Monday, January 27, 2020
POSTDOCTORAL POSITION IN EVOLUTION OF DEVELOPMENTAL MECHANISMS
Three-year NSF-supported postdoctoral position is available at University of California San Diego, Department of Scripps Institution of Oceanography, La Jolla, CA, USA to study the evolution of segmentation in chordates. This is a multi-level study focused on somite formation in the basal chordate amphioxus. The study involves dissecting the genetic mechanism of somite segmentation in embryos and larvae of the basal chordate, amphioxus. The effects of perturbing gene function on the mechanics of somite segmentation will be monitored at the single-cell level by 3-D reconstructions with serial blockface scanning electron microscopy. RNA-Seq will address questions of gene hierarchy. Applicants with a background in evo/devo and/or developmental mechanisms of amphioxus are preferred. A PhD is required. Interested applicants please submit a curriculum vitae, names, addresses and e-mail addresses for three references to Dr. Linda Z. Holland, Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla CA, 92093-0202 (tel 858-534-5607; fax 858-534-7313; email lzholland@ucsd.edu). UCSD is an equal opportunity employer.
Gold, Del Amo, and Hovel Research/Travel Awards
Gold Fellowship Announcement
Del Amo Continuing Fellowship Announcement
Hovel Travel Award
Gold Fellowship Announcement 2020 by uscbiscgrad on Scribd
Del Amo Continuing Fellowship Announcement
Del Amo Continuing Announcement 2020 by uscbiscgrad on Scribd
Hovel Travel Award
Hovel Travel Award 2020 by uscbiscgrad on Scribd
Fourth Annual Diversity, Equity, and Inclusion Week (DEI Week)
Mark your calendars for the Fourth
Annual Diversity, Equity, and Inclusion Week (DEI Week), to be held March
2-6, 2020.
Our theme this year is Climate Change in 20/20: Advancing
Diversity, Equity, and Inclusion at USC.
As said in the original memo,
DEI Week serves to nurture and produce innovative educational experiences to
meet our diversity, equity, and inclusion goals.
In response to requests, the deadline
for proposal submissions has been extended to Friday, February 7, 2020.
You can submit your proposal here: https://forms.usc.edu/usc-diversity-equity-and-inclusion-awareness-week/.
MEB Seminar | Dr. Allie Graham
Dr. Allie Graham
NSF PRFB Fellow, Oregon State University
Research Website
From the Mountains to the Sea: Comparative Genomics of Mechanisms Underlying the Physiological Response to Low Oxygen
Tuesday, January 28, 12 PM, AHF 153 (Torrey Webb Room)
Abstract: Environmental variables can exert a considerable selective pressure across the entire organism – from their genome to their physiology. Organisms living in extreme environmental conditions provide excellent systems to investigate numerous basic questions about the limits of an organism's ability to adapt, to understanding the inherent repeatability of molecular adaptation, and thus the origins of biodiversity, by examining both phenotypic and genotypic novelty. My work uses both integrative and comparative approaches to understand the mechanisms underpinning the response to such environmental variables, with a focus on oxygen availability (i.e. hypoxia). This talk will journey through my previous work on high-altitude adaptation in Andean duck species, to my current work on hypoxia in copepods (and other crustaceans), and conclude with how my discoveries opened up numerous exciting avenues for future work in aquatic invertebrates.
NSF PRFB Fellow, Oregon State University
Research Website
From the Mountains to the Sea: Comparative Genomics of Mechanisms Underlying the Physiological Response to Low Oxygen
Tuesday, January 28, 12 PM, AHF 153 (Torrey Webb Room)
Abstract: Environmental variables can exert a considerable selective pressure across the entire organism – from their genome to their physiology. Organisms living in extreme environmental conditions provide excellent systems to investigate numerous basic questions about the limits of an organism's ability to adapt, to understanding the inherent repeatability of molecular adaptation, and thus the origins of biodiversity, by examining both phenotypic and genotypic novelty. My work uses both integrative and comparative approaches to understand the mechanisms underpinning the response to such environmental variables, with a focus on oxygen availability (i.e. hypoxia). This talk will journey through my previous work on high-altitude adaptation in Andean duck species, to my current work on hypoxia in copepods (and other crustaceans), and conclude with how my discoveries opened up numerous exciting avenues for future work in aquatic invertebrates.
