Nirupa Chaudhari Flier 11-02-18 by uscbiscgrad on Scribd
Monday, October 29, 2018
MEB Seminar Series | Nathan Walworth, Ph.D.
Nathan Walworth, Ph.D.
Postdoctoral Researcher, USC, BISC
Prof. Naomi Levine’s Lab
Hitting a moving target: Microbial evolution in a dynamic ocean
Tuesday, October 30, 2018
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Microbes drive global biogeochemistry yet little is known about their microevolutionary rates and processes in response to global change. This is particularly critical in marine systems where long-term trends (e.g. warming) are overlain onto short timescale variability (e.g. eddies) and where advection moves organisms rapidly between ecoregions. The interplay between physical and evolutionary timescales was investigated using a model of adaptation coupled with an eddy-resolving climate model. Fitness increases were encoded by epigenetic modifications under short exposure times to new environments, with beneficial genetic mutations only contributing after extended exposure times. The relationship between microevolutionary and physical timescales is critical for determining future adaptation where assuming instant adaptation may bias model predictions of microbial dynamics. Decoupling between locations of selective pressure and regions of accumulation for adapted individuals was observed. These accumulation zones may act as ‘seed banks’ for novel genotypes and thus evolutionary hotspots under global change.
Postdoctoral Researcher, USC, BISC
Prof. Naomi Levine’s Lab
Hitting a moving target: Microbial evolution in a dynamic ocean
Tuesday, October 30, 2018
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Microbes drive global biogeochemistry yet little is known about their microevolutionary rates and processes in response to global change. This is particularly critical in marine systems where long-term trends (e.g. warming) are overlain onto short timescale variability (e.g. eddies) and where advection moves organisms rapidly between ecoregions. The interplay between physical and evolutionary timescales was investigated using a model of adaptation coupled with an eddy-resolving climate model. Fitness increases were encoded by epigenetic modifications under short exposure times to new environments, with beneficial genetic mutations only contributing after extended exposure times. The relationship between microevolutionary and physical timescales is critical for determining future adaptation where assuming instant adaptation may bias model predictions of microbial dynamics. Decoupling between locations of selective pressure and regions of accumulation for adapted individuals was observed. These accumulation zones may act as ‘seed banks’ for novel genotypes and thus evolutionary hotspots under global change.
Monday, October 22, 2018
Thesis Center Office Hours + FAQ for Students
Sam Mantell of the Graduate School will be holding Thesis Center Office Hours. If you will be submitting a thesis/dissertation manuscript this term and need one-on-one assistance with Thesis Center, please schedule an appointment to meet with him.
Office Hours will be held on UPC, in STU 301, and on HSC, in CHP 219, between 10 /18 and 10/24. Office Hours appointments can be scheduled on the Graduate School website, in the Graduate Events page.
Attached, you will find Thesis Center FAQ for Students.
Office Hours will be held on UPC, in STU 301, and on HSC, in CHP 219, between 10 /18 and 10/24. Office Hours appointments can be scheduled on the Graduate School website, in the Graduate Events page.
Attached, you will find Thesis Center FAQ for Students.
Thesis Center FAQ for Students by uscbiscgrad on Scribd
The Irving and Jeanne Glovin Award 2018-19
Attached, you will find this year's announcement for the Glovin Award. This award is granted to a graduate student who demonstrates scholarly excellence and wishes to carry out research into and produce an essay related to the nature of good human conduct. The award consists of a $2,500 research stipend for the student and a $500 research grant for the recipient's project advisor.
Applications are due no later than Friday, November 2, 2018.
Applications are due no later than Friday, November 2, 2018.
Glovin Award Announcement 2018-19 by uscbiscgrad on Scribd
Sunday, October 21, 2018
MEB Seminar Series | Daniel Pondella, Ph.D.
Daniel Pondella, Ph.D.
