The document discusses the strengths, weaknesses, opportunities, and threats (SWOT) of using whole genome sequencing (WGS) for surveillance and diagnostics of zoonotic bacteria. It provides a case study of using WGS to track the nosocomial transmission of Pseudomonas aeruginosa between patients and the hospital water supply. WGS was able to identify transmission routes and microevolution of the bacteria with single nucleotide resolution. However, challenges include the need for robust and standardized analysis methods as well as experimental design considerations. Overall, WGS provides opportunities for improved outbreak tracking, classification, and diagnostics if its strengths are leveraged and weaknesses addressed.
Applications of Whole Genome Sequencing (WGS) technology on food safety manag...ExternalEvents
http://tiny.cc/faowgsworkshop
Applications of genome sequencing technology on food safety management-United States of America. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infectio...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
Added Value of Open data sharing using examples from GenomeTrakrExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Added Value of Open data sharing using examples from GenomeTrakr. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
Whole Genome Sequencing (WGS) for surveillance of foodborne infections in Den...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS for surveillance of foodborne infections in Denmark; benefits and potential drawbacks on performance and cost. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Whole Genome Sequencing (WGS) for food safety management in France: Example...ExternalEvents
http://tiny.cc/faowgsworkshop
Potential usefulness of genome sequencing technology on food safety management - France. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Progress report 2016: GMI proficiency testing: Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Standards for public health genomic epidemiology - Biocuration 2015Melanie Courtot
A presentation introducing genomic epidemiology and its application in public health. It also explains the need for standards to support the Canadian Integrated Rapid Infectious Disease Analysis platform which implements genomic epidemiology analyses for detection and investigation of infectious disease outbreaks caused by food-borne pathogens.
Applications of Whole Genome Sequencing (WGS) technology on food safety manag...ExternalEvents
http://tiny.cc/faowgsworkshop
Applications of genome sequencing technology on food safety management-United States of America. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infectio...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Real-Time Genome Sequencing of Resistant Bacteria Provides Precision Infection Control in an Institutional Setting. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
Added Value of Open data sharing using examples from GenomeTrakrExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Added Value of Open data sharing using examples from GenomeTrakr. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management and GMI-9, 23-25 May 2016, Rome, Italy.
Whole Genome Sequencing (WGS) for surveillance of foodborne infections in Den...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS for surveillance of foodborne infections in Denmark; benefits and potential drawbacks on performance and cost. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Whole Genome Sequencing (WGS) for food safety management in France: Example...ExternalEvents
http://tiny.cc/faowgsworkshop
Potential usefulness of genome sequencing technology on food safety management - France. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Progress report 2016: GMI proficiency testing: Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
Standards for public health genomic epidemiology - Biocuration 2015Melanie Courtot
A presentation introducing genomic epidemiology and its application in public health. It also explains the need for standards to support the Canadian Integrated Rapid Infectious Disease Analysis platform which implements genomic epidemiology analyses for detection and investigation of infectious disease outbreaks caused by food-borne pathogens.
Whole Genome Sequencing (WGS) for food safety management: Perspectives from K...ExternalEvents
http://tiny.cc/faowgsworkshop
Use of genome sequencing technology on food safety management- Kenya's Perspectives. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
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.
Dr. Ying Fang - Emerging swine disease diagnostics and characterization: conn...John Blue
Emerging swine disease diagnostics and characterization: connecting basic research to real-world applications - Dr. Ying Fang, Kansas State University, from the 2017 North American PRRS/National Swine Improvement Federation Joint Meeting, December 1‐3, 2017, Chicago, Illinois, USA.
More presentations at http://www.swinecast.com/2017-north-american-prrs-nsif-joint-meeting
Cómo distinguir una investigación seria de una fraudulentaantenasysalud
Segunda presentación del Dr. Mike Repacholi, presidente emérito del ICNIPR (Comisión Internacional de Protección contra la Radiación No Ionizante) y Miembro del Comité Asesor Internacional del Proyecto de EMF Internacional de la Organización Mundial de la Salud, durante el II Foro Internacional “Antenas y Telecomunicaciones; Inclusiòn, Desarrollo y Salud Humana. Repacholi ofreció una disertación focalizada a resaltar las diferencias entre investigaciones científicas serias y fraudulentas que muchas veces ganan gran atención de la prensa generando temor entre la población respecto a las presuntas relaciones entre la radiación que emiten las antenas y sus efectos en la salud.