Tuesday, January 21, 2020
Interested in a trip to DC? Council of Graduate Schools Advocacy
We have received the following call for nominations (see below) from Vice Provost Sally Pratt. If you are interested in putting yourself forward for the nomination, please speak with your faculty advisor as soon as possible. The deadline for nominations is Wednesday, January 29th. Please contact Doug Burleson, if you have any questions.
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I am writing to invite one or two students to participate in Council of Graduate Schools Advocacy Days and visit to congressional offices to advocate for graduate education. The students may come from master’s or PhD programs. The Graduate School will cover travel expenses and hotel accommodations. The students must be available for the entire duration of the visit in April (see below). A Graduate School Committee will make the final selection.
From the student
· CV
· a short statement of interest (250-500 words)
From the student’s advisor or program director
· A short statement of support (250 words max)
The Council of Graduate Schools website is https://cgsnet.org/
Council of Graduate Schools Spring 2020 Advocacy Days in Washington, DC Announcement
The Council of Graduate Schools (CGS) is sponsoring an event for graduate school deans to visit legislative offices to advocate for graduate education. Due to the success of last year’s initial program, CGS is once again providing an opportunity for two graduate students to accompany the graduate dean on the visit.
Event Dates:
Wednesday, April 22, 2020
Capitol Hill visit preparation and training workshop
Thursday April 23, 2020
Visit to Capitol Hill offices
---
I am writing to invite one or two students to participate in Council of Graduate Schools Advocacy Days and visit to congressional offices to advocate for graduate education. The students may come from master’s or PhD programs. The Graduate School will cover travel expenses and hotel accommodations. The students must be available for the entire duration of the visit in April (see below). A Graduate School Committee will make the final selection.
From the student
· CV
· a short statement of interest (250-500 words)
From the student’s advisor or program director
· A short statement of support (250 words max)
The Council of Graduate Schools website is https://cgsnet.org/
Council of Graduate Schools Spring 2020 Advocacy Days in Washington, DC Announcement
The Council of Graduate Schools (CGS) is sponsoring an event for graduate school deans to visit legislative offices to advocate for graduate education. Due to the success of last year’s initial program, CGS is once again providing an opportunity for two graduate students to accompany the graduate dean on the visit.
Event Dates:
Wednesday, April 22, 2020
Capitol Hill visit preparation and training workshop
Thursday April 23, 2020
Visit to Capitol Hill offices
Marine & Environmental Biology Seminar | Dr. Phillip Cleves
Dr. Phillip Cleves
Post-Doctoral Research Fellow, Stanford University
Research Profile |
Molecular and cellular bases of cnidarian-dinoflagellate symbiosis and its breakdown
Tuesday, January 21, 12 PM, AHF 153 (Torrey Webb Room)
Abstract: The symbiosis between corals and dinoflagellate algae is essential to the energetic requirements of coral-reef ecosystems. However, coral reefs are in danger due to elevated ocean temperatures and other stresses that lead to the breakdown of this symbiosis and coral "bleaching". Despite the importance of coral reefs, the molecular basis of how corals maintain a healthy symbiosis and avoid bleaching is poorly understood, in part because of the lack of a tractable genetic model system. The small anemone Aiptasia is symbiotic with algal strains like those in reef-building corals but has many experimental advantages, making it an attractive laboratory model for cnidarian symbiosis. To explore the transcriptional basis of heat-induced bleaching, we used RNAseq to identify genes that are differentially expressed during a time course of heat stress of symbiotic and aposymbiotic Aiptasia strains. We observed a strong upregulation of hundreds of genes at times long before bleaching begins in symbiotic anemones. The putative promoters of these early stress-response genes are enriched for binding sites for the NFB and HSF1 transcription factors, suggesting that many of these genes share core transcriptional control. The overall expression patterns were similar between the symbiotic and aposymbiotic anemones, indicating that many of the expression changes are not specific to the presence of the algae. Nonetheless, reducing HSF1 activity with a pharmacological inhibitor resulted in more severe bleaching, suggesting that this symbiont-independent stress response is protective against bleaching.
Genetic tools are needed to allow rigorous functional testing of the roles of candidate genes in symbiosis and bleaching. Recently, we have developed methods for knocking down and overexpressing genes of interest in Aiptasia. Meanwhile, we have successfully used the CRISPR/Cas9 technology to create genetic changes in embryos of the coral Acropora millepora. We used this technology to knock out HSF1 and demonstrated its role in coral heat tolerance. Through the establishment of both gain-of-function and loss-of-function methods in both Aiptasia and corals, it will be possible to exploit the year-round spawning of Aiptasia to perform initial tests of gene function in cnidarian-algal symbiosis and then further test the discoveries made using similar technologies in corals.
