This document summarizes a study comparing gene family sizes across fungal genomes. It finds that changes in gene family copy numbers may be an important mechanism for adaptation. Using comparative genomics tools that model gene family evolution, the study identifies unexpectedly large expansions or contractions of specific gene families in lineages of interest, such as human pathogens. This may provide insights into the genetic basis of traits like pathogenesis. The analysis screens multiple fungal genomes, including pathogens like Coccidioides species, to find candidate gene families with lineage-specific changes in copy number that distinguish phenotypic groups.
Mobiles Lernen” - ein Überblick über Szenarien und Technologien (Folien Prof....e-teaching.org
Lernen spielt sich längst nicht nur im Hörsaal, Seminarraum oder Zuhause ab: Die hohe Verbreitung mobiler Endgeräte ermöglicht es zunehmend, auch an anderen Orten zu lernen. Dies bedeutet entweder, dass „Leerzeiten” unterwegs genutzt werden, um unabhängig von Ort und Zeit das eigene Wissen zu erweitern. Oder Wissen kann situiert „vor Ort” erworben werden, etwa an historischen Schauplätzen oder bei Exkursionen. Darüber hinaus ist auch noch die Nutzung mobiler Technologien im klassischen Hörsaal oder Seminarraum möglich (z.B. als Abstimmungstools).
Um bei all dieser Vielfalt einen Überblick zu bekommen, betrachtete die Auftaktveranstaltung ( http://bit.ly/1zyN9sP ) das Thema „Mobiles Lernen” aus zwei Perspektiven. Im Veranstaltungsteil zu diesen Slides ging es um zentrale pädagogische und didaktische Aspekte: Welches Lernverständnis und welche Lernziele sind beispielsweise mit den verschiedenen Einsatz- bzw. Lehrszenarien verbunden?
Unleashing the Power of the Millennial GenerationKari Wilson
The document discusses strategies for engaging millennial knowledge workers to maximize innovation. It finds that millennials will soon be the largest generation in the workforce due to their size and shared traits of being educated, innovative, and globally connected. However, their expectations of the workplace differ from previous generations in wanting career growth opportunities, frequent feedback and recognition, an emphasis on work-life balance, and a values-based culture where they feel part of something bigger. The document argues that employers must cultivate four dimensions - mentorship, values, community, and work-life integration - to better engage millennials and unleash their potential for greater innovation.
The document discusses fungal genomics resources including FungiDB and related projects. It provides information on:
1) FungiDB releasing genomes from 18 species including Aspergillus, Coccidioides, Fusarium, Neurospora, Candida, Saccharomyces, Cryptococcus, Puccinia and Rhizopus.
2) Future plans to include additional Cryptococcus genomes and the genomes of Tremella mesenterica and Neurospora crassa with RNA-seq data and GO annotations.
3) Strategies for querying fungal genomes and functional genomics data using FungiDB and related tools.
The document discusses the potential for using methane hydrate structures as an energy source by extracting methane gas from hydrate deposits in ocean floors and arctic tundra. Methane hydrate forms naturally when methane gas combines with water under high pressure and low temperatures. These methane hydrate deposits represent an enormous untapped energy source that could be harvested using engineered systems. The document outlines some design challenges for autonomous systems and vehicles that could sustainably extract methane from hydrate deposits to generate power on kilowatt scales for distributed sensor networks and unmanned vehicles. Oxygen could potentially be used to facilitate extracting the methane gas from the solid hydrate structures.
This document discusses biodiversity loss and protected areas. It notes that more tigers live in captivity than in the wild, and that species populations have declined by 30% globally. Temperate regions have seen a 29% increase in the Living Planet Index since 1970, while tropical regions have seen a 60% decline. It introduces protected areas as a way to achieve conservation and notes the World Database on Protected Areas as a resource to know where these areas are located. It emphasizes the importance of both protected areas and information about what is happening on the ground within them.
1. The document discusses lifelong learning and developing a lifelong learning tool belt. It provides numerous online resources and tools for learning including websites, conferences, and social media platforms.
2. Advice provided includes using QR codes, mobile devices, social bookmarking tools, blogs, online conferences, and developing a personal learning network to continue learning.
3. The importance of lifelong learning, being a lead learner, understanding technology's role, and collaborating with others are emphasized. Developing confidence and conviction as an educator is also discussed.
The document summarizes findings from a study of open access publishing outlets. It found around 8-10% of annual articles are published in fully or hybrid open access journals. The majority of journals and articles come from a small number of large publishers, most of which are in science, technology and medicine. Two thirds of journals and three quarters of articles are in these fields. Both large and small publishers have journals listed in impact metrics like the ISI and Scopus, showing open access publishing has similar quality indicators as non-open access.
Mobiles Lernen” - ein Überblick über Szenarien und Technologien (Folien Prof....e-teaching.org
Lernen spielt sich längst nicht nur im Hörsaal, Seminarraum oder Zuhause ab: Die hohe Verbreitung mobiler Endgeräte ermöglicht es zunehmend, auch an anderen Orten zu lernen. Dies bedeutet entweder, dass „Leerzeiten” unterwegs genutzt werden, um unabhängig von Ort und Zeit das eigene Wissen zu erweitern. Oder Wissen kann situiert „vor Ort” erworben werden, etwa an historischen Schauplätzen oder bei Exkursionen. Darüber hinaus ist auch noch die Nutzung mobiler Technologien im klassischen Hörsaal oder Seminarraum möglich (z.B. als Abstimmungstools).
Um bei all dieser Vielfalt einen Überblick zu bekommen, betrachtete die Auftaktveranstaltung ( http://bit.ly/1zyN9sP ) das Thema „Mobiles Lernen” aus zwei Perspektiven. Im Veranstaltungsteil zu diesen Slides ging es um zentrale pädagogische und didaktische Aspekte: Welches Lernverständnis und welche Lernziele sind beispielsweise mit den verschiedenen Einsatz- bzw. Lehrszenarien verbunden?
Unleashing the Power of the Millennial GenerationKari Wilson
The document discusses strategies for engaging millennial knowledge workers to maximize innovation. It finds that millennials will soon be the largest generation in the workforce due to their size and shared traits of being educated, innovative, and globally connected. However, their expectations of the workplace differ from previous generations in wanting career growth opportunities, frequent feedback and recognition, an emphasis on work-life balance, and a values-based culture where they feel part of something bigger. The document argues that employers must cultivate four dimensions - mentorship, values, community, and work-life integration - to better engage millennials and unleash their potential for greater innovation.
The document discusses fungal genomics resources including FungiDB and related projects. It provides information on:
1) FungiDB releasing genomes from 18 species including Aspergillus, Coccidioides, Fusarium, Neurospora, Candida, Saccharomyces, Cryptococcus, Puccinia and Rhizopus.
