BISC Award Recipients by on Scribd
Monday, April 29, 2019
MBBO Ph.D. Dissertation Defense | Erin McParland
Erin McParland
Ph.D. Candidate, MBBO Graduate Program (PI: Dr. Naomi Levine)
The dynamic regulation of DMSP production by marine phytoplankton
Wednesday, May 8, 2019
10 AM
AHF 153 (Torrey Webb Room)
Abstract: Dimethylsulfoniopropionate (DMSP) is a labile sulfur and carbon metabolite that significantly contributes to both the cycling of marine dissolved organic carbon and the balance of Earth’s albedo. DMSP is produced by the majority of eukaryotic marine phytoplankton and by many prokaryotes, but despite decades of research, the cellular mechanism and environmental drivers of DMSP production remain unknown. My thesis confirms that the cellular mechanism of DMSP is differentiated by the cellular concentrations of DMSP in different producers, where high DMSP producers (e.g. dinoflagellates and haptophytes) constitutively produce DMSP and low DMSP producers (e.g. cyanobacteria and diatoms) actively regulate DMSP production in response to environmental stress. However, with natural community experiments and global model predictions, my thesis demonstrates that variability of in situ DMSP production is driven by the biomass of high producers. My thesis highlights the potential for predicting in situ DMSP concentrations with a high DMSP producer marker gene and demonstrates the importance of accurately capturing the sub-dominant community for prediction of DMSP, or other similar metabolites produced by a small fraction of the marine microbial community.
Ph.D. Candidate, MBBO Graduate Program (PI: Dr. Naomi Levine)
The dynamic regulation of DMSP production by marine phytoplankton
Wednesday, May 8, 2019
10 AM
AHF 153 (Torrey Webb Room)
Abstract: Dimethylsulfoniopropionate (DMSP) is a labile sulfur and carbon metabolite that significantly contributes to both the cycling of marine dissolved organic carbon and the balance of Earth’s albedo. DMSP is produced by the majority of eukaryotic marine phytoplankton and by many prokaryotes, but despite decades of research, the cellular mechanism and environmental drivers of DMSP production remain unknown. My thesis confirms that the cellular mechanism of DMSP is differentiated by the cellular concentrations of DMSP in different producers, where high DMSP producers (e.g. dinoflagellates and haptophytes) constitutively produce DMSP and low DMSP producers (e.g. cyanobacteria and diatoms) actively regulate DMSP production in response to environmental stress. However, with natural community experiments and global model predictions, my thesis demonstrates that variability of in situ DMSP production is driven by the biomass of high producers. My thesis highlights the potential for predicting in situ DMSP concentrations with a high DMSP producer marker gene and demonstrates the importance of accurately capturing the sub-dominant community for prediction of DMSP, or other similar metabolites produced by a small fraction of the marine microbial community.
MBBO Ph.D. Dissertation Defense | Pingping Qu
Pingping Qu
Ph.D. Candidate, MBBO Graduate Program (PI: Dr. David Hutchins)
Thermal Acclimation and Adaptation of Key Phytoplankton Groups and Interactions with Other Global Change Variables
Wednesday, May 1, 2019
11 AM
AHF 153 (Torrey Webb Room)
Abstract: Marine phytoplankton play critical roles in global primary productivity, carbon export and biogeochemistry. The relationships between environmental forcing and key phytoplankton groups in marine ecosystems need more attention, especially under global change scenarios. Among many other environmental changes, phytoplankton communities in the euphotic zone are anticipated to be most sensitive to concurrent ocean acidification, warming, more thermal variability and reduced nutrient supplies.
Marine diatoms play critical roles in global primary productivity, carbon export and the food web. Marine diazotrophic cyanobacteria are equally important as a source of new nitrogen through nitrogen fixation. In order to better understand the possible responses of marine diatoms and diazotrophs to a changing ocean environment, my studies focused on the synergistic effects of multiple climate change variables on an important diatom, as well as the responses of two keystone diazotrophs to thermal variability and to long-term selection by warming.
