The Mycobacterium tuberculosis genome contains approximately 4.4 million base pairs, 4,183 genes, and 1 chromosome. It was one of the first bacterial genomes to be fully sequenced in 1998. Recent research findings include discovering more genetic variation between strains than expected, including long sequence polymorphisms, and that both the host and bacterial genome affect the disease process and specific strains are adapted to particular human populations.
Organoids are small 3D tissues that mimic the function of organs. They were first developed in 2007 and have since been used to model many organs including the brain, pancreas, and heart. While organoids are still in the early stages of research, they show promise for medical and scientific uses. Organoids are made by harvesting stem cells from an organ and culturing them in a gel environment where they self-organize into ball-like structures that resemble miniature organs. Researchers hope organoids can be used for drug testing and personalized medicine without the need for animal testing. As techniques for growing organoids continue to advance, so too will their potential applications.
This document describes a proposed starting MSc project that will apply site- and time-heterogeneous evolutionary models to mitochondrial phylogenomic analysis. The project aims to improve phylogenetic inference by accounting for variation in evolutionary rates across sites and lineages. Supervisors for the project include researchers from CIBIO and the University of Vigo. Relevant literature on mitochondrial DNA evolution, phylogenomics, and evolutionary rates in specific taxa are also cited.
Antonio Ahn is a medical researcher from New Zealand. He received his PhD in pathology from the University of Otago, where he currently works as a lab demonstrator. His research focuses on bioinformatics analysis of RNA-seq and methylation data to study protein-coding genes, lncRNAs, transposable elements, and immune cell infiltration in cancer. He has published several papers on epigenetic changes and drug resistance in melanoma.
Meritxell Huch - Wellcome Trust/Cancer Research UK Gurdon Institute, Universi...Fundación Ramón Areces
El jueves 8 de febrero de 2018 se realizó en la Fundación Ramón Areces un Ciclo de Conferencias sobre células madre y organoides, en colaboración con Springer Nature.
The document summarizes basic principles of genetics including alleles, dominant and recessive traits, and how traits are inherited from parents. It then discusses the goals and accomplishments of the Human Genome Project which was completed in 2000, two years ahead of schedule. The document notes some social, ethical, and legal implications of the project, including issues around genetic discrimination and patenting of DNA sequences. It also describes different types of genetic disorders like single gene disorders, chromosomal abnormalities, and multifactorial disorders.
The Mycobacterium tuberculosis genome contains approximately 4.4 million base pairs, 4,183 genes, and 1 chromosome. It was one of the first bacterial genomes to be fully sequenced in 1998. Recent research findings include discovering more genetic variation between strains than expected, including long sequence polymorphisms, and that both the host and bacterial genome affect the disease process and specific strains are adapted to particular human populations.
Organoids are small 3D tissues that mimic the function of organs. They were first developed in 2007 and have since been used to model many organs including the brain, pancreas, and heart. While organoids are still in the early stages of research, they show promise for medical and scientific uses. Organoids are made by harvesting stem cells from an organ and culturing them in a gel environment where they self-organize into ball-like structures that resemble miniature organs. Researchers hope organoids can be used for drug testing and personalized medicine without the need for animal testing. As techniques for growing organoids continue to advance, so too will their potential applications.
This document describes a proposed starting MSc project that will apply site- and time-heterogeneous evolutionary models to mitochondrial phylogenomic analysis. The project aims to improve phylogenetic inference by accounting for variation in evolutionary rates across sites and lineages. Supervisors for the project include researchers from CIBIO and the University of Vigo. Relevant literature on mitochondrial DNA evolution, phylogenomics, and evolutionary rates in specific taxa are also cited.
Antonio Ahn is a medical researcher from New Zealand. He received his PhD in pathology from the University of Otago, where he currently works as a lab demonstrator. His research focuses on bioinformatics analysis of RNA-seq and methylation data to study protein-coding genes, lncRNAs, transposable elements, and immune cell infiltration in cancer. He has published several papers on epigenetic changes and drug resistance in melanoma.
Meritxell Huch - Wellcome Trust/Cancer Research UK Gurdon Institute, Universi...Fundación Ramón Areces
El jueves 8 de febrero de 2018 se realizó en la Fundación Ramón Areces un Ciclo de Conferencias sobre células madre y organoides, en colaboración con Springer Nature.
The document summarizes basic principles of genetics including alleles, dominant and recessive traits, and how traits are inherited from parents. It then discusses the goals and accomplishments of the Human Genome Project which was completed in 2000, two years ahead of schedule. The document notes some social, ethical, and legal implications of the project, including issues around genetic discrimination and patenting of DNA sequences. It also describes different types of genetic disorders like single gene disorders, chromosomal abnormalities, and multifactorial disorders.
In a speech for the Global Health Program at the Council on Foreign Relations in New York City, Calit2 director Larry Smarr addresses the issue of biological diversity and the importance of monitoring the microbiome.
WikiGenomes and Chlambase provide a semantic data model in Wikidata for integrating microbial genomics data. They model taxonomic and gene/protein relationships as Wikidata items and properties. A Python bot gathers data from sources and writes it to Wikidata. WikiGenomes serves as a centralized database for sequenced microbial genomes. It provides gene reports and supports community annotation directly in Wikidata. This engages domain experts and facilitates data access.
The mouse rodent model (root vole, Microtus oeconomus Pall.) in the ecotoxity...Maria Drahulian
The contamination of vast areas with radionuclides after the Chernobyl disaster has particularly acutely posed the problem of predicting the consequences of its chronic effects on ecosystems. Mouse rodents, due to their wide range of distribution, attachment to habitats, close contact with the upper layers of the soil (the most intensively accumulating pollutants, as well as rapid reproduction rates, are widely used as objects for bioindication of ecotoxicity
The document summarizes key points about the human genome project and its impacts over the past 10 years as well as opportunities for the next 10 years. It discusses how the human genome project revealed the blueprint for building a human in 2001 and enabled greater understanding of gene functions and their medical impacts. It then outlines focus areas for genomic medicine in the coming decade like diagnostics, disease biology insights, cancer genome characterization, and clinical informatics. The role of the human microbiome in health and disease is also summarized along with challenges in bioinformatics like data analysis, integration and tools. Ethical and societal issues related to genomics research and medicine are also highlighted.