Post-Doctoral Research Fellow, Stanford University
Research Profile |
Molecular and cellular bases of cnidarian-dinoflagellate symbiosis and its breakdown
Tuesday, January 21, 12 PM, AHF 153 (Torrey Webb Room)
Abstract: The symbiosis between corals and dinoflagellate algae is essential to the energetic requirements of coral-reef ecosystems. However, coral reefs are in danger due to elevated ocean temperatures and other stresses that lead to the breakdown of this symbiosis and coral "bleaching". Despite the importance of coral reefs, the molecular basis of how corals maintain a healthy symbiosis and avoid bleaching is poorly understood, in part because of the lack of a tractable genetic model system. The small anemone Aiptasia is symbiotic with algal strains like those in reef-building corals but has many experimental advantages, making it an attractive laboratory model for cnidarian symbiosis. To explore the transcriptional basis of heat-induced bleaching, we used RNAseq to identify genes that are differentially expressed during a time course of heat stress of symbiotic and aposymbiotic Aiptasia strains. We observed a strong upregulation of hundreds of genes at times long before bleaching begins in symbiotic anemones. The putative promoters of these early stress-response genes are enriched for binding sites for the NFB and HSF1 transcription factors, suggesting that many of these genes share core transcriptional control. The overall expression patterns were similar between the symbiotic and aposymbiotic anemones, indicating that many of the expression changes are not specific to the presence of the algae. Nonetheless, reducing HSF1 activity with a pharmacological inhibitor resulted in more severe bleaching, suggesting that this symbiont-independent stress response is protective against bleaching.
Genetic tools are needed to allow rigorous functional testing of the roles of candidate genes in symbiosis and bleaching. Recently, we have developed methods for knocking down and overexpressing genes of interest in Aiptasia. Meanwhile, we have successfully used the CRISPR/Cas9 technology to create genetic changes in embryos of the coral Acropora millepora. We used this technology to knock out HSF1 and demonstrated its role in coral heat tolerance. Through the establishment of both gain-of-function and loss-of-function methods in both Aiptasia and corals, it will be possible to exploit the year-round spawning of Aiptasia to perform initial tests of gene function in cnidarian-algal symbiosis and then further test the discoveries made using similar technologies in corals.
Molecular & Computational Biology Colloquium | Dr. Jacob Musser
Dr. Jacob Musser
Post-Doctoral Fellow, EMBL, Developmental Biology Unit (Heidelberg)
Research Profile | Abstract
Few cell types, many functions: The evolutionary origin of division of labor among animal cells
Thursday, January 23, 10:30-11:45 AM, RRI 101
Abstract: Sponges are the sister group to nearly all other animals, and lack a nervous system, musculature, and gut. However, genes encoding important neuronal proteins, including key synaptic proteins, have been found in sponge genomes. Using single-cell RNAseq, single-molecule FISH, and Focused Ion Beam SEM (FIB-SEM) we generate a comprehensive molecular and morphological characterization of cell types in Spongilla lacustris, a freshwater demosponge. We identify many specialized cell types bearing functional and regulatory signatures similar to those of other animals. This includes contractile epithelial cells, which we demonstrate experimentally are responsive to nitric oxide signaling, phagocytes involved in innate immunity, and digestive cells that express a nearly complete set of postsynaptic genes. Remarkably, we also find immune cells expressing presynaptic genes and show via FIB-SEM that they send long projections that directly contact and enwrap microvilli of 'postsynaptic' digestive cells. This reveals new evidence linking neuronal and immune function in sponges, and suggests a primordial neuro-immune system cleared intruders and controlled ciliary beating for feeding.