In my first chapter, the physiological responses of the widespread centric diatom Coscinodiscus sp. to interactions between three climate-change variables (elevated CO2, warming, and nitrate availability) were investigated to better understand the interactions of multiple global changes on large, carbon-exporting diatoms. The second one examined how short-term thermal variability affects the growth and physiology of the diazotrophic cyanobacterium Trichodesmium erythraeum GBRTRLI101, as well as the interaction between temperature variation and phosphate availability. The third chapter tested the physiological responses and compared and contrasted acclimation and adaptation of Trichodesmium erythraeum IMS101 and Crocosphaera WH0005 under long-term experimental selection at different temperatures, exploring possible ecological and biogeochemical implications of ways that these two representative diazotrophic cyanobacteria may cope with future warmer conditions.
Ph.D. Candidate, MBBO Graduate Program (PI: Dr. David Hutchins)
Thermal Acclimation and Adaptation of Key Phytoplankton Groups and Interactions with Other Global Change Variables
Wednesday, May 1, 2019
11 AM
AHF 153 (Torrey Webb Room)
Abstract: Marine phytoplankton play critical roles in global primary productivity, carbon export and biogeochemistry. The relationships between environmental forcing and key phytoplankton groups in marine ecosystems need more attention, especially under global change scenarios. Among many other environmental changes, phytoplankton communities in the euphotic zone are anticipated to be most sensitive to concurrent ocean acidification, warming, more thermal variability and reduced nutrient supplies.
Marine diatoms play critical roles in global primary productivity, carbon export and the food web. Marine diazotrophic cyanobacteria are equally important as a source of new nitrogen through nitrogen fixation. In order to better understand the possible responses of marine diatoms and diazotrophs to a changing ocean environment, my studies focused on the synergistic effects of multiple climate change variables on an important diatom, as well as the responses of two keystone diazotrophs to thermal variability and to long-term selection by warming.
In my first chapter, the physiological responses of the widespread centric diatom Coscinodiscus sp. to interactions between three climate-change variables (elevated CO2, warming, and nitrate availability) were investigated to better understand the interactions of multiple global changes on large, carbon-exporting diatoms. The second one examined how short-term thermal variability affects the growth and physiology of the diazotrophic cyanobacterium Trichodesmium erythraeum GBRTRLI101, as well as the interaction between temperature variation and phosphate availability. The third chapter tested the physiological responses and compared and contrasted acclimation and adaptation of Trichodesmium erythraeum IMS101 and Crocosphaera WH0005 under long-term experimental selection at different temperatures, exploring possible ecological and biogeochemical implications of ways that these two representative diazotrophic cyanobacteria may cope with future warmer conditions.
Monday, April 22, 2019
MEB Graduate Student Seminars
Yi-Chun Yeh (PI: Dr. Jed Fuhrman)
Long-term dynamics of free-living and particle-associated prokaryotic communities at the San Pedro Ocean Time-series
Abstract: The free-living and particle-associated marine prokaryotes have been proved to differ in their diversity and composition, but drivers of their long-term dynamics are poorly understood. We thus investigated surface to bottom dynamics of free-living (0.2-1.2 µm) and particle-associated (1.2-80 µm) prokaryotes at the San Pedro Ocean Time Series (SPOT) during 2000-2018 by using ssu rRNA tag sequencing. We assessed factors influencing the temporal variation of community composition by canonical correspondence analysis (CCA), and community turnover by the β-nearest taxon index (βNTI), a measure designed to assess the extent of stochastic vs. deterministic drivers. The results showed free-living and particle-associated prokaryotic communities both have strong seasonality at the surface and the deep chlorophyll maximum (DCM), though seasonal variation decreased in warm years, notably after 2012. Moreover, the free-living fraction exhibited a relatively stable dynamic without decreasing in average similarity over time, whereas the particle-associated fraction was undergoing directional change.
Melissa DellaTorre (PI: Dr. Donal Manahan)
Mechanisms of food and temperature impacts on growth in the ocean
Abstract: Variations in sources of energy and temperature have major impacts on the survival and growth of organisms. For marine larval forms, the degree to which food availability can alter physiological tolerances to thermal stress remains unknown. In this presentation, the physiological mechanisms of growth that are impacted by food quantity and temperature will be analyzed, in addition to food-temperature interactions. The goal of these studies is to understand resilience potential to future scenarios of ocean change.
