The document discusses the genetic basis of social organization in fire ant populations. Researchers used RAD sequencing of haploid males to discover SNPs and genotype individuals at over 2,400 loci. Principal component analysis separated individuals into two clusters corresponding to their social form (single or multiple queen), with the first principal component explaining over 12% of the variance. A region on chromosome 13 containing the Gp-9 gene was completely associated with social form. This research identified a major gene influencing an important social trait using next-generation sequencing techniques.
Step‐by‐Step Evolution of Vertebrate Blood Coagulation Madhusudan Katti
Department of Biology, Consortium for Evolutionary Studies & Tri Beta Biological Honor Society, California State University, Fresno present:
Step‐by‐Step Evolution of Vertebrate Blood Coagulation
by
Dr. Russell F. Doolittle
Dept. Chemistry & Biochemistry and Molecular Biology , University of California, San Diego
Abstract
The availability of whole genome sequences for a variety of vertebrates is making it possible to reconstruct the step-by-step evolution of complex phenomena like blood coagulation, an event that in mammals involves the interplay of more than two dozen genetically encoded factors. Gene inventories for different organisms are revealing when during vertebrate evolution certain factors first made their appearance or, on occasion, disappeared from some lineages. The whole genome sequence databases of two protochordates and seven non-mammalian vertebrates were examined in search of some 20 genes known to be associated with blood clotting in mammals. No genuine orthologs were found in the protochordate genomes (sea squirt and amphioxus). As for vertebrates, although the jawless fish have genes for generating the thrombin-catalyzed conversion of fibrinogen to fibrin, they lack several clotting factors, including two thought to be essential for the activation of thrombin in mammals. Fish in general lack genes for the “contact factor” proteases, the predecessor forms of which make their first appearance in tetrapods. The full complement of factors known to be operating in humans doesn’t occur until pouched marsupials (opossum), at least one key factor still being absent in egg-laying mammals like platypus.
On: Friday, January 29, 2010
At: 3:00‐‐‐4:00 PM
In: Science II, Room 109
1. Variation in the genome of the fungal wheat pathogen Zymoseptoria tritici facilitates rapid evolution through mechanisms like gaining virulence mutations, chromosomal rearrangements that result in gene loss or gain, and transposable element activity providing a source of evolutionary novelty.
2. Analysis of multiple Z. tritici genomes revealed a large flexible pan-genome with a small conserved core and many lineage-specific genes, facilitating adaptation to different wheat cultivars and environments. Recent losses of core genes were enriched for secreted effectors.
3. Signatures of recent strong positive selection were detected in pathogen populations, indicating adaptive evolution in response to pressures like new resistant wheat cultivars.
Towards a functional analysis of the major factors involved in the reproducti...CIAT
This document summarizes research on the reproductive barrier between Asian and African cultivated rice species. The researchers characterized hybrid sterility in crosses between Oryza sativa and O. glaberrima. They found pollen and embryo sac abortion in hybrids, occurring during early microspore and post-meiosis stages, respectively. Sequence analysis revealed structural changes in candidate sterility genes, F-box genes at the S1 and S1A loci. Expression analysis showed highest F-box expression in hybrids during critical gametogenesis stages. This supports the hypothesis that altered F-box genes cause hybrid sterility between the two rice species.
Knowledge Management in a Knowledge Based Disciplinerobertstevens65
1) The document discusses knowledge management in biology, a knowledge-based discipline. It describes how biological knowledge can be represented computationally using ontologies that define domain entities.
2) The document provides background on biology as a field, from classic to modern biology. It also discusses the speed of DNA sequencing and number of biological databases.
3) The document specifically focuses on the human prion protein (PrP) and provides its sequence, structures, functions, domains, variants associated with disease, and more. It aims to computationally represent biological knowledge on PrP.
Este documento trata sobre la energía eólica y contiene seis secciones principales. La primera sección caracteriza el recurso eólico y explica conceptos como la potencia del viento, la teoría de la cantidad de movimiento y las variaciones espaciales y temporales del viento. La segunda sección cubre la obtención y tratamiento de datos de viento. La tercera sección trata sobre la selección de emplazamientos eólicos. La cuarta sección analiza los impactos medioambientales de la energía eólica. La qu
This document provides an overview and schedule for the course "SBC 361 Research Methods & Comms". The course is a mixture of advanced analytical skills taught in computer labs using the programming language R, and theoretical content covered in lectures and workshops. It includes two workshops on careers in science and popular science writing. Students will complete assignments involving the computer practicals and tutorials, and a mock exam. The schedule details the topics to be covered each week by different professors and teaching staff. It emphasizes the importance of attending classes, completing required work, and doing additional outside reading to succeed in the course.
The document discusses the key provisions around acceptance of deposits and issue of securities by companies under the Companies Act, 2013. It provides 10 exclusions for what does not constitute a 'deposit' according to the Act. It also outlines the conditions stipulated under Section 73 for a company to accept deposits from members, including issuing a circular, maintaining a deposit repayment reserve account, and obtaining credit ratings. Specific additional conditions are provided for eligible companies to restrict the amount of deposits accepted.
Step‐by‐Step Evolution of Vertebrate Blood Coagulation Madhusudan Katti
Department of Biology, Consortium for Evolutionary Studies & Tri Beta Biological Honor Society, California State University, Fresno present:
Step‐by‐Step Evolution of Vertebrate Blood Coagulation
by
Dr. Russell F. Doolittle
Dept. Chemistry & Biochemistry and Molecular Biology , University of California, San Diego
Abstract
The availability of whole genome sequences for a variety of vertebrates is making it possible to reconstruct the step-by-step evolution of complex phenomena like blood coagulation, an event that in mammals involves the interplay of more than two dozen genetically encoded factors. Gene inventories for different organisms are revealing when during vertebrate evolution certain factors first made their appearance or, on occasion, disappeared from some lineages. The whole genome sequence databases of two protochordates and seven non-mammalian vertebrates were examined in search of some 20 genes known to be associated with blood clotting in mammals. No genuine orthologs were found in the protochordate genomes (sea squirt and amphioxus). As for vertebrates, although the jawless fish have genes for generating the thrombin-catalyzed conversion of fibrinogen to fibrin, they lack several clotting factors, including two thought to be essential for the activation of thrombin in mammals. Fish in general lack genes for the “contact factor” proteases, the predecessor forms of which make their first appearance in tetrapods. The full complement of factors known to be operating in humans doesn’t occur until pouched marsupials (opossum), at least one key factor still being absent in egg-laying mammals like platypus.
