Pattern & Process of Tree Mortality Waves in the Mountains of the Southwestern United States. Presented by Alison Macalady at the "Perth II: Global Change and the World's Mountains" conference in Perth, Scotland in September 2010.
This document discusses the importance of understanding agriculture's past to help feed the future world. It highlights several key points:
1. Studying the past is key to understanding the future of agriculture. Early farmers began selectively breeding crops like rice in China over 6,000 years ago.
2. The science of agricultural origins was pioneered by Nikolai Vavilov in the early 20th century who identified centers of origin for crops. New techniques like radiocarbon dating and DNA analysis are unlocking more information.
3. Agricultural diversity is important for the future as genes from crop wild relatives and landraces can be transferred to crops to provide benefits like flood tolerance. Understanding patterns of genetic diversity is crucial.
A Grand Challenge of Genome Sequencing: Complete Genomics of Human and Microb...Larry Smarr
11.06.15
Enabling Genomic Medicine Roundtable: A Grand Challenge of Genome Sequencing: Complete Genomics of Human and Microbiome DNA: Comparing Healthy with IBD
Presented by: Larry Smarr, UCSD (Calit2)
San Francisco California
Seminar abstract: I will be talking about two ongoing research projects in my laboratory: (1) evolution of thermal niches in seaweeds, (2) biodiversity of endolithic algae in coral skeletons and its relationship with the environment. Using evolutionary models in an explicit phylogenetic framework, patterns of evolution in environmental traits such as the sea surface temperature (SST) affinities of species can be studied. Based on case studies in the green algae Codium and Halimeda, it is shown that lineages behave differently when it comes to their evolution of SST affinities, and that there is a strong correlation between the evolution of SST affinities and rates of species diversification. For the second part of the talk, I will focus on our recent work on environmental sequencing of coral skeletons. These feature unexpectedly high biodiversity of limestone-boring algae as well as many unknown inhabitants. Our first results indicate that the diversity of algal endoliths may be linked to environmental conditions, but this hypothesis needs further testing.
Jack Gilbert: Welcome to the 1st International EMP Meeting: the first 10,000 ...GigaScience, BGI Hong Kong
This document summarizes the First International EMP meeting and the Earth Microbiome Project's pilot study. The EMP aims to catalog microbial diversity globally by sequencing 10,000 environmental samples. So far over 60,000 samples have been pledged from over 50 researchers worldwide. Analysis of initial samples shows robust seasonal patterns in species richness. The EMP also aims to correlate taxonomic data with environmental parameters and functional gene profiles to better understand microbial communities and predict assemblages.
This study aims to determine if there is a relationship between ploidy number and branching patterns in big sagebrush (Artemisia tridentata ssp. tridentata). Sage-grouse prefer to nest in U-shaped branching that is found in big sagebrush. However, some burned areas have regrown with V-shaped branching instead. The focus is on using flow cytometry to analyze the ploidy (number of sets of chromosomes) of sagebrush samples. Preliminary results found a nuclear DNA content lower than expected, possibly due to cell wall material interfering. Further optimization of the nuclei isolation procedure is needed to accurately determine ploidy levels and investigate impacts on branching patterns.
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.21
Invited Talk
Center for Earth Observations and Applications
Advisory Committee
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
La Jolla, CA
The increase in resolution and taxon sampling of algal phylogenies resulting from the various algal tree of life projects and other initiatives worldwide opens tremendous opportunity to learn more about the evolution of all aspects of algal biology. Using evolutionary modeling techniques in a phylogenetic context, hypotheses about the evolution of particular traits and their interaction with speciation-extinction dynamics become testable. I will illustrate this with three case studies. First, I will investigate the evolution of the thermal niche of seaweeds, showing how it affects latitudinal diversity patterns. Second, I will test the hypothesis that the evolution of cellular trace element requirements (stoichiometry) is dominated by endosymbiosis events. Third, I will investigate the evolution of morphological traits typically used in species-level systematics, focusing on its implications for the prevalence of cryptic diversity. These case studies show the potential and limitations of the approach, and offer new insights in algal evolution from the very recent to the very ancient, and across the various subdisciplines of algal biology.
Modeling Myxozoan Disease in Pacific Salmon: How Will Climate Change Affect P...Oregon Sea Grant
This document summarizes the research goals of studying how climate change will affect the distribution and severity of a myxozoan parasite (Ceratomyxa shasta) in Pacific salmon. The research aims to monitor parasite levels over time in rivers, study how changing water temperatures may impact parasite lifecycles, predict potential changes in the parasite's geographic range based on climate models, and develop a risk assessment of how disease severity may change in salmon populations.
This document discusses the importance of understanding agriculture's past to help feed the future world. It highlights several key points:
1. Studying the past is key to understanding the future of agriculture. Early farmers began selectively breeding crops like rice in China over 6,000 years ago.