CitrusCyc: Metabolic Pathway Databases for the C. clementina and C. sinensis...Surya Saha
CitrusCyc is a metabolic pathway database for the Citrus clementina and Citrus sinensis genomes. It was constructed using the Pathway Tools software and contains pathways, reactions, enzymes and genes derived from the annotated citrus genomes and the MetaCyc database. The database contains over 25,000 proteins and 40,000 transcripts with EC numbers for both citrus species. It provides visualizations of metabolic pathways and allows for overlay of RNA-seq expression data. Future work includes manual curation of pathways and development of a Meta-CitrusCyc database.
The human genome project was a large, international scientific research project that began in 1990 with the goal of mapping the entire human genome and determining the sequence of chemical base pairs that make up human DNA. It was coordinated by the US Department of Energy and National Institutes of Health. By 2003, the project had generated a rough draft of the human genome sequence and identified most human genes. The goals of the project included developing chromosome maps, sequencing the human genome, analyzing genetic variation, and identifying all human genes. The project has led to many medical and other applications such as improved disease diagnosis, drug development, and agriculture.
What is bioinformatics?
About human genome
Human genome project
Aim of human genome project
History
Sequencing Strategy
Benefits of Human Genome Project research
Disadvantages of human genome project
Conclusion
References
Genetic mapping is used to determine the specific location of genes on chromosomes. Knowing gene locations can help identify genetic diseases and their underlying causes. One document describes how researchers used genetic techniques to identify a gene (PSR1) in algae that increases lipid production without subjecting the algae to stress. This could allow for lipid extraction and energy production while preserving the algae species. A second document discusses a new method developed by the University of Haifa to reduce the number of possible genetic effects to study from millions to thousands. The method was tested successfully in a plant with over 7,000 genes. This type of research can help identify genetic diseases more easily and determine the best treatments.
This document provides a summary of Aaron M Bender's background and experience. It includes his contact information, educational background which includes a PhD in Molecular Biology from the University of Wyoming, and extensive research experience including positions at ArcherDX, the University of Kansas Molecular Probes Core Laboratory, the University of Kansas, and the Mayo Clinic where he conducted research in areas such as cancer genetics, chemical biology, next generation sequencing, and the use of model organisms like C. elegans. He has over 15 publications in peer-reviewed journals.
The researchers exposed wild type and p53 heterozygous mice to multi-walled carbon nanotubes (MWCNTs) to evaluate pulmonary disease. They found that while no mice developed mesothelioma, p53 heterozygous mice exhibited significantly larger granulomas in the lungs compared to wild type mice, indicating susceptibility to pulmonary fibrosis. The study suggests the p53 gene is a susceptibility factor for lung fibrosis in mice exposed to MWCNTs.
Stem cells are totipotent cells that can differentiate into any body cell type. Scientists first researched mouse bone marrow stem cells in 1963 and have since tried using bone marrow stem cells for transplants. Stem cells can potentially be used to treat nervous system diseases, injuries, genetic disorders, and more because they can become any cell needed. However, embryonic stem cell research requires destroying embryos and carries cancer risks, causing ethical debates. Now, scientists can turn adult skin cells into stem cells to avoid rejection and new methods avoid cancer risks.
Cellular network biology: Proteome-wide analysis of heterogeneous dataLars Juhl Jensen
This document discusses three topics: proteome analysis using mass spectrometry to identify proteins and modifications, network biology to build association networks between proteins, and text mining to extract biological information from literature to integrate diverse data sources and build networks. Mass spectrometry is used to analyze proteomes at large scale but has missing values, while networks identify enriched functions and show evolutionary conservation. Text mining extracts data from over 10,000 papers to integrate into networks due to the large number of databases with different formats. It uses natural language processing and co-mentioning to capture relationships beyond proteins from literature and other sources.
The document summarizes the key aspects of the Human Genome Project. It began in 1990 as a collaborative effort to sequence the entire human genome. Major milestones included a working draft in 2000 covering over 90% of the genome, and completion in 2003, two years ahead of schedule. The goals were to identify all human genes, develop genetic maps, and make the data publicly available. It helped locate genes associated with diseases and traits but also raised ethical issues around privacy and use of genetic information.
The Human Genome Project had several stated goals:
1) Identify all the approximately 20,000-25,000 genes in human DNA.
2) Determine the sequences of the 3 billion chemical base pairs that make up human DNA.
3) Store this information in databases.
4) Improve tools for data analysis.
5) Transfer related technologies to the private sector.
6) Address the ethical, legal, and social issues that may arise from the project.
This document discusses genetic mapping and its various medical applications. It describes how genetic mapping is used to identify the positions of genes within genomes and locate genes associated with certain traits or diseases. Specifically, it mentions two studies: one that used genetic mapping in mice to identify the pituitary tumor transforming gene's role in liver fibrosis, and another that mapped genes responsible for leaf rust resistance in wheat. The document also outlines some of genetic mapping's utility in medical fields like assessing disease predispositions, genetically engineering crop resistance, and examining fetal genetics during high-risk pregnancies.
The Genomics Revolution: The Good, The Bad, and The Ugly (UEOP16 Keynote)Emiliano De Cristofaro
The document discusses the genomics revolution and its implications for privacy. It outlines the good of genetic testing and medicine, the bad of collecting sensitive genomic data that is hard to anonymize, and the ugly challenges of balancing privacy and the greater good. It then reviews the history of genome sequencing and cost reductions. The remainder summarizes privacy issues like re-identification risks, kin privacy, and challenges of data sharing. It also outlines cryptography techniques being explored to enable private genomic computation and testing on encrypted genomes. Open problems remain around long-term data storage and usability of privacy techniques.