On: Friday, January 29, 2010
At: 3:00‐‐‐4:00 PM
In: Science II, Room 109
1. Variation in the genome of the fungal wheat pathogen Zymoseptoria tritici facilitates rapid evolution through mechanisms like gaining virulence mutations, chromosomal rearrangements that result in gene loss or gain, and transposable element activity providing a source of evolutionary novelty.
2. Analysis of multiple Z. tritici genomes revealed a large flexible pan-genome with a small conserved core and many lineage-specific genes, facilitating adaptation to different wheat cultivars and environments. Recent losses of core genes were enriched for secreted effectors.
3. Signatures of recent strong positive selection were detected in pathogen populations, indicating adaptive evolution in response to pressures like new resistant wheat cultivars.
Towards a functional analysis of the major factors involved in the reproducti...CIAT
This document summarizes research on the reproductive barrier between Asian and African cultivated rice species. The researchers characterized hybrid sterility in crosses between Oryza sativa and O. glaberrima. They found pollen and embryo sac abortion in hybrids, occurring during early microspore and post-meiosis stages, respectively. Sequence analysis revealed structural changes in candidate sterility genes, F-box genes at the S1 and S1A loci. Expression analysis showed highest F-box expression in hybrids during critical gametogenesis stages. This supports the hypothesis that altered F-box genes cause hybrid sterility between the two rice species.
Knowledge Management in a Knowledge Based Disciplinerobertstevens65
1) The document discusses knowledge management in biology, a knowledge-based discipline. It describes how biological knowledge can be represented computationally using ontologies that define domain entities.
2) The document provides background on biology as a field, from classic to modern biology. It also discusses the speed of DNA sequencing and number of biological databases.
3) The document specifically focuses on the human prion protein (PrP) and provides its sequence, structures, functions, domains, variants associated with disease, and more. It aims to computationally represent biological knowledge on PrP.
Este documento trata sobre la energía eólica y contiene seis secciones principales. La primera sección caracteriza el recurso eólico y explica conceptos como la potencia del viento, la teoría de la cantidad de movimiento y las variaciones espaciales y temporales del viento. La segunda sección cubre la obtención y tratamiento de datos de viento. La tercera sección trata sobre la selección de emplazamientos eólicos. La cuarta sección analiza los impactos medioambientales de la energía eólica. La qu
This document provides an overview and schedule for the course "SBC 361 Research Methods & Comms". The course is a mixture of advanced analytical skills taught in computer labs using the programming language R, and theoretical content covered in lectures and workshops. It includes two workshops on careers in science and popular science writing. Students will complete assignments involving the computer practicals and tutorials, and a mock exam. The schedule details the topics to be covered each week by different professors and teaching staff. It emphasizes the importance of attending classes, completing required work, and doing additional outside reading to succeed in the course.
The document discusses the key provisions around acceptance of deposits and issue of securities by companies under the Companies Act, 2013. It provides 10 exclusions for what does not constitute a 'deposit' according to the Act. It also outlines the conditions stipulated under Section 73 for a company to accept deposits from members, including issuing a circular, maintaining a deposit repayment reserve account, and obtaining credit ratings. Specific additional conditions are provided for eligible companies to restrict the amount of deposits accepted.
This document provides summaries of 15 mobile applications. They cover a variety of domains including education, healthcare, entertainment, business, and more. Each application summary includes a description of its purpose and key features. Special features highlighted among the applications include customized content and interfaces, integration of external APIs, analytics and recommendation capabilities, and tools for enhancing user experiences.
The document discusses analyzing ancient plant and insect DNA extracted from ice core samples in Greenland. Key points:
- Plant and insect DNA was recovered from silty ice samples taken between 2-3 km deep in the Dye 3 and JEG ice cores in Greenland, dating back to before the last glacial period.
- The DNA was identified as coming from tree species like pine and alder, indicating a boreal forest environment in southern Greenland at the time, rather than today's Arctic conditions.
- Other plant species identified include those from orders like Asterales, Poales, Rosales and Malpighiales. Insect DNA from Lepidoptera was also recovered.
2015 12-18- Avoid having to retract your genomics analysis - Popgroup Reprodu...Yannick Wurm
Brief (15min) talk I gave at #PopGroup49 in Edinburgh providing a few simple methods to reduce risk in genomics analyses.
Please cite: Avoid having to retract your genomics analysis (2015) Y Wurm. The Winnower 2, e143696.68941 https://thewinnower.com/papers/avoid-having-to-retract-your-genomics-analysis
V3 basic pm training overview thammasatRobert Twiddy
This document provides an overview of a project management fundamentals course. The course teaches the fundamentals of project management, discusses the roles of project managers and team members, and practices core project management techniques. However, the course does not provide enough training to sit for the Project Management Professional certification exam. The course objectives are to describe project manager roles, understand fundamental project management concepts, learn from case studies, and know where to find additional resources and training.
Mr. Robert Twiddy provides strategic consulting services including project management training and coaching to executives. He is currently a visiting professor and strategy advisor in Thailand. He has experience providing balanced scorecard, project management, and IT consulting. The presentation introduces project portfolio management (PPM) including the overall model, strategic alignment using balanced scorecard, frameworks for project selection, and tools for PPM. Participants will learn about introducing PPM to their organization through establishing processes, metrics, and strategic linkage between projects and programs. They will also learn about PPM certification and tools to support the PPM lifecycle.
Keynote talk given at Fairdom User meeting http://fair-dom.org/communities/users/barcelona-2016-first-user-meeting/ .