2. The science of agricultural origins was pioneered by Nikolai Vavilov in the early 20th century who identified centers of origin for crops. New techniques like radiocarbon dating and DNA analysis are unlocking more information.
3. Agricultural diversity is important for the future as genes from crop wild relatives and landraces can be transferred to crops to provide benefits like flood tolerance. Understanding patterns of genetic diversity is crucial.
A Grand Challenge of Genome Sequencing: Complete Genomics of Human and Microb...Larry Smarr
11.06.15
Enabling Genomic Medicine Roundtable: A Grand Challenge of Genome Sequencing: Complete Genomics of Human and Microbiome DNA: Comparing Healthy with IBD
Presented by: Larry Smarr, UCSD (Calit2)
San Francisco California
Seminar abstract: I will be talking about two ongoing research projects in my laboratory: (1) evolution of thermal niches in seaweeds, (2) biodiversity of endolithic algae in coral skeletons and its relationship with the environment. Using evolutionary models in an explicit phylogenetic framework, patterns of evolution in environmental traits such as the sea surface temperature (SST) affinities of species can be studied. Based on case studies in the green algae Codium and Halimeda, it is shown that lineages behave differently when it comes to their evolution of SST affinities, and that there is a strong correlation between the evolution of SST affinities and rates of species diversification. For the second part of the talk, I will focus on our recent work on environmental sequencing of coral skeletons. These feature unexpectedly high biodiversity of limestone-boring algae as well as many unknown inhabitants. Our first results indicate that the diversity of algal endoliths may be linked to environmental conditions, but this hypothesis needs further testing.
Jack Gilbert: Welcome to the 1st International EMP Meeting: the first 10,000 ...GigaScience, BGI Hong Kong
This document summarizes the First International EMP meeting and the Earth Microbiome Project's pilot study. The EMP aims to catalog microbial diversity globally by sequencing 10,000 environmental samples. So far over 60,000 samples have been pledged from over 50 researchers worldwide. Analysis of initial samples shows robust seasonal patterns in species richness. The EMP also aims to correlate taxonomic data with environmental parameters and functional gene profiles to better understand microbial communities and predict assemblages.
This study aims to determine if there is a relationship between ploidy number and branching patterns in big sagebrush (Artemisia tridentata ssp. tridentata). Sage-grouse prefer to nest in U-shaped branching that is found in big sagebrush. However, some burned areas have regrown with V-shaped branching instead. The focus is on using flow cytometry to analyze the ploidy (number of sets of chromosomes) of sagebrush samples. Preliminary results found a nuclear DNA content lower than expected, possibly due to cell wall material interfering. Further optimization of the nuclei isolation procedure is needed to accurately determine ploidy levels and investigate impacts on branching patterns.
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...Larry Smarr
06.09.21
Invited Talk
Center for Earth Observations and Applications
Advisory Committee
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
La Jolla, CA
The increase in resolution and taxon sampling of algal phylogenies resulting from the various algal tree of life projects and other initiatives worldwide opens tremendous opportunity to learn more about the evolution of all aspects of algal biology. Using evolutionary modeling techniques in a phylogenetic context, hypotheses about the evolution of particular traits and their interaction with speciation-extinction dynamics become testable. I will illustrate this with three case studies. First, I will investigate the evolution of the thermal niche of seaweeds, showing how it affects latitudinal diversity patterns. Second, I will test the hypothesis that the evolution of cellular trace element requirements (stoichiometry) is dominated by endosymbiosis events. Third, I will investigate the evolution of morphological traits typically used in species-level systematics, focusing on its implications for the prevalence of cryptic diversity. These case studies show the potential and limitations of the approach, and offer new insights in algal evolution from the very recent to the very ancient, and across the various subdisciplines of algal biology.
Modeling Myxozoan Disease in Pacific Salmon: How Will Climate Change Affect P...Oregon Sea Grant
This document summarizes the research goals of studying how climate change will affect the distribution and severity of a myxozoan parasite (Ceratomyxa shasta) in Pacific salmon. The research aims to monitor parasite levels over time in rivers, study how changing water temperatures may impact parasite lifecycles, predict potential changes in the parasite's geographic range based on climate models, and develop a risk assessment of how disease severity may change in salmon populations.
1) Researchers inoculated soil microcosms with switchgrass and tracked changes in microbial communities over 62 transfers.
2) Initial diversity decreased from 30 phyla to mainly Firmicutes (>99%) despite rare OTUs accounting for most diversity.
3) A stable yet specialized community developed, maintaining high species diversity among closely related organisms.
The Human Gut Microbiome: A New Diagnostic for Disease?Larry Smarr
The document summarizes research on analyzing human gut microbiomes to better understand health and disease. It describes how the researchers used 25 CPU-years of computing and analyzed over 2.7 trillion DNA bases to map and compare the microbial ecology between healthy individuals and those with inflammatory bowel disease. Their analyses revealed major differences in microbial phyla between healthy and diseased states. Machine learning techniques discovered specific protein families that differentiate disease subtypes and healthy cohorts. The researchers aim to develop a novel microbiome-based diagnostic for disease by continuing to study gut microbiome dynamics using larger datasets and populations over time.