1) The study aimed to visualize the interaction between the HIV-1 p24 capsid protein and the viral envelope using freeze-fracture electron microscopy. 2) By arresting viral bud release through site-directed mutagenesis of the p6Gag protein, which increased virion density, the researchers obtained multiple fracture planes throughout the virion. 3) Freeze-fracture involves freezing samples under high pressure to form amorphous ice, fracturing with a super-cooled blade, etching in a high vacuum, shadowing with heavy metals, and imaging with transmission electron microscopy at 1.1 nm resolution to visualize the viral envelope and capsid interaction.
Beyond the Tsunami: Dealing with Life Sciences DataChris Southan
This document discusses the rapid growth of life sciences data and the need to develop infrastructure to manage this data. It notes that the amount of sequence data in databases has grown enormously in recent years and projects like the 1000 Genomes Project will generate vast amounts of new data. Developing sustainable data archives, databases, data sharing resources, and tools for data analysis and mining will be crucial to maximize the scientific benefits from these large datasets. International collaboration on data infrastructure projects like ELIXIR will be essential to support data-driven discovery in biology and medicine.
The document discusses the "EFRUZHU Cancer (Carcinogenesis) Theory" which proposes that carcinogenesis is triggered by four main factors: 1) mutations that alter group identity, 2) inadequate or inefficient energy, 3) chronic inflammation, and 4) suppression of normal DNA sequences. It also suggests that carcinogenesis involves a person having both mutated and normal DNA identities that continuously recombine in a manner similar to crossover cloning, leading to metastatic conditions.
1. Whole genome sequencing is becoming more affordable and widespread, allowing for large datasets and personalized medicine applications.
2. However, genomic data is extremely sensitive and can be used to identify individuals and their relatives, even when anonymized. Once a genome is leaked, it cannot be revoked.
3. Computer scientists are exploring techniques to protect genomic privacy, such as differential privacy and secure computation, but enabling privacy-preserving genomic research remains a challenge.
The document discusses using whole genome sequencing (WGS) and building a global genome library as powerful research and public health tools. It describes the Global Meningitis Genome Library initiative which aims to create a comprehensive, representative collection of WGS data for four major causes of meningitis. The initiative will integrate this genome library within the PubMLST.org platform for open access data sharing, analysis and visualization to support epidemiological research and surveillance on a global scale.
In a speech for the Global Health Program at the Council on Foreign Relations in New York City, Calit2 director Larry Smarr addresses the issue of biological diversity and the importance of monitoring the microbiome.
WikiGenomes and Chlambase provide a semantic data model in Wikidata for integrating microbial genomics data. They model taxonomic and gene/protein relationships as Wikidata items and properties. A Python bot gathers data from sources and writes it to Wikidata. WikiGenomes serves as a centralized database for sequenced microbial genomes. It provides gene reports and supports community annotation directly in Wikidata. This engages domain experts and facilitates data access.
The mouse rodent model (root vole, Microtus oeconomus Pall.) in the ecotoxity...Maria Drahulian
The contamination of vast areas with radionuclides after the Chernobyl disaster has particularly acutely posed the problem of predicting the consequences of its chronic effects on ecosystems. Mouse rodents, due to their wide range of distribution, attachment to habitats, close contact with the upper layers of the soil (the most intensively accumulating pollutants, as well as rapid reproduction rates, are widely used as objects for bioindication of ecotoxicity
The document summarizes key points about the human genome project and its impacts over the past 10 years as well as opportunities for the next 10 years. It discusses how the human genome project revealed the blueprint for building a human in 2001 and enabled greater understanding of gene functions and their medical impacts. It then outlines focus areas for genomic medicine in the coming decade like diagnostics, disease biology insights, cancer genome characterization, and clinical informatics. The role of the human microbiome in health and disease is also summarized along with challenges in bioinformatics like data analysis, integration and tools. Ethical and societal issues related to genomics research and medicine are also highlighted.
CitrusCyc: Metabolic Pathway Databases for the C. clementina and C. sinensis...Surya Saha
CitrusCyc is a metabolic pathway database for the Citrus clementina and Citrus sinensis genomes. It was constructed using the Pathway Tools software and contains pathways, reactions, enzymes and genes derived from the annotated citrus genomes and the MetaCyc database. The database contains over 25,000 proteins and 40,000 transcripts with EC numbers for both citrus species. It provides visualizations of metabolic pathways and allows for overlay of RNA-seq expression data. Future work includes manual curation of pathways and development of a Meta-CitrusCyc database.
The human genome project was a large, international scientific research project that began in 1990 with the goal of mapping the entire human genome and determining the sequence of chemical base pairs that make up human DNA. It was coordinated by the US Department of Energy and National Institutes of Health. By 2003, the project had generated a rough draft of the human genome sequence and identified most human genes. The goals of the project included developing chromosome maps, sequencing the human genome, analyzing genetic variation, and identifying all human genes. The project has led to many medical and other applications such as improved disease diagnosis, drug development, and agriculture.
What is bioinformatics?
About human genome
Human genome project
Aim of human genome project
History
Sequencing Strategy
Benefits of Human Genome Project research
Disadvantages of human genome project
Conclusion
References
Genetic mapping is used to determine the specific location of genes on chromosomes. Knowing gene locations can help identify genetic diseases and their underlying causes. One document describes how researchers used genetic techniques to identify a gene (PSR1) in algae that increases lipid production without subjecting the algae to stress. This could allow for lipid extraction and energy production while preserving the algae species. A second document discusses a new method developed by the University of Haifa to reduce the number of possible genetic effects to study from millions to thousands. The method was tested successfully in a plant with over 7,000 genes. This type of research can help identify genetic diseases more easily and determine the best treatments.