I begin by summarising how we apply molecular approaches to understand social behaviour in ants. Subsequently, I give an overview of the data-handling challenges the genomic bioinformatics community faces. Finally, I give an overview of some of the tools and approaches my lab have developed to help us get things done better, faster, more reliably and more reproducibly.
The document appears to be about the genome of the red fire ant Solenopsis invicta. It summarizes some key findings from sequencing and analyzing the fire ant genome. These include an expansion of gene families related to lipid processing and cuticular hydrocarbons. It also found over 420 putative olfactory receptor genes, more than any other insect genome sequenced. Additionally, the genome appears to have a functional DNA methylation system.
50% social chromosomes in ants, 50% bioinformatics for genomics in emerging model organisms. Given at #CTBio http://pathogenomics.bham.ac.uk/blog/2013/07/cream-teas-and-bioinformatics-balti-and-bioinformatics-goes-on-its-holidays/
Apologies - videos and transitions are largely missing as part of the PDF conversion.
The work referenced here includes:
http://dx.doi.org/10.1038/nature11832
http://dx.doi.org/10.1073/pnas.1009690108
http://sequenceserver.com
https://github.com/yeban/afra & http://afra.sbcs.qmul.ac.uk
https://github.com/monicadragan/GeneValidator
This document summarizes research on social evolution in ants. It discusses various ant species like leaf-cutter ants, weaver ants, and Forelius pusillus ants. It also discusses fire ants and their single and multiple queen social forms which are associated with their Gp-9 gene. Genome sequencing of the fire ant revealed expansion of odor receptor genes and other findings. The document covers topics like kin selection, evolution of eusociality, and using modern technologies to study insect societies.
The document discusses genomic analysis of the fire ant Solenopsis invicta. It notes that the genome sequencing of a Gp-9 B male fire ant revealed an expansion of lipid-processing gene families and over 420 putative olfactory receptors, more than any other insect. It also identified a functional DNA methylation system. Previous research had linked the fire ant's social structure to its Gp-9 locus, but genome sequencing provided more genomic context around this gene and others related to social behavior and chemical signaling.
The document discusses genomic research on fire ants. It summarizes that the genome of a fire ant was sequenced, which revealed an expansion of lipid-processing and olfactory receptor genes. Over 400 putative olfactory receptors were identified, more than any other insect sequenced so far. The genome also contains a functional DNA methylation system. Previous research on fire ants linked their social structure to a single gene (Gp-9), but sequencing of the entire genome allowed further investigation into other genes that may be linked.
The document discusses developing a fungicide program for 2011 to control diseases on creeping bentgrass putting greens, highlighting the need to identify key diseases, determine when they are typically active based on historical weather, and select fungicides to target the expected diseases, adjusting treatments based on actual weather conditions.
The document summarizes a proposed study that aims to investigate convergent evolution of wing morphologies in birds and bats at the molecular level. The study involves using CRISPR/Cas9 gene editing to knockout genes in the BMP pathway (Bmp3) and sonic hedgehog (Shh) pathway in bat and chicken embryos. The expected results are that knockout of Bmp3 will result in shorter forelimbs and wingspans, and knockout of Shh will result in increased bone size and density in the ulna bone of both bats and chickens, supporting the hypothesis that convergent traits evolved through shared genetic mechanisms. Possible complications involve incomplete gene knockout or upregulation of other genes compensating for the knockout.
This document discusses the experience of a researcher in genomics with applying FAIR and open approaches. It notes that making data and analysis methods FAIR and open can increase visibility, drive citations, and facilitate collaboration. However, it also enables competition to more easily access and utilize resources without contributing. Striking the right balance between openness and protecting competitive advantages is challenging. Overall, the researcher finds FAIR and open principles have greatly increased the impact and robustness of their work, but there are also costs to consider.
2018 08-reduce risks of genomics researchYannick Wurm
Geoffrey Chang, a protein crystallographer at The Scripps Research Institute, had his career trajectory disrupted when several of his high-profile papers describing protein structures had to be retracted. An in-house software program Chang's lab used to process diffraction data from protein crystals introduced a sign error that inverted the structures, invalidating biological interpretations. This included a 2001 Science paper describing the structure of the MsbA protein. A 2006 Nature paper by Swiss researchers casting doubt on Chang's MsbA structure led him to discover the software error. Chang and his co-authors sincerely regretted the confusion and unproductive research caused by the need to retract their influential papers.
Geoffrey Chang was a prominent structural biologist who received prestigious early career awards. However, his work came under scrutiny when other researchers discovered errors in his published protein structures due to a problem with his in-house data analysis software. This led Chang to retract 5 of his papers describing protein structures. The retractions were costly for Chang's career and reputation as well as for other researchers who had performed follow-up work based on the incorrect structures. The incident highlights the importance of using well-tested, reproducible analysis methods in scientific research.
This document provides an agenda for a spring school on bioinformatics and population genomics, including practical sessions on analyzing genomic data from reads to reference genomes and gene predictions in 6 steps: inspecting and cleaning reads, genome assembly, assessing assembly quality, predicting protein-coding genes, assessing gene prediction quality, and assessing the overall process quality using biological measures. It also addresses wifi issues that could reduce bandwidth and lists the VM password.
This document provides information about a spring school on bioinformatics and population genomics that includes practical sessions. The sessions will cover topics like short read cleaning, genome assembly, gene prediction, quality control, mapping reads to call variants, visualizing variants, analyzing variants through PCA and measuring diversity and differentiation, inferring population sizes and gene flow, and analyzing gene expression from raw sequencing data to expression levels. The document lists the team of practitioners leading the sessions and encourages participants to share their favorite software packages.
This document contains information about programming in R, including practical examples. It discusses accessing and subsetting data, using regular expressions for text search, creating functions, and using loops. Examples are provided to demonstrate creating vectors, accessing subsets of vectors, using regular expressions to find patterns in text, creating functions to convert between units or estimate values, and using for loops to repeat operations over multiple elements. The document suggests R is useful for working with big data in biology and other fields due to its ability to automate tasks, integrate with other tools, and handle large datasets through programming.