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
This document summarizes a lecture about analyzing the human microbiome and its relationship to human health. It discusses how the human body contains 100 trillion microbial cells that contain 100 times as many genes as human DNA. Analysis of the speaker's own gut microbiome over time revealed changes in bacterial phyla between healthy and inflammatory bowel disease states. Collecting biomarkers from the speaker's body over years showed oscillations linked to gut microbes and immune response. Ongoing research aims to better understand dynamics of the human immune system and gut microbiome.
Deciphering the Dynamic Coupling of the Human Immune System and the Gut Micro...Larry Smarr
This document discusses Dr. Larry Smarr's research into understanding the relationship between the human immune system and gut microbiome in Crohn's disease. Dr. Smarr sequenced his own genome to identify genetic polymorphisms associated with higher risk of Crohn's disease. He also conducted fine-time resolution sampling to study the distinct dynamics of the innate and adaptive immune system in health and disease. Additionally, he found major shifts in the gut microbiome between healthy individuals and those with two forms of inflammatory bowel disease.
Description of my initial results to identify NeSL-1 full length and truncated elements. Previously only identified in C elegans, multiple copies were identified in C brenneri, C japonica, and C remanei. A single truncated copy was seen ijn C briggsae. Completed in 2010.
This document discusses several key concepts in population genetics:
1) Genetic variation is important for adaptation, environmental change, conservation, and divergence of populations. Variation allows populations to survive over time while lack of variation leads to extinction.
2) Population genetics studies genetic structure, allele frequencies, and how they change over time due to evolutionary processes like mutation, genetic drift, natural selection, and gene flow.
3) The Hardy-Weinberg principle describes how allele and genotype frequencies remain stable without these evolutionary forces acting on a population.
Kelsey Beachman - Fall 2015, Final PresentationKelsey Beachman
The document summarizes a study that investigated how the pigmentation of the sea anemone Condylactis gigantea changes under thermal stress. Six C. gigantea were placed in either a control or treatment aquarium tank, with the treatment tank increasing in temperature by 1 degree Celsius every other day. Photos of the anemones were taken and their colors were measured and analyzed using a colorimetry method. The results showed that while the data wasn't statistically significant, there was a trend of the anemones in the treatment tank becoming lighter in color over time compared to the control tank anemones. Future research with improved controls and a longer study period could provide more definitive results on the temperature threshold at
Rigor Mortis and Intestinal Necrosis During C. elegans Deathjunaedrx
This study examines organismal death in C. elegans by observing two phenomena: 1) a wave of body wall muscle contraction (rigor mortis-like) called death contraction (DC) and 2) a wave of intestinal necrosis causing blue fluorescence (DF). The researchers find that DC occurs in an anterior-to-posterior wave through muscle contraction. DC waves correlate with and precede DF waves. Both are accompanied by calcium release and a drop in ATP levels. Long-lived daf-2 mutants show resistance to DC, suggesting organismal death pathways can be modulated to extend lifespan.
This study examined the nesting patterns and movements of spectacled eiders on Kigigak Island in Alaska from 1998-2012. The researchers found that:
1) Nest success had a significant effect on dispersal distance between consecutive years, with unsuccessful nests dispersing farther on average than successful nests.
2) There was no significant variation found in average yearly dispersal distances between years.
3) Comparisons to a previous 1992-1997 study found differences in dispersal distances of unsuccessful nests, which the authors attributed to differences in sample sizes, data selection, and analysis methods between the studies.
Project by Amy Huynh, Dylan Sonett, Mauri Malta, Dr. Jesse Zaneveld. Partnered with the Global Coral Microbiome Project. Presented in 2019 at the University of Washington Bothell Biology Presentations.
Impact of the koka reservoir on malaria, Solomon Kibret, Matthew McCartney and Jonathan Lautze. Challenge Program on Water and Food, 2nd International Forum on Water and Food, Addis Ababa, Ethiopia
November 2008
The document discusses several key themes of biology including how we know an organism is alive, cell structure and function, reproduction, metabolism, homeostasis, heredity, evolution, natural selection, and interdependence. It also discusses how science has improved our lives through topics like saving the environment, food supply, the human genome project, and fighting disease. The scientific process of making observations, asking questions, collecting data, designing experiments with hypotheses, controls, and variables is also outlined.
Observing the Dynamics of the Human Immune System Coupled to the Microbiome i...Larry Smarr
Calit2 Director Larry Smarr delivered this presentation to the CASIS Workshop on Biomedical Research Aboard the ISS at Columbia University in NY, NY, on May 28, 2014.