This document provides a summary of Aaron M Bender's background and experience. It includes his contact information, educational background which includes a PhD in Molecular Biology from the University of Wyoming, and extensive research experience including positions at ArcherDX, the University of Kansas Molecular Probes Core Laboratory, the University of Kansas, and the Mayo Clinic where he conducted research in areas such as cancer genetics, chemical biology, next generation sequencing, and the use of model organisms like C. elegans. He has over 15 publications in peer-reviewed journals.
The researchers exposed wild type and p53 heterozygous mice to multi-walled carbon nanotubes (MWCNTs) to evaluate pulmonary disease. They found that while no mice developed mesothelioma, p53 heterozygous mice exhibited significantly larger granulomas in the lungs compared to wild type mice, indicating susceptibility to pulmonary fibrosis. The study suggests the p53 gene is a susceptibility factor for lung fibrosis in mice exposed to MWCNTs.
Stem cells are totipotent cells that can differentiate into any body cell type. Scientists first researched mouse bone marrow stem cells in 1963 and have since tried using bone marrow stem cells for transplants. Stem cells can potentially be used to treat nervous system diseases, injuries, genetic disorders, and more because they can become any cell needed. However, embryonic stem cell research requires destroying embryos and carries cancer risks, causing ethical debates. Now, scientists can turn adult skin cells into stem cells to avoid rejection and new methods avoid cancer risks.
Cellular network biology: Proteome-wide analysis of heterogeneous dataLars Juhl Jensen
This document discusses three topics: proteome analysis using mass spectrometry to identify proteins and modifications, network biology to build association networks between proteins, and text mining to extract biological information from literature to integrate diverse data sources and build networks. Mass spectrometry is used to analyze proteomes at large scale but has missing values, while networks identify enriched functions and show evolutionary conservation. Text mining extracts data from over 10,000 papers to integrate into networks due to the large number of databases with different formats. It uses natural language processing and co-mentioning to capture relationships beyond proteins from literature and other sources.
The document summarizes the key aspects of the Human Genome Project. It began in 1990 as a collaborative effort to sequence the entire human genome. Major milestones included a working draft in 2000 covering over 90% of the genome, and completion in 2003, two years ahead of schedule. The goals were to identify all human genes, develop genetic maps, and make the data publicly available. It helped locate genes associated with diseases and traits but also raised ethical issues around privacy and use of genetic information.
The Human Genome Project had several stated goals:
1) Identify all the approximately 20,000-25,000 genes in human DNA.
2) Determine the sequences of the 3 billion chemical base pairs that make up human DNA.
3) Store this information in databases.
4) Improve tools for data analysis.
5) Transfer related technologies to the private sector.
6) Address the ethical, legal, and social issues that may arise from the project.
This document discusses genetic mapping and its various medical applications. It describes how genetic mapping is used to identify the positions of genes within genomes and locate genes associated with certain traits or diseases. Specifically, it mentions two studies: one that used genetic mapping in mice to identify the pituitary tumor transforming gene's role in liver fibrosis, and another that mapped genes responsible for leaf rust resistance in wheat. The document also outlines some of genetic mapping's utility in medical fields like assessing disease predispositions, genetically engineering crop resistance, and examining fetal genetics during high-risk pregnancies.
The Genomics Revolution: The Good, The Bad, and The Ugly (UEOP16 Keynote)Emiliano De Cristofaro
The document discusses the genomics revolution and its implications for privacy. It outlines the good of genetic testing and medicine, the bad of collecting sensitive genomic data that is hard to anonymize, and the ugly challenges of balancing privacy and the greater good. It then reviews the history of genome sequencing and cost reductions. The remainder summarizes privacy issues like re-identification risks, kin privacy, and challenges of data sharing. It also outlines cryptography techniques being explored to enable private genomic computation and testing on encrypted genomes. Open problems remain around long-term data storage and usability of privacy techniques.
1) The study aimed to visualize the interaction between the HIV-1 p24 capsid protein and the viral envelope using freeze-fracture electron microscopy. 2) By arresting viral bud release through site-directed mutagenesis of the p6Gag protein, which increased virion density, the researchers obtained multiple fracture planes throughout the virion. 3) Freeze-fracture involves freezing samples under high pressure to form amorphous ice, fracturing with a super-cooled blade, etching in a high vacuum, shadowing with heavy metals, and imaging with transmission electron microscopy at 1.1 nm resolution to visualize the viral envelope and capsid interaction.
Beyond the Tsunami: Dealing with Life Sciences DataChris Southan
This document discusses the rapid growth of life sciences data and the need to develop infrastructure to manage this data. It notes that the amount of sequence data in databases has grown enormously in recent years and projects like the 1000 Genomes Project will generate vast amounts of new data. Developing sustainable data archives, databases, data sharing resources, and tools for data analysis and mining will be crucial to maximize the scientific benefits from these large datasets. International collaboration on data infrastructure projects like ELIXIR will be essential to support data-driven discovery in biology and medicine.
The document discusses the "EFRUZHU Cancer (Carcinogenesis) Theory" which proposes that carcinogenesis is triggered by four main factors: 1) mutations that alter group identity, 2) inadequate or inefficient energy, 3) chronic inflammation, and 4) suppression of normal DNA sequences. It also suggests that carcinogenesis involves a person having both mutated and normal DNA identities that continuously recombine in a manner similar to crossover cloning, leading to metastatic conditions.
1. Whole genome sequencing is becoming more affordable and widespread, allowing for large datasets and personalized medicine applications.
2. However, genomic data is extremely sensitive and can be used to identify individuals and their relatives, even when anonymized. Once a genome is leaked, it cannot be revoked.
3. Computer scientists are exploring techniques to protect genomic privacy, such as differential privacy and secure computation, but enabling privacy-preserving genomic research remains a challenge.