2) Future plans to include additional Cryptococcus genomes and the genomes of Tremella mesenterica and Neurospora crassa with RNA-seq data and GO annotations.
3) Strategies for querying fungal genomes and functional genomics data using FungiDB and related tools.
The document discusses the potential for using methane hydrate structures as an energy source by extracting methane gas from hydrate deposits in ocean floors and arctic tundra. Methane hydrate forms naturally when methane gas combines with water under high pressure and low temperatures. These methane hydrate deposits represent an enormous untapped energy source that could be harvested using engineered systems. The document outlines some design challenges for autonomous systems and vehicles that could sustainably extract methane from hydrate deposits to generate power on kilowatt scales for distributed sensor networks and unmanned vehicles. Oxygen could potentially be used to facilitate extracting the methane gas from the solid hydrate structures.
This document discusses biodiversity loss and protected areas. It notes that more tigers live in captivity than in the wild, and that species populations have declined by 30% globally. Temperate regions have seen a 29% increase in the Living Planet Index since 1970, while tropical regions have seen a 60% decline. It introduces protected areas as a way to achieve conservation and notes the World Database on Protected Areas as a resource to know where these areas are located. It emphasizes the importance of both protected areas and information about what is happening on the ground within them.
1. The document discusses lifelong learning and developing a lifelong learning tool belt. It provides numerous online resources and tools for learning including websites, conferences, and social media platforms.
2. Advice provided includes using QR codes, mobile devices, social bookmarking tools, blogs, online conferences, and developing a personal learning network to continue learning.
3. The importance of lifelong learning, being a lead learner, understanding technology's role, and collaborating with others are emphasized. Developing confidence and conviction as an educator is also discussed.
The document summarizes findings from a study of open access publishing outlets. It found around 8-10% of annual articles are published in fully or hybrid open access journals. The majority of journals and articles come from a small number of large publishers, most of which are in science, technology and medicine. Two thirds of journals and three quarters of articles are in these fields. Both large and small publishers have journals listed in impact metrics like the ISI and Scopus, showing open access publishing has similar quality indicators as non-open access.
Online fundraising has become increasingly important as the internet allows nonprofits to reach broader audiences at lower costs. Effective online fundraising strategies include making donations easy through multiple payment options, building personal connections to inspire recurring donations, and demonstrating impact to develop long-term donor relationships. Nonprofits should integrate online and offline fundraising to maximize results.
1. The document discusses various topics related to finance and funding including partnerships, investments, fundraising, and exits.
2. Key points include pitching to investors and informal backers, strategies for increasing chances of success, and preparing for eventual exit through acquisition or IPO.
3. Statistics are provided on typical exit values for startups of different sizes, with larger exits more common for those securing multiple rounds of funding from experienced investors.
The document provides tips for an Egyptian vacation, including suggestions to visit popular tourist sites along the Nile River, sleep in a room full of Egyptian artifacts, and interact with local vendors to learn about their culture and bargain for souvenirs. It also recommends experiencing a traditional Egyptian breakfast, avoiding harassment by telling others you prefer bottled water, and making a treacherous three-hour taxi ride downtown to reach the non-existent seat belt.
This document provides an overview of open access in medicine. It discusses two main forms of open access: gold OA which is publishing in an open access journal, and green OA which is self-archiving in an institutional repository or PubMed Central. It notes that PubMed Central provides open access to over 19 million citations and links to full-text articles. The document also discusses the NIH public access policy which requires researchers receiving NIH funds to submit final peer-reviewed manuscripts to PubMed Central. Overall, the summary provides a high-level introduction to open access models and policies in the medical literature.
Findes der millioner i velfærdsteknologi?Lakeside A/S
Oplæg afholdt i forbindelse med InnovationX arrangement maj 2011. Innovation X er en fælles platform for erhvervs- og innovationsaktører i Nordjylland. Formålet er at give små og mellemstore virksomheder, erhvervsledere og iværksættere et overblik over mulighederne for rådgivning, innovation og samarbejde.
Ariu - Workshop on Applications of Pattern Analysis 2010 - PosterPluribus One
This document summarizes an application of Hidden Markov Models (HMMs) to analyze HTTP payloads:
1. An HMM is used to associate a probability to each sequence of bytes in an HTTP payload and obtain an overall probability for the payload.
2. Real HTTP payload data collected from various sources on the internet is used to train the HMM.
3. The trained HMM can then be used to detect anomalies in new HTTP payloads by flagging payloads with significantly different probabilities as potential attacks or malware.
1. The document discusses a study analyzing the effectiveness of mindfulness meditation techniques in reducing stress levels and improving mental health outcomes.
2. The study found mindfulness meditation helped lower stress levels and improve mood in participants by reducing rumination and worry.
3. Mindfulness training was shown to decrease activity in the brain regions associated with rumination and increase activity in regions involved in attention and emotional regulation.
This document provides guidelines for the management of dementia. It discusses general management including activities of daily living, environment, caregivers, rehabilitation, and palliative care. It also covers management of cognitive impairment and behavioral/psychological symptoms, including both non-pharmacological and pharmacological approaches. Key topics include risk factors for dementia, types of dementia, diagnosing tools like the MMSE, and recommendations for treatment and care.
LUNAR PITS: SUBLUNAREAN VOIDS AND THE NATURE OF MARE EMPLACEMENTSérgio Sacani
The document discusses lunar pits observed by the Lunar Reconnaissance Orbiter Camera (LROC) team. Specifically:
1) The LROC has observed pits up to 65 meters in diameter and 80-88 meters deep that are thought to be collapsed lava tubes. Imaging these pits could help confirm the lava tube hypothesis.
2) The LROC will conduct meter-scale mapping of polar regions to locate safe landing sites for future robotic and human missions by identifying permanently shadowed and illuminated regions.
3) Repeated imaging of lunar regions during respective summers and winters will help characterize the illumination environment to determine optimal sampling and logistical strategies for each proposed landing site.
The document discusses presentations made by Quartz, President of Quartz Design and author of "Slide:ology", and Barr Neyfold, author of "Visual Explanations" and the very popular presentation "A Tale of Two Brains", on how slideware will dramatically change from the way it is used today. Recently, I had the chance to attend a one-day workshop offered by both of these revolutionaries, "Slide:ology" and "Visual Explanations", and I came away a changed man. You can read more about "Slide:ology" and Barr Neyfold's work at their websites.
A summary for learning the muscles of the hip including their attachments, innervation, etc., without having to have too many books open. Resources: "Grey's anatomy", "Taschenatlas Anatomie", "McMinn's Clinical Atlas of Human Anatomy" and Wikipedia. Awaiting further proof-reading!