This document discusses how advances in genetic sequencing and computing are enabling humans to read and understand the "software of life" encoded in their human and microbiome DNA. It notes that the human microbiome contains millions of microbial genes compared to the 23,000 genes in human cells. The author details how the cost of DNA sequencing has fallen over 100,000-fold, allowing sequencing of both human and microbial genomes. Machine learning will be needed to understand differences between healthy and diseased states by analyzing enormous genomic and microbiome datasets. The author provides an example of analyzing their own gut microbiome over time and comparing to healthy/IBD populations.
Lecture slides on Estimating Species Divergence Times in RevBayes (https://github.com/revbayes/revbayes).
By Tracy Heath and Tanja Stadler
** this version was taught at the 2014 NESCent Academy Course: Phylogenetic analysis using RevBayes, 8/27/2014 (https://www.nescent.org/sites/academy/Phylogenetic_analysis_using_RevBayes) **
The document discusses the evolution of populations through various mechanisms of microevolution including natural selection, genetic drift, gene flow, mutation, and sexual reproduction. It explains how natural selection can lead to adaptive evolution as populations become better suited to their environments over generations. Genetic drift, founder effects, and bottlenecks are described as random processes that can reduce genetic variation within populations. The interaction between these microevolutionary forces and gene flow between populations influences evolutionary change.
The document discusses the evolution of populations through various mechanisms of microevolution including natural selection, genetic drift, gene flow, mutation, and sexual reproduction. It explains how natural selection can lead to adaptive evolution as populations become better suited to their environments over generations. Genetic drift, founder effects, and bottlenecks are described as random processes that can reduce genetic variation within populations. The interaction between these microevolutionary forces and gene flow between populations influences evolutionary change.
1. The document discusses how extreme climate events like droughts and floods are becoming more common and impactful.
2. It presents a simulation model to study the eco-evolutionary responses of populations to increasing climate trends and variability, as well as more frequent extreme events.
3. The model examines how these factors influence population extinction risk and genetic adaptation over time.
Water temperatures affects susceptibility to ranavirusmgray11
This document summarizes a study that tested how water temperature affects the pathogenicity of ranavirus in four amphibian species. The study found that at higher temperatures (25C vs 10C): 1) Mortality from ranavirus was greater for wood frogs, spotted salamanders, and green frogs; 2) Infection prevalence was higher in all species tested; and 3) Wood frogs experienced 100% infection but no mortality at 10C, whereas 80-90% mortality occurred at 15C. These results support the hypothesis that higher temperatures increase ranavirus replication and pathogenicity, likely by increasing virus replication rates while suppressing immune function in amphibians. Future research should retest other species and temperatures to further elucidate
Can patterns of ranavirus emergence be used to assess conservation threat?mgray11
This document discusses patterns of ranavirus emergence in amphibian populations and the threats they pose to conservation. It summarizes evidence that some populations experience persistent disease emergence and population declines over 80%, while others experience temporary emergence that does not result in long-term impacts. The document also discusses evidence that amphibians may be evolving responses to ranavirus, such as changes in sexual selection and immune gene diversity, but that novel ranavirus strains in Europe pose a serious threat due to lack of coevolution. Overall, the document examines how ranavirus emergence patterns can help assess threats to amphibian species conservation.
1) Researchers inoculated soil microcosms with switchgrass and tracked changes in microbial communities over 62 transfers.
2) Initial diversity decreased from 30 phyla to mainly Firmicutes (>99%) despite rare OTUs accounting for most diversity.
3) A stable yet specialized community developed, maintaining high species diversity among closely related organisms.
The Human Gut Microbiome: A New Diagnostic for Disease?Larry Smarr
The document summarizes research on analyzing human gut microbiomes to better understand health and disease. It describes how the researchers used 25 CPU-years of computing and analyzed over 2.7 trillion DNA bases to map and compare the microbial ecology between healthy individuals and those with inflammatory bowel disease. Their analyses revealed major differences in microbial phyla between healthy and diseased states. Machine learning techniques discovered specific protein families that differentiate disease subtypes and healthy cohorts. The researchers aim to develop a novel microbiome-based diagnostic for disease by continuing to study gut microbiome dynamics using larger datasets and populations over time.
Assay Lab Within Your Body: Biometrics and BiomesLarry Smarr
This document summarizes a lecture about analyzing the human microbiome and its relationship to human health. It discusses how the human body contains 100 trillion microbial cells that contain 100 times as many genes as human DNA. Analysis of the speaker's own gut microbiome over time revealed changes in bacterial phyla between healthy and inflammatory bowel disease states. Collecting biomarkers from the speaker's body over years showed oscillations linked to gut microbes and immune response. Ongoing research aims to better understand dynamics of the human immune system and gut microbiome.
Deciphering the Dynamic Coupling of the Human Immune System and the Gut Micro...Larry Smarr
This document discusses Dr. Larry Smarr's research into understanding the relationship between the human immune system and gut microbiome in Crohn's disease. Dr. Smarr sequenced his own genome to identify genetic polymorphisms associated with higher risk of Crohn's disease. He also conducted fine-time resolution sampling to study the distinct dynamics of the innate and adaptive immune system in health and disease. Additionally, he found major shifts in the gut microbiome between healthy individuals and those with two forms of inflammatory bowel disease.