Ariel Levi Simons (PI: Dr. Sergey Nuzhdin)
Using 𝞪, 𝞫, and 𝞯 diversity in describing the health of stream-based benthic macroinvertebrate communities
Abstract: Ecological monitoring of streams has frequently focused on measures describing the taxonomic, and sometimes functional, α diversity of benthic macroinvertebrates (BMIs) within a single sampled community. However, as many ecological processes effectively link BMI stream communities there is a need to describe groups of communities using measures of regional diversity. Here we demonstrate a role for incorporating both a traditional pairwise measure of community turnover, β diversity, in assessing community health as well as ζ diversity, a more generalized framework for describing similarity between multiple communities. Using 4395 samples of BMI stream communities in California, we constructed a model using measures of α, β, and ζ diversity which could account for most of the among-watershed variation in the mean health of communities, as described by the California Streams Condition Index (CSCI).
Tuesday, April 23, 2019
12 PM
AHF 153 (Torrey Webb Room)
Long-term dynamics of free-living and particle-associated prokaryotic communities at the San Pedro Ocean Time-series
Abstract: The free-living and particle-associated marine prokaryotes have been proved to differ in their diversity and composition, but drivers of their long-term dynamics are poorly understood. We thus investigated surface to bottom dynamics of free-living (0.2-1.2 µm) and particle-associated (1.2-80 µm) prokaryotes at the San Pedro Ocean Time Series (SPOT) during 2000-2018 by using ssu rRNA tag sequencing. We assessed factors influencing the temporal variation of community composition by canonical correspondence analysis (CCA), and community turnover by the β-nearest taxon index (βNTI), a measure designed to assess the extent of stochastic vs. deterministic drivers. The results showed free-living and particle-associated prokaryotic communities both have strong seasonality at the surface and the deep chlorophyll maximum (DCM), though seasonal variation decreased in warm years, notably after 2012. Moreover, the free-living fraction exhibited a relatively stable dynamic without decreasing in average similarity over time, whereas the particle-associated fraction was undergoing directional change.
Melissa DellaTorre (PI: Dr. Donal Manahan)
Mechanisms of food and temperature impacts on growth in the ocean
Abstract: Variations in sources of energy and temperature have major impacts on the survival and growth of organisms. For marine larval forms, the degree to which food availability can alter physiological tolerances to thermal stress remains unknown. In this presentation, the physiological mechanisms of growth that are impacted by food quantity and temperature will be analyzed, in addition to food-temperature interactions. The goal of these studies is to understand resilience potential to future scenarios of ocean change.
Ariel Levi Simons (PI: Dr. Sergey Nuzhdin)
Using 𝞪, 𝞫, and 𝞯 diversity in describing the health of stream-based benthic macroinvertebrate communities
Abstract: Ecological monitoring of streams has frequently focused on measures describing the taxonomic, and sometimes functional, α diversity of benthic macroinvertebrates (BMIs) within a single sampled community. However, as many ecological processes effectively link BMI stream communities there is a need to describe groups of communities using measures of regional diversity. Here we demonstrate a role for incorporating both a traditional pairwise measure of community turnover, β diversity, in assessing community health as well as ζ diversity, a more generalized framework for describing similarity between multiple communities. Using 4395 samples of BMI stream communities in California, we constructed a model using measures of α, β, and ζ diversity which could account for most of the among-watershed variation in the mean health of communities, as described by the California Streams Condition Index (CSCI).
Tuesday, April 23, 2019
12 PM
AHF 153 (Torrey Webb Room)
MCB Colloquium Series | Dr. Susan Strome
Dr. Susan Strome
Distinguished Professor, UC Santa Cruz, MCD Biology
Lab Website
Passing an epigenetic “memory of germline" from parents to offspring
Friday, April 26, 2019
12 PM
RRI 101
Abstract: The Strome lab investigates the molecular mechanisms used by germ cells to establish and maintain their identity, immortality, and totipotency. They study germ cells in C. elegans using a variety of approaches, including genetics, genomics, and imaging. Their current focus is on regulation of chromatin states and the involvement of those states in transmitting an epigenetic “memory of germline” from parent germ cells to germ cells in offspring.
