The Human Microbiome Project Consortium established a population-scale framework to study the human microbiome through standardized protocols. They obtained samples from 15-18 body sites from 242 healthy adults over multiple time points. They generated over 5,000 microbial profiles from 16S rRNA genes and over 3.5 terabases of metagenomic sequence data. They also sequenced approximately 800 reference strains isolated from the human body. Collectively, these data and resources represent the largest collection of human microbiome data and provide a framework for current and future microbiome studies.
Inhibitors for Attachment Protein BabA of Helicobacter pyloriPremier Publishers
Helicobacter pylori causes gastric pathologies to human after attachment to gastric epithelial layer via BabA protein, which is considered as one of the most important virulence factors. The study aimed to find inhibitors to this protein using structure-based drug design (SBDD) approach on the protein 3D structure (pdb ID 4zh0) . Large number of molecules / ligands were obtained as the protein gets many binding pockets. Checking and filtering the compounds depending on different parameters such as types of toxicity , ADME (absorption, distribution, metabolism, and excretion ) characters and others , only 6 molecules were obtained , these were redocked with the protein , they gave reasonable binding affinity at root-mean-square deviation (RMSD) of zero which represented by mode 1 of results performed by AutoDock vina.
The document describes the SalivaPRINT Toolkit, a tool for analyzing protein profiles from capillary electrophoresis. It builds a molecular feature matrix from electrophoresis output files that can then be used for data analysis and machine learning. The toolkit includes commands for building the matrix from output files, classifying samples using naïve Bayes, and identifying important molecular weight ranges for stratifying phenotypes. It provides an independent tool for high-throughput analysis of electrophoresis profiles from large population studies.
This document provides an overview of the November 2000 issue of JALA (Journal of Analytical Laboratories Automation). It describes the development of a novel robotic system for the New York Cancer Project biorepository in collaboration with the Medical Automation Research Center. The biorepository receives 50-100 blood samples per day which are processed robotically to extract, quantify, aliquot and store DNA, plasma and RNA to be accessible to investigators. The robotic system aims to provide rapid random access to the hundreds of thousands of DNA samples stored for high-throughput analysis in studies of gene-environment interactions and cancer risk.
MseqDR consortium: a grass-roots effort to establish a global resource aimed ...Human Variome Project
The success of whole exome sequencing (WES) for highly heterogeneous disorders, such as mitochondrial disease, is limited by substantial technical and bioinformatics challenges to correctly identify and prioritize the extensive number of sequence variants present in each patient. The likelihood of success can be greatly improved if a large cohort of patient data is assembled in which sequence variants can be systematically analysed, annotated, and interpreted relative to known phenotype. This effort has engaged and united more than 100 international mitochondrial clinicians, researchers, and bioinformaticians in the Mitochondrial Disease Sequence Data Resource (MSeqDR) consortium that formed in June 2012 to identify and prioritize the specific WES data analysis needs of the global mitochondrial disease community. Through regular web-based meetings, we have familiarized ourselves with existing strengths and gaps facing integration of MSeqDR with public resources, as well as the major practical, technical, and ethical challenges that must be overcome to create a sustainable data resource. We have now moved forward toward our common goal by establishing a central data resource (http://mseqdr.org/) that has both public access and secure web-based features that allow the coherent compilation, organization, annotation, and analysis of WES and mtDNA genome data sets generated in both clinical- and research-based settings of suspected mitochondrial disease patients. The most important aims of the MSeqDR consortium are summarized in the MSeqDR portal within the Consortium overview sections. Consortium participants are organized in 3 working groups that include (1) Technology and Bioinformatics; (2) Phenotyping, databasing, IRB concerns and access; and (3) Mitochondrial DNA specific concerns. The online MSeqDR resource is organized into discrete sections to facilitate data deposition and common reannotation, data visualization, data set mining, and access management. With the support of the United Mitochondrial Disease Foundation (UMDF) and the NINDS/NICHD U54 supported North American Mitochondrial Disease Consortium (NAMDC), the MSeqDR prototype has been built. Current major components include common data upload and reannotation using a novel HBCR based annotation tool that has also been made publicly available through the website, MSeqDR GBrowse that allows ready visualization of all public and MSeqDR specific data including labspecific aggregate data visualization tracks, MSeqDR-LSDB instance of nearly 1250 mitochondrial disease and mitochodnrial localized genes that is based on the Locus Specific Database model, exome data set mining in individuals or families using the GEM.app tool, and Account & Access Management. Within MSeqDR GBrowse it is now possible to explore data derived from MitoMap, HmtDB, ClinVar, UCSC-NumtS, ENCODE, 1000 genomes, and many other resources that bioinformaticians recruited to the project are organizing.
1) Researchers have created a new online resource called the IUPHAR/MMV Guide to Malaria Pharmacology (GtoMPdb) to curate information on antimalarial compounds and their molecular targets in Plasmodium.
2) The database currently contains 25 Plasmodium molecular targets and 57 antimalarial ligands that were manually curated from scientific literature.
3) A new customized online portal provides open access to the antimalarial data and allows browsing by parasite lifecycle stage, target species, and other features to help malaria research.
The National Center for Biotechnology Information (NCBI) Pathogen Analysis Pi...ExternalEvents
The document describes the NCBI Pathogen Analysis Pipeline which supports real-time sequencing of foodborne pathogens. The pipeline performs k-mer analysis, genome assembly, annotation, placement, clustering, SNP analysis, and tree construction on sequencing data submitted to NCBI. It provides automated bacterial assembly and a SNP analysis pipeline for clustering isolates and identifying outbreaks. The pipeline is demonstrated on examples of outbreaks linked to stone fruit and chicken kiev. NCBI aims to build a database of sequenced antibiotic resistant isolates with standardized metadata and maintain reference databases of antibiotic resistance genes.
The Human Variome Database in Australia in 2014 - Graham TaylorHuman Variome Project
There are a number of genetics and genomics initiatives underway in Australia, including the Australian node of the Human Variome Project (HVPA), as well as many active research collaborations including familial cancer, endocrine disease, and developmental delay. Most of these projects work with disease-specific databases on a research basis, with the risk that such archives may be ephemeral. HVPA is the only database that is directly integrated with accredited clinical reporting of variants. As such it is designed to capture variants that have passed scrutiny as diagnostically robust, and have therefore already been curated by qualified staff. Registered users access the HVPA database via a secure Internet portal.
I will describe three recent developments of the HVPA database and portal: the upgraded search interface, linkage to other datasets via BioGrid using hash-based de-identified case matching, and the introduction of a genome wide database using LOVD3. Finally I will discuss the future direction of the HVPA and the questions of utility, quality control and sustainability of genetic variation databases.