The document discusses using whole genome sequencing (WGS) and building a global genome library as powerful research and public health tools. It describes the Global Meningitis Genome Library initiative which aims to create a comprehensive, representative collection of WGS data for four major causes of meningitis. The initiative will integrate this genome library within the PubMLST.org platform for open access data sharing, analysis and visualization to support epidemiological research and surveillance on a global scale.
The document discusses recent findings in ancient DNA research. It summarizes a 2014 Nature article that analyzed ancient human genomes from present-day Europeans and suggested three ancestral populations. It also lists 27 other relevant published ancient DNA studies from the past few years. Key criteria for evaluating the reliability of ancient DNA analyses are discussed, such as the journal and researchers involved, sample handling, contamination controls, and consistency of results.
This document summarizes content mining of biomedical literature and policy developments surrounding it. It defines content mining as using automated methods to exploit knowledge in biomedical literature. Examples discussed include building phylogenetic trees, extracting chemical reactions, and improving genome annotation. Legal considerations around copyright, databases, and contracts are also addressed. Developments in relevant UK and EU laws from 2011-2015 aimed to support these transformative technologies and help researchers.
Microbial Metagenomics Drives a New CyberinfrastructureLarry Smarr
06.03.03
Invited Talk
School of Biological Sciences
University of California, Irvine
Title: Microbial Metagenomics Drives a New Cyberinfrastructure
Irvine, CA
This document reports on the first high-quality draft genome sequence of Pasteurella multocida sequence type 128 isolated from the infected bone of a woman bitten by a dog. The genome was sequenced and assembled into 23 contigs totaling 2.3 megabases. Annotation identified over 2,000 protein-coding genes, 10 rRNAs, and 50 tRNAs. Comparison to other P. multocida genomes confirmed the identification as P. multocida and determined it was sequence type 128, which has only been reported once before from a sheep in New Zealand. The genome provides new genomic resources that can improve understanding of P. multocida pathogenesis.
ContentMine (EMBL-EBI Industry Programme)Jenny Molloy
ContentMine extracts millions of facts from scientific literature using automated content mining techniques. It began in the 1980s with work on extracting logical representations from text passages and has grown to include extracting phylogenetic trees, chemical reactions, clinical trial data and more for reuse. ContentMine addresses issues like limited data sharing by extracting raw data from papers into reusable formats. It also considers legal issues around copyright and data rights. The goal is to make more scientific knowledge accessible through automated content mining.
Lam C. Tsoi is a Research Assistant Professor at the University of Michigan in the Departments of Dermatology and Computational Medicine and Bioinformatics. He received his Ph.D. in Biomedical Science from the Medical University of South Carolina in 2010. His research focuses on using genomics data and computational approaches to provide biological insights into human cutaneous diseases such as psoriasis. He has published over 20 papers on identifying genetic risk loci and biological mechanisms for psoriasis and other autoimmune diseases.
Bats and rodents as a source of emerging human disease in KenyaILRI
Poster by E. Cook, E. Dobson, A. Kiyong'a, J Akoko, A. Ogendo, M. Bronsvoort, S. Kemp, B. Agwanda and E. Fèvre presented at the Australasian Society for Infectious Diseases (ASID) annual scientific meeting, Canberra, Australia, 20-23 March 2013.
The document discusses the Human Genetics Historical Library located at Cardiff University. It provides details about the library's collections, donors, key items including works by Galton, Lysenko, Koltsov, and Watson and Crick. The library houses resources on the history of genetics and heredity from 1557 to present day, including books, archives, photographs, and newspapers. It also notes recent developments like an exhibition in the library's building and the cataloguing of the Polani collection.
Improved two-photon imaging of living neurons in brain tissue through tempora...julian choy
This document describes a study that optimized two-photon imaging of living neurons in brain tissue by temporally gating the incident laser to reduce photon flux while maximizing fluorescence signal. The study found that gating the laser at the sampling frequency compromised cell viability despite high fluorescence. An optimum gating frequency range was identified that maintained cell viability while preserving fluorescence levels in two-photon images. Cell viability was monitored by measuring changes in membrane input resistance during whole-cell patch recording of neurons.
Evolution of microbiomes and the evolution of the study and politics of micro...Jonathan Eisen
The document discusses the evolution of microbiomes and the study of microbiomes. It notes that microbiomes can be both overhyped yet underappreciated. It provides background on the rise of interest in microbiomes since the 2000s due to technological advances enabling their study as well as appreciation of their important functions. The author then discusses their own research focusing on using phylogenomic methods to study microbial communities and symbioses, especially how microbes and microbiomes help hosts adapt to stress. Examples discussed include chemosymbioses, pathogen resistance, environmental changes, and more.
Marine Host-Microbiome Interactions: Challenges and OpportunitiesJonathan Eisen
This document summarizes a talk given by Jonathan Eisen on marine host-microbiome interactions. It discusses various topics researched in Eisen's lab, including phylogenomic methods and tools, microbial phylogenomics and evolvability, reference data resources, communication in science, and model systems. Specific projects are mentioned, such as automated genome trees, phylogenetic marker genes, the GEBA project, and dark matter microbes. The document then introduces the concept of the host-microbiome stress triangle and gives examples of stress types including nutrient acquisition, pathogens, and environmental change. It concludes by discussing a potential project on seagrass microbiomes in collaboration with Jay Stachowicz's lab.
Biodiversity & Citizen Science in the Genomic Erasratnasi
Presentation at STARMUS Science Festival - Life and the Universe. An overview of the evolution of the LifeScanner project in light of insights from the Maker movement.
Maria A. Diroma – MEWAs: sviluppo di un sistema bioinformatico per studi di a...eventi-ITBbari
MEWAs (Mitochondriome-Exome Wide Associations): sviluppo di un sistema bioinformatico per studi di associazione fra l’intero esoma nucleare e il DNA mitocondriale in fenotipi fisiologici o patologici.
