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Antibiogram, Genomic and Phylogeny of Stool and Seafood Isolates from Some Cholera-Prone Coastal Communities in Rivers State, Nigeria

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Journal of Biosciences and Medicines 2023年第4期11卷 385-406页

作者： Chidimma Anthonia Azike Vivian Nkemkanma Agi Easter Godwin Nwokah Amba Ollor Ollor Clement Ugochukwu Nyenke Confidence Kinikanwo Wachukwu Rivers State University Port Harcourt Nigeria PAMO University of Medical Sciences Port Harcourt Nigeria

Cholera is a significant public health threat across the globe, especially in coastal regions with poor water supply. This study was carried out to determine the antibiogram, genomic, and phylogeny of stool and seafood isolates from some cholera-prone coastal communities in Rivers State, Nigeria. A total of 400 stool samples and 42 different seafood were aseptically collected and examined using standard microbiology and molecular techniques. An antibiogram of isolates from seafood and stool samples was assayed. Genes for virulence, resistance, and relatedness of bacteria identified were also determined. The isolates from the stool and seafood were examined for susceptibility to some selected antibiotics. The findings showed the prevalence rate of cholera in the communities as follows: 16% in Kaa, 30% in Andoni, 4% in Ogu/Bolo, and 10% in Abua/Odual. The isolates from stool were susceptible to Ciprofloxacin and Gentamycin with a susceptibility rate of 94.12% each while 100% resistance was recorded against Amoxicillin-clavulanic acid, 94.12% against Amikacin and 88.24% against Colistin. For the sea foods, the isolates were susceptible to gentamycin and ciprofloxacin with a susceptibility rate of 91.43% and 82.86% respectively. Resistance was also recorded against Colistin (88.57%) and Azithromycin (82.86%). Testing the isolates for the presence of 16SrRNA genes showed that all were positive with 1500 bp 16SrRNA gene band size. TEM, OXA, SHV, and CTX-M resistant genes were detected whereas the virulence genes were TDH and AcrB. The phylogenetic analysis revealed isolates from seafood to be Aeromonas dhakensis, Vibrio parahaemolyticus, Vibrio azureus, and Providencia rettgeri, while in stool samples they were Enterobacter sichuanensis, Enterobacter hormaechei, Providencia sneebia, and Proteus vulgaris. Providencia stuartii, Proteus mirabilis, Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae were common isolates from both seafood and stool samples. Thi

关键词： Cholera Antibiogram genomics Phylogeny Virulence Coastal

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The “3 Genomic Numbers” Discovery: How Our Genome Single-Stranded DNA Sequence Is “Self-Designed” as a Numerical Whole

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Applied Mathematics 2013年第10期4卷 37-53页

作者： Jean-Claude Perez IBM Emeritus Bordeaux France

This article proves the existence of a hyper-precise global numerical meta-architecture unifying, structuring, binding and controlling the billion triplet codons constituting the sequence of single-stranded DNA of the entire human genome. Beyond the evolution and erratic mutations like transposons within the genome, it’s as if the memory of a fossil genome with multiple symmetries persists. This recalls the “intermingling” of information characterizing the fractal universe of chaos theory. The result leads to a balanced and perfect tuning between the masses of the two strands of the huge DNA molecule that constitute our genome. We show here how codon populations forming the single-stranded DNA sequences can constitute a critical approach to the understanding of junk DNA function. Then, we suggest revisiting certain methods published in our 2009 book “Codex Biogenesis”. In fact, we demonstrate here how the universal genetic code table is a powerful analytical filter to characterize single-stranded DNA sequences constituting chromosomes and genomes. We can then show that any genomic DNA sequence is featured by three numbers, which characterize it and its 64 codon populations with correlations greater than 99%. The number “1” is common to all sequences, expressing the second law of Chargaff. The other 2 numbers are related to each specific DNA sequence case characterizing life species. For example, the entire human genome is characterized by three remarkable numbers 1, 2, and Phi = 1.618 the golden ratio. Associated with each of these three numbers, we can match three axes of symmetry, then “imagine” a kind of hyperspace formed by these codon populations. Then we revisit the value (3-Phi)/2 which is probably universal and common to both the scale of quarks and atomic levels, balancing and tuning the whole human genome codon population. Finally, we demonstrate a new kind of duality between “form and substance” overlapping the whole human genome: we will show that—simult

