scholarly journals Experience of using modern genomic technologies to study microorganisms and their communities

2021 ◽  
pp. 159-167
Author(s):  
E. V. Voropaev ◽  
I. O. Stoma ◽  
D. V. Tapalski
Keyword(s):  
Risk Groups ◽  
Metagenomic Analysis ◽  
Minimal Amount ◽  
Genomic Technologies ◽  
Bacterial Microbiome ◽  
Genomic Studies ◽  
H Pylori ◽  
Sequencing Platforms ◽  
Modern Genomic ◽  
Medical University

Objective. The aim of this work was to review the main results of genomic studies of microorganisms and their communities performed on the base of the Research Laboratory of Gomel State Medical University.Materials and methods. Genomic, transcriptomic and metagenomic analysis of the microorganisms of the stomach and respiratory tract.Results. The capabilities of modern next-generation sequencing platforms have been analyzed, and the authors` own results of the use of genomic, transcriptomic and metagenomic analysis of the microbiota in patients with various gastric and respiratory pathologies have been described.Conclusion. The analysis of the obtained data has revealed peculiarities of the structure of the microbial communities of the stomach of the patients infected with H. pylori with different gastric pathology: the proportion participation of H. pylori in the metagenome of the samples with different forms of gastric cancer did not exceed 25 %, of gastritis — 6 %, of peptic ulcer — 1 %. At the same time, the minimal amount of H. pylori in all the cases could reach 0.1 %. A signifcant degree of CagA and CagY loci variability of H. pylori was detected. Streptoccocus genus bacteria dominated (36 %) in the bacterial microbiome of a patient diagnosed with the coronavirus disease, and in the viral microbiome, SARS-CoV-2 constituted 59 % of the total number of viruses in the material. The analysis of 13 strains of Klebsiella pneumoniae with multiple and extreme resistance to antibiotics has found that the studied strains belong to fve MLST-types, three of which are classifed as high epidemic risk groups.

The Roles of Twin Studies and Modern Genomic Technologies in Integrative Health Science

2018 ◽  
pp. 34-46
Author(s):  
Robert F. Krueger ◽  
Susan C. South
Keyword(s):  
Allostatic Load ◽  
Twin Studies ◽  
Transcriptional Response ◽  
The United States ◽  
Health Science ◽  
Research Strategies ◽  
Integrative Health ◽  
Genomic Technologies ◽  
Health And Illness ◽  
Modern Genomic

This chapter focuses on genetically informative research design and strategy in integrative health science (IHS). A feature of IHS is studying individual differences in health outcomes together and in a multidisciplinary manner. The chapter focuses on the advantages of using genetically informative research strategies for IHS. Genetically informative strategies are tools to enrich inferences within the IHS paradigm. They help parse the meaning of observed associations between exposures and outcomes. Two strategies are considered for the Midlife in the United States study : (1) Gene × Environment interactions and (2) correlations between education and allostatic load. A strategy likely to be employed in IHS research involves using segments of RNA to understand mechanisms underlying health and illness, focusing on the conserved transcriptional response to adversity (CTRA). The conclusion is that IHS and genetically informative research strategies are natural allies in understanding origins of health and illness in the population at large.

scholarly journals Potential Application of Genomic Technologies in Breeding for Fungal and Oomycete Disease Resistance in Pea

Agronomy ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1260
Author(s):  
Ambuj B. Jha ◽  
Krishna K. Gali ◽  
Zobayer Alam ◽  
V. B. Reddy Lachagari ◽  
Thomas D. Warkentin
Keyword(s):  
Disease Resistance ◽  
Genome Sequence ◽  
Potential Application ◽  
Ascochyta Blight ◽  
Gene Families ◽  
Snp Markers ◽  
Growth And Yield ◽  
Current Status ◽  
Genomic Technologies ◽  
Sequencing Platforms

Growth and yield of pea crops are severely affected by various fungal diseases, including root rot, Ascochyta blight, powdery mildew, and rust, in different parts of the world. Conventional breeding methods have led to enhancement of host plant resistance against these diseases in adapted cultivars, which is the primary option to minimize the yield losses. To support the breeding programs for marker-assisted selection, several successful attempts have been made to detect the genetic loci associated with disease resistance, based on SSR and SNP markers. In recent years, advances in next-generation sequencing platforms, and resulting improvements in high-throughput and economical genotyping methods, have been used to make rapid progress in identification of these loci. The first reference genome sequence of pea was published in 2019 and provides insights on the distribution and architecture of gene families associated with disease resistance. Furthermore, the genome sequence is a resource for anchoring genetic linkage maps, markers identified in multiple studies, identification of candidate genes, and functional genomics studies. The available pea genomic resources and the potential application of genomic technologies for development of disease-resistant cultivars with improved agronomic profile will be discussed, along with the current status of the arising improved pea germplasm.