This document provides an overview and summary of the book "Plant Cytogenetics: Methods and Protocols". It begins with an introduction to the field of cytogenetics and its importance in understanding genetics. It then summarizes some of the key techniques described in the book, including C-banding to study chromosome structure, genomic in situ hybridization (GISH) and fluorescence in situ hybridization (FISH) to locate sequences on chromosomes, fiber-FISH for high resolution analysis, and tyramide signal amplification to identify homoeologous chromosomes. The summary also mentions techniques like analyzing recombination, using radiation to create chromosome breaks, optical mapping, flow sorting chromosomes, constructing BAC libraries, and chromosome microdis
Why Life is Difficult, and What We MIght Do About ItAnita de Waard
This document discusses connecting biological knowledge through claim-evidence networks. It outlines some of the challenges in biology like variability between specimens and gene expression changes. It then proposes that claim-evidence networks can be used to connect biological knowledge by linking experimental evidence to claims. Steps to build these networks include identifying claims in documents, structuring the evidence in databases, and automatically connecting the claims and evidence. Examples of efforts that link drug interactions to evidence and predict protein interactions across species are provided. However, it notes that more still needs to be done to fully realize this approach.
Researchers used zinc-finger nucleases (ZFNs) to generate knockout rats by targeting three genes - green fluorescent protein (GFP), Immunoglobulin M (IgM), and Rab38. ZFNs were microinjected into rat embryos to induce mutations in the target genes. Of 295 founder animals screened, 35 (12%) contained targeted mutations, including full knockout of the GFP transgene in some animals. Mutations were transmitted to offspring, demonstrating the ability of ZFNs to disrupt genes and induce heritable mutations in the rat genome. This technique allows for targeted genetic modification of the rat, an important model for studying human disease.
Similar to The MRF Genome Library: Epidemiology of meningococcal disease-causing lineages in England and Wales from 2010/11 to 2011/12 (20)
The document discusses the Global Meningitis Genome Partnership (GMGP), which aims to address inequities in genomic surveillance capacity for meningitis pathogens between high-income and low-income countries. It outlines what has been achieved so far, including establishing standardized metadata for sequencing and epidemiological data. The GMGP is working to incorporate genome surveillance into regional surveillance strategies, initially focusing on Neisseria meningitidis, Streptococcus pneumoniae, Haemophilus influenzae, and Streptococcus agalactiae in Africa. Open data sharing is encouraged according to clear governance policies. Standardizing metadata and curating sequencing data in a central library are discussed to facilitate consistent analysis and data visualization for public health benefit
- There was a significant reduction in cases of invasive bacterial infections like pneumococcal disease, H. influenzae, and meningococcal disease in 2020 coinciding with COVID-19 containment measures across many countries. Vaccination coverage rates have decreased dramatically in Brazil representing a potential risk of rebound in infectious disease rates. Maintaining disease surveillance is important to inform authorities on current disease burden and carriage rates even though some diseases were reduced during the pandemic.
This document discusses optimal schedules for controlling pneumococcal infection in countries with high and low carriage. It notes that the African Meningitis Belt has seen sub-optimal pneumococcal conjugate vaccine (PCV) coverage due to geopolitical factors and vulnerable populations. Outbreaks in Ghana pre- and post-PCV introduction show that herd protection may be inadequate. Research is needed to better understand pneumococcal biology and prevention. Improving PCV access and coverage, including schedules with boosters and catch-up campaigns targeting 5-29 year olds, may help prevent outbreaks. Strengthening surveillance systems allows rapid response.
Professor Muhamed-Kheir TAHA MD, PhD, HDR presented on lessons and impacts for meningitis in the COVID-19 era. Data showed cumulative cases of invasive meningococcal disease (IMD) from 2014-2020 in France as well as distribution of IMD cases from 2011-2020. Vaccine use in France declined during the COVID-19 pandemic in 2020, with reduced doses of the 5-month and 12-month vaccines. Distribution of IMD cases by age group from 2011-2021 showed an immunity gap in childhood due to the pandemic. Conclusions were that reduced pathogen circulation may decrease herd immunity, social distancing was associated with lower vaccine uptake, and countries need plans to promote
Progress is being made on developing a combined MenABCWY vaccine. Studies are underway evaluating the immunogenicity and safety of combining different meningococcal vaccines that target serogroups A, C, W, Y. Combining the vaccines could simplify immunization schedules, reduce costs by needing fewer doses, and increase vaccination uptake by reducing the number of required injections. However, a combined vaccine may also increase reactogenicity and interfere with the immune response to other concomitant vaccines. Ongoing studies are evaluating different potential MenABCWY vaccine combinations to determine the optimal formulation.
This document discusses pneumococcal genomics, vaccines, and antibiotic resistance. It examines how pneumococcal carriage and disease changes following vaccination as non-vaccine serotypes increase. The author analyzed carriage samples from Native American communities before and after vaccination, finding 35 sequence clusters but vaccination did not change overall carriage prevalence. The document explores how the accessory genome varies between locations and how negative frequency dependent selection structures pneumococcal populations. Models are developed to predict which sequence clusters may increase or decrease following vaccination based on accessory genome content and frequency dependent fitness. Comparisons are made between predicted and actual changes in sequence cluster prevalence post-vaccination.
Cryptococcal meningitis is responsible for 15% of AIDS-related deaths globally. A strategic framework is needed to end cryptococcal meningitis deaths by 2030 by addressing gaps in screening, diagnosis, and access to critical antifungal medicines. Key targets include expanding access to CD4 and cryptococcal antigen tests, improving availability of lumbar puncture and antifungal drugs, and increasing research to develop better diagnostics and treatments.
This document summarizes changes in invasive meningococcal disease (IMD) cases in Germany during the COVID-19 pandemic. It finds that overall IMD cases decreased during the first pandemic period (PP) in 2020 compared to pre-pandemic levels, with the largest declines in children ages 1-4 and 5-9. However, IMD cases increased again after restrictions eased. The decrease in IMD cases during increased restrictions correlates with decreased mobility based on Google mobility indices.