Risk management: Social media usage in enterprisesdaenu
The usage of social media platforms is increasing rapidly and now also more and more enterprises start to have their own presence on different social media platforms. Even if an enterprise is present on a social media platform, it isn‘t given that the own employees are allowed to access these platforms mostly due to the existing risks. One of the biggest risks is the loss of the reputation of a enterprise that only with a continuos monitoring of the social media platforms can be reduced. With a clear social media governance including a clear strategy and a risk analysis an enterprise can train their employees in a awareness program.
8 Steps to Maximize Your Financial Aid PackageBrian Davidson
The document discusses financial aid options for a student-athlete. It provides 3 steps:
1) Calculate how much money the student will need for school tuition and expect to receive from the university for their academic/athletic scholarship.
2) Consider if the student's family income makes them eligible for other need-based financial aid from the university.
3) Explore hidden money that some colleges have available for students they need for their athletic teams.
For the small business and individual business person:
This is an English explanation of the following questions:
1) Why use social media?
2) How will it benefit my business?
3) What's the point?
And yet, as a small business or individual business person.....
1) Are you focused on your business & too busy to learn about Social Media?
2) Do you have time to learn about Social Media technology?
3) Are you confused by all the different Social Media Tools?
4) Do you understand why Social Media is so important?
5) Have you figured out how to use Social Media to market your business?
SocialNet Productions can help:
Let us:
1) Set up your Social Media Network
2) Create your marketing plan
3) Guide you into the world of Social Media
The document provides an overview of an investment manager's macro strategy and portfolio management process. It discusses:
1. The manager focuses on long-term profit opportunities brought about by an ever-increasing energy and commodity demand fueled by increasing population and accelerated industrialization.
2. They manage portfolios through dedicated sub-strategies including clean energy, water, agriculture, traditional energy, carbon and emissions trading, commodities and natural resources, and other hedge sectors.
3. The current timing is ideal for an experienced and diligent group of investors like themselves, as the cash flow rich integrated energy companies, sovereign wealth funds, utilities and technology companies around the world are spending vast amounts of money on these sectors.
The study measured heart rate responses during synchronized swimming routines to analyze breath holding and body position changes, finding that heart rate increased during breath holding periods and inverted positions compared to other parts of the routine. Data was collected from elite synchronized swimmers during competition using wearable heart rate monitors. Results provide insight into physiological demands of synchronized swimming routines.
Presentacion utilizada en la sesión del Monday Reading Club del mes de Octubre en la que hablamos de "Como aprovechar los movimientos sociales en Internet" siendo el libro de apoyo "El Mundo GroundSwell"
This portfolio summarizes Peeranut Wongsiri's architectural projects from 2010 to 2015 while studying at Chulalongkorn University in Thailand. It includes preliminary designs for a hotel, apartment buildings, restaurants, and retail stores showcasing her skills in architectural and interior design. The portfolio demonstrates her ability to thoughtfully consider site context, program needs, and aesthetic qualities in her designs.
Effects of physical exercise in cerebrovascular mechanisms of adaptation to a...Enrike G. Argandoña
Microvascular environment plays a fundamental role in the adaptive response to increases in activity, involving an increase in energy demand. To puntual increases in demand, the response is effected by changes in local flow, but if demand remains high, angiogenic process is triggered through the formation of new capillaries from preexisting vessels. The trigger factor of angiogenesis is local neuronal hypoxia as result of increased activity, mediated by angioglioneurins whose main exponent is VEGF. There are situations in which hypoxia is not from an increased activity, but a decrease in available oxygen, as occurs in the altitude exposure.
Our goal is to study the changes underlying microvascular acute adaptation to moderate altitude and the possible effects of physical exercise.
Wistar rats bred to 400 m (P47) and transported to a height of 2800m on a journey of 35 minutes. We used the following cohorts of 7 rats each: a group was housed indoors in standard laboratory conditions, another group had free access to
an exercise wheel. As controls, we used animals born at 400m. After 48 h, animals were sacrificed and after neuropathological examination by conventional histology, capillary density was quantified using computer assisted stereology on thick sections processed using Butyryl Cholinesterase Histochemistry (Argandoña, Brain Res, 1996).
Three cortical areas were quantified, motor, somatosensory and visual cortices.
Rats with free access to exercise wheel showed higher vascular density in response to hypoxia, while the rest showed similar values. Differences were significant in all three areas, being highest in the motor cortex.
The acute adaptation to moderate altitude is an increasingly relevant issue given the increase in displacements at moderate or high altitudes, with serious consequences such as Acute Mountain Sickness, which in its most severe degree leads to
Brain edema. Our results show that exercise can play a protective role through adaptive angiogenesis.
The document discusses dental complications from head and neck radiotherapy, including changes to taste, xerostomia, salivary gland damage, oral infections like candidiasis, rapid dental decay, osteoradionecrosis, and recommendations for preventive dental care before, during, and after radiation therapy to minimize complications and promote oral health. A multidisciplinary approach between dentists and radiation oncologists is emphasized to plan treatment, monitor oral health issues, and provide ongoing dental care and patient education.
This document provides an overview of the FungiDB database, which contains genomic and functional genomic data for 18 fungal species. Key points include:
- FungiDB takes advantage of infrastructure developed for the Eukaryotic Pathogen Genome Database.
- 18 fungal genomes from 3 fungal phyla are included in the current release.
- The database allows browsing of gene pages, genome browsers, and querying to enable data mining across fungal species.
This document summarizes the FungiDB database, which provides comparative genomics resources for fungal genomes. It includes 18 fungal genomes from Ascomycota, Basidiomycota and Zygomycota phyla. Users can perform gene and genome queries, view gene pages, analyze orthology and synteny between species. The database is powered by infrastructure from other pathogen databases and aims to facilitate research in fungal genomics, evolution and functional annotation. Feedback is sought from users to improve the resource.
Online fundraising has become increasingly important as the internet allows nonprofits to reach broader audiences at lower costs. Effective online fundraising strategies include making donations easy through multiple payment options, building personal connections to inspire recurring donations, and demonstrating impact to develop long-term donor relationships. Nonprofits should integrate online and offline fundraising to maximize results.
1. The document discusses various topics related to finance and funding including partnerships, investments, fundraising, and exits.
2. Key points include pitching to investors and informal backers, strategies for increasing chances of success, and preparing for eventual exit through acquisition or IPO.
3. Statistics are provided on typical exit values for startups of different sizes, with larger exits more common for those securing multiple rounds of funding from experienced investors.
The document provides tips for an Egyptian vacation, including suggestions to visit popular tourist sites along the Nile River, sleep in a room full of Egyptian artifacts, and interact with local vendors to learn about their culture and bargain for souvenirs. It also recommends experiencing a traditional Egyptian breakfast, avoiding harassment by telling others you prefer bottled water, and making a treacherous three-hour taxi ride downtown to reach the non-existent seat belt.
