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Aug 2018 DOI 10.14302/issn.2576-6694.jbbs-18-2173
Bioinformatic tools is widely used to manage the enormous genomic and proteomic data involving DNA/protein sequences management, drug designing, homology modelling, motif/domain prediction ,docking, annotation and dynamic simulation etc. Bioinformatics offers a wide range of applications in numerous disciplines such as genomics. Proteomics, comparative genomics, nutrigenomics, microbial genome, biodefense, forensics etc. Thus it offers promising future to accelerate scientific research in biotechnology
Apr 2018 DOI 10.14302/issn.2326-0793.jpgr-18-2004
Human proteome project was revolutionized about 40 years ago with purpose of summarizing whole proteomic data at one place. It was launched after human genome project to map and observe all proteins. The goal related proteomic study is to draft the entire human proteome in disease diagnosis by using bioinformatics tools. Pillars of human proteome project provide different databases related to proteins at transcriptional and translational level. Human proteome organization(HUPO) published biology disease HUPO whose aim is to measure protein and proteome by life and processes related to human diseases. Different human organ like plasma, liver, brain and diabetic base project are used to characterize human disease and health. Major data resources accumulated in databases like peptides Atlas, GPMDB and neXtProt for proteins. Matrices of human proteome project identify and characterize the protein products as Post translational modification (PTM), splice various isoforms from 20,300 proteins. Matrices related to different years make proteomes counterpart by magnify the research biomedical community with high output of instruments and specimen pre-analytical protocols. CALIPHO multidisciplinary group provides information about protein complexities, interactions, function and structure complexities after Uniport and Swissprot. Different bioinformatics tools are used for structural and functional annotations of protein, disease diagnosis and mutations due to protein. Extensive study of human proteome project has been proved helpful in disease treatment at translational and post- translational levels. In future, human proteome project along with bioinformatics will include protein profiling, biomarkers, Mass spectrophotometer technique and cross analysis of different proteome projects.
Oct 2014 DOI 10.14302/issn.2374-9431.jbd-13-212
Diabetes mellitus type 2 (DMT2) is a complex polygenic disorder. DMT2 is a result of insulin resistance and destruction of pancreatic β-cell or dysfunction. Therefore, glucose builds up in the bloodstream, leading to nerve damage, blindness, organ failures and sometimes death. Recently, some recently discovered genes play a key role in regulating the sensitivity to insulin. Scientists have long known that the disease often runs in families, and other genetic links. Human genetic discoveries will keep improving our knowledge about diabetes for many years to come. Varieties of prospective diabetic researches were developed to diagnose and control DMT2. Researchers spent thousands of millions of dollars to address DMT2. Pioneers of advanced biotechnology developed bioinformatics tools that changed the course of research about the role of metabolomics in DMT2. It will facilitate the identification of possible causes of DMT2 in genome studies. The present article aimed at reviewing the research studies per training to metabolomics and bioinformatics in genome studies in relation to DMT2.
May 2025 DOI 10.14302/issn.2641-5526.jmid-25-5466
Information on adverse drug event (ADE) assessment and prevention within Electronic Health Records (EHRs) is difficult for clinicians to use and produces wide-ranging results. Challenges include inconsistent ADE and drug product definition and documentation, workflows, terminology standardization, interoperability, and clinical decision support (CDS) to inform clinical decision-making within EHRs. These factors contribute to care issues for clinicians, such as alert fatigue and provider burden for clinicians and medical errors, patient harm, and even death for patients. Clinicians play the primary role in documenting, reviewing, detecting, and preventing ADEs within EHRs. It is essential that clinicians, clinical informaticists, nursing informaticists, pharmacy informaticists, and the health informatics profession understand the current electronic ADE paradigm to advocate for improved detection and prevention of ADEs within EHRs.
Nov 2022 DOI 10.14302/issn.2690-4721.ijcm-22-4341
Bacteria of the genus Staphylococcus are pathogenic Gram-positive bacteria responsible for various infections, including skin suppuration, which can be severe or chronic. The objective of this study was to confirm Staphylococci strain’s identification isolated by bacteriological methods from biological products of CHU-B patients, by molecular methods based on the analysis of the gene coding for 16S rRNA. In total, 30 strains of Staphylococci were isolated including 8 (26.66%) community strains, 22 (73.33%) hospital strains. The products of the amplification of gene fragments encoding 16S rRNA from 10 strains of Staphylococci including 6 strains of Staphylococcus aureus (S. aureus) and 4 Coagulase Negative Staphylococci (CNS) were sequenced. The sequences obtained were subjected to bioinformatics analysis to confirm the results of conventional bacteriological methods. Six (6) S. aureus strains, 2 Staphylococcus haemolyticus strains, 1 uncultured bacterium clone nbw618g09c1, and one Staphylococcus sp. have been identified. These results made it possible to confirm the effectiveness of the molecular method and to show the limits of traditional bacteriological methods in the complete identification of bacteria.