Search interface
The search interface has to provide useful tools for clinicians and lab scientists so that the HPVA project offers them direct benefits and incentivises them to participate. Following a request for feedback from users, a series of improvements were implemented, initially on a demonstration server and then on the live server following review by the Steering Committee. The highest priorities were for more information about numbers of times particular variants were
recorded, the ability to search by range and to filter by pathogenicity. There was also interest in enabling direct uploading of VCF files and the automated calculation of pathogenicity scores. Many of these features are now implemented and examples will be presented.
Linkage to other datasets
We have implemented the hash key algorithm and work is in progress with BioGrid to link variation data to clinical data sets.
Genome wide database
We have established an HVPA LOVD3 database and are working with the Human Genetics Society of Australasia on a pilot study to sequence the exomes of two trios and review the data using this database.
Inhibitors for Attachment Protein BabA of Helicobacter pyloriPremier Publishers
Helicobacter pylori causes gastric pathologies to human after attachment to gastric epithelial layer via BabA protein, which is considered as one of the most important virulence factors. The study aimed to find inhibitors to this protein using structure-based drug design (SBDD) approach on the protein 3D structure (pdb ID 4zh0) . Large number of molecules / ligands were obtained as the protein gets many binding pockets. Checking and filtering the compounds depending on different parameters such as types of toxicity , ADME (absorption, distribution, metabolism, and excretion ) characters and others , only 6 molecules were obtained , these were redocked with the protein , they gave reasonable binding affinity at root-mean-square deviation (RMSD) of zero which represented by mode 1 of results performed by AutoDock vina.
The document describes the SalivaPRINT Toolkit, a tool for analyzing protein profiles from capillary electrophoresis. It builds a molecular feature matrix from electrophoresis output files that can then be used for data analysis and machine learning. The toolkit includes commands for building the matrix from output files, classifying samples using naïve Bayes, and identifying important molecular weight ranges for stratifying phenotypes. It provides an independent tool for high-throughput analysis of electrophoresis profiles from large population studies.
This document provides an overview of the November 2000 issue of JALA (Journal of Analytical Laboratories Automation). It describes the development of a novel robotic system for the New York Cancer Project biorepository in collaboration with the Medical Automation Research Center. The biorepository receives 50-100 blood samples per day which are processed robotically to extract, quantify, aliquot and store DNA, plasma and RNA to be accessible to investigators. The robotic system aims to provide rapid random access to the hundreds of thousands of DNA samples stored for high-throughput analysis in studies of gene-environment interactions and cancer risk.
MseqDR consortium: a grass-roots effort to establish a global resource aimed ...Human Variome Project
The success of whole exome sequencing (WES) for highly heterogeneous disorders, such as mitochondrial disease, is limited by substantial technical and bioinformatics challenges to correctly identify and prioritize the extensive number of sequence variants present in each patient. The likelihood of success can be greatly improved if a large cohort of patient data is assembled in which sequence variants can be systematically analysed, annotated, and interpreted relative to known phenotype. This effort has engaged and united more than 100 international mitochondrial clinicians, researchers, and bioinformaticians in the Mitochondrial Disease Sequence Data Resource (MSeqDR) consortium that formed in June 2012 to identify and prioritize the specific WES data analysis needs of the global mitochondrial disease community. Through regular web-based meetings, we have familiarized ourselves with existing strengths and gaps facing integration of MSeqDR with public resources, as well as the major practical, technical, and ethical challenges that must be overcome to create a sustainable data resource. We have now moved forward toward our common goal by establishing a central data resource (http://mseqdr.org/) that has both public access and secure web-based features that allow the coherent compilation, organization, annotation, and analysis of WES and mtDNA genome data sets generated in both clinical- and research-based settings of suspected mitochondrial disease patients. The most important aims of the MSeqDR consortium are summarized in the MSeqDR portal within the Consortium overview sections. Consortium participants are organized in 3 working groups that include (1) Technology and Bioinformatics; (2) Phenotyping, databasing, IRB concerns and access; and (3) Mitochondrial DNA specific concerns. The online MSeqDR resource is organized into discrete sections to facilitate data deposition and common reannotation, data visualization, data set mining, and access management. With the support of the United Mitochondrial Disease Foundation (UMDF) and the NINDS/NICHD U54 supported North American Mitochondrial Disease Consortium (NAMDC), the MSeqDR prototype has been built. Current major components include common data upload and reannotation using a novel HBCR based annotation tool that has also been made publicly available through the website, MSeqDR GBrowse that allows ready visualization of all public and MSeqDR specific data including labspecific aggregate data visualization tracks, MSeqDR-LSDB instance of nearly 1250 mitochondrial disease and mitochodnrial localized genes that is based on the Locus Specific Database model, exome data set mining in individuals or families using the GEM.app tool, and Account & Access Management. Within MSeqDR GBrowse it is now possible to explore data derived from MitoMap, HmtDB, ClinVar, UCSC-NumtS, ENCODE, 1000 genomes, and many other resources that bioinformaticians recruited to the project are organizing.
1) Researchers have created a new online resource called the IUPHAR/MMV Guide to Malaria Pharmacology (GtoMPdb) to curate information on antimalarial compounds and their molecular targets in Plasmodium.
2) The database currently contains 25 Plasmodium molecular targets and 57 antimalarial ligands that were manually curated from scientific literature.
3) A new customized online portal provides open access to the antimalarial data and allows browsing by parasite lifecycle stage, target species, and other features to help malaria research.
The National Center for Biotechnology Information (NCBI) Pathogen Analysis Pi...ExternalEvents
The document describes the NCBI Pathogen Analysis Pipeline which supports real-time sequencing of foodborne pathogens. The pipeline performs k-mer analysis, genome assembly, annotation, placement, clustering, SNP analysis, and tree construction on sequencing data submitted to NCBI. It provides automated bacterial assembly and a SNP analysis pipeline for clustering isolates and identifying outbreaks. The pipeline is demonstrated on examples of outbreaks linked to stone fruit and chicken kiev. NCBI aims to build a database of sequenced antibiotic resistant isolates with standardized metadata and maintain reference databases of antibiotic resistance genes.
The Human Variome Database in Australia in 2014 - Graham TaylorHuman Variome Project
There are a number of genetics and genomics initiatives underway in Australia, including the Australian node of the Human Variome Project (HVPA), as well as many active research collaborations including familial cancer, endocrine disease, and developmental delay. Most of these projects work with disease-specific databases on a research basis, with the risk that such archives may be ephemeral. HVPA is the only database that is directly integrated with accredited clinical reporting of variants. As such it is designed to capture variants that have passed scrutiny as diagnostically robust, and have therefore already been curated by qualified staff. Registered users access the HVPA database via a secure Internet portal.