Professor, Occidental College, Biology; Director, Vantuna Research Group
Research Group Website
More Big Fish, Restoring the Southern California Rocky Reef Ecosystem
Tuesday, October 23
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Southern California has one of the most dynamic and productive marine rocky-reef ecosystems in the world. Its characteristic giant kelp beds are a visual reminder from the surface of the majestic expanse found below. Unfortunately, despite its potential we have observed decades of chronic decline in ecosystem health and services. This decline in health for rocky reefs and kelp beds is a result of pollution, habitat loss and overfishing and is particularly problematic for coastal communities where the loss of commercial and recreational fishing opportunities has negatively affected the economy of the region. Traditional management actions can have positive changes, are generally passive (like changing a fishery regulation) but usually work on multi-year to multi-decadal time scales. While my research has highlighted these positive longterm impacts including the return of ‘big fish’ (giant seabass, white seabass, leopard shark, soupfins etc.), my current research is focused on creating solutions that work in short time scales, what I refer to as active management. My colleagues and I are currently developing and implementing a variety of restoration and enhancement techniques to restore the Southern California rocky reef ecosystem using the Palos Verdes Peninsula as the starting point for the region. To support the science behind understanding the efficacy of these technique, I focus on developing ecosystem-based spatial and timeseries models primarily utilizing marine fishes to evaluate and improve our restoration efforts. Considering the challenges our coastline continues to face, immediately improving the health of our rocky-reef ecosystem and associated fisheries is paramount.
Professor, Occidental College, Biology; Director, Vantuna Research Group
Research Group Website
More Big Fish, Restoring the Southern California Rocky Reef Ecosystem
Tuesday, October 23
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Southern California has one of the most dynamic and productive marine rocky-reef ecosystems in the world. Its characteristic giant kelp beds are a visual reminder from the surface of the majestic expanse found below. Unfortunately, despite its potential we have observed decades of chronic decline in ecosystem health and services. This decline in health for rocky reefs and kelp beds is a result of pollution, habitat loss and overfishing and is particularly problematic for coastal communities where the loss of commercial and recreational fishing opportunities has negatively affected the economy of the region. Traditional management actions can have positive changes, are generally passive (like changing a fishery regulation) but usually work on multi-year to multi-decadal time scales. While my research has highlighted these positive longterm impacts including the return of ‘big fish’ (giant seabass, white seabass, leopard shark, soupfins etc.), my current research is focused on creating solutions that work in short time scales, what I refer to as active management. My colleagues and I are currently developing and implementing a variety of restoration and enhancement techniques to restore the Southern California rocky reef ecosystem using the Palos Verdes Peninsula as the starting point for the region. To support the science behind understanding the efficacy of these technique, I focus on developing ecosystem-based spatial and timeseries models primarily utilizing marine fishes to evaluate and improve our restoration efforts. Considering the challenges our coastline continues to face, immediately improving the health of our rocky-reef ecosystem and associated fisheries is paramount.
Computational Biology Colloquium | Kelley Harris, Ph.D.
Kelley Harris, Ph.D.
Assistant Professor, University of Washington, Department of Genome Sciences
Lab Website
Using archaic introgression to probe enhancer function and evolution
Thursday, October 25, 2018
2 PM
RRI 101
Abstract: After Neanderthals interbred with humans, their DNA was selectively purged from many functional regions of the genome. Protein coding regions, for example, tend to have less Neanderthal DNA than regions that evolve more neutrally, and this imbalance implies that Neanderthal genes put hybrids at a fitness disadvantage compared to contemporaries without hybrid ancestry. As such, the landscape of Neanderthal introgression provides a snapshot of selection that occurred about 50,000 years ago as a result of the differences that arose over 300,000 years of Neanderthal/human divergence. To deduce how much of this selection may have been driven by gene regulation rather than gene sequence, we examine how high-confidence Neanderthal variants annotated by Sankararaman, et al. are distributed in enhancer regions annotated by the ENCODE project, calculating the binomial enrichment/depletion of Neanderthal variants in enhancers compared to a set of control variants matched for allele frequency and the local intensity of background selection. We find that enhancers appear to have tolerated Neanderthal introgression slightly better than genes or promoters have, but are still significantly depleted of introgression more than expected based on their relatively modest level of sequence conservation. We find that highly pleiotropic enhancers active in many tissue types are the most intolerant to introgression, whereas tissue-specific enhancers are relatively tolerant to Neanderthal DNA, perhaps because changes to the sequences of tissue-specific enhancers are easier to buffer and therefore less damaging to regulatory function. Every cell type profiled by ENCODE appears somewhat intolerant to the presence of Neanderthal DNA in its complement of enhancers, but the magnitude of this intolerance varies by tissue type. Introgression depletion is correlated across tissues with skew in the site frequency spectrum toward rare variants, but this correlation is imperfect, indicating that the introgression landscape provides additional information about genomic functionality that cannot be gleaned from conservation information alone. Fetal enhancers, in particular, seem to tolerate new mutations better than brain enhancers do, but of the two categories, fetal enhancers are less tolerant of introgression. Fetal enhancers that are classified as human accelerated regions (HARs) show the strongest introgression intolerance of all, suggesting that enhancers in this pathway have experienced more functionally significant changes since the human/Neanderthal split than other pathways that exhibit more enhancer sequence conservation overall.