Post-Doctoral Fellow, EMBL, Developmental Biology Unit (Heidelberg)
Research Profile | Abstract
Few cell types, many functions: The evolutionary origin of division of labor among animal cells
Thursday, January 23, 10:30-11:45 AM, RRI 101
Abstract: Sponges are the sister group to nearly all other animals, and lack a nervous system, musculature, and gut. However, genes encoding important neuronal proteins, including key synaptic proteins, have been found in sponge genomes. Using single-cell RNAseq, single-molecule FISH, and Focused Ion Beam SEM (FIB-SEM) we generate a comprehensive molecular and morphological characterization of cell types in Spongilla lacustris, a freshwater demosponge. We identify many specialized cell types bearing functional and regulatory signatures similar to those of other animals. This includes contractile epithelial cells, which we demonstrate experimentally are responsive to nitric oxide signaling, phagocytes involved in innate immunity, and digestive cells that express a nearly complete set of postsynaptic genes. Remarkably, we also find immune cells expressing presynaptic genes and show via FIB-SEM that they send long projections that directly contact and enwrap microvilli of 'postsynaptic' digestive cells. This reveals new evidence linking neuronal and immune function in sponges, and suggests a primordial neuro-immune system cleared intruders and controlled ciliary beating for feeding.
Quantitative & Computational Biology Faculty Candidate Seminar | Yang Yang
Yang Yang
Ph.D. Candidate, Carnegie Mellon University, Computational Biology
Research Website
Computational Methods for Multi-Species Comparison of 3D Genome Structure and Function
Thursday, January 23, 2 PM, RRI 101
Abstract: Recent development in chromatin interaction mapping technologies have greatly advanced the study of three-dimensional (3D) genome organization, which is closely related to vital genome functions such as DNA replication timing (RT) and transcription. However, the principles underlying 3D genome organization and the detailed patterns on how the 3D genome has changed in mammalian evolution remain largely unclear. In this talk, I will primarily introduce two probabilistic models that I have developed during my Ph.D. research: Phylo-HMGP and Phylo-HMRF, which provide the new generic frameworks for genome-wide comparison of continuous genomic features, including RT and Hi-C data for 3D genome structures. The methods incorporate the temporal dependencies of species in the context of evolution with the spatial dependencies of genomic loci, to identify genome-wide evolutionary patterns of continuous genomic features. Real data applications to the RT data and Hi-C data from multiple primate species demonstrated the effectiveness of the models and offered high resolution characterization of evolutionary patterns of 3D genome structure and function. Together, the methods have the potential to help reveal genomic regions with conserved or species-specific structural and regulatory roles, and provide key insights into nuclear organization and function through cross-species comparisons.
Ph.D. Candidate, Carnegie Mellon University, Computational Biology
Research Website
Computational Methods for Multi-Species Comparison of 3D Genome Structure and Function
Thursday, January 23, 2 PM, RRI 101
Abstract: Recent development in chromatin interaction mapping technologies have greatly advanced the study of three-dimensional (3D) genome organization, which is closely related to vital genome functions such as DNA replication timing (RT) and transcription. However, the principles underlying 3D genome organization and the detailed patterns on how the 3D genome has changed in mammalian evolution remain largely unclear. In this talk, I will primarily introduce two probabilistic models that I have developed during my Ph.D. research: Phylo-HMGP and Phylo-HMRF, which provide the new generic frameworks for genome-wide comparison of continuous genomic features, including RT and Hi-C data for 3D genome structures. The methods incorporate the temporal dependencies of species in the context of evolution with the spatial dependencies of genomic loci, to identify genome-wide evolutionary patterns of continuous genomic features. Real data applications to the RT data and Hi-C data from multiple primate species demonstrated the effectiveness of the models and offered high resolution characterization of evolutionary patterns of 3D genome structure and function. Together, the methods have the potential to help reveal genomic regions with conserved or species-specific structural and regulatory roles, and provide key insights into nuclear organization and function through cross-species comparisons.
Monday, January 13, 2020
Stanford PRISM - Stanford Postdoc Recruitment Now Accepting Applications
The application is now open for our fifth PRISM cohort. Stanford PRISM is a recruitment opportunity for late-stage graduate students from diverse backgrounds to explore postdoctoral training at Stanford.
Please forward the following message to your colleagues and any graduate students planning to complete their PhDs by June 2021 who might be interested in considering postdoctoral training at Stanford.
Stanford PRISM
PRISM (Postdoctoral Recruitment Initiative in Sciences and Medicine) is an opportunity for select late-stage graduate students from broadly diverse backgrounds to come to Stanford for a recruitment weekend, interview with potential mentors, and get the inside scoop on postdoctoral training at Stanford. The purpose of this program is to encourage those who might not currently consider a postdoctoral position at Stanford to get a first-hand look at whether Stanford might be a good fit for them. Our goal is to match excellent trainees to excellent mentors at Stanford.