scholarly journals Role of Legal Principles in Eliminating and Minimizing the Risks of Genomic Technologies

Lex Russica ◽  
2019 ◽  
pp. 121-128 ◽  
Author(s):  
M. N. Maleina
Keyword(s):  
Genetic Information ◽  
Personal Data ◽  
Negative Consequences ◽  
Genetic Characteristics ◽  
Legal Principles ◽  
Genomic Technologies ◽  
Preventive Actions ◽  
The Individual ◽  
Modern Genomic

The use of modern genomic technologies, along with the benefits to the man and society, can lead to negative consequences. Such risks exist both in the process and after the production, isolation, modification, storage of DNA. Prior to detailed legislative regulation of relations regarding the use of genomic technologies for medicinal purposes and not for medical reasons, legal principles become vital.The paper formulates the following basic legal principles of genomic technologies application: the principle of preventive actions of the state to protect citizens from the risks of using genomic technologies; the principle of preserving the human genome as a special species; the principle of guaranteeing the inviolability of the individual of every citizen when using genomic technologies; the principle of priority of life and health of citizens over the interests of science and society; the principle of equality of citizens regardless of genetic characteristics; the principle of protection of genetic information of every citizen as part of personal data; the principle of guaranteeing access to the citizen’s own genetic information. Legal principles can be used to resolve a dispute by analogy of law.

scholarly journals The role of the gastric bacterial microbiome in gastric cancer: Helicobacter pylori and beyond

2019 ◽  
Vol 12 ◽  
pp. 175628481989406 ◽  
Author(s):  
Christian Schulz ◽  
Kerstin Schütte ◽  
Julia Mayerle ◽  
Peter Malfertheiner
Keyword(s):  
Gastric Cancer ◽  
Helicobacter Pylori ◽  
Bacterial Pathogen ◽  
Gastric Carcinogenesis ◽  
Nucleotide Sequencing ◽  
Wide Field ◽  
Current State ◽  
Organ Systems ◽  
Bacterial Microbiome ◽  
H Pylori

A link between chronic inflammation and carcinogenesis has been depicted in many organ systems. Helicobacter pylori is the most prevalent bacterial pathogen, induces chronic gastritis and is associated with more than 90% of cases of gastric cancer (GC). However, the introduction of nucleotide sequencing techniques and the development of biocomputional tools have surpassed traditional culturing techniques and opened a wide field for studying the mucosal and luminal composition of the bacterial gastric microbiota beyond H. pylori. In studies applying animal models, a potential role in gastric carcinogenesis for additional bacteria besides H. pylori has been demonstrated. At different steps of gastric carcinogenesis, changes in bacterial communities occur. Whether these microbial changes are a driver of malignant disease or a consequence of the histologic progression along the precancerous cascade, is not clear at present. It is hypothesized that atrophy, as a consequence of chronic gastric inflammation, alters the gastric niche for commensals that might further urge the development of H. pylori-induced GC. Here, we review the current state of knowledge on gastric bacteria other than H. pylori and on their synergism with H. pylori in gastric carcinogenesis.

scholarly journals Bi-allelic GAD1 variants cause a neonatal onset syndromic developmental and epileptic encephalopathy

Brain ◽  
2020 ◽  
Vol 143 (5) ◽  
pp. 1447-1461 ◽  
Author(s):  
Nicolas Chatron ◽  
Felicitas Becker ◽  
Heba Morsy ◽  
Miriam Schmidts ◽  
Katia Hardies ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Epileptic Encephalopathy ◽  
Allelic Loss ◽  
Loss Of Function ◽  
Seizure Onset ◽  
Joint Contractures ◽  
Epileptic Encephalopathies ◽  
Genomic Technologies ◽  
Pes Equinovarus ◽  
Modern Genomic