Host: Mark Chaisson
Assistant Professor, University of Washington, Department of Genome Sciences
Lab Website
Using archaic introgression to probe enhancer function and evolution
Thursday, October 25, 2018
2 PM
RRI 101
Abstract: After Neanderthals interbred with humans, their DNA was selectively purged from many functional regions of the genome. Protein coding regions, for example, tend to have less Neanderthal DNA than regions that evolve more neutrally, and this imbalance implies that Neanderthal genes put hybrids at a fitness disadvantage compared to contemporaries without hybrid ancestry. As such, the landscape of Neanderthal introgression provides a snapshot of selection that occurred about 50,000 years ago as a result of the differences that arose over 300,000 years of Neanderthal/human divergence. To deduce how much of this selection may have been driven by gene regulation rather than gene sequence, we examine how high-confidence Neanderthal variants annotated by Sankararaman, et al. are distributed in enhancer regions annotated by the ENCODE project, calculating the binomial enrichment/depletion of Neanderthal variants in enhancers compared to a set of control variants matched for allele frequency and the local intensity of background selection. We find that enhancers appear to have tolerated Neanderthal introgression slightly better than genes or promoters have, but are still significantly depleted of introgression more than expected based on their relatively modest level of sequence conservation. We find that highly pleiotropic enhancers active in many tissue types are the most intolerant to introgression, whereas tissue-specific enhancers are relatively tolerant to Neanderthal DNA, perhaps because changes to the sequences of tissue-specific enhancers are easier to buffer and therefore less damaging to regulatory function. Every cell type profiled by ENCODE appears somewhat intolerant to the presence of Neanderthal DNA in its complement of enhancers, but the magnitude of this intolerance varies by tissue type. Introgression depletion is correlated across tissues with skew in the site frequency spectrum toward rare variants, but this correlation is imperfect, indicating that the introgression landscape provides additional information about genomic functionality that cannot be gleaned from conservation information alone. Fetal enhancers, in particular, seem to tolerate new mutations better than brain enhancers do, but of the two categories, fetal enhancers are less tolerant of introgression. Fetal enhancers that are classified as human accelerated regions (HARs) show the strongest introgression intolerance of all, suggesting that enhancers in this pathway have experienced more functionally significant changes since the human/Neanderthal split than other pathways that exhibit more enhancer sequence conservation overall.
Host: Mark Chaisson
Monday, October 15, 2018
This week on campus | 10/15-10/21
Below is a curated list of events on campus that may be of interest to BISC students.
Monday, October 15
The Boba Truck at SOTO Building
TAI CHI - Movement Meditation Series
Tuesday, October 16
USC Stem Cell Seminar: Martin Lotz, Scripps
Curator's Walkthrough
USC Spatial Brown Bag Series
Interview and Negotiation Workshop
USC Dornsife Career Pathways Work it Series | Close it: Salary negotiation and job offers
KUNDALINI YOGA - Movement Meditation Series
Wednesday, October 17
Justin's Sampling at Seeds
Trojan Farmers Market
Research Gateway Scholars Program
USC Global Fellows Internship Program Information Session
Feel Better Workshops Drop-In - USC Student Health
Music@RushHour: Lisztomania Part I
Trojan Scary Farm
Let's Talk - International Student Workshops - Drop-in
USC Interfaith Council
Thursday, October 18
Study Abroad in Madrid Info Session - USC Madrid
IYENGAR YOGA - Movement Meditation Series
Major2Career Oppor2nity Peace Corps
CommuniTEA
Feel Better Workshops Drop-In - USC Student Health
Los Angeles Philharmonic: Romeo & Juliet with Gustavo Dudamel and Benjamin Millepied
Jazz Duos: Voice & Guitar
Friday, October 19
Ming Hsieh Institute Symposium
LABYRINTH - Movement Meditation Series
Yoga at Fisher
Mindful Yoga
USC Stem Cell Student/Postdoc Seminar
Probability and Statistics Seminar: Diffusion-Limited Annihilating Systems
Late Night SC Griffith Park Night Hike