I will describe three recent developments of the HVPA database and portal: the upgraded search interface, linkage to other datasets via BioGrid using hash-based de-identified case matching, and the introduction of a genome wide database using LOVD3. Finally I will discuss the future direction of the HVPA and the questions of utility, quality control and sustainability of genetic variation databases.
Search interface
The search interface has to provide useful tools for clinicians and lab scientists so that the HPVA project offers them direct benefits and incentivises them to participate. Following a request for feedback from users, a series of improvements were implemented, initially on a demonstration server and then on the live server following review by the Steering Committee. The highest priorities were for more information about numbers of times particular variants were
recorded, the ability to search by range and to filter by pathogenicity. There was also interest in enabling direct uploading of VCF files and the automated calculation of pathogenicity scores. Many of these features are now implemented and examples will be presented.
Linkage to other datasets
We have implemented the hash key algorithm and work is in progress with BioGrid to link variation data to clinical data sets.
Genome wide database
We have established an HVPA LOVD3 database and are working with the Human Genetics Society of Australasia on a pilot study to sequence the exomes of two trios and review the data using this database.
Literature Based Framework for Semantic Descriptions of e-Science resourcesHammad Afzal
Hammad Afzal gave a seminar at the National University of Sciences and Technology in Islamabad about developing a literature-based framework for semantic descriptions of e-Science resources. He discussed using natural language processing techniques to automatically generate semantic profiles of bioinformatics resources by extracting information from relevant scientific literature. His approach involved building a controlled vocabulary from literature and then mining literature to find semantic descriptions of resources.
How bioinformatic and sequencing data might inform the regulatory process - O...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
A machine learning and bioinformatics approach was used to identify non-invasive miRNA biomarkers for early detection of non-small cell lung cancer (NSCLC). 13 miRNAs were found to be consistently underexpressed in NSCLC tissue, blood and serum across 4 datasets. Kaplan-Meier analysis showed 6 miRNAs had prognostic power. A random forest model identified a 3-miRNA panel (miR-320e, miR-103a, miR-526b) that detected NSCLC with 91.5% accuracy. These miRNAs were also prognostic for lung adenocarcinoma survival. An online tool called BiomarkerGenie was created to automate biomarker selection from omics data.
Keynote presented at the Phenotype Foundation first annual meeting.
Describes data sharing, data annotation and the needs for further tool and ontology and ontology mapping development.
Amsterdam, January 18, 2016
This document discusses sensing technologies for precision phenotyping in vegetable crops. It begins with an overview of the importance of precision phenotyping in plant breeding to characterize quantitative traits. It then reviews various proximal and remote sensing technologies that can be used for non-destructive high-throughput phenotyping, focusing on those applicable in protected horticulture. Optical and thermal sensors are highlighted as the most widely used. The document concludes by discussing challenges in managing large phenotyping data and integrating with other omics disciplines.
The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 22 member states. EMBL was created in 1974 and operates from five sites, performing basic research in molecular biology and molecular medicine. A key function of EMBL is the EMBL Nucleotide Sequence Database, maintained at the European Bioinformatics Institute, which incorporates and distributes nucleotide sequences from public sources as part of an international collaboration.
The document discusses data sharing and analysis platforms for rare diseases like RD-Connect and MatchMaker Exchange, describing RD-Connect's genome-phenome analysis platform that enables variant identification and diagnosis. It also summarizes RD-Connect's role in facilitating data integration and sharing across resources to overcome bottlenecks in rare disease research like lack of data and samples.
This document discusses major biological databases. It describes three types of biological databases: primary databases that contain original experimental data, secondary databases that contain additional derived information from primary databases, and composite databases that combine data from multiple sources. The document focuses on describing GenBank, a primary sequence database maintained by the National Center for Biotechnology Information. It provides details on how sequences are submitted to GenBank and how entries are formatted, including information contained in various fields like LOCUS, DEFINITION, and FEATURES. The document also briefly introduces the European Molecular Biology Laboratory database, EMBL, which collaborates with GenBank and DDBJ to exchange nucleotide sequence data daily.
Bioinformatics databases: Current Trends and Future PerspectivesUniversity of Malaya
Data is the most powerful resource in any field or subject of study. In Biology, data comes from scientists and their actions, while any institution that makes sense of the data collected, will be in the forefront in their respective research field. In the beginning of any data collection endeavour, it is critical to find proper management techniques to store data and to maximise its utilisation. This presentation reflects upon the current trends and techniques of data modeling, architecture with a highlight on the uses of database, focusing on Bioinformatics examples and case studies. Finally, the future of bioinformatics databases is highlighted to give an overview of the modeling techniques to accommodate the biological data escalation in coming years.
Biological databases are collections of experimental and theoretical biological data that are organized so their contents can be easily accessed, managed, updated, and retrieved. The activity of preparing a database can be divided into collecting data in an accessible form and making it available to a multi-user system. Two important biological databases are GenBank, which contains publicly available nucleotide and protein sequences, and the Protein Data Bank, which houses 3D structures of proteins, nucleic acids, and carbohydrates.
Bioinformatics: Building the cornerstones of Sequence Homology and its use fo...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
How can Whole Genome Sequencing information be used to address data requireme...OECD Environment
This document discusses the potential use of whole genome sequencing data to address regulatory requirements for approval of microorganisms as active ingredients in plant protection products in the EU. It analyzes how genome sequencing could be used for species assignment, relationship to pathogens, distinction between Bacillus strains, production of metabolites, antibiotic resistance, genetic stability, risk assessment, and unequivocal identification of strains. While noting some potential benefits, it also describes limitations and problems with relying solely on genome sequencing data. It concludes that genome sequencing can be useful to exclude some issues but should not be a standard requirement, and that only reports on analyses—not the genome sequences themselves—should be included in dossiers.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
The document discusses several drug and medication databases:
- The FDA drug database contains information on drugs approved in the US since 1939 and allows searching by drug or ingredient name. It also includes drugs undergoing clinical trials.
- PubChem is an NIH database containing over 90 million chemical compounds and their biological properties. It can be searched by structure, name, and other properties.
- PubMed provides access to MEDLINE references and citations on biomedical topics from the National Library of Medicine.
- DrugBank combines drug and drug target data and contains over 9,500 drug entries including FDA-approved and experimental drugs. It is freely accessible online.