Syntropy
Greek syn (together) and tropos (tendency)
A deep, unifying, self-organizing force that is omnipresent in the universe, bringing a tendency towards energy concentration, order, organization and life, in contrast to entropy.
Guy Dauncey is a futurist who works to develop a positive vision of a sustainable future, and to translate that vision into action. He lives on Vancouver Island, in Canada.
He is founder of the BC Sustainable Energy Association, co-founder of the Victoria Car Share Cooperative, and the author or co-author of ten books, including The Climate Challenge: 101 Solutions to Global Warming and most recently Journey to the Future: A Better World Is Possible.
He is an Honorary Member of the Planning Institute of BC, a Fellow of the Findhorn Foundation in Scotland, and a Fellow of the Royal Society for the Arts, founded in Britain in 1754.
His websites are www.earthfuture.com, www.journeytothefuture.ca and www.thepracticalutopian.ca.
Whole Genome Sequencing (WGS) for food safety management: Perspectives from K...ExternalEvents
http://tiny.cc/faowgsworkshop
Use of genome sequencing technology on food safety management- Kenya's Perspectives. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
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.
Dr. Ying Fang - Emerging swine disease diagnostics and characterization: conn...John Blue
Emerging swine disease diagnostics and characterization: connecting basic research to real-world applications - Dr. Ying Fang, Kansas State University, from the 2017 North American PRRS/National Swine Improvement Federation Joint Meeting, December 1‐3, 2017, Chicago, Illinois, USA.
More presentations at http://www.swinecast.com/2017-north-american-prrs-nsif-joint-meeting
Cómo distinguir una investigación seria de una fraudulentaantenasysalud
Segunda presentación del Dr. Mike Repacholi, presidente emérito del ICNIPR (Comisión Internacional de Protección contra la Radiación No Ionizante) y Miembro del Comité Asesor Internacional del Proyecto de EMF Internacional de la Organización Mundial de la Salud, durante el II Foro Internacional “Antenas y Telecomunicaciones; Inclusiòn, Desarrollo y Salud Humana. Repacholi ofreció una disertación focalizada a resaltar las diferencias entre investigaciones científicas serias y fraudulentas que muchas veces ganan gran atención de la prensa generando temor entre la población respecto a las presuntas relaciones entre la radiación que emiten las antenas y sus efectos en la salud.
Syntropy
Greek syn (together) and tropos (tendency)
A deep, unifying, self-organizing force that is omnipresent in the universe, bringing a tendency towards energy concentration, order, organization and life, in contrast to entropy.
Guy Dauncey is a futurist who works to develop a positive vision of a sustainable future, and to translate that vision into action. He lives on Vancouver Island, in Canada.
He is founder of the BC Sustainable Energy Association, co-founder of the Victoria Car Share Cooperative, and the author or co-author of ten books, including The Climate Challenge: 101 Solutions to Global Warming and most recently Journey to the Future: A Better World Is Possible.
He is an Honorary Member of the Planning Institute of BC, a Fellow of the Findhorn Foundation in Scotland, and a Fellow of the Royal Society for the Arts, founded in Britain in 1754.
His websites are www.earthfuture.com, www.journeytothefuture.ca and www.thepracticalutopian.ca.
This project is revising diagnostic tools for all high-priority Dacini fruit fly species in the National Fruit Fly Strategy and their non-pest relatives including offshore and Australian endemics.
Borders vs. Amazon: Comparative Analysis of Organizational Design InfluencesTeo Tertel
Project objective is to apply course concepts to understand how an organization\'s design influences its performance and to draft a proposed change to enhance the company\'s performance.
Comparative Analysis of SWOT and TOWS, Company Diagnostics, Force Field Analysis, and Recommendations for Borders.