Feb 2019 DOI 10.14302/issn.2471-7061.jcrc-18-2526
There is currently no validated micro(mi)RNA diagnostic stool test to screen for colon cancer (CC) on the market because of the complexity of fecal density, vulnerability of stool to daily changes, and the presence of three sources of miRNAs in stool (cell-free from fecal homogenates, exsosomal miRNAs from fecal exosomes, and fecal colonocytes). To address these complexities, we have first carried out a microarray miRNA experiment, using Affymetrix GeneChip miRNA 2.0 Arrays, on immunocaptured and enriched stool colonocytes of 15 subjects (three healthy controls and twelve colon cancer patients [three TNM stage 0-1 (e.g., polyps◻ ³ 1 cm, villous or tubvillous, or with high grade dysplasia), three stage 2, three stage 3, and three stage 4 in triplicates to select a smaller panel of 14 preferentially expressed mature miRNAs associated with colon cancer (12 Up-Regulated, miR-19a, miR-20a, miR-21, miR-31, miR-34a, miR-96, miR-106a, miR-133a, miR-135b, miR-206, miR-224 and miR-302; and 2 Down-Regulated, miR-143 and miR-145). In a subsequent validation study carried out on total small RNA extracted by immunocapture, followed by RT that employed TaqMan® miRNA Reverse Transcription (RT) Kit and a Custom TaqMan RT Primer Pool, absolute quantification of miRNAs, in copies/µl, was measured using a chip-based Absolute QuantStudio 3D Digital PCR analysis. To ensure that we have chosen human and not bacterial small total RNA, we have carried out coextraction protocols with E. coli K1 strain RS18, compare Agilent electrophoretic patterns, and also sequenced random samples throughout this research using mRNA/miRNA sequencing. Our initial quantitative dPCR miRNA data presented herein showe that the quantitative changes in the expression of a few mature miRNA genes in stool, which are associated with right and left colon cancer, would provide for a more convenient, sensitive and specific diagnostic screening markers thatare more useful than those test markers currently available on the market, such as the low-sensitivity (<15%) fecal occult blood test (FOBT); result in better compliance; and is more economical than the invasive and expensive colonoscopy exam in colon cancer, which can be cured if that cancer is detected at the early TNM stages, and that becomes incurable and deadly if not diagnosed before metastasis. Initial test performance characteristics of the miRNA approach showed that the test has a high numerical predictive value in colon cancer. Moreover, underpinning of the miRNA markers as a function of total RNA showed that the test can numerically differentiate between control subjects and colon cancer patients, particularly at the early stages of that curable cancer. We propose to extend our initial research results to a larger prospective and randomized five-years nested case-control study, to validate the expression of the above 14 miRNAs, in stool of 180 individuals in an epidemiologically designed study, using (30 controls and 150 colon cancer patients (thirty precancerous polyps (stage 0-1), forty five stage 2, and seventy-five colon cancer stages 3 or 4). chosen randomly by an epidemiological method from 900 control and CC subjects to allow for an adequate time to collect the required 900 stool samples, as well as allowing for statistically valid analysis, standardized test conditions, and to provide a mean for determining the true sensitivity and specificity of a miRNA-screening approach in noninvasive human stool. Power-analysis has indicated that a total of 180 individuals, which will take us 5 years to enroll in testing, is an appropriate number of subjects to standardize and validate our proposed miRNA screening test. We may find out at the end of the proposed validation study in stool that fewer miRNAs, or even one miRNA, may suffice to serve as an efficient and a quantitative marker for the non-invasive diagnostic screening of colon cancer in human stool. The above approach when combined with bioinformatics analysis, to correlate miRNA seed data with our previously published messenger (m)RNA target data in stool, allows for a thorough mechanistic understanding of how miRNA genes regulate mRNA expression, and would offer a better comprehensive diagnostic screening test for the non-invasive early detection stage (0-1) of colon cancer. In order to show the clinical sensitivity and specificity of the proposed miRNA test, the absolute miRNA PCR values, in copies/µl, will be correlated with FOBT, colonoscopy, and pathology data. Standardization will establish test’s performance characteristics (sample selection, optimal sample running conditions, preservation and storage) to ensure that the assay will perform the same way in any laboratory, by any trained personnel, anywhere in the World. Ultimately, a smaller number of selected validated miRNAs (<10) showing increased and reduced expression could suffice to give quantitative miRNAs colon cancer expression values, useful for the early diagnostic screening of that curable cancer.