This document provides summaries of 15 mobile applications. They cover a variety of domains including education, healthcare, entertainment, business, and more. Each application summary includes a description of its purpose and key features. Special features highlighted among the applications include customized content and interfaces, integration of external APIs, analytics and recommendation capabilities, and tools for enhancing user experiences.
The document discusses analyzing ancient plant and insect DNA extracted from ice core samples in Greenland. Key points:
- Plant and insect DNA was recovered from silty ice samples taken between 2-3 km deep in the Dye 3 and JEG ice cores in Greenland, dating back to before the last glacial period.
- The DNA was identified as coming from tree species like pine and alder, indicating a boreal forest environment in southern Greenland at the time, rather than today's Arctic conditions.
- Other plant species identified include those from orders like Asterales, Poales, Rosales and Malpighiales. Insect DNA from Lepidoptera was also recovered.
2015 12-18- Avoid having to retract your genomics analysis - Popgroup Reprodu...Yannick Wurm
Brief (15min) talk I gave at #PopGroup49 in Edinburgh providing a few simple methods to reduce risk in genomics analyses.
Please cite: Avoid having to retract your genomics analysis (2015) Y Wurm. The Winnower 2, e143696.68941 https://thewinnower.com/papers/avoid-having-to-retract-your-genomics-analysis
V3 basic pm training overview thammasatRobert Twiddy
This document provides an overview of a project management fundamentals course. The course teaches the fundamentals of project management, discusses the roles of project managers and team members, and practices core project management techniques. However, the course does not provide enough training to sit for the Project Management Professional certification exam. The course objectives are to describe project manager roles, understand fundamental project management concepts, learn from case studies, and know where to find additional resources and training.
Mr. Robert Twiddy provides strategic consulting services including project management training and coaching to executives. He is currently a visiting professor and strategy advisor in Thailand. He has experience providing balanced scorecard, project management, and IT consulting. The presentation introduces project portfolio management (PPM) including the overall model, strategic alignment using balanced scorecard, frameworks for project selection, and tools for PPM. Participants will learn about introducing PPM to their organization through establishing processes, metrics, and strategic linkage between projects and programs. They will also learn about PPM certification and tools to support the PPM lifecycle.
Keynote talk given at Fairdom User meeting http://fair-dom.org/communities/users/barcelona-2016-first-user-meeting/ .
I begin by summarising how we apply molecular approaches to understand social behaviour in ants. Subsequently, I give an overview of the data-handling challenges the genomic bioinformatics community faces. Finally, I give an overview of some of the tools and approaches my lab have developed to help us get things done better, faster, more reliably and more reproducibly.
The document appears to be about the genome of the red fire ant Solenopsis invicta. It summarizes some key findings from sequencing and analyzing the fire ant genome. These include an expansion of gene families related to lipid processing and cuticular hydrocarbons. It also found over 420 putative olfactory receptor genes, more than any other insect genome sequenced. Additionally, the genome appears to have a functional DNA methylation system.
50% social chromosomes in ants, 50% bioinformatics for genomics in emerging model organisms. Given at #CTBio http://pathogenomics.bham.ac.uk/blog/2013/07/cream-teas-and-bioinformatics-balti-and-bioinformatics-goes-on-its-holidays/
Apologies - videos and transitions are largely missing as part of the PDF conversion.
The work referenced here includes:
http://dx.doi.org/10.1038/nature11832
http://dx.doi.org/10.1073/pnas.1009690108
http://sequenceserver.com
https://github.com/yeban/afra & http://afra.sbcs.qmul.ac.uk
https://github.com/monicadragan/GeneValidator
This document summarizes research on social evolution in ants. It discusses various ant species like leaf-cutter ants, weaver ants, and Forelius pusillus ants. It also discusses fire ants and their single and multiple queen social forms which are associated with their Gp-9 gene. Genome sequencing of the fire ant revealed expansion of odor receptor genes and other findings. The document covers topics like kin selection, evolution of eusociality, and using modern technologies to study insect societies.
The document discusses genomic analysis of the fire ant Solenopsis invicta. It notes that the genome sequencing of a Gp-9 B male fire ant revealed an expansion of lipid-processing gene families and over 420 putative olfactory receptors, more than any other insect. It also identified a functional DNA methylation system. Previous research had linked the fire ant's social structure to its Gp-9 locus, but genome sequencing provided more genomic context around this gene and others related to social behavior and chemical signaling.
The document discusses genomic research on fire ants. It summarizes that the genome of a fire ant was sequenced, which revealed an expansion of lipid-processing and olfactory receptor genes. Over 400 putative olfactory receptors were identified, more than any other insect sequenced so far. The genome also contains a functional DNA methylation system. Previous research on fire ants linked their social structure to a single gene (Gp-9), but sequencing of the entire genome allowed further investigation into other genes that may be linked.
The document discusses developing a fungicide program for 2011 to control diseases on creeping bentgrass putting greens, highlighting the need to identify key diseases, determine when they are typically active based on historical weather, and select fungicides to target the expected diseases, adjusting treatments based on actual weather conditions.
The document summarizes a proposed study that aims to investigate convergent evolution of wing morphologies in birds and bats at the molecular level. The study involves using CRISPR/Cas9 gene editing to knockout genes in the BMP pathway (Bmp3) and sonic hedgehog (Shh) pathway in bat and chicken embryos. The expected results are that knockout of Bmp3 will result in shorter forelimbs and wingspans, and knockout of Shh will result in increased bone size and density in the ulna bone of both bats and chickens, supporting the hypothesis that convergent traits evolved through shared genetic mechanisms. Possible complications involve incomplete gene knockout or upregulation of other genes compensating for the knockout.