Distinguished Professor, UC Santa Cruz, MCD Biology
Lab Website
Passing an epigenetic “memory of germline" from parents to offspring
Friday, April 26, 2019
12 PM
RRI 101
Abstract: The Strome lab investigates the molecular mechanisms used by germ cells to establish and maintain their identity, immortality, and totipotency. They study germ cells in C. elegans using a variety of approaches, including genetics, genomics, and imaging. Their current focus is on regulation of chromatin states and the involvement of those states in transmitting an epigenetic “memory of germline” from parent germ cells to germ cells in offspring.
Monday, April 15, 2019
MEB Seminar Series | Dr. Shana Goffredi
Dr. Shana Goffredi
Associate Professor, Occidental College, Biology/Biochemistry
Lab Website
Extreme Alliances: Relationships between deep-sea animals and bacteria
Tuesday, April 16, 2019
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Forty years ago, scientists discovered invertebrates at the bottom of the ocean that forever changed how we view life on this planet. Abundant, thriving communities were not expected in the deep-sea, due to the very low levels of organic carbon that arrive at these depths from above. Certain worms, bivalves, and others, however, have forged relationships with bacteria, in order to harness inorganic sources of energy, typically foreign to animals. Symbiosis is the best of both worlds -- Morphological diversity of animals, and the Physiological diversity of bacteria. This seminar will highlight examples of deep-sea animal-bacterial symbioses from a variety of animal groups - some recently discovered, revealing surprising new relationships between animals and bacteria, and some among the oldest known.
Associate Professor, Occidental College, Biology/Biochemistry
Lab Website
Extreme Alliances: Relationships between deep-sea animals and bacteria
Tuesday, April 16, 2019
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Forty years ago, scientists discovered invertebrates at the bottom of the ocean that forever changed how we view life on this planet. Abundant, thriving communities were not expected in the deep-sea, due to the very low levels of organic carbon that arrive at these depths from above. Certain worms, bivalves, and others, however, have forged relationships with bacteria, in order to harness inorganic sources of energy, typically foreign to animals. Symbiosis is the best of both worlds -- Morphological diversity of animals, and the Physiological diversity of bacteria. This seminar will highlight examples of deep-sea animal-bacterial symbioses from a variety of animal groups - some recently discovered, revealing surprising new relationships between animals and bacteria, and some among the oldest known.
Watershed Stewards Program now accepting applications for Year 26
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2019 CGS/ProQuest Distinguished Dissertation Awards
Initial Nomination Packages due to grad school by Monday June 17, 2019 via this link.
Three letters of Recommendation for selected applicants due to graduate school by Monday July 1, 2019.
Sponsored jointly by Council of Graduate Schools (CGS) and ProQuest Dissertations Publishing, these dissertation awards are made annually to individuals who, in the opinion of the award committee, have completed dissertations representing original work that makes an unusually significant contribution to their disciplines.
2019 Fields of Competition
There are two broad fields of competition for the 2019 dissertation awards:
• Biological Sciences: biology; botany; zoology; ecology; embryology; entomology; genetics; nutrition; plant pathology; plant physiology; anatomy; biochemistry; biophysics; microbiology; pathology; pharmacology; physiology; and related fields. Also included are agriculture, forestry, and related fields.
• Humanities and Fine Arts: history; philosophy; language; linguistics; literature; archaeology; jurisprudence; the history, theory and criticism of the arts; ethics; comparative religion; and those aspects of the social sciences that employ historical or philosophical approaches.
If a dissertation is multi- or interdisciplinary in nature, a significant portion of the work must be comprised by at least one of the 2019 fields of competition.
Eligibility
• USC may nominate one person in the field of humanities and fine arts and one person in the field of biological sciences (for a total of two nominations maximum).
• The effective date of the degree awarded, or the completion of doctoral degree requirements and dissertation, must lie in the period of July 1, 2017 to June 30, 2019, inclusive, for each nominee selected.
Nomination Package
A complete nomination package includes the following components in this order:
1. An abstract of the nominee’s dissertation (not to exceed 10 double-spaced pages). Appendices containing other material, such as charts, tables, and/or references, may be included as additional pages (not to exceed 10 pages).
2. The nominee’s curriculum vitae (not to exceed five pages). Note: The initial nomination package must be sent as a single pdf document with the file saved as: last name of the nominee and institution (i.e. Smith_USC)
Selected students will also need to submit:
1. Three letters of recommendation evaluating the significance and quality of the dissertation work. One of these letters is to be from the nominee's dissertation supervisor, another from a member of the nominee's dissertation committee, and the third from a person of the nominee's choice.