This document provides an overview of open access in medicine. It discusses two main forms of open access: gold OA which is publishing in an open access journal, and green OA which is self-archiving in an institutional repository or PubMed Central. It notes that PubMed Central provides open access to over 19 million citations and links to full-text articles. The document also discusses the NIH public access policy which requires researchers receiving NIH funds to submit final peer-reviewed manuscripts to PubMed Central. Overall, the summary provides a high-level introduction to open access models and policies in the medical literature.
Findes der millioner i velfærdsteknologi?Lakeside A/S
Oplæg afholdt i forbindelse med InnovationX arrangement maj 2011. Innovation X er en fælles platform for erhvervs- og innovationsaktører i Nordjylland. Formålet er at give små og mellemstore virksomheder, erhvervsledere og iværksættere et overblik over mulighederne for rådgivning, innovation og samarbejde.
Ariu - Workshop on Applications of Pattern Analysis 2010 - PosterPluribus One
This document summarizes an application of Hidden Markov Models (HMMs) to analyze HTTP payloads:
1. An HMM is used to associate a probability to each sequence of bytes in an HTTP payload and obtain an overall probability for the payload.
2. Real HTTP payload data collected from various sources on the internet is used to train the HMM.
3. The trained HMM can then be used to detect anomalies in new HTTP payloads by flagging payloads with significantly different probabilities as potential attacks or malware.
1. The document discusses a study analyzing the effectiveness of mindfulness meditation techniques in reducing stress levels and improving mental health outcomes.
2. The study found mindfulness meditation helped lower stress levels and improve mood in participants by reducing rumination and worry.
3. Mindfulness training was shown to decrease activity in the brain regions associated with rumination and increase activity in regions involved in attention and emotional regulation.
This document provides guidelines for the management of dementia. It discusses general management including activities of daily living, environment, caregivers, rehabilitation, and palliative care. It also covers management of cognitive impairment and behavioral/psychological symptoms, including both non-pharmacological and pharmacological approaches. Key topics include risk factors for dementia, types of dementia, diagnosing tools like the MMSE, and recommendations for treatment and care.
LUNAR PITS: SUBLUNAREAN VOIDS AND THE NATURE OF MARE EMPLACEMENTSérgio Sacani
The document discusses lunar pits observed by the Lunar Reconnaissance Orbiter Camera (LROC) team. Specifically:
1) The LROC has observed pits up to 65 meters in diameter and 80-88 meters deep that are thought to be collapsed lava tubes. Imaging these pits could help confirm the lava tube hypothesis.
2) The LROC will conduct meter-scale mapping of polar regions to locate safe landing sites for future robotic and human missions by identifying permanently shadowed and illuminated regions.
3) Repeated imaging of lunar regions during respective summers and winters will help characterize the illumination environment to determine optimal sampling and logistical strategies for each proposed landing site.
The document discusses presentations made by Quartz, President of Quartz Design and author of "Slide:ology", and Barr Neyfold, author of "Visual Explanations" and the very popular presentation "A Tale of Two Brains", on how slideware will dramatically change from the way it is used today. Recently, I had the chance to attend a one-day workshop offered by both of these revolutionaries, "Slide:ology" and "Visual Explanations", and I came away a changed man. You can read more about "Slide:ology" and Barr Neyfold's work at their websites.
A summary for learning the muscles of the hip including their attachments, innervation, etc., without having to have too many books open. Resources: "Grey's anatomy", "Taschenatlas Anatomie", "McMinn's Clinical Atlas of Human Anatomy" and Wikipedia. Awaiting further proof-reading!
Risk management: Social media usage in enterprisesdaenu
The usage of social media platforms is increasing rapidly and now also more and more enterprises start to have their own presence on different social media platforms. Even if an enterprise is present on a social media platform, it isn‘t given that the own employees are allowed to access these platforms mostly due to the existing risks. One of the biggest risks is the loss of the reputation of a enterprise that only with a continuos monitoring of the social media platforms can be reduced. With a clear social media governance including a clear strategy and a risk analysis an enterprise can train their employees in a awareness program.
8 Steps to Maximize Your Financial Aid PackageBrian Davidson
The document discusses financial aid options for a student-athlete. It provides 3 steps:
1) Calculate how much money the student will need for school tuition and expect to receive from the university for their academic/athletic scholarship.
2) Consider if the student's family income makes them eligible for other need-based financial aid from the university.
3) Explore hidden money that some colleges have available for students they need for their athletic teams.
For the small business and individual business person:
This is an English explanation of the following questions:
1) Why use social media?
2) How will it benefit my business?
3) What's the point?
And yet, as a small business or individual business person.....
1) Are you focused on your business & too busy to learn about Social Media?
2) Do you have time to learn about Social Media technology?
3) Are you confused by all the different Social Media Tools?
4) Do you understand why Social Media is so important?
5) Have you figured out how to use Social Media to market your business?
SocialNet Productions can help:
Let us:
1) Set up your Social Media Network
2) Create your marketing plan
3) Guide you into the world of Social Media
The document provides an overview of an investment manager's macro strategy and portfolio management process. It discusses:
1. The manager focuses on long-term profit opportunities brought about by an ever-increasing energy and commodity demand fueled by increasing population and accelerated industrialization.
2. They manage portfolios through dedicated sub-strategies including clean energy, water, agriculture, traditional energy, carbon and emissions trading, commodities and natural resources, and other hedge sectors.
3. The current timing is ideal for an experienced and diligent group of investors like themselves, as the cash flow rich integrated energy companies, sovereign wealth funds, utilities and technology companies around the world are spending vast amounts of money on these sectors.
The study measured heart rate responses during synchronized swimming routines to analyze breath holding and body position changes, finding that heart rate increased during breath holding periods and inverted positions compared to other parts of the routine. Data was collected from elite synchronized swimmers during competition using wearable heart rate monitors. Results provide insight into physiological demands of synchronized swimming routines.
Presentacion utilizada en la sesión del Monday Reading Club del mes de Octubre en la que hablamos de "Como aprovechar los movimientos sociales en Internet" siendo el libro de apoyo "El Mundo GroundSwell"
This portfolio summarizes Peeranut Wongsiri's architectural projects from 2010 to 2015 while studying at Chulalongkorn University in Thailand. It includes preliminary designs for a hotel, apartment buildings, restaurants, and retail stores showcasing her skills in architectural and interior design. The portfolio demonstrates her ability to thoughtfully consider site context, program needs, and aesthetic qualities in her designs.