GASCAN: A Novel Database for Gastric Cancer Genes and Primersijdmtaiir
GasCan is a specialized and unique database of
gastric cancer protein encoding genes expressed in human and
mouse. The features that make GasCan unique are availability
of gene information, availability of primers for each gene, with
their features and conditions given that are useful in PCR
amplification, especially in cloning experiments and to make it
more unique built in programmed sequence analysis facility is
provided that analyze gene sequences in database itself,
resulting sequence analysis information can be valuable for
researchers in different experiments. Furthermore, DNA
sequence analysis tool is provided that can be access freely.
GasCan will expand in future to other species, genes and cover
more useful information of other species. Flexible database
design, expandability and easy access of information to all of
the users are the main features of the database. The Database is
publicly available at http://www.gastric-cancer.site40.net.
A well-conceived and executed preclinical and clinical
radiolabeled ADME program will provide you with a detailed
assessment of the total fate (mass balance, route, and rate of excretion,
tissue distribution, metabolic pathways, and identity and quantity of
metabolites) of your drug candidate to support regulatory submissions.
Biological databases provide various types of molecular biology data including sequences, structures, and functional information. Sequence databases like GenBank provide nucleotide sequences while UniProt provides protein sequences. Structure databases like PDB provide 3D protein structures. These databases contain sequences, annotations, references, and tools for analysis. They are periodically updated and cross-referenced for comprehensive molecular data.
This document describes resources for genomic variation from the National Center for Biotechnology Information (NCBI). It begins with a quick description and case study example. It then describes the Medical Genetics Summary resource and other variation resources available from NCBI. It concludes with additional general information about NCBI and genomic variation.
The document discusses the National Center for Biotechnology Information (NCBI). It provides background that NCBI is part of the National Library of Medicine and houses databases relevant to biotechnology and biomedicine. It describes some of NCBI's major databases, including GenBank for DNA sequences and PubMed for biomedical literature. The document also discusses the BLAST tool and provides examples of some of NCBI's databases, such as the Nucleotide, Protein, and Structural databases.
1) The gut microbiota is now a major focus of research across many disciplines due to its contributions to health and disease.
2) Changes in the composition of the gut microbiota are linked to changes in human behavior and the rising prevalence of immune and metabolic disorders.
3) Discoveries about the gut microbiota promise to realize personalized medicine and nutrition and change conventional dietary management approaches.
This study investigated the effects of the probiotic Bifidobacterium breve CNCM I-4035 and its cell-free culture supernatant (CFS) on human dendritic cells (DCs) and how the DCs respond to the pathogenic bacteria Salmonella typhi. The CFS decreased pro-inflammatory cytokines in DCs challenged with S. typhi, while live B. breve induced both pro- and anti-inflammatory cytokines. Both live B. breve and CFS activated Toll-like receptor signaling pathways in DCs. CFS increased expression of TLR9 and related genes more than live B. breve in the presence of S. typhi. The results suggest B. breve affects the
Literature Based Framework for Semantic Descriptions of e-Science resourcesHammad Afzal
Hammad Afzal gave a seminar at the National University of Sciences and Technology in Islamabad about developing a literature-based framework for semantic descriptions of e-Science resources. He discussed using natural language processing techniques to automatically generate semantic profiles of bioinformatics resources by extracting information from relevant scientific literature. His approach involved building a controlled vocabulary from literature and then mining literature to find semantic descriptions of resources.
How bioinformatic and sequencing data might inform the regulatory process - O...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
A machine learning and bioinformatics approach was used to identify non-invasive miRNA biomarkers for early detection of non-small cell lung cancer (NSCLC). 13 miRNAs were found to be consistently underexpressed in NSCLC tissue, blood and serum across 4 datasets. Kaplan-Meier analysis showed 6 miRNAs had prognostic power. A random forest model identified a 3-miRNA panel (miR-320e, miR-103a, miR-526b) that detected NSCLC with 91.5% accuracy. These miRNAs were also prognostic for lung adenocarcinoma survival. An online tool called BiomarkerGenie was created to automate biomarker selection from omics data.
Keynote presented at the Phenotype Foundation first annual meeting.
Describes data sharing, data annotation and the needs for further tool and ontology and ontology mapping development.
Amsterdam, January 18, 2016
This document discusses sensing technologies for precision phenotyping in vegetable crops. It begins with an overview of the importance of precision phenotyping in plant breeding to characterize quantitative traits. It then reviews various proximal and remote sensing technologies that can be used for non-destructive high-throughput phenotyping, focusing on those applicable in protected horticulture. Optical and thermal sensors are highlighted as the most widely used. The document concludes by discussing challenges in managing large phenotyping data and integrating with other omics disciplines.
The European Molecular Biology Laboratory (EMBL) is a molecular biology research institution supported by 22 member states. EMBL was created in 1974 and operates from five sites, performing basic research in molecular biology and molecular medicine. A key function of EMBL is the EMBL Nucleotide Sequence Database, maintained at the European Bioinformatics Institute, which incorporates and distributes nucleotide sequences from public sources as part of an international collaboration.
The document discusses data sharing and analysis platforms for rare diseases like RD-Connect and MatchMaker Exchange, describing RD-Connect's genome-phenome analysis platform that enables variant identification and diagnosis. It also summarizes RD-Connect's role in facilitating data integration and sharing across resources to overcome bottlenecks in rare disease research like lack of data and samples.
This document discusses major biological databases. It describes three types of biological databases: primary databases that contain original experimental data, secondary databases that contain additional derived information from primary databases, and composite databases that combine data from multiple sources. The document focuses on describing GenBank, a primary sequence database maintained by the National Center for Biotechnology Information. It provides details on how sequences are submitted to GenBank and how entries are formatted, including information contained in various fields like LOCUS, DEFINITION, and FEATURES. The document also briefly introduces the European Molecular Biology Laboratory database, EMBL, which collaborates with GenBank and DDBJ to exchange nucleotide sequence data daily.
Bioinformatics databases: Current Trends and Future PerspectivesUniversity of Malaya
Data is the most powerful resource in any field or subject of study. In Biology, data comes from scientists and their actions, while any institution that makes sense of the data collected, will be in the forefront in their respective research field. In the beginning of any data collection endeavour, it is critical to find proper management techniques to store data and to maximise its utilisation. This presentation reflects upon the current trends and techniques of data modeling, architecture with a highlight on the uses of database, focusing on Bioinformatics examples and case studies. Finally, the future of bioinformatics databases is highlighted to give an overview of the modeling techniques to accommodate the biological data escalation in coming years.
Biological databases are collections of experimental and theoretical biological data that are organized so their contents can be easily accessed, managed, updated, and retrieved. The activity of preparing a database can be divided into collecting data in an accessible form and making it available to a multi-user system. Two important biological databases are GenBank, which contains publicly available nucleotide and protein sequences, and the Protein Data Bank, which houses 3D structures of proteins, nucleic acids, and carbohydrates.
