WERA 2009
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The document summarizes research from the University of Washington on pathogens affecting shellfish species and genomics research on the Pacific oyster and other shellfish. It describes work identifying the pathogen Vibrio tubiashii, sequencing its genome, and finding genes related to disease tolerance. It also discusses genomics research on Crassostrea gigas and other species looking at responses to Vibrio challenge and disease resistance related to prostaglandins.
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Does DNA methylation facilitate phenotypic plasticity in marine invertebrates?
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Short read sequencing and shellfish
This document discusses using short-read sequencing to characterize genomes in aquacultured shellfish. It presents research on (1) disease tolerance in hard clams using RNA-seq, (2) environmental stress response in Manila clams to ocean acidification through RNA-seq, and (3) DNA methylation patterns in the Pacific oyster using MBD-seq. The availability of shared genomic and transcriptomic sequences from short-read sequencing can help improve aquaculture production by facilitating increased application of the technology.
FISH441: Oysters, acidification and methylation
This study examined the DNA methylation levels of Pacific oysters (Crassostrea gigas) exposed to varying acidified conditions. The researchers found that oysters exposed to low pH conditions exhibited higher levels of DNA methylation compared to oysters in control or high pH treatments. Both diploid and triploid oysters showed similar stress responses to ocean acidification through changes in DNA methylation levels. The results suggest that epigenetic modifications play a role in the phenotypic plasticity of oysters to environmental stressors like ocean acidification.
FISH441: Oyster acidification: gene and protein expression
The document describes an experiment that examined the stress response of Pacific oysters (Crassostrea gigas) to acidification. The objectives were to determine if acidification would induce a stress response, by analyzing expression of genes and proteins involved in the stress response. Oysters of two ploidies (2n and 3n) were exposed to normal and low pH conditions. Results found no significant difference in expression of the heat shock protein HSP70 between pH conditions. Expression of the metalloprotein metallothionein was also analyzed and found to be lower in oysters exposed to low pH. This suggests acidification may induce a stress response in Pacific oysters.
FISH441: Oyster Hypoxia and acclimation
This document summarizes a study on the impacts of hypoxia on gene expression in the Pacific oyster (Crassostrea gigas). The study found that: 1) Hsp70 expression was lower in oysters acclimated to low dissolved oxygen conditions, indicating an adaptive stress response; 2) HIF-1α expression was also lower in low oxygen acclimated oysters; and 3) hrIGF-1 expression was higher in oysters acclimated to low oxygen, suggesting it helps the oysters adapt, grow and survive in hypoxic conditions. The results demonstrate the oysters' ability to adapt their gene expression in response to low oxygen levels through phenotypic plasticity.
Timmins Schiffman PCSGA 2011
This document summarizes a study on the effects of ocean acidification on the development and physiology of Pacific oyster larvae. The study exposed oyster larvae to different levels of CO2 representing current and elevated future atmospheric CO2 levels. Results showed higher CO2 levels delayed development, decreased calcification and growth, and increased expression of stress response genes. The study suggests ocean acidification could negatively impact oyster larvae development and physiology.
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Elene Dorfmeier's presentation: How will a changing climate impact Vibrio tubiashii growth and pathogenicity to Pacific oyster larvae?
FISH510 Lec 1
This course will discuss innovations in sequencing technologies that have become major tools in aquatic sciences. The class will include presentations from researchers using these technologies, discussions of challenges working with non-model organisms, and a survey of available data analysis tools. Students will learn about applications of large-scale sequencing data to address issues in ecology and natural resource management. As technologies continue advancing rapidly, the course will also cover bioinformatics challenges.
FISH441 Group Project (Oysters)
The document summarizes a study that used an integrated molecular approach to examine the response of the Pacific oyster, Crassostrea gigas, to multiple stressors. The study exposed oysters to copper, a common pollutant, and Vibrio tubiashii, a bacterial pathogen. It measured the expression of genes involved in stress response, including heat shock protein 70 (Hsp70), metallothionein IV, and copper oxidase, at the mRNA and protein levels. The results showed that V. tubiashii inhibited the expression of metallothionein IV and copper oxidase, leaving the oysters more vulnerable to copper toxicity. The study demonstrated how one stressor can compromise an
Timmins-Schiffman P2010
This document summarizes research on how environmental stressors like ocean acidification and elevated temperatures affect Pacific oyster larvae physiology and survival when exposed to disease. The research examines the effects of these stressors individually and in combination on oyster larval development, temperature impacts on the oyster-Vibrio relationship, and an ongoing study on ocean acidification and Vibrio exposure.