Effects of physical exercise in cerebrovascular mechanisms of adaptation to a...Enrike G. Argandoña
Microvascular environment plays a fundamental role in the adaptive response to increases in activity, involving an increase in energy demand. To puntual increases in demand, the response is effected by changes in local flow, but if demand remains high, angiogenic process is triggered through the formation of new capillaries from preexisting vessels. The trigger factor of angiogenesis is local neuronal hypoxia as result of increased activity, mediated by angioglioneurins whose main exponent is VEGF. There are situations in which hypoxia is not from an increased activity, but a decrease in available oxygen, as occurs in the altitude exposure.
Our goal is to study the changes underlying microvascular acute adaptation to moderate altitude and the possible effects of physical exercise.
Wistar rats bred to 400 m (P47) and transported to a height of 2800m on a journey of 35 minutes. We used the following cohorts of 7 rats each: a group was housed indoors in standard laboratory conditions, another group had free access to
an exercise wheel. As controls, we used animals born at 400m. After 48 h, animals were sacrificed and after neuropathological examination by conventional histology, capillary density was quantified using computer assisted stereology on thick sections processed using Butyryl Cholinesterase Histochemistry (Argandoña, Brain Res, 1996).
Three cortical areas were quantified, motor, somatosensory and visual cortices.
Rats with free access to exercise wheel showed higher vascular density in response to hypoxia, while the rest showed similar values. Differences were significant in all three areas, being highest in the motor cortex.
The acute adaptation to moderate altitude is an increasingly relevant issue given the increase in displacements at moderate or high altitudes, with serious consequences such as Acute Mountain Sickness, which in its most severe degree leads to
Brain edema. Our results show that exercise can play a protective role through adaptive angiogenesis.
The document discusses dental complications from head and neck radiotherapy, including changes to taste, xerostomia, salivary gland damage, oral infections like candidiasis, rapid dental decay, osteoradionecrosis, and recommendations for preventive dental care before, during, and after radiation therapy to minimize complications and promote oral health. A multidisciplinary approach between dentists and radiation oncologists is emphasized to plan treatment, monitor oral health issues, and provide ongoing dental care and patient education.
This document provides an overview of the FungiDB database, which contains genomic and functional genomic data for 18 fungal species. Key points include:
- FungiDB takes advantage of infrastructure developed for the Eukaryotic Pathogen Genome Database.
- 18 fungal genomes from 3 fungal phyla are included in the current release.
- The database allows browsing of gene pages, genome browsers, and querying to enable data mining across fungal species.
This document summarizes the FungiDB database, which provides comparative genomics resources for fungal genomes. It includes 18 fungal genomes from Ascomycota, Basidiomycota and Zygomycota phyla. Users can perform gene and genome queries, view gene pages, analyze orthology and synteny between species. The database is powered by infrastructure from other pathogen databases and aims to facilitate research in fungal genomics, evolution and functional annotation. Feedback is sought from users to improve the resource.
This document discusses a talk given by Jason Stajich on comparative and evolutionary genomics of filamentous fungi using next generation sequencing. Stajich is from the Plant Pathology and Microbiology department at the University of California, Riverside. He discussed how next generation sequencing has allowed for comparative genomics studies of many fungal species, which has provided insights into fungal diversity, ecology, and evolution. He highlighted several examples of fungal genomes that have been sequenced and analyzed to learn about relationships between different fungal taxa.
This document discusses open questions in bioinformatics and computational biology from an evolutionary and molecular biology perspective. It outlines where biological data is coming from, current approaches to analyzing large datasets, and problems that remain around efficiently searching, interfacing with, and finding patterns in huge amounts of sequencing data. Future directions include more biologically focused research using these computational tools.
Evolution and exploration of the transcriptional landscape in two filamentous...Jason Stajich
The document summarizes comparative genomic analyses of the human pathogenic fungi Coccidioides immitis and Coccidioides posadasii. Genomes from 13 strains of the two Coccidioides species were sequenced and analyzed to reconstruct their evolutionary history and population structure. Phylogenetic analysis of the strains supported the distinction of the two species and identified potential introgression between species. Comparative genomics was also used to search for genetic differences underlying variations in virulence and distribution between strains that may provide insight into the molecular basis of Coccidioides pathogenesis.
Connecting ultrastructure to molecules: Studying evolution of molecular comp...Jason Stajich
- Comparative genomics can help inventory genes shared or missing between fungal species and trace evolutionary transitions from aquatic to terrestrial lifestyles.
- Studying genome sequences from early diverging fungi can illuminate three major evolutionary transitions in fungi - cellular division, cell wall composition, and septa formation.
- Transitions include changing from centrioles to spindle pole bodies for cell division and gaining genes involved in making β(1,3)-glucan while potentially losing cellulose in cell walls.
Comparative genomics of the fungal kingdomJason Stajich
This document discusses comparative genomics of fungi using available fungal genome sequences. It describes how comparative genomics can be used to identify shared, unique, gained and lost genes between species to study evolution. More than 65 fungal genomes are available with more in development, allowing for the study of genome organization, evolution of multicellularity, cell wall evolution and ancestral gene content. Gene prediction and annotation methods are discussed to generate consensus gene models from multiple tools.
Comparative genomics of fung: studying adaptation through gene family evolutionJason Stajich
Comparative genomics of fungi can provide insights into how fungi adapt to different environments through gene family evolution. Analysis of gene family sizes in fungi found that they often follow a power law distribution, with some gene families having many copies while others are singletons. Expansion of gene families involved in functions like secondary metabolism and pathogenesis have allowed adaptation to new niches. Case studies on Onygenales and chytrid fungi identified family expansions of genes related to virulence as well as contractions of families for plant cell wall degradation, indicating evolutionary shifts in lifestyle. Local duplications were found to be a major driver of family expansions in some species. Comparisons of gene content beyond just orthologs can provide clues about phenotypic
Evolution of gene family size change in fungiJason Stajich
The document discusses gene family size changes in fungi. It notes that gene duplications are important for new gene and function evolution. It analyzed gene family sizes across 37 fungal genomes using computational methods to identify lineage-specific expansions. The analysis used probabilistic models to evaluate gene family size changes along phylogenetic branches and identify families with unusually large size increases or decreases in specific lineages.
Comparative Genomics with GMOD and BioPerlJason Stajich
BioPerl is an open source toolkit for bioinformatics data manipulation written in Perl. It contains modules for reading and writing sequence data in common formats, manipulating sequences, parsing BLAST reports and multiple sequence alignments. BioPerl objects represent sequences, features, annotations and search results in a flexible and extensible way. The toolkit is widely used for tasks like sequence analysis, parsing bioinformatics software output, and accessing biological databases.
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A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
বাংলাদেশের অর্থনৈতিক সমীক্ষা ২০২৪ [Bangladesh Economic Review 2024 Bangla.pdf] কম্পিউটার , ট্যাব ও স্মার্ট ফোন ভার্সন সহ সম্পূর্ণ বাংলা ই-বুক বা pdf বই " সুচিপত্র ...বুকমার্ক মেনু 🔖 ও হাইপার লিংক মেনু 📝👆 যুক্ত ..
