November 2020 to May 2021. All plates were checked, classifying them as positive or negative morphologically identification of Acanthamoeba spp. where PCR analysis, which entails the targeted amplification of nucleic acids, has been carried out, and where The 18s rRNA gene's DF3 region was the focus of the isolated strains' sequences. Three patients had Acanthamoeba spp. infections, according to the findings. then the sequence analysis was performed using the NCBI tool, which showed the presence of 2 different genotypes, two strains were grouped into the T3 genotype, one from T4, then they were registered in GeneBank under number accession (MZ427912, MZ349042) respectively. To our knowledge, these are the first reported cases of Acanthamoeba keratitis in Iraq.

Using Bioinformatics and NCBI Tools to Sequence and Structure Analysis of Transcription Factor 7 Like 2 Gene (TCF7L2) in Iraqi Diabetic Mellitus Type II Patients

In this paper, the study aimed to analyze the sequence and structure of Transcription Factor 7 Like 2 gene (TCF7L2) in Iraqi Diabetic Mellitus Type II (T2DM) Patients and was compared with standard sequence form National Center of Bioinformatics Tools (NCBI) using BLAST. Ten blood samples of (T2DM) Iraqi patients, was collected from Al-Mustansiriya University National Diabetes Centre in Baghdad Province/Iraq (17-65 year). DNA was extracted from whole blood of patients’ samples using the Quick-DNA™ Blood MiniPrep kit, then it was sent to Korea at Macrogen Corporartion Company, where they used automated DNA sequencing for sequence analysis. The results of the sequence analysis of (T2DM) patients’ samples, we found: six missense mutations, one deletion mutation, and three silent mutations detected using BLAST in (NCBI). All mutations appeared at the same sites of the gene which controls the rate of genetic information transcription that indicates to have a relationship with (T2DM). These mutations were recorded on the (NCBI). The physicochemical properties of (TCF7L2) determined in the present study included; alpha-helical structure and 3-Dimension structure appeared contrast when compared with the gene template. Briefly, mutations effected (TCF7L2) which influences the structure, physicochemical properties of the protein, and the secretion of insulin hormone which maintains glucose level in blood.

DEVELOPMENT OF A CRISPR-BASED ANTIVIRAL SYSTEM AGAINST BOHV-1

<h3>Background</h3> Bovine Herpesvirus type 1 (BoHV-1) infection has no cure and infected animals become lifelong carriers, greatly impacting health and productivity of herds worldwide. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas (CRISPR associated) tool has been widely explored for the development of antiviral strategies due to its ability to precisely edit genetic sequences. In this manner, we have designed a CRISPR-based antiviral system against BoHV-1 through the tetracycline-inducible expression of the Cas9 nuclease and a guide RNA (gRNA) homologous to a viral sequence in genetically modified bovine cells. <h3>Methods</h3> The in silico design of the antiviral system was based on the literature. BoHV-1 and bovine (Bos taurus taurus) genome were obtained from GenBank and basic molecular vectors from Addgene. Sequence analysis of appropriate targets were performed with Snapgene and Serial Cloner. Primers for cloning were obtained using the NCBI tool Primer BLAST. The gRNA for bovine DNA cleavage was selected from literature considering cleavage efficiency and potential off-target effects. The gRNA for the viral genome cleavage was designed using the CRISPR gRNA design tool from ATUM and CHOPCHOP. <h3>Results</h3> The developed molecular vector allows the delivery of the necessary machinery to perform a cleavage in the chromosome 25 of the bovine DNA between the FSCN1 and the ACTB genes, where the sequence of the antiviral mechanism will be inserted by homologous recombination (HR). The cleavage site has already been reported as safe for the insertion of sequences into the bovine genome. The HR fragment has the Cas9 nuclease sequence and a tetracycline-inducible expression system capable of conditioning the expression of the nuclease gene to the presence of the antibiotic. In addition, the fragment has a sequence for the expression of a gRNA targeting an essential sequence for virus replication, the UL52 gene. The expressed Cas9 enzyme and gRNA form a ribonucleoprotein complex capable of cleaving only the virus genome leading to its inactivation and preventing its replication in the genetically modified cells stimulated by tetracycline. <h3>Conclusion</h3> The mechanism and elements developed explore new applications of the CRISPR-Cas tool to combat viral diseases that currently have no cure. The ease of altering the gRNA target makes the proposed system highly flexible and can possibly be applied to different diseases caused by viruses.