Description of my initial results to identify NeSL-1 full length and truncated elements. Previously only identified in C elegans, multiple copies were identified in C brenneri, C japonica, and C remanei. A single truncated copy was seen ijn C briggsae. Completed in 2010.
This document discusses several key concepts in population genetics:
1) Genetic variation is important for adaptation, environmental change, conservation, and divergence of populations. Variation allows populations to survive over time while lack of variation leads to extinction.
2) Population genetics studies genetic structure, allele frequencies, and how they change over time due to evolutionary processes like mutation, genetic drift, natural selection, and gene flow.
3) The Hardy-Weinberg principle describes how allele and genotype frequencies remain stable without these evolutionary forces acting on a population.
Kelsey Beachman - Fall 2015, Final PresentationKelsey Beachman
The document summarizes a study that investigated how the pigmentation of the sea anemone Condylactis gigantea changes under thermal stress. Six C. gigantea were placed in either a control or treatment aquarium tank, with the treatment tank increasing in temperature by 1 degree Celsius every other day. Photos of the anemones were taken and their colors were measured and analyzed using a colorimetry method. The results showed that while the data wasn't statistically significant, there was a trend of the anemones in the treatment tank becoming lighter in color over time compared to the control tank anemones. Future research with improved controls and a longer study period could provide more definitive results on the temperature threshold at
Rigor Mortis and Intestinal Necrosis During C. elegans Deathjunaedrx
This study examines organismal death in C. elegans by observing two phenomena: 1) a wave of body wall muscle contraction (rigor mortis-like) called death contraction (DC) and 2) a wave of intestinal necrosis causing blue fluorescence (DF). The researchers find that DC occurs in an anterior-to-posterior wave through muscle contraction. DC waves correlate with and precede DF waves. Both are accompanied by calcium release and a drop in ATP levels. Long-lived daf-2 mutants show resistance to DC, suggesting organismal death pathways can be modulated to extend lifespan.
This study examined the nesting patterns and movements of spectacled eiders on Kigigak Island in Alaska from 1998-2012. The researchers found that:
1) Nest success had a significant effect on dispersal distance between consecutive years, with unsuccessful nests dispersing farther on average than successful nests.
2) There was no significant variation found in average yearly dispersal distances between years.
3) Comparisons to a previous 1992-1997 study found differences in dispersal distances of unsuccessful nests, which the authors attributed to differences in sample sizes, data selection, and analysis methods between the studies.
Project by Amy Huynh, Dylan Sonett, Mauri Malta, Dr. Jesse Zaneveld. Partnered with the Global Coral Microbiome Project. Presented in 2019 at the University of Washington Bothell Biology Presentations.
Impact of the koka reservoir on malaria, Solomon Kibret, Matthew McCartney and Jonathan Lautze. Challenge Program on Water and Food, 2nd International Forum on Water and Food, Addis Ababa, Ethiopia
November 2008
The document discusses several key themes of biology including how we know an organism is alive, cell structure and function, reproduction, metabolism, homeostasis, heredity, evolution, natural selection, and interdependence. It also discusses how science has improved our lives through topics like saving the environment, food supply, the human genome project, and fighting disease. The scientific process of making observations, asking questions, collecting data, designing experiments with hypotheses, controls, and variables is also outlined.
Observing the Dynamics of the Human Immune System Coupled to the Microbiome i...Larry Smarr
Calit2 Director Larry Smarr delivered this presentation to the CASIS Workshop on Biomedical Research Aboard the ISS at Columbia University in NY, NY, on May 28, 2014.
This document discusses how advances in genetic sequencing and computing are enabling humans to read and understand the "software of life" encoded in their human and microbiome DNA. It notes that the human microbiome contains millions of microbial genes compared to the 23,000 genes in human cells. The author details how the cost of DNA sequencing has fallen over 100,000-fold, allowing sequencing of both human and microbial genomes. Machine learning will be needed to understand differences between healthy and diseased states by analyzing enormous genomic and microbiome datasets. The author provides an example of analyzing their own gut microbiome over time and comparing to healthy/IBD populations.
Lecture slides on Estimating Species Divergence Times in RevBayes (https://github.com/revbayes/revbayes).
By Tracy Heath and Tanja Stadler
** this version was taught at the 2014 NESCent Academy Course: Phylogenetic analysis using RevBayes, 8/27/2014 (https://www.nescent.org/sites/academy/Phylogenetic_analysis_using_RevBayes) **
The document discusses the evolution of populations through various mechanisms of microevolution including natural selection, genetic drift, gene flow, mutation, and sexual reproduction. It explains how natural selection can lead to adaptive evolution as populations become better suited to their environments over generations. Genetic drift, founder effects, and bottlenecks are described as random processes that can reduce genetic variation within populations. The interaction between these microevolutionary forces and gene flow between populations influences evolutionary change.