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তাই একজন নাগরিক হিসাবে এই তথ্য গুলো আপনার জানা প্রয়োজন ...।
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How to Manage Your Lost Opportunities in Odoo 17 CRMCeline George
Odoo 17 CRM allows us to track why we lose sales opportunities with "Lost Reasons." This helps analyze our sales process and identify areas for improvement. Here's how to configure lost reasons in Odoo 17 CRM
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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.
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1. Fungal phylogenomics: Getting lost in the moldy forest
Jason E Stajich
Dept of Plant Pathology & Microbiology
University of California, Riverside
http://lab.stajich.org
http://fungalgenomes.org/blog
http://fungiDB.org
twitter{stajichlab,hyphaltip,fungalgenomes,fungidb}
2. Fungi have diverse forms, ecology, and associations
Cryptococcus neoformans X. Lin Coprinopsis cinerea Ellison & Stajich Aspergillus niger. N Read Glomus sp. Univ Sydney Rozella allomycis. James et al
Puccinia graminis J. F. Hennen Batrachochytrium dendrobatidis
Laccaria bicolor Martin et al. Neurospora crassa. Hickey & Reed Phycomyces blakesleansus T. Ootaki
J. Longcore
Ustilago maydis Kai Hirdes Amanita phalloides. M Wood Xanthoria elegans. Botany POtD Rhizopus stolonifera. Blastocadiela simplex Stajich & Taylor
3. Fungi are an old group of organisms
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4. Awash in Fungal Genomes
• Mid-2011: Genomes from 150+ species sequenced and ~400 more in progress/pipeline
• Several multi-strain resequencing projects (Neurospora - Ellison PNAS 2011),
Saccharomyces (Liti Nature 2009), Coccidoides (Neafsey Genome Res 2010) and many in
progress/proposed.
• Many of sequenced genomes were focused around plant, animal pathogens, and some
specific evolutionary questions.
• Now are starting to fill out the tree more to capture the diversity of kingdom and also for
studies of molecular evolution among many related species.
• Also efforts targeting specific questions - pathogens and their relatives; wood rotting
fungi; flagellated and non-flagellated forms; extremophiles; comparison of growth forms
(e.g. yeast forms from phylogenetically very different species)
5. Genome sizes of fungi are 8Mb-100Mb = easy(ish) to
sequence Melampsora, Blumeria,
Puccinia
Genome size of fungi
(many Transposable
100
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80
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Mushrooms Francis Martin
Flickr:/fmartin1954/2338045504/
http://en.wikipedia.org/wiki/File:Barleypowderymildew.jpg
40
Ashbya, Malassezia, Candida
other yeasts
20
http://www.biologie.uni-osnabrueck.de/Genetik/index.php?menuid=12
6. Need to cover more of the phylogenetic diversity: 1000
Fungal genomes project
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Blue = completed or in progress, Red= proposed for Tier One sampling,
Green = remaining unsampled families Numbers or Percent of Families in each clade and their current or proposed genome sampling
7. Tools to access this data
• Genome databases at sequencing centers and NCBI
• Comprehensive and integrated systems are not as well developed in Fungi, but some
examples of excellent tools highlighted at http://tools.fungalgenomes.org/
• Ensembl Fungi, MicrobesOnline, JGI’s Mycocosm, Comparative Fungal Genomics, and
some targeted to specific clades e.g. Saccharomyces (SGD), Aspergillus (AspGD),
Candida (CGD)
• We have launched FungiDB - http://fungidb.org to support integrating functional
genomics data for data mining as well as standard ‘Gene’ pages for genes.
8. Searching with FungiDB:
A strategy for drug targets
C.neoformans genes with
- no hits in other eukaryotes
(excepting fungi), bacteria
- has S.cerevisiae orthologs
that have EC terms
OR orthologs in other fungi
with GO metabolic terms
associated
9. Searching with FungiDB:
A strategy for reannotation
2885 C.neoformans genes with desc “"conserved hypothetical
protein” but 1327 can be assigned name from ortholog in any
fungus with EC #, GO terms, or Pfam domains
10. Gene page and genome browser
Synteny Views
Data mining interface
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11. Using comparative genomics towards understand
pathogen evolution
• How do traits like pathogenecity evolve?
• Can comparative genomics indicate meaningful differences that can lead to
understanding the basis for pathogenesis?
• Contrasting genomes of pathogens with non-pathogens can suggest recent genomic
changes that might be testable in the lab
• Gene duplication is thought to be important source for evolutionary innovation - What
role might gene family size change play in adaptation?
12. Models for comparing gene family size changes
• A model for gene family size change that incorporates the birth-death process of gene
families which follow a power law distribution (Hahn et al, Genome Res 2005)
• Implemented in a program called CAFE to find unexpectedly large lineage or clade-
specific changes in gene family sizes (Hahn Lab @Indiana Univ) (De Bie et al,
Bioinformatics 2006)
• Can screen genome family sizes across multiple species to find expectedly large
changes (based on counts) which can be verified using gene tree-species tree
reconciliation approaches like Notung (Chen, Durand, Farach-Colton, J Comp Bio 2000)
13. Short Life
Coccidioides Granuloma
• Fungal pathogen Doctorfungus.com
Spherule
M. McGinnis
genomics: Gene families Endospores Long Life
and appetite differences
14. Human pathogen Coccidioides
• Coccidioides (Valley fever) - 2 species C. immitis and C. posadasii
• Is a primary human pathogen - infects healthy people
(most human pathogenic fungi are opportunistic)
• Endemic in US Southwest, Mexico
• Requires laboratory BSL3 and is a Select Agent
• Genomes of 2 species (Sharpton et al Genome Res 2009) and then 18 strains
(Neafsey et al Genome Res 2010)
• Comparative analyses of Coccidoides spp
16. Coccidioides ecology
Soil?
Short Life
Granuloma
D octorfungus. com
M. McGinnis
Spherule
Endospores Long Life
pocket mice?
17. Two species of Coccidioides are allopatric
C.immitis
C.posadasii
EVOLUTION
Fisher et al, 2000
18. Studying the evolution of a pathogen
• Comparing sequences from two Coccidioides species, closely
related outgroup, and more distant ougroups species:
• Evidence for recent positive selection
• What gene family differences can be identified that distinguish
phenotypic groups (mammalian pathogens from non-
pathogens)
• Evidence for recent introgression which contains candidate
genes for pathogenesis
19. Gene family changes
• Another mechanism for adaptation may be changes in copy
number of a gene family
• Gene duplication is a source of novelty allowing for changes
in the function of one copy if the other maintains original
function
• Expansions of copy number may also be an easy way to get
more protein for a particular process
• How important is copy number change in adaptation?