USC Thornton Chamber Singers & Concert Choir: Radiant Dawn
Saturday, October 20
Metropolitan Opera Live in HD: Giuseppe Verdi's “Aida”
Monday, October 15
The Boba Truck at SOTO Building
TAI CHI - Movement Meditation Series
Tuesday, October 16
USC Stem Cell Seminar: Martin Lotz, Scripps
Curator's Walkthrough
USC Spatial Brown Bag Series
Interview and Negotiation Workshop
USC Dornsife Career Pathways Work it Series | Close it: Salary negotiation and job offers
KUNDALINI YOGA - Movement Meditation Series
Wednesday, October 17
Justin's Sampling at Seeds
Trojan Farmers Market
Research Gateway Scholars Program
USC Global Fellows Internship Program Information Session
Feel Better Workshops Drop-In - USC Student Health
Music@RushHour: Lisztomania Part I
Trojan Scary Farm
Let's Talk - International Student Workshops - Drop-in
USC Interfaith Council
Thursday, October 18
Study Abroad in Madrid Info Session - USC Madrid
IYENGAR YOGA - Movement Meditation Series
Major2Career Oppor2nity Peace Corps
CommuniTEA
Feel Better Workshops Drop-In - USC Student Health
Los Angeles Philharmonic: Romeo & Juliet with Gustavo Dudamel and Benjamin Millepied
Jazz Duos: Voice & Guitar
Friday, October 19
Ming Hsieh Institute Symposium
LABYRINTH - Movement Meditation Series
Yoga at Fisher
Mindful Yoga
USC Stem Cell Student/Postdoc Seminar
Probability and Statistics Seminar: Diffusion-Limited Annihilating Systems
Late Night SC Griffith Park Night Hike
USC Thornton Chamber Singers & Concert Choir: Radiant Dawn
Saturday, October 20
Metropolitan Opera Live in HD: Giuseppe Verdi's “Aida”
MEB Seminar Series | Anne Dekas, Ph.D.
Anne Dekas, Ph.D.
Assistant Professor, Stanford University
Lab Website
Linking function to phylogeny in marine microbes: two stories from the dark ocean
October 16
12 PM
AHF 153 (Torrey Webb Room)
RESEARCH OVERVIEW
Microorganisms collectively shape the chemistry of our planet, and have for billions of years. Understanding the activity and metabolic capabilities of microbes in the modern environment is therefore critical to understanding the history of the Earth, as well as the future of our climate.
The Dekas Lab focuses on understanding the microbiology and biogeochemistry of the deep sea: the largest and least explored habitat on the surface of our planet. We investigate the diversity, distribution and activity of marine bacteria and archaea driving carbon, nitrogen, and sulfur cycling, with a focus on processes directly and indirectly involved in the production and consumption of greenhouse gases (e.g. CH4, CO2 and N2O). Using techniques from both molecular biology and isotope geochemistry, we answer questions such as: (1) “who” is doing “what” (linking phylogenetic identity to physiological function), (2) what are the biogeochemical controls on metabolic rates, (3) how do specific metabolisms affect global scale biogeochemical cycles and climate, and (4) will these metabolisms act as a positive or negative feedback to climate change?
Assistant Professor, Stanford University
Lab Website
Linking function to phylogeny in marine microbes: two stories from the dark ocean
October 16
12 PM
AHF 153 (Torrey Webb Room)
RESEARCH OVERVIEW
Microorganisms collectively shape the chemistry of our planet, and have for billions of years. Understanding the activity and metabolic capabilities of microbes in the modern environment is therefore critical to understanding the history of the Earth, as well as the future of our climate.
The Dekas Lab focuses on understanding the microbiology and biogeochemistry of the deep sea: the largest and least explored habitat on the surface of our planet. We investigate the diversity, distribution and activity of marine bacteria and archaea driving carbon, nitrogen, and sulfur cycling, with a focus on processes directly and indirectly involved in the production and consumption of greenhouse gases (e.g. CH4, CO2 and N2O). Using techniques from both molecular biology and isotope geochemistry, we answer questions such as: (1) “who” is doing “what” (linking phylogenetic identity to physiological function), (2) what are the biogeochemical controls on metabolic rates, (3) how do specific metabolisms affect global scale biogeochemical cycles and climate, and (4) will these metabolisms act as a positive or negative feedback to climate change?