关键词： Genetic Code Codon Populations Junk DNA Cancer genomics Chromosomal Translocations Genomes Diversity Chromosomes Diversity Whole Human Genome DNA Sequence “Phi” the Golden Ratio Fibonacci Numbers Information Theory Symmetry Cellular Automata Chargaff’s Codon Level Symmetry Principle Fractal Self-Similarity “e” Euler’s Number “Pi” form and Substance Redundancy Encryption

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PPPM (Predictive, Preventive and Personalized Medicine) as a New Model of the National and International Healthcare Services and Thus a Promising Strategy to Prevent a Disease: From Basics to Practice

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International Journal of Clinical Medicine 2014年第14期5卷 855-870页

作者： I. A. Sadkovsky O. Golubnitschaja M. A. Mandrik M. A. Studneva H. Abe H. Schroeder E. N. Antonova F. Betsou T. A. Bodrova K. Payne S. V. Suchkov Department of Medicine Genetics and Comparative Pathology University of Alabama at Birmingham (UAB) Birmingham USA European Association for Predictive Preventive and Personalized Medicine (EPMA) Brussels EU Rheinische Friedrich-Wilhelms-University of Bonn Bonn Germany I.M. Sechenov First Moscow State Medical University Moscow Russia I.M. Sechenov First Moscow State Medical University Moscow Russia A.I. Evdokimov Moscow State Medical & Dental University Moscow Russia United Cultural Convention (UCC) Cambridge UK Institute of Population Health and Health Economics University of Manchester Manchester UK International Society for Personalized Medicine (ISPM) Tokyo Japan National Research University “Higher School of Economics” Moscow Russia Université du Luxembourg and IBBL (Integrated BioBank of Luxembourg) Luxembourg EU

Nowadays the system of public health is constructed in such a manner so that its main objective is the recovery of an already sick person, while prediction and prevention receive little attention. Meanwhile the development of these aspects of medicine can lead to the ability to control morbidity among the population, to identify chronic and genetic diseases in the early stages of development, and thus to prevent their further progression. This will reduce traditionally high costs of sick people treatment and the number of disabled population, and improve the quality and duration of life. The elaboration of new fields of science that are working on the study and interpretation of data obtained during laboratory and clinical research, creation of new methods for diagnosis, prognosis and treatment, provides an opportunity now to implement a new strategy, called PPPM, and gets promising results, which should lead to further development of an existing medicine.

关键词： Predictive Preventive and Personalized Medicine Biomarkers Subclinical Metabolomics genomics Proteomics Bioinformatics Public Health Predisposition

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Genome sequencing and next-generation sequence data analysis: A comprehensive compilation of bioinformatics tools and databases

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American Journal of Molecular Biology 2013年第2期3卷 115-130页

作者： Jose C. Jimenez-Lopez Emma W. Gachomo Sweta Sharma Simeon O. Kotchoni Department of Biochemistry Cell and Molecular Biology of Plants Estacion Experimental del Zaidin High Council for Scientific Research (CSIC) Granada Spain Department of Biology Rutgers University Camden USA