24. Keratinases in Onygenales
SignalP
Subtilisin_N
• Onygenales are Keratinophilic
• Domains: Peptidase S8, Subtilisin domains
• Large expansion of putative keratinases in Onygenales
27. Population genomics
• Revealed no loci with evidence for
balancing selection - so little
evidence for long standing host-
pathogen battle as in Plasmodium.
• Sliding window FST analysis
revealed some regions of reduced
divergence and followup revealed a
regions of recent intergression.
Directionality looks to be mostly
from Cp and into Ci.
• One gene implicated in
pathogenesis, MEP4, is found in
introgressed region
28. Towards identifying genes underlying adaptation
Sharpton et al. Genome Res 2009
Neafsey et al, Genome Res 2010
29. Towards identifying genes underlying adaptation
• Coccidioides is found in desert soil and associated with animals - perhaps has a long term
animal association without inducing response from the host.
Sharpton et al. Genome Res 2009
Neafsey et al, Genome Res 2010
30. Towards identifying genes underlying adaptation
• Coccidioides is found in desert soil and associated with animals - perhaps has a long term
animal association without inducing response from the host.
• Loss of genes involved in plant product metabolism suggests nutritional shift in Onygenales
from relatives in Eurotiales
Sharpton et al. Genome Res 2009
Neafsey et al, Genome Res 2010
31. Towards identifying genes underlying adaptation
• Coccidioides is found in desert soil and associated with animals - perhaps has a long term
animal association without inducing response from the host.
• Loss of genes involved in plant product metabolism suggests nutritional shift in Onygenales
from relatives in Eurotiales
• Expansion of only a few gene families, seem to be involved in metabolism - none are
Coccidioides specific though.
Sharpton et al. Genome Res 2009
Neafsey et al, Genome Res 2010
32. Towards identifying genes underlying adaptation
• Coccidioides is found in desert soil and associated with animals - perhaps has a long term
animal association without inducing response from the host.
• Loss of genes involved in plant product metabolism suggests nutritional shift in Onygenales
from relatives in Eurotiales
• Expansion of only a few gene families, seem to be involved in metabolism - none are
Coccidioides specific though.
• From population genetics analysis - failed to find regions under balancing selection suggesting
there is not a long-term arms race between host and pathogen.
Sharpton et al. Genome Res 2009
Neafsey et al, Genome Res 2010
33. Towards identifying genes underlying adaptation
• Coccidioides is found in desert soil and associated with animals - perhaps has a long term
animal association without inducing response from the host.
• Loss of genes involved in plant product metabolism suggests nutritional shift in Onygenales
from relatives in Eurotiales
• Expansion of only a few gene families, seem to be involved in metabolism - none are
Coccidioides specific though.
• From population genetics analysis - failed to find regions under balancing selection suggesting
there is not a long-term arms race between host and pathogen.
• Evidence for introgression between the species and perhaps imported novel alleles that are
important for adaptation in both species to their animal hosts.
Sharpton et al. Genome Res 2009
Neafsey et al, Genome Res 2010
34. Batrachochytrium dendrobatidis (Bd)- a major cause of
amphibian decline
Bd is a Chytrid
http://cisr.ucr.edu/chytrid_fungus.html
fungus
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35. Bd genome sequence projects
• 2 strains sequenced at JGI and Broad; allow whole genome comparison between strains
• Found that genome is diploid, but with large regions with loss of heterozygocity (LOH)
• Identified gene family changes that might suggest mechanisms of pathogenecity
• Greater understanding of what the early fungus was like
• With collaborators we are sequencing 20 more strains for population genomics to better
understand population dynamics, trace origin of diversity, and understand the LOH as
independent or shared events.
36. Bd grows intercellularly
Formally described by Joyce Longcore (U Maine) (Mycologia 1999)
Rick Speare, Lee Berger, Alax Haytt
James Cook University, Townsville, Australia
http://www.jcu.edu.au/school/phtm/PHTM/frogs/chpr1/fc13.htm
37. Phylogenomic profiling
• For each gene in the the target (Bd) genome, look to see which have homologs in other
fungi, animals, plants
• Classify genes by its profile as to when it must have arisen based on identified homologs
• Also compare well-studied organisms (S. cerevisiae, N. crassa) to see which genes were
missing
• For Bd/Chytrids several trends appeared
• Missing: some cell wall genes, spindle-pole body
• Present in Bd but not other non-chytrid fungi: Flagella, some signaling pathways,
effector like proteins
• Some expansions of gene families
38. Fungal cell wall evolution- a view from earliest branches
Ergosterol Yeast Cell Wall
What is the fungal cell wall
made of? Sugar polymers
Some fungi also have
Selitrennikoff CP, AEM 2001 α (1,3) glucan
42. B. dendrobatidis cell wall biochemical analysis
Cellulose
β (1,3)- β(1,6)- α(1,3)-
β(1,4)- Chitin
glucan glucan glucan
glucan
X X X ✓ ✓
A putative cellulose synthase gene can be found in genome of Bd
but also found in N. crassa and other Fungi with JP Latgé, M. Fisher
43. B. dendrobatidis cell wall biochemical analysis
Cellulose
β (1,3)- β(1,6)- α(1,3)-
β(1,4)- Chitin
glucan glucan glucan
glucan
X X X ✓ ✓
A putative cellulose synthase gene can be found in genome of Bd
but also found in N. crassa and other Fungi with JP Latgé, M. Fisher
100X higher MIC for Caspofungin than C. albicans with N.A.R Gow & M. Fisher
44. Expansion of CBM18 domain - Chitin binding gene family
0 100 200 300 800 900 1000
400 500 600 700
Length - aa
BD_03764 C C C DE 471-aa
TL
BD_05538 O E D DE DL
*
746-aa
BD_05531 O D 439-aa
LL
** BD_07015 O E D DE 503-aa
BD_08806 O D DE 503-aa
* ** BD_05161 O D DE 444-aa Deactylase Like
BD_05540 O E D DE 478-aa
BD_05533 D DE 368-aa
BD_05536 D DE 321-aa
BD_06123 A TYR
*
635-aa
BD_06122 A TYR 673-aa Tyrosinase Like
BD_06121 A B B B A TYR 771-aa