Gmr2301 Breeding Transgenic Cattle For Human Therapeutics Avi Dey
Small breed cattle & pigs now can be part of small farm new product development via emerging agribio technology with recent breakthroughs in bioscience/bioengineering.
This presentation talks about the Diagnostics & Healthcare industry in India.It includes Marketing Mix,STPD Analysis,SWOT Analysis of some of the top healthcare organizations.
Deciphering DNA sequences is essential for virtually all branches of biological research. With the
advent of capillary electrophoresis (CE)-based Sanger sequencing, scientists gained the ability to
elucidate genetic information from any given biological system. This technology has become widely
adopted in laboratories around the world, yet has always been hampered by inherent limitations in
throughput, scalability, speed, and resolution that often preclude scientists from obtaining the essential
information they need for their course of study. To overcome these barriers, an entirely new technology
was required—Next-Generation Sequencing (NGS), a fundamentally different approach to sequencing
that triggered numerous ground-breaking discoveries and ignited a revolution in genomic science.
GenomeTrakr: Whole-Genome Sequencing for Food Safety and A New Way Forward in...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
GenomeTrakr: Whole-Genome Sequencing for Food Safety and A New Way Forward in the Microbiological Testing & Traceability for Foodborne Pathogens. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
This year's 3rd Annual TCGC: The Clinical Genome Conference, held June 10-12, 2014 in San Francisco, is a three-day event that weaves together the science of sequencing and the business of implementing genomics in the clinic. It uniquely illustrates the mutual influence of those areas and the need to therefore consider the needs, challenges and opportunities of both - from next-generation sequencing and variant interpretation to insurance reimbursement and electronic health records - throughout the entire research process.Learn more at http://www.clinicalgenomeconference.com
Whole Genome Sequencing (WGS) for surveillance of foodborne infections in Den...ExternalEvents
http://tiny.cc/faowgsworkshop
Applications of genome sequencing technology on food safety management - Denmark. Presentation from the FAO expert workshop on practical applications of Whole Genome Sequencing (WGS) for food safety management - 7-8 December 2015, Rome, Italy.
Common languages in genomic epidemiology: from ontologies to algorithmsJoão André Carriço
Presentation for 2nd Conference Rapid Microbial NGS and Bioinformatics: Translation Into Practice
Hamburg/Germany, June 9-11, 2016
http://rami-ngs.org/
An overview of genomic epidemiology, Canada's IRIDA project for genome-based outbreak investigation, and a breathless romp through the awesome potential of the MinION
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain the viral diversity in the environment that is often missed in studies targeting specific potential reservoirs.
It’s an example of how data analysis can contribute to effective COVID-19 policies. But it also presents challenges, from ensuring that individuals’ privacy is protected to the need to independently verify its accuracy.
Additional value of prenatal genomic array testing in fetuses with isolated structural ultrasound abnormalities and a normal karyotype: a systematic review of the literature
M.C. de Wit, M.I. Srebniak, L.C.P. Govaerts, D. Van Opstal, R.J.H. Galjaard and A.T.J.I. Go
Link to free access article: http://onlinelibrary.wiley.com/doi/10.1002/uog.12575/abstract
Research investigating the use a genome-informed approach to develop diagnostic tools, for the detection of exotic phytopathogenic bacteria that pose a threat to Australian agriculture.
Exploiting NLP for Digital Disease InformaticsNigel Collier
Exploiting These are the slides from my talk at the Department of Computer Science at Sheffield University. The talk covers broad ground in my experience of applying natural language processing to knowledge discovery from various media including social media, news and the scientific literature.
Presentation delivered 8th August 2016, at the European Association for Potato Research (EAPR) meeting, Dundee - outlining classification of bacterial plant pathogens with
Introductory slides for the Python hands-on session of the Research Data Visualisation Workshop run by the Software Sustainability Institute, University of Manchester 28th July 2016.
Materials for the session are available at https://github.com/widdowquinn/Teaching-Data-Visualisation
Guest lecture on comparative genomics for University of Dundee BS32010, delivered 21/3/2016
Workshop/other materials available at DOI:10.5281/zenodo.49447
Keynote presentation, 4th February 2015, León, México - part of the 2015 Genomics Research on Plant-Parasite Interactions to Increase Food Production UK-MX Workshop.