Award Information:
Two CGS/ProQuest Distinguished Dissertation Awards, each consisting of an award of $2,000 and a certificate of recognition, will be presented at the CGS Annual Meeting Awards Luncheon on December 5, 2019, in Nashville, TN. Reasonable travel expenses of award recipients will be covered. Only the winners and the nominating deans will be notified of the outcomes of the competition prior to the Awards Luncheon.
Selection Process:
The Council of Graduate Schools will name an Award Committee whose members have established records in the disciplinary areas under consideration. Additional consultation may be sought at the discretion of the committee members. The nominated dissertations should represent original work making an unusually significant contribution to the disciplines. Both methodological and substantive quality will be judged.
Please Note: The CGS/ProQuest Award operates on a two-year cycle with regard to fields of competition. The fields of competition for 2020 will be Mathematics, Physical Sciences & Engineering, and the Social Sciences.
Three letters of Recommendation for selected applicants due to graduate school by Monday July 1, 2019.
Sponsored jointly by Council of Graduate Schools (CGS) and ProQuest Dissertations Publishing, these dissertation awards are made annually to individuals who, in the opinion of the award committee, have completed dissertations representing original work that makes an unusually significant contribution to their disciplines.
2019 Fields of Competition
There are two broad fields of competition for the 2019 dissertation awards:
• Biological Sciences: biology; botany; zoology; ecology; embryology; entomology; genetics; nutrition; plant pathology; plant physiology; anatomy; biochemistry; biophysics; microbiology; pathology; pharmacology; physiology; and related fields. Also included are agriculture, forestry, and related fields.
• Humanities and Fine Arts: history; philosophy; language; linguistics; literature; archaeology; jurisprudence; the history, theory and criticism of the arts; ethics; comparative religion; and those aspects of the social sciences that employ historical or philosophical approaches.
If a dissertation is multi- or interdisciplinary in nature, a significant portion of the work must be comprised by at least one of the 2019 fields of competition.
Eligibility
• USC may nominate one person in the field of humanities and fine arts and one person in the field of biological sciences (for a total of two nominations maximum).
• The effective date of the degree awarded, or the completion of doctoral degree requirements and dissertation, must lie in the period of July 1, 2017 to June 30, 2019, inclusive, for each nominee selected.
Nomination Package
A complete nomination package includes the following components in this order:
1. An abstract of the nominee’s dissertation (not to exceed 10 double-spaced pages). Appendices containing other material, such as charts, tables, and/or references, may be included as additional pages (not to exceed 10 pages).
2. The nominee’s curriculum vitae (not to exceed five pages). Note: The initial nomination package must be sent as a single pdf document with the file saved as: last name of the nominee and institution (i.e. Smith_USC)
Selected students will also need to submit:
1. Three letters of recommendation evaluating the significance and quality of the dissertation work. One of these letters is to be from the nominee's dissertation supervisor, another from a member of the nominee's dissertation committee, and the third from a person of the nominee's choice.
Award Information:
Two CGS/ProQuest Distinguished Dissertation Awards, each consisting of an award of $2,000 and a certificate of recognition, will be presented at the CGS Annual Meeting Awards Luncheon on December 5, 2019, in Nashville, TN. Reasonable travel expenses of award recipients will be covered. Only the winners and the nominating deans will be notified of the outcomes of the competition prior to the Awards Luncheon.
Selection Process:
The Council of Graduate Schools will name an Award Committee whose members have established records in the disciplinary areas under consideration. Additional consultation may be sought at the discretion of the committee members. The nominated dissertations should represent original work making an unusually significant contribution to the disciplines. Both methodological and substantive quality will be judged.
Please Note: The CGS/ProQuest Award operates on a two-year cycle with regard to fields of competition. The fields of competition for 2020 will be Mathematics, Physical Sciences & Engineering, and the Social Sciences.
Monday, April 8, 2019
Ambassadors of the Future Award - Summer funding opportunity
Prize: Five $5,000 awards are available
Established to support graduate students majoring in the natural sciences who have demonstrated a commitment to work with the Hungarian community.