Monday, October 8, 2018
Subscribe to U.S. Coastal Research Program's Quarterly Bulletin
Anyone interested in collaborative coastal research should sign up for the U.S. Coastal Research Program's Quarterly Bulletin.
E-mail info@uscoastalresearch.org
ABOUT USCRP: Founded in 2016, the U.S. Coastal Research Program (USCRP) was formed as a grass-roots collaboration of researchers from Federal agencies, academia, & NGOs to better coordinate coastal research, enhance funding sources, & strengthen academic programs to build a skilled workforce.
E-mail info@uscoastalresearch.org
ABOUT USCRP: Founded in 2016, the U.S. Coastal Research Program (USCRP) was formed as a grass-roots collaboration of researchers from Federal agencies, academia, & NGOs to better coordinate coastal research, enhance funding sources, & strengthen academic programs to build a skilled workforce.
This week on campus | 10/8-10/14
Below is a curated list of events on campus that may be of interest to BISC students.
Monday, October 8
Research Gateway Scholars Program
TAI CHI - Movement Meditation Series
Jazz Night: USC Thornton Concert Jazz Orchestra performs music from “West Side Story”
Tuesday, October 9
USC Stem Cell Seminar: Mo Ebrahimkhani, Arizona State University
Pasadena Career Fair & Job Fair
Interview and Negotiation Workshop
USC Dornsife Career Pathways Work it Series | Close it: Salary negotiation and job offers
KUNDALINI YOGA - Movement Meditation Series
Wednesday, October 10
San Diego Career Fair & Job Fair
Columbia’s Sustainability Graduate Programs
Feel Better Workshops Drop-In - USC Student Health
Music@RushHour: USC Brass Ensemble
USC Interfaith Council
Popular Music: First-Year Showcase
Thursday, October 11
Trojan Family Weekend 2018
USC Stem Cell and BCRegMed Virtual Symposium
Trojan Farmers Market
San Francisco Career Fair & Job Fair
IYENGAR YOGA - Movement Meditation Series
Keep Up with Social Media: Your Online Presence
CommuniTEA
Feel Better Workshops Drop-In - USC Student Health
Film Screening: Alone in the Game
Friday, October 12
12th Annual USC Stevens Student Innovator Showcase
LABYRINTH - Movement Meditation Series
Yoga at Fisher
Prospective Student Day: Master of Education in Postsecondary Administration and Student Affairs (PASA) and Educational Counseling (EC) Programs
Professional Writing: Essentials of Email
USC Stem Cell Student/Postdoc Seminar
Research Gateway Scholars Program
Concerto Night with the USC Thornton Symphony
Popular Music: Second-Year Showcase
Saturday, October 13
USC Football vs. Colorado
Chinese Calligraphy Classes
Chinese Brushpainting Classes
Monday, October 8
Research Gateway Scholars Program
TAI CHI - Movement Meditation Series
Jazz Night: USC Thornton Concert Jazz Orchestra performs music from “West Side Story”
Tuesday, October 9
USC Stem Cell Seminar: Mo Ebrahimkhani, Arizona State University
Pasadena Career Fair & Job Fair
Interview and Negotiation Workshop
USC Dornsife Career Pathways Work it Series | Close it: Salary negotiation and job offers
KUNDALINI YOGA - Movement Meditation Series
Wednesday, October 10
San Diego Career Fair & Job Fair
Columbia’s Sustainability Graduate Programs
Feel Better Workshops Drop-In - USC Student Health
Music@RushHour: USC Brass Ensemble
USC Interfaith Council
Popular Music: First-Year Showcase
Thursday, October 11
Trojan Family Weekend 2018
USC Stem Cell and BCRegMed Virtual Symposium
Trojan Farmers Market
San Francisco Career Fair & Job Fair
IYENGAR YOGA - Movement Meditation Series
Keep Up with Social Media: Your Online Presence
CommuniTEA
Feel Better Workshops Drop-In - USC Student Health
Film Screening: Alone in the Game
Friday, October 12
12th Annual USC Stevens Student Innovator Showcase
LABYRINTH - Movement Meditation Series
Yoga at Fisher
Prospective Student Day: Master of Education in Postsecondary Administration and Student Affairs (PASA) and Educational Counseling (EC) Programs
Professional Writing: Essentials of Email
USC Stem Cell Student/Postdoc Seminar
Research Gateway Scholars Program
Concerto Night with the USC Thornton Symphony
Popular Music: Second-Year Showcase
Saturday, October 13
USC Football vs. Colorado
Chinese Calligraphy Classes
Chinese Brushpainting Classes
MEB Seminar Series | Daniel E. Crocker, Ph.D.