Abstract Developmental and epileptic encephalopathies are a heterogeneous group of early-onset epilepsy syndromes dramatically impairing neurodevelopment. Modern genomic technologies have revealed a number of monogenic origins and opened the door to therapeutic hopes. Here we describe a new syndromic developmental and epileptic encephalopathy caused by bi-allelic loss-of-function variants in GAD1, as presented by 11 patients from six independent consanguineous families. Seizure onset occurred in the first 2 months of life in all patients. All 10 patients, from whom early disease history was available, presented with seizure onset in the first month of life, mainly consisting of epileptic spasms or myoclonic seizures. Early EEG showed suppression-burst or pattern of burst attenuation or hypsarrhythmia if only recorded in the post-neonatal period. Eight patients had joint contractures and/or pes equinovarus. Seven patients presented a cleft palate and two also had an omphalocele, reproducing the phenotype of the knockout Gad1−/− mouse model. Four patients died before 4 years of age. GAD1 encodes the glutamate decarboxylase enzyme GAD67, a critical actor of the γ-aminobutyric acid (GABA) metabolism as it catalyses the decarboxylation of glutamic acid to form GABA. Our findings evoke a novel syndrome related to GAD67 deficiency, characterized by the unique association of developmental and epileptic encephalopathies, cleft palate, joint contractures and/or omphalocele.

scholarly journals GWAS of a soybean breeding collection from South East and South Kazakhstan for resistance to fungal diseases

2018 ◽  
Vol 22 (5) ◽  
pp. 536-543 ◽  
Author(s):  
A. Zatybekov ◽  
S. Abugalieva ◽  
S. Didorenko ◽  
A. Rsaliyev ◽  
Y. Turuspekov
Keyword(s):  
Genome Wide Association Study ◽  
Field Evaluation ◽  
Fungal Diseases ◽  
Brown Spot ◽  
The South ◽  
Genome Wide ◽  
Genomic Studies ◽  
Local Breeding ◽  
Efficient Breeding ◽  
Modern Genomic

Soybean (Glycine max(L.) Merr) is an essential food, feed, and technical culture. In Kazakhstan the area under soybean is increasing every year, helping to solve the problem of protein deficiency in human nutrition and animal feeding. One of the main problems of soybean production is fungal diseases causing yields losses of up to 30 %. Modern genomic studies can be applied to facilitate efficient breeding research for improvement of soybean fungal disease tolerance. Therefore, the objective of this genome-wide association study (GWAS) was analysis of a soybean collection consisting of 182 accessions in relation to fungal diseases in the conditions of South East and South Kazakh­stan. Field evaluation of the soybean collection suggested thatFusariumspp. andCercospora sojinaaffected plants in the South region (RIBSP), andSeptoria glycines– in the South East region (KRIAPP). The major objective of the study was identification of QTL associated with resistance to fusarium root rot (FUS), frogeye leaf spot (FLS), and brown spot (BS). GWAS using 4 442 SNP (single nucleotide polymorphism) markers of Illumina iSelect array allowed for identification of fifteen marker trait associations (MTA) resistant to the three diseases at two different stages of growth. Two QTL both for FUS (chromosomes 13 and 17) and BS (chromosomes 14 and 17) were genetically mapped, including one presumably novel QTL for BS (chromo­some 17). Also, five presumably novel QTL for FLS were genetically mapped on chromosomes 2, 7, and 15. The results can be used for improvement of the local breeding projects based on marker-assisted selection approach.          

scholarly journals Antimicrobial Sensitivity Pattern of Helicobacter pylori Isolates among Subgroup of Bangladeshi Patients

2014 ◽  
Vol 8 (2) ◽  
pp. 49-52
Author(s):  
MMSU Islam ◽  
Shamsun Nahar ◽  
Mst Naznin Sarker ◽  
ASM Salimullah ◽  
Mohammad Asadur Rahman ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Diarrhoeal Disease ◽  
Cross Sectional Study ◽  
Dilution Method ◽  
Agar Dilution Method ◽  
Cross Sectional ◽  
Antimicrobial Sensitivity ◽  
Sensitivity Pattern ◽  
H Pylori ◽  
Medical University