· GPA of 3.0 or higher
· Preference given to students who foster cooperation between USC and individuals and/or institutions with Hungarian affiliation.
Hungarian international students are welcome to apply.
Submit the following to Kim Allen by April 26th:
STARS report
CV
A brief statement discussing how you have shown a commitment to fostering cooperation between USC and individuals and/or institutions with Hungarian affiliation.
Established to support graduate students majoring in the natural sciences who have demonstrated a commitment to work with the Hungarian community.
· GPA of 3.0 or higher
· Preference given to students who foster cooperation between USC and individuals and/or institutions with Hungarian affiliation.
Hungarian international students are welcome to apply.
Submit the following to Kim Allen by April 26th:
STARS report
CV
A brief statement discussing how you have shown a commitment to fostering cooperation between USC and individuals and/or institutions with Hungarian affiliation.
MCB Colloquium Series | Dr. David M. Gilbert
Dr. David M. Gilbert
J. Herbert Taylor Distinguished Professor of Molecular Biology, Florida State University, Dept. of Biological Science
Lab Website
Regulation of Replication Timing and Chromosome Architecture
Friday, April 12
12 PM
RRI 101
Abstract: The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide earlyto- late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these ‘‘early replication control elements’’ (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.
J. Herbert Taylor Distinguished Professor of Molecular Biology, Florida State University, Dept. of Biological Science
Lab Website
Regulation of Replication Timing and Chromosome Architecture
Friday, April 12
12 PM
RRI 101
Abstract: The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide earlyto- late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these ‘‘early replication control elements’’ (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.
MEB Graduate Student Seminars
ELAINA GRAHAM (PI: Prof. John Heidleberg)
Efforts in enrichment of novel photoautotroph identified through metagenomics
Abstract: Aerobic anoxygenic phototrophs are ubiquitous throughout the global ocean, making up to 11% of the community in some locations. Traditionally aerobic anoxygenic phototrophs have been associated with photoheterotrophy while anaerobic anoxygenic phototrophs were associated with facultative photoautotrophy. Using draft genomes generated from the Tara Oceans metagenomic dataset, 11 draft genomes were identified that lacked key genes for survival in suboxic environments and possessed key genes with the potential for anoxygenic phototrophy via Type-II photochemical reaction centers, carbon fixation via the Calvin-Benson-Bassham cycle, and lithotrophic energy utilization via the oxidation of sulfite and/or thiosulfate. To further study this group and characterize its carbon fixation capability and metabolism there is a need to enrich or isolate the organism. Here we have used comparative genomics to predict the potential metabolism and designed a low nutrient autotrophic medium to enrich for this group using sea water collected at the surface from the San Pedro Ocean Time series (SPOT).
JOSH KLING (PI: Prof. David Hutchins and Prof. Feixue Fu)
Thermal Diversity in a Coastal Marine Synechoccus Population Selected Under Low- and High Temperatures
Abstract: Synechococcus is a photoautroph found from the equator to near polar waters and contributes together with other picocyanobacteria as much as 25% of net primary productivity in the ocean. The effect of temperature on intraspecific Synechococcus diversity and evolution is well documented; however, it is usually expressed as changing the distribution and relative abundance of distinct clades. To probe for diverse phenotypes, we enriched for photoautotrophs from water collected at the Narragansett Bay Time-series and grown at unseasonably low (18° C) and high (30°) temperatures. From these enrichments, we isolated multiple Synechococcus sp. and quantified their thermal niche by generating thermal performance curves for each, which revealed distinct thermotypes characterized by different maximum temperature limits and optimal temperatures. To understand the genotypic diversity underlying observed phenotypic diversity, we sequenced the genomes of 8 strains, and we found evidence that suggests that variation in genes underlying accessory photosynthetic pigments appears to be related to thermal phenotype in our Synechococcus strains.
JASON WANG (PI: Prof. Donal Manahan)
Challenges with linking genes to organismal function
Abstract: The leading edge of biological discovery is enabled by a limited number of “model” organisms, with sophisticated resources for the study of genes and their function. Studies of most organisms, however, lack such resources, in particular for the study of functional genomics. The increasing availability of completed genomes and the use of biotechnology in “non-model” organisms offer new opportunities to bridge gaps in understanding biological function, from genes to the whole-organism. I will present some recent steps taken to understand the function of an expanded set of orthologous genes that have been identified in developmental stages of marine invertebrates. These studies have implications for understanding the molecular biological basis of nutrient uptake, with predicting links to whole-organism growth rates.