genomics has become a ground-breaking field in all areas of the life sciences. The advanced genomics and the development of high-throughput techniques have lately provided insight into whole-genome characterization of a wide range of organisms. In the post-genomic era, new technologies have revealed an outbreak of prerequisite genomic sequences and supporting data to understand genome wide functional regulation of gene expression and metabolic pathways reconstruction. However, the availability of this plethora of genomic data presents a significant challenge for storage, analyses and data management. Analysis of this mega-data requires the development and application of novel bioinformatics tools that must include unified functional annotation, structural search, and comprehensive analysis and identification of new genes in a wide range of species with fully sequenced genomes. In addition, generation of systematically and syntactically unambiguous nomenclature systems for genomic data across species is a crucial task. Such systems are necessary for adequate handling genetic information in the context of comparative functional genomics. In this paper, we provide an overview of major advances in bioinformatics and computational biology in genome sequencing and next-generation sequence data analysis. We focus on their potential applications for efficient collection, storage, and analysis of genetic data/information from a wide range of gene banks. We also discuss the importance of establishing a unified nomenclature system through a functional and structural genomics approach.

关键词： Databases Computational Biology genomics Proteomics Next-Generation Sequencing

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The Status of the “Biopsychosocial” Model in Health Psychology: Towards an Integrated Approach and a Critique of Cultural Conceptions

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Open Journal of Medical Psychology 2012年第4期1卷 51-62页

作者： Andrew R. Hatala Department of Psychology University of Saskatchewan Saskatoon Canada

The current status of the “Biopsychosocial” Model in health psychology is contested and arguably exists in a stage of infancy. Despite original goals, medical researchers have developed theoretical and empirical integrations across bio-psycho-social domains only to a limited extent. This review article addresses this issue by making connections across research findings in health psychology and related medical fields in order to strengthen the associations across bio-psycho-social domains. In particular, research in sociosomatics, neuroplasticity and psychosocial genomics are introduced and explored. The role of “culture” as conceived of within the Biopsychosocial Model is also ambiguous and somewhat problematic. Arthur Klienman’s conceptions of culture as what is at stake for individuals in their local social and moral worlds is adopted to offer a critique of previous perspectives of culture and question its role amidst bio-psycho-social domains. Overall, a multilevel integrative or ‘holistic’ perspective is advanced to strengthen the Biopsychosocial Model for use within health psychology and biomedical research. In the end, some clinical implications are discussed.

关键词： Biopsychosocial Model Health Psychology Culture Sociomatics Psychosocial genomics

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Proteomics and Its Applications in Diagnosis of Auto Immune Diseases

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Open Journal of Immunology 2016年第1期6卷 14-33页

作者： Gebrehiwot Gebretsadik M. K. C. Menon Department of Medical Biochemistry College of Health and Medical Sciences Haramaya University Haramaya Ethiopia Department of Medical Biochemistry College of Health Sciences Addis Ababa University Addis Ababa Ethiopia

Although the proteomics and its applications in detecting autoimmune diseases are a prominently discussed issue, this review will focus particularly some prominent aspects regarding clinical utility of these techniques in prognosis, diagnosis, and treatment of these diseases. The impact of immunofluorescent techniques, enzyme immunoassays and use of proteomics biomarkers in the characterization of the auto immune diseases is briefly discussed. The necessity of adopting existing technologies of protein chemistry, predisposition testing, targeted monitoring and prevention of diseases through nutrition coupled with lifestyle changes will be focused as modern diagnostic tools in realizing the changeover from isolated medicine to personalized medicine. Use of biological fluids, in order to identify low abundance proteins as biomarkers in detecting autoimmune diseases is attempted in the study of serum/plasma proteomics.

关键词： Proteomics Autoimmune Diseases Biomarkers genomics

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Progress in pancreatic cancer therapeutics: The potential to exploit molecular targets

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World Journal of Pharmacology 2015年第2期4卷 180-192页

作者： Kiruthikah Thillai Debashis Sarker Paul Ross Department of Medical Oncology Guy's and St Thomas NHS Trust

Pancreatic ductal adenocarcinoma is an aggressive and devastating disease associated with poor survival outcomes. Even though signifcant advances have been made towards understanding the intricate pathology of this cancer, several important aspects remain unknown. Recently, key genetic mutations within the tumour have been identified, but the exact role they play in tumourigenesis has yet to be *** many years, the micro-tumour environment and stroma was thought to aid proliferation but there is now emerging research that suggests the contrary. Several novel targeted agents in pre-clinical and early clinical studies have been promising but it remains to be seen whether they will have a signifcant impact on patient outcomes. In this review we discuss the unique nature of pancreatic cancer biology, current treatment options and summarise the latest results from pre-clinical and clinical research. We also discuss the future strategies that are needed to improve outcomes for this disease.