1) The PSERENADE project analyzed surveillance data from over 50 sites in 34 countries to assess the impact of PCV10 and PCV13 introduction on pneumococcal meningitis incidence globally in children under 5 years old and adults 18 years and older.
2) For both age groups, PCV10 and PCV13 significantly reduced meningitis caused by serotypes covered by the vaccines, with almost elimination in children under 5 years old within 5 years. Herd protection was observed in adults as well.
3) PCV13 significantly reduced meningitis from additional serotypes it covers compared to PCV10, though serotype 19A increased with PCV10 and serotype 3 trends were unclear
This study examined sequelae in 49 pediatric patients with invasive meningococcal disease (IMD) in Chile between 2009-2019. The researchers found that 59% of patients experienced sequelae at hospital discharge, with neurological disorders being the most common at 59.2%. Risk factors for sequelae included age under 1 year old, shock, and meningeal signs at admission. Sequelae were also associated with a clinical diagnosis of meningitis with meningococcemia. The study concludes that multidisciplinary follow-up is needed to reduce the long-term impacts of IMD in children.
National Center for Immunization & Respiratory Diseases
Rapid Diagnostic Tests for Bacterial Meningitis Pathogens: where we are now and what’s next.
Xin Wang Chief, Bacterial Meningitis Laboratory Director WHO Collaborating Center for Meningitis MVPDB/DBD/NCIRD/CDC Meningitis Research Foundation Conference Nov 1-3, 2021
The document discusses the current state of rapid diagnostic tests for bacterial meningitis pathogens and outlines a vision for their future development and deployment. It describes existing tests and their limitations. Potential new platforms are identified that could meet targets outlined in a target product profile. Advanced technologies like sequencing and CRISPR/Cas are also discussed
Gonorrhea is a sexually transmitted infection caused by the bacterium Neisseria gonorrhoeae that can lead to serious health complications if left untreated. There is an urgent need for a gonorrhea vaccine due to increasing antibiotic resistance and the potential for the disease to become untreatable. However, vaccine development faces several difficulties as N. gonorrhoeae is highly variable, able to avoid the immune system, and past vaccine trials have shown no efficacy. Continued research is focused on identifying conserved antigens that could induce a protective immune response through vaccination.
Dr. Sami Gottlieb of the World Health Organization discussed the potential for meningococcal B (MenB) vaccines to help prevent gonococcal infection on a global scale. MenB vaccines have shown preliminary efficacy against gonorrhea in clinical trials and epidemiological data. WHO is working to define priority populations for gonorrhea vaccines and assess how existing MenB programs could be leveraged. Effectiveness may depend on disease epidemiology, vaccine characteristics, target populations, and integration with current immunization systems. Ongoing trials of MenB vaccines against gonorrhea will provide critical data to inform introduction decisions.
Gavi has supported the rollout of the Meningococcal A Conjugate Vaccine (MenAfrivac) in 26 African countries since 2010 through routine immunization and preventive campaigns for those aged 1-29. No cases of meningococcal A have been identified in the African meningitis belt since 2018. In 2018, non-A outbreaks prompted Gavi to authorize support for multivalent meningococcal conjugate vaccines contingent on regulatory approval, review processes, and cost targets being met. The estimated cost per death averted for the risk-based multivalent meningococcal conjugate vaccine program would be $6,300 to $13,400.
While pneumococcal disease primarily burdens infants in their first year of life, relying on herd effects from PCV schedules could help protect others indirectly and reduce costs. However, caution is needed, as indirect protection depends on direct protection of main transmitters, and key questions remain around who transmits, the duration of protection from boosters, and lessons from cRCTs comparing 2-dose and 3-dose schedules in Malawi and Gambia. Programmatic concerns like booster dose coverage, incomplete dosing, travel/border effects, and lack of surveillance also warrant consideration.
The document discusses Nepal's introduction of the PCV 10 vaccine using a 2+1 schedule of administration at 6 weeks, 10 weeks, and 9 months. A trial found this schedule to be equally effective as a 3+0 schedule. Surveillance data showed declines in invasive pneumococcal disease cases and pneumonia with consolidation following vaccine introduction. Pneumococcal carriage among children with clinical pneumonia under 2 years old declined significantly, but no decrease was seen in older children. Short term impact was observed using the 2+1 schedule, but continued surveillance is needed to assess long term vaccine impact.
The document discusses optimal vaccination schedules for pneumococcal disease in countries with high and low disease carriage. It summarizes studies comparing 1+1 and 2+1 vaccination schedules for PCV10 and PCV13 vaccines. The studies found immunogenicity was equivalent or higher for many serotypes with 1+1 schedules. The UK switched to a 1+1 schedule in 2020 and ongoing surveillance will monitor its impact on invasive pneumococcal disease cases. Future studies will evaluate the impact of the schedule change and potential for disease rebound over time.
Rasamanikya is a excellent preparation in the field of Rasashastra, it is used in various Kushtha Roga, Shwasa, Vicharchika, Bhagandara, Vatarakta, and Phiranga Roga. In this article Preparation& Comparative analytical profile for both Formulationon i.e Rasamanikya prepared by Kushmanda swarasa & Churnodhaka Shodita Haratala. The study aims to provide insights into the comparative efficacy and analytical aspects of these formulations for enhanced therapeutic outcomes.
These lecture slides, by Dr Sidra Arshad, offer a quick overview of the physiological basis of a normal electrocardiogram.