This document discusses the experience of a researcher in genomics with applying FAIR and open approaches. It notes that making data and analysis methods FAIR and open can increase visibility, drive citations, and facilitate collaboration. However, it also enables competition to more easily access and utilize resources without contributing. Striking the right balance between openness and protecting competitive advantages is challenging. Overall, the researcher finds FAIR and open principles have greatly increased the impact and robustness of their work, but there are also costs to consider.
2018 08-reduce risks of genomics researchYannick Wurm
Geoffrey Chang, a protein crystallographer at The Scripps Research Institute, had his career trajectory disrupted when several of his high-profile papers describing protein structures had to be retracted. An in-house software program Chang's lab used to process diffraction data from protein crystals introduced a sign error that inverted the structures, invalidating biological interpretations. This included a 2001 Science paper describing the structure of the MsbA protein. A 2006 Nature paper by Swiss researchers casting doubt on Chang's MsbA structure led him to discover the software error. Chang and his co-authors sincerely regretted the confusion and unproductive research caused by the need to retract their influential papers.
Geoffrey Chang was a prominent structural biologist who received prestigious early career awards. However, his work came under scrutiny when other researchers discovered errors in his published protein structures due to a problem with his in-house data analysis software. This led Chang to retract 5 of his papers describing protein structures. The retractions were costly for Chang's career and reputation as well as for other researchers who had performed follow-up work based on the incorrect structures. The incident highlights the importance of using well-tested, reproducible analysis methods in scientific research.
This document provides an agenda for a spring school on bioinformatics and population genomics, including practical sessions on analyzing genomic data from reads to reference genomes and gene predictions in 6 steps: inspecting and cleaning reads, genome assembly, assessing assembly quality, predicting protein-coding genes, assessing gene prediction quality, and assessing the overall process quality using biological measures. It also addresses wifi issues that could reduce bandwidth and lists the VM password.
This document provides information about a spring school on bioinformatics and population genomics that includes practical sessions. The sessions will cover topics like short read cleaning, genome assembly, gene prediction, quality control, mapping reads to call variants, visualizing variants, analyzing variants through PCA and measuring diversity and differentiation, inferring population sizes and gene flow, and analyzing gene expression from raw sequencing data to expression levels. The document lists the team of practitioners leading the sessions and encourages participants to share their favorite software packages.
This document contains information about programming in R, including practical examples. It discusses accessing and subsetting data, using regular expressions for text search, creating functions, and using loops. Examples are provided to demonstrate creating vectors, accessing subsets of vectors, using regular expressions to find patterns in text, creating functions to convert between units or estimate values, and using for loops to repeat operations over multiple elements. The document suggests R is useful for working with big data in biology and other fields due to its ability to automate tasks, integrate with other tools, and handle large datasets through programming.
This document describes oSwitch, a tool that allows easy access to other operating systems via one-line commands. It works by wrapping Docker containers, allowing commands to be run in different OS environments without disrupting the user's current environment. The document provides an example usage where a user is able to run an "abyss-pe" command in a Biolinux container after it is not found in their native OS. It notes how oSwitch aims to preserve the user's current working directory, login shell, home directory and file permissions during usage.
This document provides an outline for a lecture on the genetic basis of evolution. It begins with introducing key terms like gene, locus, allele, genotype, and phenotype. It then discusses genetic drift and how drift is influenced by population size. Selection is also introduced and defined as a process where individuals with different genotypes have different fitnesses. The document emphasizes that both genetic drift and selection influence evolution, and neither process should be overemphasized. It aims to move people away from only considering selection (pan-selectionism) and highlights the importance of genetic drift.
This document discusses human evolution and recent insights from genomics. It summarizes that Neanderthals were the closest evolutionary relatives to modern humans and lived in Europe and Western Asia until disappearing 30,000 years ago. A draft sequence of the Neanderthal genome from three individuals was presented, composed of over 4 billion nucleotides. Comparisons with five modern human genomes identified regions potentially affected by selection in ancestral modern humans, involving genes related to metabolism, cognition, and skeletal development. Analysis suggests Neanderthals shared more genetic variants with non-Africans, indicating gene flow from Neanderthals into their ancestors occurred before Eurasian groups diverged.
1. The document discusses best practices for scientific software development, including writing code for people rather than computers, automating repetitive tasks, using version control, and conducting code reviews.
2. Specific approaches and tools recommended are planning for mistakes, automated testing, continuous integration, and using a coding style guide. R and Ruby style guides are provided as examples.
3. The benefits of following such practices are improving productivity, reducing errors, making code easier to read and maintain, and allowing scientists to focus on scientific questions rather than software issues. Reproducible and sustainable software is the overall goal.
This document provides an introduction to regular expressions (regex) for text search and pattern matching. It explains that regex allows for powerful text searches beyond simple keywords. Various special symbols and constructs are demonstrated that allow matching complex patterns and variants in text. Examples show matching names, sequences, microsatellite repeats and more with regex. Functions, loops and logical operators in R programming are also briefly covered.
The document discusses major geological drivers of evolution including tectonic plate movement, vulcanism, climate change, and meteorite impacts. Tectonic plate movement has caused continental drift and formation of supercontinents like Pangaea, affecting species distributions. Vulcanism causes both local and global climate changes through emission of gases and particles and formation of new land barriers and islands. Climate changes over geological timescales have also impacted evolution. Meteorite impacts have precipitated mass extinctions. These geological forces alter Earth's conditions and drive evolution through large-scale migrations, speciation events, mass extinctions, and adaptive radiations.
This document discusses computational methods and challenges for genome assembly using next-generation sequencing data. It describes the four main stages of genome assembly as preprocessing filtering, graph construction, graph simplification, and postprocessing filtering. Each stage processes the data from the previous stage to build the assembly graph and reduce complexity, though some assemblers delay filtering steps.
This document outlines the course SBC322 Ecological and Evolutionary Genomics. It discusses how new genomic technologies have changed ecology and evolution research by merging molecular and ecological approaches. It aims to critically evaluate research questions, methods, experimental designs and applications in ecological and evolutionary genomics. The course will improve students' skills in critically reading literature, understanding interdisciplinary science, and oral and written scientific communication through interactive small group work, informal and formal presentations, blog posts, and peer review.