Highly Discriminatory Diagnostic Primer Design From Whole Genome DataLeighton Pritchard
Presented at the GMI (Global Microbial Identifier) satellite meeting, sponsored by the UK Department for Environment, Food and Rural Affairs (DEFRA), organised by the Food and Environment Research Agency (FERA), Bedern Hall, York, 10th September 2014.
Presentation summarising the 2013 ICSB conference in Copenhagen, a requirement of James Hutton Institute Visits Abroad funding. Presented at the Cellular and Molecular Sciences seminar series.
Golden Rules of Bioinformatics.
Presented as part of a full-day introductory bioinformatics course - the example data and source for the slides can be found at https://github.com/widdowquinn/Teaching-Intro-to-Bioinf
Keynote presentation from Plant and Pathogen Bioinformatics workshop at EMBL-EBI, 8-11 July 2014
Slides and teaching material are available at https://github.com/widdowquinn/Teaching-EMBL-Plant-Path-Genomics
Repeatable plant pathology bioinformatic analysis: Not everything is NGS dataLeighton Pritchard
Presentation on use of Galaxy for plant pathology bioinformatics, presented by Peter Cock, at the Genomics for Non-Model Organisms workshop, ISMB/ECCB, Vienna, Austria, 19 July 2011
Presentation delivered 29th October 2012, at the CoZee workshop in Dundee (see CoZee zoonosis network site for more information: http://www.cozee-zoonosis.net/).
[For clarity: our diagnostics work did not at the time form part of the excellent E.coli O104:H4 genome analysis crowd-sourcing consortium work, which can be found at https://github.com/ehec-outbreak-crowdsourced/BGI-data-analysis/wiki - we talked about it here because it was good work, and without their efforts we couldn't have done what we did]
Slides for the afternoon session on "Introduction to Bioinformatics", delivered at the James Hutton Institute, 29th, 20th May and 5th June 2014, by Leighton Pritchard and Peter Cock.
Slides cover introductory guidance and links to resources, theory and use of BLAST tools, and a workshop featuring some common tools and tasks.
Presentation given as part of the EMBO Workshop on Plant-Microbe Interactions, at The Sainsbury Laboratory, Norwich, 20th June 2012. This presentation describes bioinformatic and statistical considerations for the prediction of plant pathogen effectors from genome sequences and annotation, with several literature examples.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Toxic effects of heavy metals : Lead and Arsenicsanjana502982
Heavy metals are naturally occuring metallic chemical elements that have relatively high density, and are toxic at even low concentrations. All toxic metals are termed as heavy metals irrespective of their atomic mass and density, eg. arsenic, lead, mercury, cadmium, thallium, chromium, etc.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
1. Sequencing and Beyond?
Risks and SWOT for
sequencing-led surveillance
and diagnostics of zoonotic
bacteria
Leighton Pritchard1;2;3
1Information and Computational Sciences,
2Centre for Human and Animal Pathogens in the Environment,
3Dundee Eector Consortium,
The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA
2. Acceptable Use Policy
Recording of this talk, taking photos, discussing the content using
email, Twitter, blogs, etc. is permitted (and encouraged),
providing distraction to others is minimised.
This presentation will be available on SlideShare.
3. Table of Contents
SWOT analysis
Case Study
Nosocomial P.aeruginosa acquisition
Strengths
Weaknesses
Opportunities
Threats
Acknowledgements
Without Whom. . .
4. What is SWOT?
A generic structured planning/categorisation method
Identify the objective, and identify internal and external factors
that can help or harm reaching that objective.
Strengths: characteristics of sequencing approaches that may
be helpful
Weaknesses: characteristics of sequencing approaches that
might be harmful
Opportunities: external elements that could be helpful
Threats: external elements that may be harmful
Its purpose is to guide strategies that might help achieve objectives.
6. Table of Contents
SWOT analysis
Case Study
Nosocomial P.aeruginosa acquisition
Strengths
Weaknesses
Opportunities
Threats
Acknowledgements
Without Whom. . .