Bioinformatics: Building the cornerstones of Sequence Homology and its use fo...OECD Environment
24 June 2019: This OECD seminar presented and discussed the potential use of genome sequence, bioinformatic tools and databases in a regulatory decision process for microbial pesticides.
How can Whole Genome Sequencing information be used to address data requireme...OECD Environment
This document discusses the potential use of whole genome sequencing data to address regulatory requirements for approval of microorganisms as active ingredients in plant protection products in the EU. It analyzes how genome sequencing could be used for species assignment, relationship to pathogens, distinction between Bacillus strains, production of metabolites, antibiotic resistance, genetic stability, risk assessment, and unequivocal identification of strains. While noting some potential benefits, it also describes limitations and problems with relying solely on genome sequencing data. It concludes that genome sequencing can be useful to exclude some issues but should not be a standard requirement, and that only reports on analyses—not the genome sequences themselves—should be included in dossiers.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
The document discusses several drug and medication databases:
- The FDA drug database contains information on drugs approved in the US since 1939 and allows searching by drug or ingredient name. It also includes drugs undergoing clinical trials.
- PubChem is an NIH database containing over 90 million chemical compounds and their biological properties. It can be searched by structure, name, and other properties.
- PubMed provides access to MEDLINE references and citations on biomedical topics from the National Library of Medicine.
- DrugBank combines drug and drug target data and contains over 9,500 drug entries including FDA-approved and experimental drugs. It is freely accessible online.
GASCAN: A Novel Database for Gastric Cancer Genes and Primersijdmtaiir
GasCan is a specialized and unique database of
gastric cancer protein encoding genes expressed in human and
mouse. The features that make GasCan unique are availability
of gene information, availability of primers for each gene, with
their features and conditions given that are useful in PCR
amplification, especially in cloning experiments and to make it
more unique built in programmed sequence analysis facility is
provided that analyze gene sequences in database itself,
resulting sequence analysis information can be valuable for
researchers in different experiments. Furthermore, DNA
sequence analysis tool is provided that can be access freely.
GasCan will expand in future to other species, genes and cover
more useful information of other species. Flexible database
design, expandability and easy access of information to all of
the users are the main features of the database. The Database is
publicly available at http://www.gastric-cancer.site40.net.
A well-conceived and executed preclinical and clinical
radiolabeled ADME program will provide you with a detailed
assessment of the total fate (mass balance, route, and rate of excretion,
tissue distribution, metabolic pathways, and identity and quantity of
metabolites) of your drug candidate to support regulatory submissions.
Biological databases provide various types of molecular biology data including sequences, structures, and functional information. Sequence databases like GenBank provide nucleotide sequences while UniProt provides protein sequences. Structure databases like PDB provide 3D protein structures. These databases contain sequences, annotations, references, and tools for analysis. They are periodically updated and cross-referenced for comprehensive molecular data.
This document describes resources for genomic variation from the National Center for Biotechnology Information (NCBI). It begins with a quick description and case study example. It then describes the Medical Genetics Summary resource and other variation resources available from NCBI. It concludes with additional general information about NCBI and genomic variation.
The document discusses the National Center for Biotechnology Information (NCBI). It provides background that NCBI is part of the National Library of Medicine and houses databases relevant to biotechnology and biomedicine. It describes some of NCBI's major databases, including GenBank for DNA sequences and PubMed for biomedical literature. The document also discusses the BLAST tool and provides examples of some of NCBI's databases, such as the Nucleotide, Protein, and Structural databases.
1) The gut microbiota is now a major focus of research across many disciplines due to its contributions to health and disease.
2) Changes in the composition of the gut microbiota are linked to changes in human behavior and the rising prevalence of immune and metabolic disorders.
3) Discoveries about the gut microbiota promise to realize personalized medicine and nutrition and change conventional dietary management approaches.
This study investigated the effects of the probiotic Bifidobacterium breve CNCM I-4035 and its cell-free culture supernatant (CFS) on human dendritic cells (DCs) and how the DCs respond to the pathogenic bacteria Salmonella typhi. The CFS decreased pro-inflammatory cytokines in DCs challenged with S. typhi, while live B. breve induced both pro- and anti-inflammatory cytokines. Both live B. breve and CFS activated Toll-like receptor signaling pathways in DCs. CFS increased expression of TLR9 and related genes more than live B. breve in the presence of S. typhi. The results suggest B. breve affects the
A study found that consuming milk fat promotes growth of normally rare sulphate-reducing bacteria in mice, which stimulates harmful immune responses and causes more severe colitis in mice genetically prone to inflammatory bowel disease (IBD). Milk fat increases taurine-conjugated bile acids that feed these bacteria, namely Bilophilia wadsworthia, leading them to produce metabolites like hydrogen sulfide that damage the gut. These findings help explain how certain diets may influence IBD by altering the gut microbiome in genetically susceptible individuals.
The document describes the discovery of a new basal clade within the fungal kingdom called cryptomycota.
- Cryptomycota includes organisms like Rozella that branch with fungi genetically but appear to grow and develop without synthesizing a chitin-rich cell wall, which is a defining characteristic of fungi.
- Phylogenetic trees constructed from genetic data place cryptomycota as a sister group to Rozella and identify it as a very large, uncultured group of microbes that fundamentally challenges current understanding of fungal evolution and diversity.
This document summarizes the current understanding of fungal hyphal branching. It discusses the two main types of branching (apical and lateral) and some of the internal and external factors that induce branching. Potential mechanisms underlying branch site selection are outlined, including multiple signaling pathways and subcellular structures. Finally, branching in other kingdoms is briefly compared to fungal hyphal branching. However, the molecular basis of hyphal branching remains poorly understood.
Zhao Liping is a Chinese microbiologist who studied his own microbiome to understand obesity. After gaining significant weight, he adopted a regimen of fermented foods like Chinese yam and bitter melon believed to change gut bacteria. This led to weight loss of 20 kg in 2 years along with improved health markers. His personal experience inspired him to research the role of the microbiome in conditions like diabetes and obesity. While the field is still young, Zhao hopes to establish a molecular pathway between gut microbes and obesity through human and animal studies.
Synthetic Biology for Plant ScientistsSachin Rawat
Tools of synthetic biology can be utilised to engineer metabolic pathways to optimize production of secondary metabolites and ligno-cellulose. The presentation describes an approach to develop an artificial positive feedback loop to increase accumulation of cell wall polysaccharides. These will decrease the cost of production of plant-based biofuels, paper and other plant products.