* BD_00259 K K K K K H G 577-aa
Lectin Like 1033-aa
BD_01761 F M I X L J J J J H G
* BD_00264 F N M H H G 621-aa
** BD_00271 F N M H H G 577-aa
* * BD_00287 F N M M H H G 636-aa
BD_00289 N I I 334-aa
Abramyan & Stajich, submitted
45. BD_06121 - A
TL .60 A BD_06121 - A
DL * BD_06123 - A
BD_06122 - A
LL * B BD_06121 - B
** * BD_06121 - B
BD_06121 - B
* = 1.0 * C BD_03764 - C
* BD_03764 - C
** ≥ .90 BD_03764 - C
BD_05538 - D
BD_08806 - D
.85 * BD_05540 - D
BD_07015 - D
* D ** BD_05161 - D
* BD_05536 - D
BD_05531 - D
BD_05533 - D
* E BD_05538 - E
* BD_05540 - E
BD_07015 - E
BD_00271 - F
F
* BD_00264 - F
* BD_00287 - F
BD_01761 - F
X
Domain tree shows **
G ** *
BD_01761 - X
BD_00264 - G
BD_00287 - G
BD_00271 - G
** BD_00259 - G
clade-specific grouping ** *
BD_01761 - G
BD_00271 - H
BD_00264 - H
BD_00287 - H
H BD_00287 - H
BD_00259 - H
* BD_00264 - H
BD_00271 - H
Domains evolved from mostly *I
BD_01761 - H
BD_01761 - I
BD_00289 - I
tandem duplications with some BD_00289 - I
BD_01761 - J
*J
BD_01761 - J
intergene duplications. BD_01761 - J
BD_01761 - J
*K *
BD_00259 - K
** BD_00259 - K
BD_00259 - K
** L * BD_00259 - K
BD_00259 - K
BD_01761 - L
BD_00287 - M
* BD_00271 - M
.81 M ** BD_00264 - M
BD_01761 - M
.86 BD_00287 - M
BD_00289 - N
** N BD_00264 - N
* BD_00271 - N
BD_00287 - N
BD_08806 - O
O * BD_05538 - O
* BD_05531 - O
BD_05161 - O
** * BD_07015 - O
BD_05540 - O
SP_07646
SP_07647
SP_03958
Abramyan & Stajich, submitted
46. CBM18 expansion
• Largest copy number of CBM18 in all fungi, and most number of domains (11) in a single
locus
• Evidence for positive selection among copies of the domains based on codon analyses
• CBM18 thought to bind chitin, could be involved in binding its own chitin to cloak the cells
from the host immunity
• Could also bind chitin-related molecules in animals attach more firmly to the animal cells
Abramyan & Stajich, submitted
47. Tyrosinase expansions in Bd and other fungi
Allomyces
Synthesis of
melanin, H.Whistler via Liu et al BMC Evol Biol 2006
pigments
and other
polyphenols
Hajime Muraguchi via
Stajich et al PNAS 2010
E.Medina
48. But are these changes important?
• Just observing big families in a genome is nice, but does it mean that changes are really
related to recent adaptation?
• The branches on some gene trees are short, indicating duplications are recent
• A better is to polarize the changes to the Bd branch by having a closer species than
50-100 Mya...
• So is there a species closer to Bd we can use? ...
49. Homolaphylictis polyrhiza JEL142 is a close(ish) relative
F. graminearum
1
N. crassa
1
B. cinerea
454 genome sequencing 1
U. reesii
C. immitis
MAKER genome annotation 1
1
1
T. rubrum
A. benhamiae
OrthoMCL gene families 1 1
M. canis
0.58 A. nidulans
1
P. tritici-repentis
C. cinerea
1
C. neoformans
1 *
U. maydis
1
P. graminis
1
P. blakesleeanus
A. macrogynus
S. punctatus
1 H. polyrhiza JEL142
1
B. dendrobatidis
! "! #
Joneson et al, Submitted
50. Contrasting some family sizes among the Chytrids
M36 S41 Tyrosinase CBM18
Allomyces 31 0 16 3
Spizellomyces 3 3 3 3
Hp 3-5 3 15 5
Bd 38 32 12 14-16
Fungalysin
Serine protease
Serine protease expansions in
Fungalysins - thought to be Coccidoides and relatives maybe
keratinases (break down keratin in related to breaking down on
an amphibian skin...) animal matter
Joneson et al, Submitted
51. H. polyrhiza won’t grow on frog skin; doesn’t cause
mortality in frogs
Hp- frog skin intact Bd- frog skin degraded
Joneson et al, Submitted
53. Bd summary
• Comparisons to close species can polarize some differences in lineage specific
expansions
• Findings of M36, S41 expansions seem to be recent to Bd and could be a functional
link to pathogenesis
• Expansion of Tyronsinase from counts is less compelling, but gene tree analyses
suggests recent expansions on Bd-Hp branch
• Lack of FKS1 in early Chytridiomycota lineages suggests a more recent origin of this
gene than origin of the Fungi and predicts timing of some changes in fungal cell wall
composition
• CBM18 expansion may be related to adhesion, future experiments to test this
• Future: We are employing a population genomic approach, resequencing 24 strains of Bd
and hope to understand more about origins and variation in the genome from these data.
54. Summary
• Unraveling the evolution of pathogens can be tricky, more so when mode of
pathogenesis is not obvious (e.g. not just a toxin gene)
• Comparative genomics at the scale of gene and gene families can suggest changes that
may be important in adaptation of a species.
• Connecting these molecular changes to pathogenecity is still needed to understand the
role these expansions may play - but provides rich experimental fodder for the
laboratory.
55. Acknowledgements
Coccidioides B. dendrobatidis
Tom Sharpton {UCSF} John Taylor {UC Berkeley} John Abramyan {UCR}
Dan Neafsey {Broad Institute} Edgar Medina {Universidad de Los Andes,
Bridget Barker, Marc Orbach, Steve Rounsley {U Colombia}
Arizona} Christina Cuomo {Broad Institute}
Tim James {U Michigan}
Suzanne Joneson, Tom Poorten, Erica
Stajich lab @UCR lab
Rosenblum {U Idaho}
Steven Ahrendt
Igor Grigoriev {JGI}
Divya Sain
H. polyrhiza
Yizhou Wang
Suzanne Joneson, Erica Rosenblum {U Idaho}
Yi Zhou
Shin-Han shiu {Michigan State}
Jessica De Anda Burroughs Wellcome Fund Grant Programs
Joyce Longcore {U Maine}
Annie Nguyen
Tim James {U Michigan}
W.M. KeckBiomedical Sciences
Foundation Career Awards for Medical Scientists
http://lab.stajich.org
Five-year awards for physician scientists provide $700,000 to bridge advanced postdoctoral/fellowship
training and the early years of faculty service. This award addresses the on-going problem of increasing
http://mobedac.org
the number of physician scientists and will help facilitate the transition to a career in research. Proposals
must be in the area of basic biomedical, disease-oriented, translational, or molecular, genetic, or
pharmacological epidemiology research.
Collaborative Research Travel Grants http://fungidb.org
Provide up to $15,000 in support for researchers from degree-granting institutions to travel to a labo-
Editor's Notes
\n
R. stolonifera infecting the strawberries\n\nMacro and microscales\n\n