The document provides an overview of topics covered in a bioinformatics course, including using Unix, bioinformatics algorithms, biological databases, sequencing technologies, and genome assembly and variant identification. It lists challenges for students in each topic area and provides examples of concepts that will be covered, such as using HPC systems, dynamic programming for sequence alignment, accessing databases like NCBI, processing sequencing data, and identifying variants from assembly. Images are included of different organisms like ants and sequencing technologies. The document aims to outline the scope and challenges of the bioinformatics course.
Sustainable software institute Collaboration workshopYannick Wurm
The document discusses tools for analyzing biological data. It summarizes four tools:
1. SequenceServer - A simple web interface for BLAST that handles formatting and installing BLAST locally.
2. oSwitch - Allows rapidly switching between operating systems and container environments to access specific bioinformatics software without installation.
3. GeneValidator - Helps curate gene predictions by identifying problematic predictions, choosing best alternative models, and aiding manual curation of individual genes.
4. Afra - A crowdsourcing platform that aims to crowdsource the visual inspection and correction of gene models by recruiting and training students, ensuring quality through tutorials, redundancy and senior review, and creating small, simple initial tasks.
This document provides an overview of genomic tools and best practices for scientific computing. It discusses SequenceServer, a tool for BLAST searches, and Bionode, a collection of Node.js modules for bioinformatics. It also discusses challenges with gene prediction and introduces GeneValidator, a tool for visual inspection and manual correction of gene predictions. Key points include automating repetitive tasks, writing code for people through style guides, and using version control and modularization to improve code quality and reproducibility.
This document discusses the importance of experimental design for ecological and evolutionary genomics experiments. It notes that poor experimental design can lead to insufficient or misleading data due to issues like pseudoreplication, confounding factors, or inappropriate analysis. The document advises considering factors like calibration of measurement tools, reducing subjective decision making, ensuring subjects are in natural conditions, and avoiding easy mistakes to create a robust experimental design. It also cautions that many types of experiments in ecological and evolutionary genomics, such as reference genome work, gene expression studies, field collections, population surveys, and identifying trait genes, have specific risks of going wrong if the experimental design is inadequate.
1. The document discusses best practices for scientific software development including writing code for people to read, automating repetitive tasks, using version control, and avoiding redundancy.
2. Specific approaches mentioned are planning for mistakes, automated testing, continuous integration, and using style guides to ensure code is readable and consistently formatted.
3. Knitting allows analyzing and reporting in a single file by embedding R code chunks in markdown documents.
This document contains information about various programming languages and data handling skills for bioinformatics. It includes sections on choosing a programming language, with pros and cons of languages like Excel, R, Unix command line, Java, Perl, Python and Ruby listed. Other sections cover practical skills like accessing and subsetting data in R, using regular expressions for text searches, creating functions, and using for loops. Examples of code are provided throughout.
Walmart Business+ and Spark Good for Nonprofits.pdfTechSoup
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Spark Good (walmart.com/sparkgood) is a charitable platform that enables nonprofits to receive donations directly from customers and associates.
Answers about how you can do more with Walmart!"
How to Make a Field Mandatory in Odoo 17Celine George
In Odoo, making a field required can be done through both Python code and XML views. When you set the required attribute to True in Python code, it makes the field required across all views where it's used. Conversely, when you set the required attribute in XML views, it makes the field required only in the context of that particular view.
How to Build a Module in Odoo 17 Using the Scaffold MethodCeline George
Odoo provides an option for creating a module by using a single line command. By using this command the user can make a whole structure of a module. It is very easy for a beginner to make a module. There is no need to make each file manually. This slide will show how to create a module using the scaffold method.
Main Java[All of the Base Concepts}.docxadhitya5119
This is part 1 of my Java Learning Journey. This Contains Custom methods, classes, constructors, packages, multithreading , try- catch block, finally block and more.
How to Fix the Import Error in the Odoo 17Celine George
An import error occurs when a program fails to import a module or library, disrupting its execution. In languages like Python, this issue arises when the specified module cannot be found or accessed, hindering the program's functionality. Resolving import errors is crucial for maintaining smooth software operation and uninterrupted development processes.
This slide is special for master students (MIBS & MIFB) in UUM. Also useful for readers who are interested in the topic of contemporary Islamic banking.
Exploiting Artificial Intelligence for Empowering Researchers and Faculty, In...Dr. Vinod Kumar Kanvaria
Exploiting Artificial Intelligence for Empowering Researchers and Faculty,
International FDP on Fundamentals of Research in Social Sciences
at Integral University, Lucknow, 06.06.2024
By Dr. Vinod Kumar Kanvaria
ISO/IEC 27001, ISO/IEC 42001, and GDPR: Best Practices for Implementation and...PECB
Denis is a dynamic and results-driven Chief Information Officer (CIO) with a distinguished career spanning information systems analysis and technical project management. With a proven track record of spearheading the design and delivery of cutting-edge Information Management solutions, he has consistently elevated business operations, streamlined reporting functions, and maximized process efficiency.
Certified as an ISO/IEC 27001: Information Security Management Systems (ISMS) Lead Implementer, Data Protection Officer, and Cyber Risks Analyst, Denis brings a heightened focus on data security, privacy, and cyber resilience to every endeavor.
His expertise extends across a diverse spectrum of reporting, database, and web development applications, underpinned by an exceptional grasp of data storage and virtualization technologies. His proficiency in application testing, database administration, and data cleansing ensures seamless execution of complex projects.
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Throughout his career, he has taken on multifaceted roles, from leading technical project management teams to owning solutions that drive operational excellence. His conscientious and proactive approach is unwavering, whether he is working independently or collaboratively within a team. His ability to connect with colleagues on a personal level underscores his commitment to fostering a harmonious and productive workplace environment.
Date: May 29, 2024
Tags: Information Security, ISO/IEC 27001, ISO/IEC 42001, Artificial Intelligence, GDPR
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This presentation includes basic of PCOS their pathology and treatment and also Ayurveda correlation of PCOS and Ayurvedic line of treatment mentioned in classics.