The document discusses the evolution of populations through various mechanisms of microevolution including natural selection, genetic drift, gene flow, mutation, and sexual reproduction. It explains how natural selection can lead to adaptive evolution as populations become better suited to their environments over generations. Genetic drift, founder effects, and bottlenecks are described as random processes that can reduce genetic variation within populations. The interaction between these microevolutionary forces and gene flow between populations influences evolutionary change.
1. The document discusses how extreme climate events like droughts and floods are becoming more common and impactful.
2. It presents a simulation model to study the eco-evolutionary responses of populations to increasing climate trends and variability, as well as more frequent extreme events.
3. The model examines how these factors influence population extinction risk and genetic adaptation over time.
Water temperatures affects susceptibility to ranavirusmgray11
This document summarizes a study that tested how water temperature affects the pathogenicity of ranavirus in four amphibian species. The study found that at higher temperatures (25C vs 10C): 1) Mortality from ranavirus was greater for wood frogs, spotted salamanders, and green frogs; 2) Infection prevalence was higher in all species tested; and 3) Wood frogs experienced 100% infection but no mortality at 10C, whereas 80-90% mortality occurred at 15C. These results support the hypothesis that higher temperatures increase ranavirus replication and pathogenicity, likely by increasing virus replication rates while suppressing immune function in amphibians. Future research should retest other species and temperatures to further elucidate
Can patterns of ranavirus emergence be used to assess conservation threat?mgray11
This document discusses patterns of ranavirus emergence in amphibian populations and the threats they pose to conservation. It summarizes evidence that some populations experience persistent disease emergence and population declines over 80%, while others experience temporary emergence that does not result in long-term impacts. The document also discusses evidence that amphibians may be evolving responses to ranavirus, such as changes in sexual selection and immune gene diversity, but that novel ranavirus strains in Europe pose a serious threat due to lack of coevolution. Overall, the document examines how ranavirus emergence patterns can help assess threats to amphibian species conservation.
Climate Change and Biodiversity: Implications for Bay Area Conservation by Da...OpenSpaceCouncil
This document summarizes a workshop on climate change impacts on biodiversity in the San Francisco Bay Area. Key points include:
- Climate models project the Bay Area climate to warm significantly by the late 21st century, increasing temperatures, drought conditions, and wildfire risk.
- Multiple vegetation models predict future climates will favor shrub and grasslands over forests as some tree species approach the limits of their climate tolerances.
- Vegetation transitions are expected to be patchy across the landscape and depend on factors like local propagule sources and disturbance regimes.
- Maintaining a diversity of habitats and vegetation types can help support species' ability to shift ranges under climate change.
Re-evaluating models to take on new challenges in ecology and evolutionLiliana Davalos
This document discusses models used to analyze ecological and evolutionary relationships in the Caribbean region. It summarizes species-area relationships for three Caribbean archipelagos at the last glacial maximum and present day, finding highly significant relationships. It also examines how changes in species numbers relate to changes in island area from the last glacial maximum to present. Additionally, it analyzes evolutionary relationships among bat species based on DNA sequences and anatomical features, finding some discordant relationships. The document explores various models for understanding these relationships and incorporating multiple data types.
Are ranaviruses capable of causing local population extinctions and contributing to species declines? By Dr. Matt Gray (University of Tennessee, Center for Wildlife Health)
Similar to Pattern & Process of Tree Mortality Waves in the Mountains of the Southwestern United States [Alison Macalady] (11)
The document discusses self-management of chronic conditions and its importance for sustainability of healthcare systems. It notes that:
- Chronic conditions will rise dramatically, with many people having multiple conditions.
- Expectations of care quality will increase as standards that are currently seen as inadequate will be viewed as inhumane.
- For healthcare systems to be sustainable, chronic conditions must be managed differently by empowering self-management supported by technology and expertise when needed.
This document provides links to further information to accompany a presentation on leading change for the future, including links about:
- The ALISS project, which is an open innovation process to improve health information access
- Using social assets and co-production approaches to deliver better and more sustainable community services
- Reports on public service reform in Scotland to develop new approaches that are better and cheaper
- The importance of health literacy, adult literacy, and effective communication and consultation skills between healthcare professionals and patients.
The CARE Measure is a 10-item consultation process measure developed by Dr. Stewart Mercer and colleagues to assess empathy in the patient-doctor relationship. Each item is scored from 1-5 on factors like making the patient feel at ease, listening, understanding concerns, and developing a care plan together. Scores are added up to a maximum of 50 to evaluate the consultation. The measure has been validated in over 3,000 consultations in Scotland. It can be used free of charge for research purposes, with attribution to the developers.