Este documento presenta un cuestionario de 31 preguntas sobre conceptos básicos de microbiología. Las preguntas abarcan temas como los descubridores clave en el campo de la microbiología, la morfología y estructura de las bacterias, sus mecanismos de movilidad y reproducción, así como las funciones de sus principales estructuras celulares como la membrana, pared celular, flagelos y ribosomas. El cuestionario parece ser parte de un examen o evaluación para estudiantes de microbiología.
The document discusses the role of gut microbiota in nutrition and health. It makes three key points:
1) The gut microbiota contributes nutrients and energy to the host through fermenting nondigestible dietary components, and maintains a balance with the host's metabolism and immune system in a healthy state.
2) Diet has a major influence on microbial community composition in both the short and long term, opening possibilities for manipulating health through diet.
3) There is significant interindividual variation in gut microbiota composition within populations that influences responses to drugs and diet. Achieving a better understanding of microbiota profiles that support health is important.
Los virus son elementos genéticos que se replican dentro de las células huésped aprovechando su maquinaria metabólica. Para multiplicarse, los virus deben ingresar a una célula e integrar su material genético, adquiriendo así las propiedades de la célula huésped como la heredabilidad. Sin embargo, durante la replicación viral se destruye la célula huésped, otorgándole al virus su carácter patógeno. Existen diferentes clasificaciones de virus según su genoma, huésped y forma de replicación
The document discusses fungal infections and the immune response to fungi. It notes that fungi can have symbiotic, commensal, latent, or pathogenic relationships with humans. The immune system aims to limit fungal burden through resistance, and limit host damage through tolerance. Both resistance and tolerance strategies are evolutionarily conserved in plants and vertebrates. Understanding the interplay between these strategies may help define how fungi have adapted to the mammalian immune system.
El documento describe los protozoarios. Estos son microorganismos eucariotas unicelulares que viven de forma libre o como parásitos. Pueden encontrarse en una amplia variedad de hábitats húmedos como agua dulce, marina o suelo. Algunos protozoarios son patógenos y causan enfermedades en humanos y animales.
The Human Microbiome Project was a US NIH initiative launched in 2007 to characterize the human microbiota and its role in health and disease. It involved sequencing over 2,000 microbial genomes from the human body and conducting metagenomic sequencing of microbial communities from 300 healthy individuals across multiple body sites. The second phase, the iHMP, launched in 2014 with the goals of generating resources to characterize the microbiome in health and disease states using methods like metatranscriptomics and metabolomics. Key sub-projects examined the microbiome in pregnancy/preterm birth and onset of inflammatory bowel disease.
The document summarizes microbiome biomarker data from the American Gut Project. It describes the project's goal of characterizing participants' gut, skin, and oral bacteria to better understand relationships between microbiome and lifestyle/health factors. Over 4,600 samples from 3,624 participants have been sequenced and analyzed. The analyzed samples included some from patients that provided multiple sample types (mouth & skin, mouth & stool). T-Bioinfo then performed analyses including mapping samples to identify bacteria, generating abundance tables, and using machine learning methods to identify correlations between bacterial species from different body sites. Preliminary conclusions identified outstanding samples and correlated oral and stool bacteria.
Bioinformatics is an interdisciplinary field involving biology, computer science, mathematics and statistics. It addresses large-scale biological problems from a computational perspective. Common problems include modeling biological processes at the molecular level and making inferences from collected data. A bioinformatics solution typically involves collecting statistics from biological data, building a computational model, solving a computational problem, and testing the algorithm. Bioinformatics plays a role in areas like structural genomics, functional genomics and nutritional genomics. It is used for applications such as transcriptome analysis, drug discovery, cheminformatics analysis, and more. It is an important tool in fields like molecular medicine, gene therapy, microbial genome applications, antibiotic resistance, and evolutionary studies. Biological databases are important for organizing
Presented at the Fall 2020 American Chemical Society (ACS) National Meeting (Virtual) on August 20, 2020.
Sunghwan Kim, Jian Zhang, Paul Thiessen, Asta Gindulyte, Pertti J. Hakkinen & Evan Bolton
National Library of Medicine, National Institutes of Health, Rockville, Maryland, United States
==== Abstract ====
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical information resource at the U.S. National Institutes of Health. It collects chemical information from 700+ data sources and disseminates the collected data to the public free of charge. Arguably, PubChem contains the largest amount of chemical information available in the public domain, with more than 250 million depositor-provided substance descriptions, 100 million unique chemical structures, and 265 million bioactivity outcomes from one million assays covering around twenty thousand unique protein target sequences.
Included in the many types of content in PubChem is toxicological information about chemicals, e.g., human and animal toxicity, ecotoxicity, exposure limits, exposure symptoms, and antidote & emergency treatment. Notably, a substantial amount of toxicological information from resources formerly offered by the TOXicology data NETwork (TOXNET) is now integrated into PubChem, e.g., the Hazardous Substances Data Bank (HSDB), LactMed, and LiverTox. In addition, PubChem contains a large amount of bioactivity and toxicity screening data that can be used to build toxicity prediction models based on statistical and machine-learning approaches. This presentation provides an overview of PubChem’s toxicological information as well as tools and services that help users exploit this information. It also describes how open data in PubChem can be used to develop prediction models for chemical toxicity.
Quantifying the content of biomedical semantic resources as a core for drug d...Syed Muhammad Ali Hasnain
The biomedical research community is providing large-scale data sources to enable knowledge discovery from the data alone, or from novel scientific experiments in combination with the existing knowledge.
Increasingly semantic Web technologies are being developed and used including ontologies, triple stores and combinations thereof.
The amount of data is constantly increasing as well as the complexity of data.
Since the data sources are publicly available, the amount of content can be derived giving an overview on the accessible content but also on the state of the data representation in comparison to the existing content.
For a better understanding of the existing data resources, i.e.\ judgments on the distribution of data triples across concepts, data types and primary providers, we have performed a comprehensive analysis which delivers an overview on the accessible content for semantic Web solutions.
It can be derived that the information related to genes, proteins and chemical entities form the center, whereas the content related to diseases and pathways forms a smaller portion.
Further data relates to dietary content and specific questions such as cancer prevention and toxicological effects of drugs.
The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb) is an expert-driven, open database of pharmacological targets and the substances that act on them. It contains information on over 1,800 drug targets and 1,100 related proteins. The database is curated by 500 experts and provides detailed pharmacological data as well as overviews of key properties and ligands. Specialized extensions of GtoPdb include guides to immunopharmacology and malaria pharmacology that connect their fields to drug discovery. The database is continuously updated with new targets, ligands, features and access methods.