Tuesday, April 9
12 PM
AHF 153 (Torrey Webb Room)
Efforts in enrichment of novel photoautotroph identified through metagenomics
Abstract: Aerobic anoxygenic phototrophs are ubiquitous throughout the global ocean, making up to 11% of the community in some locations. Traditionally aerobic anoxygenic phototrophs have been associated with photoheterotrophy while anaerobic anoxygenic phototrophs were associated with facultative photoautotrophy. Using draft genomes generated from the Tara Oceans metagenomic dataset, 11 draft genomes were identified that lacked key genes for survival in suboxic environments and possessed key genes with the potential for anoxygenic phototrophy via Type-II photochemical reaction centers, carbon fixation via the Calvin-Benson-Bassham cycle, and lithotrophic energy utilization via the oxidation of sulfite and/or thiosulfate. To further study this group and characterize its carbon fixation capability and metabolism there is a need to enrich or isolate the organism. Here we have used comparative genomics to predict the potential metabolism and designed a low nutrient autotrophic medium to enrich for this group using sea water collected at the surface from the San Pedro Ocean Time series (SPOT).
JOSH KLING (PI: Prof. David Hutchins and Prof. Feixue Fu)
Thermal Diversity in a Coastal Marine Synechoccus Population Selected Under Low- and High Temperatures
Abstract: Synechococcus is a photoautroph found from the equator to near polar waters and contributes together with other picocyanobacteria as much as 25% of net primary productivity in the ocean. The effect of temperature on intraspecific Synechococcus diversity and evolution is well documented; however, it is usually expressed as changing the distribution and relative abundance of distinct clades. To probe for diverse phenotypes, we enriched for photoautotrophs from water collected at the Narragansett Bay Time-series and grown at unseasonably low (18° C) and high (30°) temperatures. From these enrichments, we isolated multiple Synechococcus sp. and quantified their thermal niche by generating thermal performance curves for each, which revealed distinct thermotypes characterized by different maximum temperature limits and optimal temperatures. To understand the genotypic diversity underlying observed phenotypic diversity, we sequenced the genomes of 8 strains, and we found evidence that suggests that variation in genes underlying accessory photosynthetic pigments appears to be related to thermal phenotype in our Synechococcus strains.
JASON WANG (PI: Prof. Donal Manahan)
Challenges with linking genes to organismal function
Abstract: The leading edge of biological discovery is enabled by a limited number of “model” organisms, with sophisticated resources for the study of genes and their function. Studies of most organisms, however, lack such resources, in particular for the study of functional genomics. The increasing availability of completed genomes and the use of biotechnology in “non-model” organisms offer new opportunities to bridge gaps in understanding biological function, from genes to the whole-organism. I will present some recent steps taken to understand the function of an expanded set of orthologous genes that have been identified in developmental stages of marine invertebrates. These studies have implications for understanding the molecular biological basis of nutrient uptake, with predicting links to whole-organism growth rates.