Oct 2018 DOI 10.14302/issn.2639-3166.jar-18-2331
This study reviews the agricultural development perspective in the light of a rapid space technology development. In other words, precision agriculture as part of geoinformatics. The aim is to quantify whether the adopted technology can improve the efficiency of agricultural fields management and production to attain food security. Therefore, views of targeted groups from different States of Sudan were investigated, using stratified sampling method. Where quantitative statistics (descriptive/inductive techniques) was applied. About 800 questionnaires were distributed. The outcomes of data analysis reflected that the majority of interviewed groups 357 (82.1%) do not know the principles and application of integrated technology in the field of agricultural management. 85.3% of respondents know nothing about computer program related to precision agriculture. The majority of the respondents (84.6 %), did not get courses on precision agriculture during the under graduate study. The result also revealed that only 11.8% of the respondents use modern techniques in land preparation, 16.1 % in soil analysis, 12.5 % in the field of seed technology, and 11.4% in crop harvesting. However, 53.9% of the respondents reported that their Departments did not care about training on agricultural precision. Nevertheless, 24.3 % of the respondents got trained on precision agriculture through personal efforts, while about 19% got trained by their respective Departments. In regard to education, 16% of the respondents got trained on precision agriculture at undergraduate and only 9% after graduation. The study concludes that despite the rapid technological development, agriculture in Sudan remained lagging, and the productivity is below the expectation. It recommends that the Ministries of Agriculture in different States in Sudan should take the issue of introduction of new technology seriously to boost the agricultural development to attain food security.
Mar 2017 DOI 10.14302/issn.2326-0793.jpgr-17-1447
Factors that contribute to the onset of atherosclerosis may be elucidated by bioinformatic techniques applied to multiple sources of genomic and proteomic data. The results of genome wide association studies, such as the CardioGramPlusC4D study, expression data, such as that available from expression quantitative trait loci (eQTL) databases, along with protein interaction and pathway data available in Ingenuity Pathway Analysis (IPA), constitute a substantial set of data amenable to bioinformatics analysis. This study used bioinformatic analyses of recent genome wide association data to identify a seed set of genes likely associated with atherosclerosis. The set was expanded to include protein interaction candidates to create a network of proteins possibly influencing the onset and progression of atherosclerosis. Local average connectivity (LAC), eigenvector centrality, and betweenness metrics were calculated for the interaction network to identify top gene and protein candidates for a better understanding of the atherosclerotic disease process. The top ranking genes included some known to be involved with cardiovascular disease (APOA1, APOA5, APOB, APOC1, APOC2, APOE, CDKN1A, CXCL12, SCARB1, SMARCA4 and TERT), and others that are less obvious and require further investigation (TP53, MYC, PPARG, YWHAQ, RB1, AR, ESR1, EGFR, UBC and YWHAZ). Collectively these data help define a more focused set of genes that likely play a pivotal role in the pathogenesis of atherosclerosis and are therefore natural targets for novel therapeutic interventions.
Jan 2017 DOI 10.14302/issn.2572-3030.jcgb-16-1307
Interpreting variants of uncertain significance (VUS) for their effect on protein function, and therefore for the risk of developing cancer, has become a challenge in clinical practice for genetic counselling services. The present work combines structural bioinformatics and systems biology based mathematical modelling approaches with the aim of determining the pathogenicity of the mutation c.5434C->G (p.Pro1812Ala) in the BRCA1 gene (detected in a patient from a high risk family) and also to mechanistically understand the effect of this mutation in DNA damage response, a key process in cancer development. The results obtained showed that this mutation prevents the interaction of BRCA1 with key proteins of the cell cycle, subsequently impairing BRCA1-dependent induction of cell cycle arrest. The comparison of the molecular mechanisms associated with the native BRCA1 protein and the mutated variant function in DNA damage response showed that the latter undergoes a reduction in its ability to modulate pathways that are critical for DNA repair and cell cycle control. Therefore, this variant will not be able to exert its tumor suppressive action. Interestingly, these conclusions can be extrapolated to all mutations that, like c.5434C>G (p.Pro1812Ala) BRCA1, cause loss of BRCT domain activity.