This cross sectional study was carried out at Bangabandhu Sheikh Mujib Medical University (BSMMU) and International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR,B) from July 2008 to September 2009. Aim of the study was to find out the antimicrobial susceptibility profile of Helicobacter pylori isolates from dyspeptic patients. Total 224 dyspeptic patients from Out Patient Department (OPD) of BSMMU were initially enrolled after informed written consent. After upper GI endoscopy 157 patients were finally included who had erosions, ulcers or atrophic changes in the stomach or duodenum. Two biopsy samples were taken from each of them. Samples were incubated at 37°C in a double gas incubator with 5%O2, 10%CO2 and 85%N2. Total 82 (52.23%) samples were found positive for H. pylori. Isolated organisms were then tested for sensitivity to Amoxicillin, Clarithromycin, Tetracycline, Levofloxacin and Metronidazole by Agar dilution method. Among 82 patients 51(62.2%) were male and 31(37.8) were female with a male:female ratio 1.6:1. Patients were categorized into two groups one having gastric or duodenal ulcer (30.5%) and other having no ulcer (69.5%). Among these isolates 92.7% were sensitive to Amoxicillin, 89% to Clarithromycin, 81.7% to Tetracycline, 80.5% to Levofloxacin and only 26.8% to Metronidazole. Beside these, 81.7% isolates were sensitive to both Amoxicillin and Clarithromycin, 74.4% to Amoxicillin and Tetracycline, 73.2% to Amoxicillin and Levofloxacin, 72% to Clarithromycin and Tetracycline, 59% to Clarithromycin and Levofloxacin and 51% to Tetracycline and Levofloxacin DOI: http://dx.doi.org/10.3329/fmcj.v8i2.20280 Faridpur Med. Coll. J. 2013;8(2): 49-52

scholarly journals Feasibility of RNA and DNA Extraction from Fresh Pipelle and Archival Endometrial Tissues for Use in Gene Expression and SNP Arrays

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Heather D. Kissel ◽  
Thomas G. Paulson ◽  
Karen Liu ◽  
Xiaohong Li ◽  
Elizabeth Swisher ◽  
...  
Keyword(s):  
Gene Expression ◽  
Snp Array ◽  
Tissue Type ◽  
Expression Arrays ◽  
Ffpe Samples ◽  
Fresh Frozen ◽  
Genomic Studies ◽  
And Performance ◽  
Sequencing Platforms ◽  
Rna And Dna

Identifying molecular markers of endometrial hyperplasia (neoplasia) progression is critical to cancer prevention. To assess RNA and DNA quantity and quality from routinely collected endometrial samples and evaluate the performance of RNA- and DNA-based arrays across endometrial tissue types, we collected fresh frozen (FF) Pipelle, FF curettage, and formalin-fixed paraffin-embedded (FFPE) hysterectomy specimens (benign indications) from eight women. Additionally, neoplastic and uninvolved tissues from 24 FFPE archival hysterectomy specimens with endometrial hyperplasias and carcinomas were assessed. RNA was extracted from 15 of 16 FF and 51 of 51 FFPE samples, with yields >1.2 μg for 13/15 (87%) FF and 50/51 (98%) FFPE samples. Extracted RNA was of high quality; all samples performed successfully on the Illumina whole-genome cDNA-mediated annealing, selection, extension, and ligation (WG-DASL) array and performance did not vary by tissue type. While DNA quantity from FFPE samples was excellent, quality was not sufficient for successful performance on the Affymetrix SNP Array 6.0. In conclusion, FF Pipelle samples, which are minimally invasive, yielded excellent quantity and quality of RNA for gene expression arrays (similar to FF curettage) and should be considered for use in genomic studies. FFPE-derived DNA should be evaluated on new rapidly evolving sequencing platforms.

scholarly journals Digging Up the Human Genome: Current Progress in Deciphering Adverse Drug Reactions

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Shih-Chi Su ◽  
Wen-Hung Chung ◽  
Shuen-Iu Hung
Keyword(s):  
Adverse Drug Reactions ◽  
Genetic Variants ◽  
Human Leukocyte ◽  
Clinical Problem ◽  
Drug Reactions ◽  
Metabolizing Enzymes ◽  
Leukocyte Antigen ◽  
Genomic Technologies ◽  
Genes Encoding ◽  
Modern Genomic

Adverse drug reactions (ADRs) are a major clinical problem. In addition to their clinical impact on human health, there is an enormous cost associated with ADRs in health care and pharmaceutical industry. Increasing studies revealed that genetic variants can determine the susceptibility of individuals to ADRs. The development of modern genomic technologies has led to a tremendous advancement of improving the drug safety and efficacy and minimizing the ADRs. This review will discuss the pharmacogenomic techniques used to unveil the determinants of ADRs and summarize the current progresses concerning the identification of biomarkers for ADRs, with a focus on genetic variants for genes encoding drug-metabolizing enzymes, drug-transporter proteins, and human leukocyte antigen (HLA). The knowledge gained from these cutting-edge findings will form the basis for better prediction and management for ADRs, ultimately making the medicine personalized.

Sign in / Sign up

Export Citation Format

Share Document