Daniel E. Crocker, Ph.D.
Professor of Biology
Sonoma State University
Lab Website
Stress and reproduction in northern elephant seals
Tuesday, October 9
12 PM
AHF 153 (Torrey Webb Room)
Research Interests:
Comparative Physiology of Vertebrates; Physiological Ecology; Bioenergetics; Behavioral Ecology; Biology of Marine Mammals.
Research Program:
My research is focused on the physiological and behavioral ecology of pinnipeds, seals and sea lions. My approach is to integrate physiology and behavior with the aim of addressing ecological theory. I am investigating physiological factors that impact the reproductive and foraging strategies used by marine predators. Much of my current research is focused on the physiology and behavior of northern elephant seals. These investigations include both field and laboratory studies. My field research focuses on studies of fasting physiology and reproduction when seals are hauled out on land to breed and diving physiology and foraging when animals are at sea. My graduate students are exploring a wide variety of research areas including fasting physiology, foraging behavior and life history strategies. My lab has a strong collaborative relationship with the Institute of Marine Sciences at the University of California, Santa Cruz.
Professor of Biology
Sonoma State University
Lab Website
Stress and reproduction in northern elephant seals
Tuesday, October 9
12 PM
AHF 153 (Torrey Webb Room)
Research Interests:
Comparative Physiology of Vertebrates; Physiological Ecology; Bioenergetics; Behavioral Ecology; Biology of Marine Mammals.
Research Program:
My research is focused on the physiological and behavioral ecology of pinnipeds, seals and sea lions. My approach is to integrate physiology and behavior with the aim of addressing ecological theory. I am investigating physiological factors that impact the reproductive and foraging strategies used by marine predators. Much of my current research is focused on the physiology and behavior of northern elephant seals. These investigations include both field and laboratory studies. My field research focuses on studies of fasting physiology and reproduction when seals are hauled out on land to breed and diving physiology and foraging when animals are at sea. My graduate students are exploring a wide variety of research areas including fasting physiology, foraging behavior and life history strategies. My lab has a strong collaborative relationship with the Institute of Marine Sciences at the University of California, Santa Cruz.
CBB Colloquium Series | Fereydoun Hormozdiari, Ph.D.
Fereydoun Hormozdiari, Ph.D.
University of California Davis,
Genome Center
Lab Website
Contribution of structural variation to genome structure
Thursday October 11, 2018
2 PM
RRI 101
Abstract: Using Hi-C data we are able to study the genomic interactions, such as enhancer-promoter interactions that are the main mechanism for gene regulation. The analysis of Hi-C data has also provided evidence that genome folds into different compartments and domains. One of these types of domains discovered is called topological associated domains (TADs). Recent studies reported structural variants (SVs) that disrupted the three-dimensional genome structure by fusing two TADs, such that enhancers from one TAD interacted with genes from the other TAD, could cause severe developmental disorders. In this talk, we formally define TAD fusion and provide a combinatorial approach for assigning a score to quantify the level of TAD fusion for each deletion denoted as TAD fusion score. We show that our method correctly gives higher scores to deletions reported to cause developmental disorders as a result of disrupting genome structure in comparison to the deletions reported in the 1000 Genomes Project. We will also show that deletions that cause TAD fusion are rare and under negative selection in general population.
Host: Mark Chaisson
University of California Davis,
Genome Center
Lab Website
Contribution of structural variation to genome structure
Thursday October 11, 2018
2 PM
RRI 101
Abstract: Using Hi-C data we are able to study the genomic interactions, such as enhancer-promoter interactions that are the main mechanism for gene regulation. The analysis of Hi-C data has also provided evidence that genome folds into different compartments and domains. One of these types of domains discovered is called topological associated domains (TADs). Recent studies reported structural variants (SVs) that disrupted the three-dimensional genome structure by fusing two TADs, such that enhancers from one TAD interacted with genes from the other TAD, could cause severe developmental disorders. In this talk, we formally define TAD fusion and provide a combinatorial approach for assigning a score to quantify the level of TAD fusion for each deletion denoted as TAD fusion score. We show that our method correctly gives higher scores to deletions reported to cause developmental disorders as a result of disrupting genome structure in comparison to the deletions reported in the 1000 Genomes Project. We will also show that deletions that cause TAD fusion are rare and under negative selection in general population.