Learning objectives:
1. Define an electrocardiogram (ECG) and electrocardiography
2. Describe how dipoles generated by the heart produce the waveforms of the ECG
3. Describe the components of a normal electrocardiogram of a typical bipolar lead (limb II)
4. Differentiate between intervals and segments
5. Enlist some common indications for obtaining an ECG
6. Describe the flow of current around the heart during the cardiac cycle
7. Discuss the placement and polarity of the leads of electrocardiograph
8. Describe the normal electrocardiograms recorded from the limb leads and explain the physiological basis of the different records that are obtained
9. Define mean electrical vector (axis) of the heart and give the normal range
10. Define the mean QRS vector
11. Describe the axes of leads (hexagonal reference system)
12. Comprehend the vectorial analysis of the normal ECG
13. Determine the mean electrical axis of the ventricular QRS and appreciate the mean axis deviation
14. Explain the concepts of current of injury, J point, and their significance
Study Resources:
1. Chapter 11, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 9, Human Physiology - From Cells to Systems, Lauralee Sherwood, 9th edition
3. Chapter 29, Ganong’s Review of Medical Physiology, 26th edition
4. Electrocardiogram, StatPearls - https://www.ncbi.nlm.nih.gov/books/NBK549803/
5. ECG in Medical Practice by ABM Abdullah, 4th edition
6. Chapter 3, Cardiology Explained, https://www.ncbi.nlm.nih.gov/books/NBK2214/
7. ECG Basics, http://www.nataliescasebook.com/tag/e-c-g-basics
Promoting Wellbeing - Applied Social Psychology - Psychology SuperNotesPsychoTech Services
A proprietary approach developed by bringing together the best of learning theories from Psychology, design principles from the world of visualization, and pedagogical methods from over a decade of training experience, that enables you to: Learn better, faster!
One health condition that is becoming more common day by day is diabetes.
According to research conducted by the National Family Health Survey of India, diabetic cases show a projection which might increase to 10.4% by 2030.
share - Lions, tigers, AI and health misinformation, oh my!.pptxTina Purnat
• Pitfalls and pivots needed to use AI effectively in public health
• Evidence-based strategies to address health misinformation effectively
• Building trust with communities online and offline
• Equipping health professionals to address questions, concerns and health misinformation
• Assessing risk and mitigating harm from adverse health narratives in communities, health workforce and health system
Local Advanced Lung Cancer: Artificial Intelligence, Synergetics, Complex Sys...Oleg Kshivets
Overall life span (LS) was 1671.7±1721.6 days and cumulative 5YS reached 62.4%, 10 years – 50.4%, 20 years – 44.6%. 94 LCP lived more than 5 years without cancer (LS=2958.6±1723.6 days), 22 – more than 10 years (LS=5571±1841.8 days). 67 LCP died because of LC (LS=471.9±344 days). AT significantly improved 5YS (68% vs. 53.7%) (P=0.028 by log-rank test). Cox modeling displayed that 5YS of LCP significantly depended on: N0-N12, T3-4, blood cell circuit, cell ratio factors (ratio between cancer cells-CC and blood cells subpopulations), LC cell dynamics, recalcification time, heparin tolerance, prothrombin index, protein, AT, procedure type (P=0.000-0.031). Neural networks, genetic algorithm selection and bootstrap simulation revealed relationships between 5YS and N0-12 (rank=1), thrombocytes/CC (rank=2), segmented neutrophils/CC (3), eosinophils/CC (4), erythrocytes/CC (5), healthy cells/CC (6), lymphocytes/CC (7), stick neutrophils/CC (8), leucocytes/CC (9), monocytes/CC (10). Correct prediction of 5YS was 100% by neural networks computing (error=0.000; area under ROC curve=1.0).
These lecture slides, by Dr Sidra Arshad, offer a simplified look into the mechanisms involved in the regulation of respiration:
Learning objectives:
1. Describe the organisation of respiratory center
2. Describe the nervous control of inspiration and respiratory rhythm
3. Describe the functions of the dorsal and respiratory groups of neurons
4. Describe the influences of the Pneumotaxic and Apneustic centers
5. Explain the role of Hering-Breur inflation reflex in regulation of inspiration
6. Explain the role of central chemoreceptors in regulation of respiration
7. Explain the role of peripheral chemoreceptors in regulation of respiration
8. Explain the regulation of respiration during exercise
9. Integrate the respiratory regulatory mechanisms
10. Describe the Cheyne-Stokes breathing
Study Resources:
1. Chapter 42, Guyton and Hall Textbook of Medical Physiology, 14th edition
2. Chapter 36, Ganong’s Review of Medical Physiology, 26th edition
3. Chapter 13, Human Physiology by Lauralee Sherwood, 9th edition
The Nervous and Chemical Regulation of Respiration
The MRF Genome Library: Epidemiology of meningococcal disease-causing lineages in England and Wales from 2010/11 to 2011/12
1. The MRF
Meningococcus Genome Library
www.meningitis.org/research/genome
Dorothea Hill
University of Oxford
MRF conference 2013
Wednesday 6th November
2. ‘Publicly accessible data requires a stable home and
someone to pay the mortgage.’ Dr. Francine Berman, Research Data Alliance
Funding
MRU: Isolates
Illumina genome
sequencing
BIGS database
http://pubmlst.org
3. Whole-genome population structure with ‘Genome Comparator’:
two CC269 (lineage 2) sub-lineages.
lineage 2.2
261 loci
Incl. ST-275, ST-1161
lineage 2.1
Incl. ST-269, ST-467, ST-283
451 loci
lineage 5 (CC32)
100 loci
4. Community improvement of the MRF Genome Library.
dorothea.hill@zoo.ox.ac.uk
Jolley, K. and M. Maiden, Automated extraction of typing information for bacterial pathogens
from whole genome sequence data: Neisseria meningitidis as an exemplar. Euro Surveill, 2013.
5. Meningococcal Reference Unit:
Ray Borrow, Jay Lucidarme, Steve Gray
Pathogen genomics:
Julian Parkhill, David Harris
Maiden Group:
Martin Maiden, Keith Jolley, James Bray