7. P.aeruginosa nosocomial acquisitiona
a
Quick et al. (2014) BMJ Open 4: e006278. doi:10.1136/bmjopen-2014-006278
Motivation
Nosocomial water transmission of P.aeruginosa an urgent concern
8. P.aeruginosa nosocomial acquisitiona
a
Quick et al. (2014) BMJ Open 4: e006278. doi:10.1136/bmjopen-2014-006278
Motivation
Nosocomial water transmission of P.aeruginosa an urgent concern
Setup
Burns patients (30) screened for P.aeruginosa on admission
Samples taken from patients and environment
All P.aeruginosa isolates (141) WGS sequenced
9. P.aeruginosa nosocomial acquisitiona
a
Quick et al. (2014) BMJ Open 4: e006278. doi:10.1136/bmjopen-2014-006278
Motivation
Nosocomial water transmission of P.aeruginosa an urgent concern
Setup
Burns patients (30) screened for P.aeruginosa on admission
Samples taken from patients and environment
All P.aeruginosa isolates (141) WGS sequenced
Outcome
Clustering of isolates by room and outlet
Three patient isolates identical to water isolates from same room
Bio
12. P.aeruginosa nosocomial acquisitiona
a
Quick et al. (2014) BMJ Open 4: e006278. doi:10.1136/bmjopen-2014-006278
Methods
Illumina MiSeq WGS of 141 isolates
Metagenomic sequencing of bio
13. lm
Simulated sequencing of 55 published P. aeruginosa
BWA mapping against PAO1 reference genome
SNPs called with SAMtools VarScan
ML reconstruction with FastTree
De novo assembly with Velvet for MLST prediction
Sequences and bioinformatic methods shared online:
http://www.github.com/joshquick/snp calling scripts
16. P.aeruginosa nosocomial acquisitiona
a
Quick et al. (2014) BMJ Open 4: e006278. doi:10.1136/bmjopen-2014-006278
Strengths
A P. aeruginosa source could be tracked by WGS
Insights into transmission: water to patient a likely route
Sensitivity - identi
18. P.aeruginosa nosocomial acquisitiona
a
Quick et al. (2014) BMJ Open 4: e006278. doi:10.1136/bmjopen-2014-006278
Strengths
A P. aeruginosa source could be tracked by WGS
Insights into transmission: water to patient a likely route
Sensitivity - identi
19. es microevolution
Limitations
Small sample size: 5/30 patients infected, gave 55/141 isolates
Not clear that causal inferences are general
300-day sampling, not real-time crisis analysis
Good existing reference genome set for this bacterium
Sequencing cost: $8k; Sta cost: $15k; (infrastructure $?)
20. Table of Contents
SWOT analysis
Case Study
Nosocomial P.aeruginosa acquisition
Strengths
Weaknesses
Opportunities
Threats
Acknowledgements
Without Whom. . .
21. Strength: Illumina
Illumina sequencing is a stable, widespread technology
Low price: $50 per WGS bacterial genome
Robust software for assembly/mapping
Single assay pipeline for multiple species
Promise of (near) real-time genotyping and surveillance
22. Strength: Nature of information
(Almost) complete genome sequence information with WGS
Extremely sensitive: whole-genomes at single SNP/indel
resolution
Enables tracing of microevolution
Data is digital, and in
23. nitely sharable
Reference repositories for data: ENA/SNA, NCBI etc.
Can build on public sequence data
24. Strength: Active RD area
Technology is still moving forward: good things will get better
Nanopore promises cheap, long reads
Assembly/SNP calling tools can improve
New techniques, technologies, software, : : :
Active
26. Table of Contents
SWOT analysis
Case Study
Nosocomial P.aeruginosa acquisition
Strengths
Weaknesses
Opportunities
Threats
Acknowledgements
Without Whom. . .
27. Weakness: New technologies
New technologies may not be robust or reliable
Readily available only in more developed nations; in labs, not
farms/factories?
New sequencing technologies still to be proven (Nanopore)
Lack of plug-and-play analysis solutions: requires
statistical/computing/biological expertise
Plethora of assembly/mapping tools: results and quality vary
Stability of results/analysis
28. Weakness: Nature of information
Data integrity, availability critical for success
Siloing of data (no public submission) can happen
Inaccurate or incorrect reference/public data
Inadequate, incorrect or absent metadata (new
ontologies?)