Gavery PCSGA 2010
The document summarizes research on DNA methylation patterns and epigenetic regulation in the Pacific oyster. Results showed DNA methylation occurs in stress-related genes and may play a regulatory role in immune and stress responses. Understanding genetic and epigenetic influences could increase predictability in selective breeding of oysters. Further evaluating epigenetic mechanisms in bivalves using new methods like whole genome bisulfite sequencing may provide insights with implications for selective breeding, hybrid vigor, and how nutrition affects gene expression through DNA methylation.
Salmon Senescence
This document discusses research into the physiological processes that regulate senescence in sockeye salmon. It describes past research showing that senescence rate is influenced by environmental factors like temperature, climate, humans, salmon density, and stream toxins. Future research plans to focus on the cellular mechanisms of aging by fin clipping and tagging early and late arriving salmon in Hansen Creek, fin clipping daily, and sacrificing fish on days 6 and 7 post tagging to study physiological changes over time.
Roberts GRC
The document discusses using shellfish as bioindicators to study the impacts of environmental change, such as ocean acidification, on host-pathogen interactions and physiology through 'omic approaches like transcriptomics, proteomics, and investigating DNA methylation and the epigenome. It provides examples of research examining how changes in pH and other stressors influence immune response and pathogen virulence in oysters.
Herring SNP Sneak Peak
This document summarizes an SNP workshop that discussed challenges with NGS and SNP discovery. It then describes a study that used 454 transcriptome sequencing to discover SNPs in Pacific herring. Researchers sequenced liver and testes tissues separately, assembling over 1.7 million reads into 47,267 contigs. They identified over 16,000 SNPs between tissues and annotated corresponding genomic features. The study provides a workflow and pipeline for targeted SNP discovery.
FISH546 Discussion4
This document discusses transcriptomics and the process of working with raw sequencing data. It describes obtaining high quality reads of around 40 base pairs long from 16 million sequences. The steps of trimming raw data, assembling sequences either de novo or to a reference genome, and annotating the output consensus are outlined. Data management considerations for very large transcriptomics files are also mentioned.
Gavery Fish546
The document discusses testing whether whole genome bisulfite sequencing (WGBS) can be used to discover methylated cytosines in non-model species with limited genomic resources. It describes conducting a feasibility trial using Atlantic salmon sequences as a surrogate for the oyster genome. Short reads were generated from the salmon sequences, converted to simulate bisulfite treatment, and assembled using various tools. The results showed it was difficult to map methylated regions due to the limited reference genome available. While WGBS may be possible, improved assembly tools and reduced representation approaches are needed.
Fabrizio_capstone
The document summarizes research into the chemotaxis and foraging behaviors of Octopus rubescens. It discusses how octopuses may use chemotaxis when vision is limited, citing previous studies that found octopuses can detect chemicals. The study described in the document tested whether O. rubescens could choose between a live crab or an empty area using either vision or smell. The results provided limited evidence for distance chemotaxis but suggested octopuses may respond more to stressed prey. Further analysis of proteins and genes in stressed versus unstressed crabs was conducted to explore what chemical signals octopuses could be detecting.
Roberts Alaska Sen
This document summarizes preliminary research investigating the physiological mechanisms regulating senescence in sockeye salmon. The researchers found that cortisol signaling declines and molecular chaperone protein (HSP) is upregulated as salmon progress towards senescence. Genes controlling processes like olfaction, reproduction, learning, and immunity were differentially expressed between arriving and senescing salmon. Going forward, the researchers plan to compare gene expression patterns between populations with different senescence rates and take an unbiased approach like next-generation sequencing to further identify differences.
Roberts Insight
This document summarizes research on how environmental stressors and changes impact the expression of genes in oysters. The summary is:
[1] The research program examines how environmental stressors such as pathogens, carbon dioxide, mechanical stress, and anthropogenic activities affect the oyster stress response at the transcriptome, proteome, and epigenome levels.
[2] Studies found that multiple environmental stressors can interact to reduce an oyster's ability to respond to stress, and that characterizing gene expression in natural oyster populations exposed to different human impacts provided insight into their biology and adaptation.