Databases pathways of genomics and proteomics Sachin Kumar
The document discusses several databases related to human metabolism and pharmacology. It describes the contents and purpose of each database, including the Human Metabolome Database (HMDB), KEGG, MetaCyc, PubChem, ChEBI, DrugBank, the Therapeutic Target Database (TTD), PharmGKB, and Chemical Entities of Biological Interest (ChEBI). These databases contain chemical, clinical, molecular biology, pathway, and genomic data on human metabolites, drugs, and targets.
Bioinformatics is the application of computer technology to the management of biological information. It plays a role in areas like experimental molecular biology, genetics, genomics, and structural biology. It helps analyze and organize the large amounts of data generated by projects like the Human Genome Project. It is important for understanding diseases and developing new drug targets. It also aids research in fields like systems biology, genomics, and proteomics.
Bioinformatics is the application of computer technology to the management of biological information. It plays a role in areas like experimental molecular biology, genetics, genomics, and structural biology. It helps analyze and organize the large amounts of data generated by projects like the Human Genome Project. It is important for understanding diseases and developing new drug targets. It also aids research in fields like systems biology, genomics, and proteomics.
This document provides an overview of bioinformatics. It begins by explaining how bioinformatics emerged from the need to analyze vast amounts of genetic sequence data produced by projects like the Human Genome Project. It then defines bioinformatics as the field that develops tools and methods for understanding biological data by combining computer science, statistics, and other disciplines. The document outlines several goals and applications of bioinformatics, such as identifying genes and their functions, modeling protein structures, comparing genomes, and its uses in medicine, microbial research, and more. It also provides a brief history of important developments in bioinformatics and DNA sequencing.
Research trends in different pharmaceutical areas: Natural product chemistry
Imtiaj Hossain Chowdhury
B’Pharm (Jahangirnagar University), M’Pharm (Jahangirnagar University)
Master’s in Public Health (American International University Bangladesh)
Medical innovation calls for new models for collaborations that facilitates, government, academia and industry.
Barriers to research and ultimate commercialization will be lowered by bringing best practices from industry and academic settings.
Hippocrates platform facilitates early drug development extending from basic research to drug invention and commercialization significantly saving time and money.
The platform is designed in such way to facilitate collaboration amongst stakeholders as well as taking advantage of the vast resources currently available on the web to generate and aggregate content based on the needs of the research of the end-user.
Aim1: To study the method of genome identification through ENSEMBL browser.
Aim2: To study the method of genome identification through VISTA.
Aim3: To study the method of genome identification through UCSC Genome Browser.
Aim4: To study the method of genome and amino acid sequences through UCSC Genome Browser.
2011-10-11 Open PHACTS at BioIT World Europeopen_phacts
The document discusses the Innovative Medicines Initiative's Open PHACTS project, which aims to develop robust standards and apply them in a semantic integration platform ("Open Pharmacological Space") to integrate drug discovery data from various public and private sources. The project brings together partners from industry, academia, and non-profits to build an open infrastructure for linking drug discovery knowledge and supporting ongoing research. It outlines the technical approach, priorities, and initial progress on developing exemplar applications and a prototype "lash up" system.
Central mucoepidermoid carcinoma an up to-date analysis of 147 casesMNTan1
1. The study analyzed 147 cases of central mucoepidermoid carcinoma (CMC) reported in 36 publications to understand clinical aspects, histology, treatment and prognostic factors.
2. It found that CMC was more common in females than males, most often in the mandible, and usually low grade histologically. The main treatment was surgical resection.
3. Significant prognostic factors associated with worse survival in multivariate analysis included male sex, high histological grade, conservative rather than radical treatment, and lymph node metastasis.
Cheminformatics plays a key role in modern drug discovery by helping chemists organize and analyze the vast amounts of chemical data being produced. It combines fields like chemistry, biology, and informatics to transform data into knowledge. Specifically, cheminformatics aids in tasks like identifying drug targets, finding lead compounds, optimizing leads, and conducting pre-clinical trials through methods such as high-throughput screening, structure-activity modeling, and predictive toxicity analysis. It also provides tools for tasks like drawing and searching chemical structures in databases.
Presented by Richard Kidd at "The Future Information Needs of Pharmaceutical & Medicinal Chemistry", Monday 28 November 2011 at The Linnean Society, Burlington Square, London run by the RSC CICAG group.
History and devolopment of bioinfomatics.ppt (1)Madan Kumar Ca
Dear Sir, Madam
Name: Madan Kumar C A
Topic: History and Development of Bioinformatics
Guide: Dr. Ramesh C K
Associate Professor
Dept of Biotechnnology
Sahyadri Science College
Shivamogga
This document discusses bioinformatics and its applications in vaccine discovery. It begins with an introduction to bioinformatics, describing it as an interdisciplinary field that develops tools to analyze biological data using computer science, mathematics, and statistics. It then discusses the objectives and need for bioinformatics, as well as important bioinformatics databases. Next, it provides an overview of the concept of bioinformatics and how it has expanded from analyzing sequence data to include modeling and other areas. Finally, it details the impact of bioinformatics on vaccine discovery through approaches like reverse vaccinology, immunoinformatics, and structural vaccinology that use bioinformatics to select antigens and design new generation vaccines.
Similar to A framework for human microbiome research (20)
La Unión Europea ha acordado un paquete de sanciones contra Rusia por su invasión de Ucrania. Las sanciones incluyen restricciones a las importaciones de productos rusos clave como el acero y la madera, así como medidas contra bancos y funcionarios rusos. Los líderes de la UE esperan que las sanciones aumenten la presión económica sobre Rusia y la disuadan de continuar su agresión contra Ucrania.
El documento presenta el cronograma de actividades para un programa de verano científico que incluye tres etapas: aislamiento y purificación de péptidos naturales, bioensayos in vitro de los péptidos, y taxonomía molecular y genética. La primera etapa involucra técnicas de aislamiento como extracción con nitrógeno líquido y centrifugación, así como purificación mediante cromatografía líquida de baja presión y espectrometría de masas. La segunda etapa implica bioensayos de los pépt
1) The gut microbiota plays a key role in host development, physiology, and health by modulating the immune system and influencing organ development and metabolism.
2) The gut microbiota is dominated by anaerobic bacteria and contains over 500-1000 bacterial species from a few bacterial phyla. It outnumbers human cells 10:1 and contains many metabolic functions.
3) The gut microbiota influences the properties of the intestinal mucus layer, induces the development of lymphoid structures, and tailors immune development through effects on both the innate and adaptive immune systems.
This document summarizes recent findings that challenge the traditional definitions of innate and adaptive immunity. It provides three examples of studies that found evidence of immune specificity and memory in invertebrates like water fleas and copepods. It also notes that while mammals use immunoglobulins for antigen recognition, other phyla use different receptor systems, and that innate immune systems may be more complex than originally believed. The growing evidence from diverse species suggests a blurring of the lines between innate and adaptive immunity.