This document contains biographies of two speakers, Glenn Hinds and Tim Warren, presenting at an event on leading change for the future and supporting self-management. Glenn Hinds is a director of a training company who has almost 20 years experience as a social worker in mental health and substance abuse services. Tim Warren has a background in social work and worked in criminal justice, child protection, and health policy roles within the Scottish government focusing on long term conditions and self-management.
This document provides an agenda for an event titled "Leading Change for the Future" focused on supporting self-management. The one day event at the Centre for Health Science in Inverness includes coffee and registration, opening remarks from the chair, two keynote speakers on education solutions and self-management programs, a motivational speaker, three workshop sessions on various self-management topics, lunch and posters, a plenary on personal experiences with long-term conditions, closing remarks summarizing the workshops and next steps, and identifying actions to apply lessons in daily work.
This project was funded to develop self-management modules delivered by the University of Highlands and Islands. An audit found gaps in resources and materials, which informed a self-management competency framework. In response, two Masters level modules were developed for lead practitioners focusing on enabling change and leading change. A resource pack was also created, including an online Health Action Plan tool and self-management competency self-assessment toolkit to help practitioners support self-management. Ongoing work will improve the toolkit and embed the competencies and tools in practice, along with a champion network for support.
Self-management involves individuals managing their long-term conditions on a daily basis through self-care activities, with support from health and social care providers. The document discusses educational solutions developed by a project to support self-management through two university modules training leaders and champions of self-management. Lessons learned included the need for flexible timelines and dedicated project management. Future work involves further developing and embedding resources like a competency framework and champions network to support practice change.
OiWillo Training Co. Ltd. provides training to help with long term health conditions. The company is led by Principal Glenn Hinds who can be contacted via email at glenn@oiwillo.com regarding their training services for long term conditions.
The document contains population data from the General Register Office for Scotland on the population of NHS Highland (excluding Argyll & Bute) from 1981 to 2032 broken down by age and sex. It provides mid-year population estimates for each year over this 52-year period sourced from the General Register Office for Scotland.
The document contains a list of over 100 delegates including their name, job title, organisation, and email address. The delegates are from a variety of healthcare organizations in Scotland such as NHS Highland, Robert Gordon University, and the University of the Highlands and Islands. Their roles include nurses, physiotherapists, occupational therapists, dietitians, pharmacists, and others involved in healthcare, education, and patient organizations.
The document provides information about two Masters level modules on self management offered by the University of the Highlands and Islands (UHI) in collaboration with several health organizations. Module 1 focuses on developing an understanding of self management theories and practicing communication skills to empower individuals. It involves online learning and one face-to-face session. Module 2 focuses on leading organizational change to support self management. It is completed entirely online. Both aim to develop "self management champions" to facilitate culture change within their organizations and support long-term conditions management.
Garry Coutts has been chair of NHS Highland since 2004. He was recently appointed Rector of the University of the Highlands and Islands in November 2010. He believes that fully integrating health and social services under single management and budgets can improve care. Garry Coutts is passionate about using strategic commissioning to involve stakeholders in service planning across the public sector.
The document describes several abstracts presented at a conference on leading change for the future and supporting self-management. The abstracts discuss partnerships and resources for promoting self-management, including a partnership for delivering supported self-management in Highland and Argyll & Bute, a training toolkit for carers and telehealthcare, examples of self-management projects funded in Scotland, tools for chronic disease management using the Flinders model of self-management, using technology and education to support self-management, and developing resources to support a skilled workforce in planning for self-management.
The University of the Highlands and Islands (UHI) offers postgraduate students the opportunity to study in a supportive environment across various campuses located in the beautiful and unique setting of the Highlands and Islands of Scotland. UHI provides both taught postgraduate courses and opportunities for postgraduate research. Research strengths include diabetes, sustainable rural development, archaeology, Gaelic, and renewable energy. The Graduate School supports all postgraduate research students. International students will find assistance to study at UHI and opportunities to experience Scottish culture. Some courses are taught through the Gaelic language, helping to advance Gaelic in the 21st century.
The presentation is aimed at students who are thinking of a career in teaching in Scotland. It offers an overview of the teaching profession at both Primary and Secondary school level. In addition it will outline the nature of Teacher Education training courses as well as academic entry requirements, the application and interview process and current employment prospects.
This document summarizes the 433 abstracts accepted for the conference "Global Change and the World's Mountains" held in Perth, Scotland from September 26-30, 2010. It analyzes the geographical distribution and topical focus of the abstracts. The abstracts came primarily from Europe (194), Asia (82), and North America (67). Most papers focused on ecological systems (150) and global environmental change (92). Other popular topics included ecosystem interactions (34), social systems (28), decision-making (14), and resource use (10). The analysis found the greatest emphasis was on global environmental change and ecosystems, with fewer papers considering social drivers or entire socio-ecological systems impacted by global change.
Professor Martin Price, director of the Centre for Mountain Studies at Perth College UHI and UNESCO chair in sustainable mountain development, welcomes the "Perth II: Global Change and the World's Mountains" conference in Perth, Scotland in September 2010.