[3] DNA methylation is an important mechanism in oysters for transcriptional control that can be impacted
Mac Gavery PCSGA_2009
Thank you for the presentation. This research aims to develop a better understanding of Puget Sound ecosystem health through the use of Pacific oysters as bioindicators. A variety of methods are being utilized including examining physiological stress responses, gene expression, epigenetics, and water quality data. Preliminary results suggest potential for these approaches.
SAFS Aquaculture
This document discusses using genomic approaches in aquaculture research. It summarizes work on using genomics to study myostatin regulation in fish to increase muscle growth, disease resistance in oysters and abalone, and changes in virulence of the pathogen Vibrio tubiashii under different environmental conditions. Future work is aimed at further characterizing host-pathogen interactions and responses to environmental change through comparative microbial and host response analyses.
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Event Link:- https://meetups.mulesoft.com/events/details/mulesoft-mysore-presents-mule-event-processing-models/
Agenda
● What is event processing in MuleSoft?
● Types of event processing models in Mule 4
● Distinction between the reactive, parallel, blocking & non-blocking processing
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Mysore WhatsApp group:- https://chat.whatsapp.com/EhqtHtCC75vCAX7gaO842N
Speaker:-
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Organizers:-
Shubham Chaurasia - https://www.linkedin.com/in/shubhamchaurasia1/
Giridhar Meka - https://www.linkedin.com/in/giridharmeka
Priya Shaw - https://www.linkedin.com/in/priya-shaw
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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.
Linear Measurements: Instruments used. Linear Measurement by Tape, Ranging out Survey Lines and overcoming Obstructions; Measurements on sloping ground; Tape corrections, conventional symbols. Angular Measurements: Instruments used; Introduction to Compass Surveying, Bearings and Longitude & Latitude of a Line, Introduction to total station.
Levelling: Instrument used Object of levelling, Methods of levelling in brief, and Contour maps.
Chapter 4
Buildings: Selection of site for Buildings, Layout of Building Plan, Types of buildings, Plinth area, carpet area, floor space index, Introduction to building byelaws, concept of sun light & ventilation. Components of Buildings & their functions, Basic concept of R.C.C., Introduction to types of foundation
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.
Water Pollution: Water Quality standards, Introduction to Treatment & Disposal of Waste Water. Reuse and Saving of Water, Rain Water Harvesting. Solid Waste Management: Classification of Solid Waste, Collection, Transportation and Disposal of Solid. Recycling of Solid Waste: Energy Recovery, Sanitary Landfill, On-Site Sanitation. Air & Noise Pollution: Primary and Secondary air pollutants, Harmful effects of Air Pollution, Control of Air Pollution. . Noise Pollution Harmful Effects of noise pollution, control of noise pollution, Global warming & Climate Change, Ozone depletion, Greenhouse effect
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1. Palancharmy, Basic Civil Engineering, McGraw Hill publishers.
2. Satheesh Gopi, Basic Civil Engineering, Pearson Publishers.
3. Ketki Rangwala Dalal, Essentials of Civil Engineering, Charotar Publishing House.
4. BCP, Surveying volume 1
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WERA 2009
- 1. University of Washington WERA Update 2009 Steven Roberts
- 2. • Pathogens • Shellfish Genomics
- 3. Pathogens • Vibrio tubiashii
- 4. Vibrio tubiashii 226 million bp
- 5. Vibrio tubiashii chitinase, serine protease, RSE
- 6. Genomics • Basics • Crassostrea gigas • Disease Tolerance • Crassostrea virginica • Haliotis cracherodii • Mercenaria mercenaria
- 7. C. gigas plated hemocytes Roberts et al 2009
- 8. C. gigas plated hemocytes Roberts et al 2009
- 9. C. gigas Vibrio challenge Roberts et al 2009
- 10. C. gigas Vibrio challenge Roberts et al 2008
- 11. C. gigas Vibrio challenge Prostaglandin E2 receptor EP4 subtype
- 12. Prostaglandins Gavery; Poster
- 13. Value-added
- 14. Disease Resistance • C. virginica • H. cracherodii • M. mercenaria
- 15. C. virginica
- 16. H. cracherodii
- 17. H. cracherodii
- 18. M. mercenaria photo: Dale Leavitt (RWU)
- 19. Other stuff • Epigenetics (methylation) • Gene annotation effort? (wiki)