Unstable results between software/technology versions
Reproducibility of analyses
Genome sequence does not generally predict phenotype
32. cation of appropriate metadata (or not)
Sample deeply enough for sucient power (or not)
WGS vs metagenomics
colonies vs communities
whole genomes vs identi
34. Table of Contents
SWOT analysis
Case Study
Nosocomial P.aeruginosa acquisition
Strengths
Weaknesses
Opportunities
Threats
Acknowledgements
Without Whom. . .
41. cation/diagnostics
Comprehensive sequence data could be highly in
uential
High-resolution tracing of outbreaks/contamination/transfer
Combine with system-scale understanding of transport/trade
43. cation/diagnostics
Comprehensive sequence data could be highly in
uential
High-resolution tracing of outbreaks/contamination/transfer
Combine with system-scale understanding of transport/trade
Pangenome-based view of bacteria
Improved taxonomic (and phenotypic?) classi
58. Diagnostics design
Validate against known, unseen examples
Successful at species level in Dickeya1, sub-serotype level in E. coli 2
targets
classication
o-targets
V
IV
III
II
I
primer sets validation gels
I
II
III
IV
V
III IV V +ve -ve
III IV V +ve -ve
III IV V +ve -ve
III IV V +ve -ve
II
V
I
III
1
Pritchard et al. (2013) Plant Path. 62: 587-596. doi:10.1111/j.1365-3059.2012.02678.x
2
Pritchard et al. (2012) PLoS One 7: e34498. doi:10.1371/journal.pone.0034498
59. Diagnostics design
Distinguish at species level in Dickeya3, sub-serotype level in E.
coli 4
3
Pritchard et al. (2013) Plant Path. 62: 587-596. doi:10.1111/j.1365-3059.2012.02678.x
4
Pritchard et al. (2012) PLoS One 7: e34498. doi:10.1371/journal.pone.0034498
60. Table of Contents
SWOT analysis
Case Study
Nosocomial P.aeruginosa acquisition
Strengths
Weaknesses
Opportunities
Threats
Acknowledgements
Without Whom. . .
62. nancially
Whose responsibility is it?
How to ensure funding continuity?
Centralisation vs federation/distribution
63. Threats: Data Management
Having lots of data brings its own problems
Do analyses scale from 10s to 100s to 1000s to 10000s of
sequences? (Where do we do the computing?)
Metadata/data accuracy and provenance
Data standards (minimum information)
Common analytical standards
Timely collection/generation/release in a crisis
64. Scaling
Moving from 30 genome to 1000 genome pairwise comparisons
New algorithms, storage and visualisation tools required
65. Threats: Data Legalities
Who owns what?
Who owns public data? (and who owns the results of
analysis?)
Legal/
70. c skills
New algorithms and techniques for scale
New visualisation and other software tools
Tools/interfaces for usability
Data curators are extremely important!
Is there a skills shortage? Industry better-paid?
Old guard may not appreciate these needs
[employer] isn't interested in an equation as an academic
exercise.
You [: : :] might want to do some [computing] thing that's [...]
special, but we're not interested.
71. Table of Contents
SWOT analysis
Case Study
Nosocomial P.aeruginosa acquisition
Strengths
Weaknesses
Opportunities
Threats
Acknowledgements
Without Whom. . .
72. Acknowledgements
James Hutton Institute
Nicola Holden
Fiona Brennan
Sonia Humphris
Ian Toth
Emma Campbell
University of Aberdeen
Ken Forbes
Norval Strachan
SASA
Gerry Saddler
FERA
Valerie Bertrand
John Elphinstone
Neil Parkinson
University of Munster
Martina Bielaszewska
Helge Karch
GitHub
Benjamin Leopold
Michael Robeson
73. Licence: CC-BY-SA
By: Leighton Pritchard
This presentation is licensed under the Creative Commons
Attribution ShareAlike license
https://creativecommons.org/licenses/by-sa/4.0/