1) The gut microbiota plays a key role in host development, physiology, and health by modulating the immune system and influencing organ development and metabolism.
2) The gut microbiota is dominated by anaerobic bacteria and contains over 500-1000 bacterial species from a few bacterial phyla. It outnumbers human cells 10:1 and contains many metabolic functions.
3) The gut microbiota influences the properties of the intestinal mucus layer, induces the development of lymphoid structures, and tailors immune development through effects on both the innate and adaptive immune systems.
This document summarizes a scientific paper that analyzed the genome of the sea urchin to gain insights into its immune system. The analysis of the sea urchin genome revealed a diverse set of immune genes similar to those found in jawed vertebrates. This suggests the sea urchin has a complex immune system reliant on specialized immune cells. The findings provide a more in-depth understanding of the evolution of the immune system in invertebrate animals.
This document summarizes a study that investigated the antibacterial activity in different tissues of four marine crustacean species: northern shrimp (Pandalus borealis), hermit crab (Pagurus bernhardus), spider crab (Hyas araneus), and king crab (Paralithodes camtschatica). Extracts were prepared from tissues including haemolymph, haemocytes, exoskeleton, gills, and internal organs. The extracts were tested for antibacterial activity against four bacterial strains. Antibacterial activity was detected in extracts from several tissues in all species, mainly in haemolymph and haemocyte extracts. Differences in activity between extracts and sensitivity to heat and enzymes suggested multiple antibacterial compounds are
This study examines the antimicrobial and antibiofilm activity of a 5-kDa peptide fraction isolated from the coelomocytes (immune cells) of the sea urchin Paracentrotus lividus. The peptide fraction, called 5-CC, showed inhibitory activity against both Gram-positive and Gram-negative bacteria, as well as fungi, with minimum inhibitory concentrations ranging from 253.7 to 15.8 mg ml-1. 5-CC also inhibited the formation of Staphylococcus aureus and Staphylococcus epidermidis biofilms. At sub-MIC concentrations, 5-CC inhibited the formation of young (6-hour) and mature (24-hour) biofilms of
El documento trata sobre la investigación científica. Presenta nuevos hallazgos sobre un tema específico de la ciencia. Los resultados contribuyen al conocimiento actual sobre el tema y sugieren más investigaciones futuras.
Este documento presenta los resultados de un estudio sobre el uso de un extracto de piel de rana catesbeiana como tratamiento alternativo para la mastitis clínica en bovinos. El extracto redujo el número de bacterias causantes de mastitis y mejoró el tejido glandular dañado. Además, el extracto redujo el grado de mastitis en vacas tratadas, especialmente mastitis moderada. Finalmente, el documento propone la creación de un laboratorio para aislar y purificar péptidos antimicrobianos de la rana con fines biotecnoló
La propuesta propone crear un laboratorio para aislar y purificar sustancias naturales con aplicaciones biotecnológicas. El laboratorio se enfocaría en secuenciar y sintetizar péptidos antimicrobianos de la rana catesbeiana para desarrollar tratamientos para infecciones. La propuesta describe la infraestructura requerida como consultoras y centros de investigación que brindarían apoyo.
A lo largo de la historia se han propuesto diferentes sistemas de clasificación para los microorganismos. Inicialmente se dividían en dos reinos, plantae y animalia. Luego se propuso el reino Protista. Más tarde, la distinción entre células procariotas y eucariotas llevó a dividir los organismos en los reinos Prokaryotae/Monera y Eukaryotae. En 1969, Whittaker propuso los cinco reinos que incluían Monera, Protista, Fungi, Plantae y Animalia. Finalmente, en
El documento describe los tres dominios principales de organismos: Archaea, Bacteria y Eukarya. Señala que las archaeas son organismos procariotas que se distinguen de las bacterias por sus lípidos de membrana únicos y su ARN polimerasa compleja. También detalla las tres filas principales de archaeas: Crenarchaeota, Euryarchaeota y Korarchaeota, y proporciona ejemplos de géneros en cada fila que habitan en ambientes extremos como hábitats volcánicos, salinos y ácidos.
A lo largo de la historia se han propuesto diferentes sistemas de clasificación para los microorganismos. Inicialmente se dividían en dos reinos, plantae y animalia. Luego se propuso el reino Protista. Más adelante, con el descubrimiento de las diferencias entre células procariotas y eucariotas, los microorganismos se clasificaron en estos dos grupos. Finalmente, en 1969 Whittaker propuso la clasificación en cinco reinos que aún se usa y reconoce las relaciones evolutivas, dividiendo los organismos
Inflammation plays a key role in many chronic diseases like cancer, diabetes, obesity, and Alzheimer's. While inflammation originally served to help heal injuries, evidence now suggests it can promote the progression of diseases over time by stimulating cell proliferation, blood vessel growth, and tissue damage. For example, in cancer tumors can induce inflammation in surrounding tissue, and this helps cancer cells grow and spread. Researchers are working to block inflammation through drugs to see if this can help treat and prevent chronic diseases.
The document discusses how views of microbes have shifted over the past decade from seeing them as "evil" to recognizing that they play a key role in human health as part of the human microbiome. Research has found that microbes make up most of the cells in the human body and contribute significantly to metabolic processes. Studies sequencing microbial genomes and analyzing microbial communities in places like the gut have revealed far more microbial diversity than previously known and shown how microbes interact closely with human hosts. The microbiome is now understood to influence important functions like immune development and energy extraction from food.
Este documento es un registro de asistencia de alumnos para un curso de Microbiología en la Universidad de Guadalajara. Contiene información sobre 34 estudiantes inscritos en el curso como su número de control, nombre, y asistencia. El curso se lleva a cabo los lunes de 1-3:50pm en el aula 0105 del 11 de febrero al 11 de junio de 2011.
El documento resume las contribuciones clave de varios científicos a la historia de la microbiología, incluyendo las primeras observaciones de microbios por van Leeuwenhoek, los experimentos de Redi, Spallanzani y Pasteur que refutaron la generación espontánea, el establecimiento de los postulados de Koch para la identificación de patógenos, y el desarrollo de técnicas como cultivos puros y la vacunación. También describe los trabajos pioneros de Lister, Ivanowsky, Metchnikoff y Ehrlich
Este documento presenta un programa de microbiología dividido en 5 unidades temáticas. Cubre temas como la morfología, estructura, fisiología, taxonomía, cultivo y aplicaciones de bacterias, hongos, protozoarios y virus. El programa asigna un número específico de horas y prácticas de laboratorio a cada subtema para proporcionar a los estudiantes una comprensión integral de los microorganismos y su papel en la naturaleza, la medicina e industrias.