Study the Cytochrome P450 Gene Expression Changes in Iraqi Patients with Chronic Liver Disease

The cytochrome P450 is a chemical group of heme-containing proteins speaks to one of the biggest and most practically various superfamilies’ found in nature. Chronic liver disease (CLD) is a the process of the liver that involves a process of progressive destruction and regeneration of the liver parenchyma leading to fibrosis and cirrhosis. The aim of this study to assessment the cytochrome P450 gene expression changes of three variants, CYP1A2, CYP2B6, and CYP2E1 in Iraqi patients with chronic liver disease(hepatitis+ alcoholism and hepatitis+ non-alcoholism).CYP1A2, CYP2B6, and CYP2E1 mRNA gene expression were assessed by quantitative real time PCR (qRT-PCR) in 50 cases with CLD and 50 subjects as control. Primers for genes of interest, CYP1A2, CYP2B6, and CYP2E1mRNA and housekeeping gene (GAPDH) were designed by using NCBI tools. Fatty acid synthase (FAS) was estimated by ELISA technique. The results showing statically significant differences in FAS levels (ng/ml) between study groups, HC, HNC, and control (p-value&lt; 0.05). GEF in CYP1A2 gene showing no change between HC and control but there were statistical variations in GEF in HNC and both HC or control. GEF in CYP2B6 and CYP2E1 genes showing highly significant differences between control and both HNC and HC. In conclusion, CYP2B6 and CYP2E1 gene expression were risk factor for progression HC but not HNC through stimulation of increasing levels of FAS.

Proceedings of the 2012 MidSouth computational biology and bioinformatics society (MCBIOS) conference

The ninth annual conference of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS 2012), Making Sense of the Omics Deluge, took place in Oxford, Mississippi February 17-8 2012. This year's Conference Chairs were Dr. Dawn Wilkins, of the University of Mississippi and Dr. Doris Kupfer, also the current MCBIOS President (2011-2), from the Federal Aviation Administration. There were 170 registrants and a total of 106 abstracts (34 oral presentations and 72 poster session abstracts). Keynote speakers for 2012 were Dr. Michael Gribskov, Purdue University, who gave the opening address, After the Deluge: Bioinformatics meets big data; Dr. David J. States, OncProTech LLC, who gave his presentation remotely via WebEx entitled Data Intensive Proteomics; and Sultan Meghji, Appistry Inc. presenting the Saturday morning address, entitled Simple, Fast and Affordable - Turning the myriad of data into action - technologies to support personalized medicine and invited speaker, Dr. William Slikker, Director of the Food and Drug Administration's, National Center for Toxicological Research, presented a talk entitled Regulatory Science: Challenges and Progress outlining the role research at the FDA plays in their regulatory responsibilities. Participants also had the opportunity to attend hands-on workshops on NCBI tools, presented by Dr. Peter Cooper, NCBI/NLM/NIH staff scientist, and a collaboration workshop focused on the timber rattlesnake genome, facilitated by Dr. Ed Perkins, Army Corp of Engineers. The winners of conference awards were: Best Oral Presentations (students): 1st Place: Shana Stoddard, University of Mississippi 2nd Place: Neal Platt, Mississippi State 3rd Place: Aleksandra Markovets, UALR Best Oral Presentations (Post-Doctoral fellows): 1st Place: Mikhail Dozmorov, OMRF 2nd Place: Zhichao Liu, NCTR Best Poster (Computation): 1st Place: Shraddha Thakkar, UAMS 2nd Place: Xingyan Kuang, University of Missouri 3rd Place: Sule Dogan, Mississippi State Best Poster (Biology): 1st Place: Tamer Aldwairi, Mississippi State 2nd Place: Dilip Gautam, Mississippi State 3rd Place: Bin Pang, University of Missouri

Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference

The Eighth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society (MCBIOS’2011) was held in College Station, Texas on April 1-2, 2011. The Conference General Chair was Ulisses Braga-Neto, the MCBIOS President for the 2010-2011 term, from Texas A&M University. There were nearly 200 registrants and 140 abstracts were submitted, divided into 48 oral presentation abstracts and 92 poster session abstracts. In addition, participants attended talks by very distinguished Keynote speakers. Joan W. Bennett, from Rutgers University and Member of the National Academy of Science, presented the talk “Chromosomal Composition and Computational Competence;” Donald Geman, from The Johns Hopkins University and co-inventor of the Gibbs Sampler and Random Forest Classifiers, lectured on “Measuring Network Regulation and Differential Expression by Rank Conservation;” while John Weinstein, Chair of the Department of Bioinformatics and Computational Biology at the University of Texas M.D. Anderson Cancer Center, talked on “Personalizing Cancer Medicine in the Era of Next-Generation Sequencing: Omics and Informatics.” The conference also benefited from invited dinner and lunch speakers, who gave informal, highly informative and entertaining talks. Edward R. Dougherty, from Texas A&M University and Director of Computational Biology at the Translational Genomics Institute, asked the audience “Is Biological Science Delightful?” whereas Ernesto Marques, from the Center for Vaccine Research at the University of Pittsburgh, gave the talk “Activation of the Complement System in Dengue Infection: Opportunities for Computational Modeling.” Participants also had the opportunity to attend hands-on workshops on NCBI tools, presented by Peter Cooper from NCBI/NIH, and on protein evolution, presented by Hugh Nicholas and Troy Wymore, from the Pittsburgh Supercomputing Center. The winners of conference awards were: Best Oral Presentations (students): First place: Suzanne Matthews, Texas A&M University Second place (3-way tie): Lori Dalton, Texas A&M University Second place: Shelton Griffith, Oak Ridge National Lab Second place: Winston Haynes, Hendrix College Best Oral Presentations (Post-Doctoral fellows): Yan Li, NCTR Fan Zhang, IUPUI Best Poster (Computation): First place: Tianchuan Du, Southern University Second place: Christopher Cathey, Jackson State University Third place: Ralph Crosby, Texas A&M University Best Poster (Biology): First place: Awantika Singh, UALR/UAMS Second place: Mohammed Shahrokh Esfahani, Texas A&M University Third place: Fang-Han Hsu, Texas A&M University MCBIOS Outstanding Service Award: Dr. Jonathan D. Wren, Oklahoma Medical Research Foundation

A proteogenomic update to Yersinia: enhancing genome annotation

BackgroundModern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the time and effort that can be invested in genome annotation. The resulting gene set contains numerous errors in even the most basic form of annotation: the primary structure of the proteins.ResultsThe application of experimental proteomics data to genome annotation, called proteogenomics, can quickly and efficiently discover misannotations, yielding a more accurate and complete genome annotation. We present a comprehensive proteogenomic analysis of the plague bacterium, Yersinia pestis KIM. We discover non-annotated genes, correct protein boundaries, remove spuriously annotated ORFs, and make major advances towards accurate identification of signal peptides. Finally, we apply our data to 21 other Yersinia genomes, correcting and enhancing their annotations.ConclusionsIn total, 141 gene models were altered and have been updated in RefSeq and Genbank, which can be accessed seamlessly through any NCBI tool (e.g. blast) or downloaded directly. Along with the improved gene models we discover new, more accurate means of identifying signal peptides in proteomics data.

Genome-wide computational identification and manual annotation of human long noncoding RNA genes