Conducting Climate Change Risk and Vulnerability Assessments in Rural Mountain Communities in the Columbia Basin Region of Canada. Presented by Jeff Zukiwsky at the "Perth II: Global Change and the World's Mountains" conference in Perth, Scotland in September 2010.
Global Change in Katunskiy Biosphere Reserve: Vulnerability of ecosystems and Adaptation Strategy. Presented by Tatyana Yashina at the "Perth II: Global Change and the World's Mountains" conference in Perth, Scotland in September 2010.
Water transparency to UV radiation in montane lakes: consequences of climate-driven changes in terrestrial inputs. Presented by Craig Williamson at the "Perth II: Global Change and the World's Mountains" conference in Perth, Scotland in September 2010.
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Chapter wise All Notes of First year Basic Civil Engineering
Syllabus
Chapter-1
Introduction to objective, scope and outcome the subject
Chapter 2
Introduction: Scope and Specialization of Civil Engineering, Role of civil Engineer in Society, Impact of infrastructural development on economy of country.
Chapter 3
Surveying: Object Principles & Types of Surveying; Site Plans, Plans & Maps; Scales & Unit of different Measurements.
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Chapter 4
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Chapter 5
Transportation: Introduction to Transportation Engineering; Traffic and Road Safety: Types and Characteristics of Various Modes of Transportation; Various Road Traffic Signs, Causes of Accidents and Road Safety Measures.
Chapter 6
Environmental Engineering: Environmental Pollution, Environmental Acts and Regulations, Functional Concepts of Ecology, Basics of Species, Biodiversity, Ecosystem, Hydrological Cycle; Chemical Cycles: Carbon, Nitrogen & Phosphorus; Energy Flow in Ecosystems.
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4. BCP, Surveying volume 1
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Pattern & Process of Tree Mortality Waves in the Mountains of the Southwestern United States [Alison Macalady]
1. Pattern & Process of Tree
Mortality Waves in the
Mountains of the Southwestern
United States
Alison Macalady1 & Harald Bugmann2,1
1 Laboratory of Tree-Ring Research, University of Arizona
2 Forest Ecology, ETH Zürich, Switzerland
Photo: Craig Allen
5. Growth-mortality models
1
Mortality
Probability ?
0
Index based on radial growth
CCR >80%, (e.g. Bigler & Bugmann 2004, Ecol Appl)
– growth level over past few years
– growth trend over past years to decades
– growth sensitivity
6. Research questions
Can the probability of piñon
mortality under drought be
accurately modeled using
indices derived from diameter
growth?
What do growth-mortality
models reveal about the
drivers of tree mortality
through space and time?
9. Tree growth – typical patterns
Large Low growth
SEV 2000s release/recovery before death
of L trees!
Divergence of L
TRP 2000s and D trees
incited by 1950s
drought
10. Fitting mortality models: one site
Sevilleta, 1950s
Internal validation: 60% fitting, 40% testing
500 simulations
11. Fitting mortality models: all sites
Site/period Variable AU ROC CCR
mean
SEV 1950s 0.89 78.7%
sensitivity 50
mean
BNM 1950s 0.92 82.0%
sensitivity 25
recent
SEV 2000s 0.83 75.3%
growth 3
BNM 2000s – – –
growth
TRP 2000s 0.67 59.6%
difference 15
12. Validating mortality models
Calibration data [shown is CCR]
Validation SEV 1950s BNM 1950s SEV 2000s
SEV 1950s – 73.1 77.4
BNM 1950s 77.4 – 60.0
SEV 2000s 55.9 61.7 –
BNM 2000s 31.6 16.7 14.3
TRP 2000s 53.4 55.9 52.5
13. What’s going on?
High model accuracies associated with 1950’s and SEV
2000’s data reflect a chronic stress signal associated with
mortality risk
•Best predictors reflect the resource status of the trees over
different time periods.
•Supports carbon starvation mechanism of mortality
Lack of fit in N 2000’s models suggests other processes.
•Acute drought stress
•Increased temps driving accelerated bark beetle/fungi dynamics?
•Carbon allocation to defensive compounds (Kane and Kolb 2010,
Oikos)?
14. Conclusions
Strong influence of acute
drought stress and/or bark
beetle/fungi dynamics at
northern sites in the 2000’s
Differences in space and time
an early indicator of global
change?
Challenges of predicting
mortality under drought
15. Acknowledgements…
Acknowledgements
Craig Allen, Julio Betancourt, Tom Swetnam, Dave Breshears,
Kay Beeley, Collin Haffey, Greg Pederson, Derek Murrow, Chris
Baisan, Rex Adams, Alex Arizpe, Christof Bigler
Financial support
Science Foundation Arizona, US DOE GREF (AM)
ETH Zürich, UA Lab. Tree-Ring Research, Haury Fellowship
(HB)