Host: Mark Chaisson
Monday, October 1, 2018
MEB Seminar Series | Enrique Navarro, Ph.D.
Enrique Navarro, Ph.D.
Visiting Professor in USC’s Manahan Lab
Professor of Physiology
Department GAFFA, Faculty of Science and Technology
University of Basque Country (UPV/EHU)
Spain
Physiological mechanisms underlying differential growth in size-segregated spat groups of marine bivalves
Tuesday, October 2
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Rates of growth are highly variable in bivalve mollusks and much of this is genetically controlled. Aquaculture practices, through the artificial selection for faster growth, have brought out differentiated growth phenotypes, enabling experiments to investigate the physiological mechanisms underlying this differential expression of growth rate. Persistent physiological differences reported among these groups contrast with the flexible behavior for feeding and growth traits required to cope with changes in the food environment (phenotypic plasticity). From this perspective, the specific aims of our research were to (i) assess the extent to which physiological behavior accounting for growth performance is endogenously (genetically) determined, and (ii) to question how much of this behavior can be environmentally modulated to achieve a more effective exploitation of available food resources within the limits set by the genetic constitution of individuals.
We addressed these issues with different species of bivalves by using groups of spat from a given generation that were artificially segregated on the basis of size in order to produce two differentiated growth categories or groups, henceforth F and S for fast and slow growers, respectively. These groups were subsequently subjected to different food rations to produce growth rate variation in the laboratory while physiological components of the energy balance were determined. Both F and S phenotypes exhibited the same pattern of response and a similar capacity to compensate for variations in food availability through both short and long-term adjustments of feeding behavior which optimized food acquisition. However, phenotypic plasticity does not include constitutive differences in the physiological behavior that underlies the differential growth between F and S phenotypes maintained throughout the dietary conditions. Under standard (hatchery) feeding conditions, the faster growth of F phenotype is achieved through a combination of faster feeding (assisted by larger gills) and an increased metabolic efficiency which results in reduced unitary costs of growth. For F and S groups segregated under restrictive feeding conditions, however, fast growth appears to rely mainly on energy saving mechanisms based on reduced metabolic costs of body maintenance.
Google Scholar Profile
Visiting Professor in USC’s Manahan Lab
Professor of Physiology
Department GAFFA, Faculty of Science and Technology
University of Basque Country (UPV/EHU)
Spain
Physiological mechanisms underlying differential growth in size-segregated spat groups of marine bivalves
Tuesday, October 2
12 PM
AHF 153 (Torrey Webb Room)
Abstract: Rates of growth are highly variable in bivalve mollusks and much of this is genetically controlled. Aquaculture practices, through the artificial selection for faster growth, have brought out differentiated growth phenotypes, enabling experiments to investigate the physiological mechanisms underlying this differential expression of growth rate. Persistent physiological differences reported among these groups contrast with the flexible behavior for feeding and growth traits required to cope with changes in the food environment (phenotypic plasticity). From this perspective, the specific aims of our research were to (i) assess the extent to which physiological behavior accounting for growth performance is endogenously (genetically) determined, and (ii) to question how much of this behavior can be environmentally modulated to achieve a more effective exploitation of available food resources within the limits set by the genetic constitution of individuals.
We addressed these issues with different species of bivalves by using groups of spat from a given generation that were artificially segregated on the basis of size in order to produce two differentiated growth categories or groups, henceforth F and S for fast and slow growers, respectively. These groups were subsequently subjected to different food rations to produce growth rate variation in the laboratory while physiological components of the energy balance were determined. Both F and S phenotypes exhibited the same pattern of response and a similar capacity to compensate for variations in food availability through both short and long-term adjustments of feeding behavior which optimized food acquisition. However, phenotypic plasticity does not include constitutive differences in the physiological behavior that underlies the differential growth between F and S phenotypes maintained throughout the dietary conditions. Under standard (hatchery) feeding conditions, the faster growth of F phenotype is achieved through a combination of faster feeding (assisted by larger gills) and an increased metabolic efficiency which results in reduced unitary costs of growth. For F and S groups segregated under restrictive feeding conditions, however, fast growth appears to rely mainly on energy saving mechanisms based on reduced metabolic costs of body maintenance.
Google Scholar Profile
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