How to Setup Warehouse & Location in Odoo 17 InventoryCeline George
In this slide, we'll explore how to set up warehouses and locations in Odoo 17 Inventory. This will help us manage our stock effectively, track inventory levels, and streamline warehouse operations.
LAND USE LAND COVER AND NDVI OF MIRZAPUR DISTRICT, UPRAHUL
This Dissertation explores the particular circumstances of Mirzapur, a region located in the
core of India. Mirzapur, with its varied terrains and abundant biodiversity, offers an optimal
environment for investigating the changes in vegetation cover dynamics. Our study utilizes
advanced technologies such as GIS (Geographic Information Systems) and Remote sensing to
analyze the transformations that have taken place over the course of a decade.
The complex relationship between human activities and the environment has been the focus
of extensive research and worry. As the global community grapples with swift urbanization,
population expansion, and economic progress, the effects on natural ecosystems are becoming
more evident. A crucial element of this impact is the alteration of vegetation cover, which plays a
significant role in maintaining the ecological equilibrium of our planet.Land serves as the foundation for all human activities and provides the necessary materials for
these activities. As the most crucial natural resource, its utilization by humans results in different
'Land uses,' which are determined by both human activities and the physical characteristics of the
land.
The utilization of land is impacted by human needs and environmental factors. In countries
like India, rapid population growth and the emphasis on extensive resource exploitation can lead
to significant land degradation, adversely affecting the region's land cover.
Therefore, human intervention has significantly influenced land use patterns over many
centuries, evolving its structure over time and space. In the present era, these changes have
accelerated due to factors such as agriculture and urbanization. Information regarding land use and
cover is essential for various planning and management tasks related to the Earth's surface,
providing crucial environmental data for scientific, resource management, policy purposes, and
diverse human activities.
Accurate understanding of land use and cover is imperative for the development planning
of any area. Consequently, a wide range of professionals, including earth system scientists, land
and water managers, and urban planners, are interested in obtaining data on land use and cover
changes, conversion trends, and other related patterns. The spatial dimensions of land use and
cover support policymakers and scientists in making well-informed decisions, as alterations in
these patterns indicate shifts in economic and social conditions. Monitoring such changes with the
help of Advanced technologies like Remote Sensing and Geographic Information Systems is
crucial for coordinated efforts across different administrative levels. Advanced technologies like
Remote Sensing and Geographic Information Systems
9
Changes in vegetation cover refer to variations in the distribution, composition, and overall
structure of plant communities across different temporal and spatial scales. These changes can
occur natural.
How to Add Chatter in the odoo 17 ERP ModuleCeline George
In Odoo, the chatter is like a chat tool that helps you work together on records. You can leave notes and track things, making it easier to talk with your team and partners. Inside chatter, all communication history, activity, and changes will be displayed.
28. Allozyme screen Social form associated to Gp-9 locus
Frequency of
the most
common allele
Locus!
0.3!
0.4!
0.5!
0.6!
0.7!
0.8!
0.9!
1.0!
Single queen!Multiple queen!
Est-6!Est-4!
G
3pdh-1!C
a-4!Pgm
-4!Ddh-1!Pro-5!
Pgm
-3!Acoh-5!acoh-1!A
cy-1!Pgm
-1!Aat-2!Gp-9!
Ken Ross and colleagues
Laurent Keller and colleagues
29. Single queen form Multiple queen form
Ken Ross and colleagues
Laurent Keller and colleagues
Social form completely associated to Gp-9 locus
30. bbbbBB BB Bb bb
Ken Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
(>15% )(< 5% )
31. bbBB BB Bb
x
Gp-9 bb females rare
Ken Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
(>15% )(< 5% )
32. BB BB Bb
Ken Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
(>15% )(< 5% )
33. BB BB Bb
x
Ken Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
Social form completely associated to Gp-9 locus
(>15% )(< 5% )
34. BB BB Bb
x x
Ken Ross and colleagues
Laurent Keller and colleagues
Social form completely associated to Gp-9 locus
Single queen form Multiple queen form
(>15% )(< 5% )
35. BB BB Bb
x x x
Ken Ross and colleagues
Laurent Keller and colleagues
Single queen form Multiple queen form
(>15% )(< 5% )
Social form completely associated to Gp-9 locus
36. • Is this gene the single überregulator?
Social form completely associated to Gp-9 locus
37. • Is this gene the single überregulator?
maybe 1/14th of the genome?
•Only 14 allozyme markers
Locus!
0.3!
0.4!
0.5!
0.6!
0.7!
0.8!
0.9!
1.0!
Single queen!Multiple queen!
Est-6!Est-4!
G
3pdh-1!C
a-4!Pgm
-4!Ddh-1!Pro-5!
Pgm
-3!Acoh-5!acoh-1!A
cy-1!Pgm
-1!Aat-2!Gp-9!
Social form completely associated to Gp-9 locus
40. Single ♂:
His brothers:
11×
4×
(330bp-insert paired reads) (normal single-end reads)45× +
Sequencing from haploid males (for easier assembly):
(8,000 & 20,000bp-insert paired reads)
B 20x
The genome of a Gp-9 B fire ant
Wurm et al 2011 PNAS
10,000 scaffolds (100 biggest scaffolds: 50% of genome)
Total: 350,000,000 bp assembled.→
The other 150Mb: highly repetitive sequence
44. AACTG
Gp-9 B
Gp-9 B
GGCCT
Gp-9 B
Gp-9 B
AAGGT
Gp-9 B
Gp-9 B
CCAGT
Gp-9 b
Gp-9 b
TAAAT
Gp-9 b
Gp-9 b
GGAAT
Gp-9 b
Gp-9 b
38 Gp-9 B
males
38 Gp-9 b
males
RAD sequencing of haploid ♂ for SNP
discovery & genotyping
45. Identify polymorphism
individual x locus
genotype table
RADseq: sequencing the same 0.01% of the
genome in many individuals
A B C D E F
L1 A C A A C C
L2 G G T - T G
L3 - A G A - G
L4 C - - G G C
L5 T T C T C -
L6 G A A - - G
2419loci
38 B & 38 b
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+
Amount of variance explained per principal component
%VarianceExplained
051015202530
12.7%
6.1% 5.4% 4.8% 4.7% 3.9% 3.5% 3.2% 3.1% 2.9% 2.8% 2.6% 2.4% 2.3% 2.2% 2.0% 1.9% 1.7% 1.6%
30.2%
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20+
Amount of variance explained per principal component
%VarianceExplained
051015202530
PCA: Principal Component Analysis
49. • Is this gene the single überregulator?
maybe 1/14th of the genome?