关键词： Pancreatic cancer Adenocarcinoma Targeted therapy genomics Stroma KRAS Chemotherapy

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ANALYSIS OF EXPRESSED SEQUENCE TAGS FROM THE MARINE MICROALGA NANNOCHL OROPSIS OCULATA(EUSTIGMATOPHYCEAE)

ANALYSIS OF EXPRESSED SEQUENCE TAGS FROM THE MARINE MICROALG...

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中国海洋湖沼学会藻类学分会第七届会员大会暨第十四次学术讨论会

作者： Juan Shi Kehou Pan Jianzhong Yu Baohua Zhu Key Laboratory of Mariculture of Ministry of Education of China,Ocean University of China,Qingdao 266003.PR China

Nannochloropsis oculata(Eustigmatophyceae),a marine eukaryotic unicellular alga,is widely used in mariculture as live *** is considered to be of high nutritional value owing to its large amounts of proteins,polyunsaturated fatty acids(especially EPA)and diverse valuable *** respect that it grows well under conditions of mass culture,*** has considerable potential for commercial ***,previous studies of this microalga focused on its taxonomy,culture and biochemistry and tittle has been known at the molecular level until *** establish a molecular base is vital to understand the biological processes of this ***,we constructed a cDNA library using algal cells grown at exponential growth phase and carried out ESTs analysis.A total of 1960 non-redundant sequences(NRSs),consisting of 668 contigs and 1292 singletons,were generated for ***(Droop)Hibberd clone *** 19% of NRSs showed significant similarity(E<1e-04)to proteins registered in GenBank nonredundant protein *** COG/KOG profile database returned significant hits for 40 *** three NRSs were annotated using Gene Ontology(GO)*** revealed that a large proportion of NRSs could be unique to this *** work set the molecular basis for further studies on *** to better understand its biochemical,physiological and cellular processes.

关键词： genomics EST(expressed sequence tags) Eustigmatophyceae Nannochloropsis oculata cyclophilin α-dioxygenase

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Chemical Biology Study in Traditional Chinese Medicine:Target profiling of Bioactive Natural Products

Chemical Biology Study in Traditional Chinese Medicine:Targe...

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中国化学会第9届天然有机化学学术会议

作者：张卫东 Modern Research Center for Traditional Chinese Medicine School of PharmacySecond Military Medical University

＜正＞Traditional Chinese Medicine（TCM）,whose therapeutic efficacy has been proved by thousands of years’ clinical usage,is an important part of public healthcare and medicine research in China and Asian *** products derived from TCM are appreciated for their structural and functional diversity,which allow them to be ideal tools for the chemical biology ***,the target identification is still a big challenge for natural products with novel structure and significant bioactivity but no specific *** years,

关键词： Traditional Chinese Medicine natural products target profiling genomics proteomics molecular docking chemobioinformatics

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Analysing the genome of hexaploid wheat and its progenitors

Analysing the genome of hexaploid wheat and its progenitors

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第十四届全国植物基因组学大会

作者： Michael Bevan Fuhao Lu Cristobal Uauy Sarah Ayling Matthew Clarke Paul Bailey Manuel Spannagl Matthias Pfeifer Dan Bolser Arnaud Kerhornou Paul Kersey Klaus Mayer Mario Caccamo John Innes Centre

Bread wheat is one of the most important crops in the world that together with rice and maize provide the bulk of nutrition for humans and domesticated *** production was 661m tonnes in 2012,with increased consumption... 详细信息

关键词： genomics wheat crop improvement polyploidy

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