12 PM
AHF 153 (Torrey Webb Room)
Monday, April 1, 2019
QCB Colloquium Series | Dr. Joshua Schraiber
Dr. Joshua Schraiber
Ancestry.com DNA Science
Assistant Professor (Leave of Absence), Temple University, Institute for Genomics and Evolutionary Medicine
Through a sequencer, darkly: statistical inference from ancient DNA
Thursday, April 4
2 PM
RRI 101
Abstract: The advent of ancient DNA sequencing opened an unprecedented window into the recent evolutionary past. Hypotheses about population continuity and natural selections, once only accessible via circumstantial evidence, can now be tested directly. However, ancient DNA is often degraded and damaged, resulting in a blurry view. To get the most of out of this exciting data, we need careful statistical modeling. In this talk, I will present work on statistical methods for learning about demographic and selective history from ancient DNA. First, I will describe about a Bayesian approach for inference of natural selection from allele frequency time series. I show that accounting for demographic history has tremendous impacts on allele age estimates, and demonstrate on empirical data that modeling demography qualitatively impacts inferences about the mode of natural selection. However, assessing the strength of selection implicitly assumes that all samples are members of the same population through time. Moreover, many questions in evolutionary biology revolve around population continuity: are the individuals that live in a location now related to those that used to inhabit that area? To assess population continuity, I developed a framework to leverage genome-wide data from low coverage ancient samples. When applying this approach to ancient Europeans, I see that the history of stone age Europe is characterized by small populations and local extinction. Finally, I discuss recently completed work using deep learning to understand subtle points about the history of human-Neandertal interbreeding. We find strong evidence of multiple episodes of interbreeding across Eurasia, leading to a picture of a complex history of human-archaic interactions
Ancestry.com DNA Science
Assistant Professor (Leave of Absence), Temple University, Institute for Genomics and Evolutionary Medicine
Through a sequencer, darkly: statistical inference from ancient DNA
Thursday, April 4
2 PM
RRI 101
Abstract: The advent of ancient DNA sequencing opened an unprecedented window into the recent evolutionary past. Hypotheses about population continuity and natural selections, once only accessible via circumstantial evidence, can now be tested directly. However, ancient DNA is often degraded and damaged, resulting in a blurry view. To get the most of out of this exciting data, we need careful statistical modeling. In this talk, I will present work on statistical methods for learning about demographic and selective history from ancient DNA. First, I will describe about a Bayesian approach for inference of natural selection from allele frequency time series. I show that accounting for demographic history has tremendous impacts on allele age estimates, and demonstrate on empirical data that modeling demography qualitatively impacts inferences about the mode of natural selection. However, assessing the strength of selection implicitly assumes that all samples are members of the same population through time. Moreover, many questions in evolutionary biology revolve around population continuity: are the individuals that live in a location now related to those that used to inhabit that area? To assess population continuity, I developed a framework to leverage genome-wide data from low coverage ancient samples. When applying this approach to ancient Europeans, I see that the history of stone age Europe is characterized by small populations and local extinction. Finally, I discuss recently completed work using deep learning to understand subtle points about the history of human-Neandertal interbreeding. We find strong evidence of multiple episodes of interbreeding across Eurasia, leading to a picture of a complex history of human-archaic interactions
QCB Colloquium Series | Dr. K. Lenhard Rudolph
Dr. K. Lenhard Rudolph
Friedrich Schiller University, Fritz Lipmann Institute in Jena, Germany, Leibniz Institute on Aging
Research Group Info
Metabolism and epigenetic stress response of aging stem cells
Monday, April 1
2 PM
RRI 101
Abstract: Adult tissue stem cells contribute to the lifelong maintenance of organ homeostasis and regeneration. However, the functionality of stem cells declines during aging and there is emerging evidence for the clonal dominance of mutant stem cells. Both processes contribute to the evolution of aging associated dysfunctions and diseases but molecular mechanisms that impair the function of stem cells during aging remain incompletely understood. Our recent work revealed that alterations in epigenetic stress responses lead to an aberrant activation of developmental pathways that impair the self renewal and regenerative capacity of muscle stem cells. During my talk I will present new data on aging associated changes in vitamin-A/retinoic acid metabolism and in ATP producing pathways that contribute to alterations of gene regulation and functionality of aging stem cells.
Friedrich Schiller University, Fritz Lipmann Institute in Jena, Germany, Leibniz Institute on Aging
Research Group Info
Metabolism and epigenetic stress response of aging stem cells
Monday, April 1
2 PM
RRI 101
Abstract: Adult tissue stem cells contribute to the lifelong maintenance of organ homeostasis and regeneration. However, the functionality of stem cells declines during aging and there is emerging evidence for the clonal dominance of mutant stem cells. Both processes contribute to the evolution of aging associated dysfunctions and diseases but molecular mechanisms that impair the function of stem cells during aging remain incompletely understood. Our recent work revealed that alterations in epigenetic stress responses lead to an aberrant activation of developmental pathways that impair the self renewal and regenerative capacity of muscle stem cells. During my talk I will present new data on aging associated changes in vitamin-A/retinoic acid metabolism and in ATP producing pathways that contribute to alterations of gene regulation and functionality of aging stem cells.
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