•Only 14 allozyme markers
Social form completely associated to Gp-9 locus
BB BB Bb
Single queen form Multiple queen form
(>15% )(< 5% )
x xx
✖
✔
Locus!
0.3!
0.4!
0.5!
0.6!
0.7!
0.8!
0.9!
1.0!
Single queen!Multiple queen!
Est-6!Est-4!
G
3pdh-1!C
a-4!Pgm
-4!Ddh-1!Pro-5!
Pgm
-3!Acoh-5!acoh-1!A
cy-1!Pgm
-1!Aat-2!Gp-9!
50. Sex chromosomes
X Y
Gp-9 B
Gp-9 b
SB Sb
?
1.Why non-recombining?
“Social chromosomes”
= supergene
2.Are SB and Sb differentiated?
3.What are the differences?
51. Small portion (200,000bp) of social chromosome:
SB♂
Sb♂
• Genome of a Gp-9 B ♂
• Genome of a Gp-9 b ♂
➡SB vs Sb sequence comparison: small inversion
1. Why no recombination between SB & Sb?
Sequenced (de novo):
52. Gp-9 B
Gp-9 b
SB Sb
≥5 major rearrangements
1. Why no recombination between SB & Sb?
54. 2. Are SB and Sb differentiated?
• Yes
• Sb has (almost) no diversity (likeY)
• Differences are homogeneously distributed
(no evolutionary strata!)
Roddy Pracana et al in prep
55. 3. What are the differences
between SB and Sb?
56. X
♀
X X Y
♂
•Prediction:
SBSB SB Sb
Single queen colony Multiple queen colony
Differences between SB and Sb?
Sb is degenerating?
•genes?
Region contains 800 genes!
no strong differences
57. SB
Sb
• More, larger repetitive DNA in Sb compared to SB
• larger introns in Sb
• larger intergenic regions in Sb
• assembly worse (smaller scaffolds) in Sb
• increased dN/dS
[b] vs. [c]: p < 10-4
[a] vs. [c]: p < 10-7
Gp-9B male Gp-9b male
Region:
Genome assembly:
Normally recombining
regions from all 16
linkage groups
Normally recombining
regions from all 16
linkage groups
Sb region without
recombination
in Gp-9 Bb queens
SB region without
recombination
in Gp-9 Bb queens
Scaffoldlength(bp)
0
1,000,000
2,000,000
3,000,000
4,000,000
5,000,000
6,000,000
[a] [a], [b] [a] [c]
SB Sb
Sb is degenerating?
58. X
♀
X X Y
♂
≥5
rearrangements
SBSB SB Sb
Single queen colony Multiple queen colony
Only small differences:Young age + Purifying
selection because of ♂ haploidy
•Prediction:
Differences between SB and Sb?
•genes?
Region contains 800 genes!
no strong differences
Sb is degenerating?
59. Summary
Fire ant Solenopsis invicta queen number determined by 1990s Gp-9 marker:
•only BB workers ➔ single BB queen
•with Bb workers ➔ multiple Bb queens
Genome sequencing + RAD Genotyping >500 individuals
•Gp-9 marks ~4% of genome ➔ social chromosomes:
SB is like X; Sb is likeY
>5 Structural differences between SB and Sb ➔ no recombination
Ants are cool.
Differentiation:
Sb has (almost) no diversity (likeY)
Differences are homogeneously distributed (no strata)
60. Formica selysi
Purcell et al 2014
Convergent social chromosome architecture
J Meunier
Single queen form Multiple queen form
Alpine silver ant
Common ancestor with fire ant: 130 MYA
64. Research themes
• Biomedical approaches
• International population genomics surveys
• Monitoring via sequencing
• Major social transitions
» social chromosomes
» convergence
» eusociality, queen number, parasitism...
• Phenotypic plasticity
• Strengths of selection
• Candidate genes/pathway
Pollinator health
Genome evolution Social evolution
65. Pollinator health
• Canonical Pesticide approval process.
• Better: behaviour for everything
• Our plan 1: RNAseq
• Our plan II: Impact of pesticide exposure in the wild
• Predict: evidence of positive selection on pesticide resistance
alleles
Joe Colgan with Richard Gill & Andres Acre @ Imperial
66. Modern Bioinformatics for
Evolutionary Genomics
• Reproducibility
• Accuracy
• Sustainability
• Versioning
• Open source
• Agile & efficient
data handling
Our tools: https://wurmlab.github.io/tools
•Sequenceserver: BLAST made easy
•GeneValidator: Gene model quality visualization
•oSwitch: One-line switch to any operating-system (e.g. biolinux)
•BioNode: streaming scalable bioinformatics
•Afra: crowd-sourcing gene model curation to students
github in progress
•Flo: transferring gene predictions between genome versions
67. y.wurm@qmul.ac.uk
@yannick__
https://wurmlab.github.io
@ Queen Mary U London
Rodrigo Pracana
Anurag Priyam @yeban
Eckart Stolle
Bruno Vieira @bmpvieira
R Nichols & sbcsEvolve
R Christie & T King / ITSR Apocrita
Laurent Keller lab @ Lausanne
J Wang, D Shoemaker,O Riba-Grognuz,
M Nipitwattanaphon
Ioannis Xenarios @ SIB
DeWayne Shoemaker @ USDA
Thanks!