Jan 2016 DOI 10.14302/issn.2574-4372.jesr-15-768
The human OCT4 gene encodes a transcription factor that maintains pluripotency and self-renewal in Embryonic Stem (ES) cells. This gene generates several known transcripts by alternative promoter and alternative splicing (OCT4A, OCT4B and OCT4B1). Even though OCT4A is the main isoform responsible for stemness properties, several recent controversial studies claimed that this isoform is expressed in cancer cell lines and differentiated cells, in addition to the ES cells. Our in silico studies revealed that OCT4A promoter has a completely match binding site for hsa-miR-1285. This microRNA was detected in the human embryonic stem cells for the first time and further studies showed that miR-1285 can target some tumor suppressor genes,(TSGs), such as p53, and oncogenic genes, such as TGM2. Additional bioinformatics analysis of short RNA sequencing data from ENCODE cell lines showed that miR-1285 is expressed in different cancer cell lines and differentiated cells. In this study, we supposed that miR-1285 potentially can bind to the OCT4 promoter and might regulate transcription of the OCT4 in the human cancer cell lines and differentiated cells.
Jun 2014 DOI 10.14302/issn.2374-9431.jbd-13-330
Background: Health practitioners of different disciplines (physicians, paramedic personnel, pharmacists) should possess adequate ICT (Information and Communication Technology) skills and practical competence on these technologies. Pharmacy practice requires a relevant flow of information, collection and handling of which could be facilitated by ICT. The correct use of ICT requires a proper knowledge by professionals offering a public service. The purpose of this paper was to assess basic informatics background and computer uses in pharmacists practicing in Italy, with the aim to identify educational interventions for increasing their informatics abilities. Methods: A questionnaire was proposed to pharmacists working in Italian community pharmacies. The survey was articulated into 35 questions concerning computer basic knowledge, ICT facilities, computer skills, habits, and uses in pharmacy practice. Results: The questionnaire was completed by ~45% (No. 224) of responders, the 96.9% of which used computer. Only 7.8% of interviewed people employed e-mail to communicate with health authorities and less than 2% used it to be in contact with physicians or other health professionals. Less than 40% used ICT for training courses. The results revealed a relevant percentage (90.8%) of self-learners to computer use, while only 9.2% was trained by specific courses. Conclusion: Basic knowledge of community pharmacists on ICT technological infrastructure is quite low. Although pharmacists play an essential role in health services, they have apparently limited computer skills. This suggests the need of educational and training efforts for enlarging computer and ICT resources competent use in daily pharmacy practice.
Mar 2014 DOI 10.14302/issn.2326-0793.jpgr-13-333
Carbofuran is a broad spectrum pesticide used in agricultural fields and domestic places throughout the world. It is one of the deadly toxic carbamate pesticide that kills the pest by inhibiting the crucial enzyme of nervous system known as acetyl cholinesterase. In the present study, we report how carbofuran increases the different spectrum of cholesterols, including free cholesterol and esterified cholesterol in the fish hepatocytes. It is observed that induced-cholesterol can inhibit the enzymatic activity such as Ca++-ATPase, which is a critical protein for maintaining the calcium homoeostasis in the cellular microenvironment. Carbofuran integrates into human body through foods and drinks. As trace of carbofuran is identified in our daily food and drinks, we examined the homology of Ca++-ATPase between the fish and human, so our data can illuminate the effects of carbofuran on this crucial enzyme. While studying the homology with the help of bioinformatics, we recognized that there is around 70% homology in the protein sequence of Ca++-ATPase between fish Heteropneustesfossilisand human (Homo sapiens), which appears as sufficient to simulate our fish-model data in human. This study demonstrates that carbofuran affects our day-to-day life by inhibiting Ca++-ATPase through modulation of lipid synthesis, a critical regulatory system that controls overall homeostasis in our body.
Jan 2014 DOI 10.14302/issn.2326-0793.jpgr-sp1-edt-1
A primer explains how proteomics scales from single‑protein analysis to whole‑organism studies, touching on technologies, bioinformatics, and applications.