Experimental evidence suggests that half or more of the mammalian transcriptome consists of noncoding RNA. Noncoding RNAs are divided into short noncoding RNAs (including microRNAs) and long noncoding RNAs (lncRNAs). We defined complementary DNAs (cDNAs) lacking any positive-strand open reading frames (ORFs) longer than 30 amino acids, as well as cDNAs lacking any evidence of interspecies conservation of their longer-than-30-amino acid ORFs, as noncoding. We have identified 5446 lncRNA genes in the human genome from approximately 24,000 full-length cDNAs, using our new ORF-prediction pipeline. We combined them nonredundantly with lncRNAs from four published sources to derive 6736 lncRNA genes. In an effort to distinguish standalone and antisense lncRNA genes from database artifacts, we stratified our catalog of lncRNAs according to the distance between each lncRNA gene candidate and its nearest known protein-coding gene. We concurrently examined the protein-coding capacity of known genes overlapping with lncRNAs. Remarkably, 62% of known genes with "hypothetical protein" names actually lacked protein-coding capacity. This study has greatly expanded the known human lncRNA catalog, increased its accuracy through manual annotation of cDNA-to-genome alignments, and revealed that a large set of hypothetical-protein genes in GenBank lacks protein-coding capacity. In addition, we have developed, independently of existing NCBI tools, command-line programs with high-throughput ORF-finding and BLASTP-parsing functionality, suitable for future automated assessments of protein-coding capacity of novel transcripts.

Prevalence and geographic distribution of Hepatitis C Virus genotypes in Indian patient cohort

Viral hepatitis represents a major global health problem with 170 million Hepatitis C Virus (HCV) carriers worldwide, and 12–13 million HCV carriers in India. HCV genotypes are of clinical significance in indicating drug responsiveness and prognosis of the patient. The HCV genotypes are of epidemiologic significance as well, as they are indicative of transmission route of infection and have not been extensively studied in the Indian context. In the current study, HCV genotyping was examined in 2118 patients from different geographic regions of India. HCV was detected by PCR amplification of 5′ UTR and core-envelope1 regions, followed by genotyping using nucleotide sequencing and analysis with NCBI tool ( http://www.ncbi.nlm.nih.gov/projects/genotyping/formpage.cgi). HCV genotype distribution in the 2118 Indian patients demonstrated prevalence of HCV3 (3a/3b primarily) in 62% and HCV1 (1a/1b primarily) in 31% patients. The predominance of HCV3 was significant in northern ( p = 0.01) and eastern ( p = 0.008) regions of India. HCV types 2, 4, 5, and 6 were detected in 0.05–4.5% of the patient group. Thus, our studies demonstrate HCV genotype prevalence in the cohort group in different regions of India.

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R.Availability: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website.Contact: yidong@mail.nih.gov

Reliability of Rapid Subtyping Tools Compared to That of Phylogenetic Analysis for Characterization of Human Immunodeficiency Virus Type 1 Non-B Subtypes and Recombinant Forms

Human immunodeficiency virus type 1 (HIV-1) subtyping is often estimated on the basis of pol sequences by using online websites instead of phylogenetic analysis (phy). We evaluated the reliability of distinct rapid subtyping tools versus phy with a large panel of HIV-1 non-B subtypes and circulating recombinant forms (CRF). pol sequences (277 protease [PR] and 171 reverse transcriptase [RT] sequences) previously assigned by phy to eight distinct HIV-1 non-B subtypes were obtained from 277 HIV-infected patients. Phy was run again to identify CRF. Subtyping was then performed using three rapid tools (the Stanford, NCBI, and REGA online tools). Thirty-three additional clade B sequences were tested as controls. New phylogenetic analyses reclassified two-thirds of pol sequences previously assigned to HIV-1 non-B clades as CRF. CRF02_AG variants were correctly assigned by the Stanford and NCBI tools for 92 to 97% and 96 to 99% of PR-RT sequences, respectively, while they were correctly assigned by the REGA tool for only 18 to 32% of PR-RT sequences. The Stanford, NCBI, and REGA tools failed to assign pure non-B clades correctly for 24 to 33%, 35%, and 57 to 64% of PR-RT sequences, respectively. For PR-RT sequences from CRF other than CRF02_AG, discrepancies occurred in 98 to 100%, 18 to 43%, and 80 to 87% of sequences, respectively. The concordance between those tools and phy was almost complete for subtype B assignment. Rapid subtyping tools show relatively low agreement with phy in identifying HIV-1 non-B clades and CRF other than CRF02_AG. The Stanford tool shows the best concordance with phy for the assignment of pure non-B clades, while the NCBI tool performs better at identifying CRF. Before entering routine clinical use, rapid subtyping tools should be optimized and updated periodically. Larger numbers of different non-B subtypes and CRF sequences should be included.