This opportunity is open to all. We especially encourage those from backgrounds underrepresented in academia to apply, including but not limited to: African Americans, Latinos, Native Americans, Pacific Islanders, Filipinos, those with disabilities, first generation college-goers, those from disadvantaged socio-economic backgrounds, and those underrepresented on the basis of gender identity or expression or sexual orientation. Applications consist of an application form, a CV, a research statement, a recommendation from your graduate advisor, and the names of up to 6 potential mentors at Stanford.
For more information or to apply, go to http://postdocs.stanford.edu/PRISM
PRISM Spring 2020 dates: May 20-23, 2020
Deadline: March 2, 2020
Please forward the following message to your colleagues and any graduate students planning to complete their PhDs by June 2021 who might be interested in considering postdoctoral training at Stanford.
Stanford PRISM
PRISM (Postdoctoral Recruitment Initiative in Sciences and Medicine) is an opportunity for select late-stage graduate students from broadly diverse backgrounds to come to Stanford for a recruitment weekend, interview with potential mentors, and get the inside scoop on postdoctoral training at Stanford. The purpose of this program is to encourage those who might not currently consider a postdoctoral position at Stanford to get a first-hand look at whether Stanford might be a good fit for them. Our goal is to match excellent trainees to excellent mentors at Stanford.
This opportunity is open to all. We especially encourage those from backgrounds underrepresented in academia to apply, including but not limited to: African Americans, Latinos, Native Americans, Pacific Islanders, Filipinos, those with disabilities, first generation college-goers, those from disadvantaged socio-economic backgrounds, and those underrepresented on the basis of gender identity or expression or sexual orientation. Applications consist of an application form, a CV, a research statement, a recommendation from your graduate advisor, and the names of up to 6 potential mentors at Stanford.
For more information or to apply, go to http://postdocs.stanford.edu/PRISM
PRISM Spring 2020 dates: May 20-23, 2020
Deadline: March 2, 2020
Marine biology field course in South Africa
Are you looking for an exciting opportunity to study biodiversity and further your marine biology skills this year in the kelp forests of South Africa? Cape RADD facilitates a 2 week and 4 week field course for students who want to learn more about the marine environment, conservation and research through hands on field experience and diver development. The Cape RADD course runs every month and includes training in multiple data collection and field operation techniques, theoretical workshops on analysis techniques and tools like R and GIS. Come spend a month abroad, scuba diving and freediving in one of the most beautiful parts of the world.
Visit www.caperadd.com or email info@caperadd.com for more details.
Visit www.caperadd.com or email info@caperadd.com for more details.
QCB Colloquium | Dr. Serghei Mangul
Dr. Serghei Mangul
Assistant Professor, USC School of Pharmacy
Lab Website
Dumpster diving in RNA-sequencing to study the immune receptor repertoires and microbial communities
Thursday, January 16, 2 PM, RRI 101
Abstract: Assay-based approaches provide a detailed view of the adaptive immune system by profiling T- and B-cell receptor (TCR/BCR) repertoires. However, these methods are costly, time-consuming, and lack the scale of RNA sequencing (RNA-seq). The seminar will introduce bioinformatic methods that mine discarded sequences and produce rich research level data including T and B cell receptor sequences, microbiome, genome-wide germline genotypes, and rDNA and mtDNA copy number. We have applied our methods to GTEx multi-tissue RNA-Seq data (n=8,555) and Profile OncoPanel cancer sequencing data (n=20,000). We validated the accuracy of our methods and showed their utility through replication of known genetic associations. The presented systematic atlas of immunological sequences data contains one of the largest collections of immune receptor sequencing across a broad range of tissue. Additionally, we investigated the functional mechanisms underlying connections between the immune system, microbiome, and disease.
Assistant Professor, USC School of Pharmacy
Lab Website
Dumpster diving in RNA-sequencing to study the immune receptor repertoires and microbial communities
Thursday, January 16, 2 PM, RRI 101
Abstract: Assay-based approaches provide a detailed view of the adaptive immune system by profiling T- and B-cell receptor (TCR/BCR) repertoires. However, these methods are costly, time-consuming, and lack the scale of RNA sequencing (RNA-seq). The seminar will introduce bioinformatic methods that mine discarded sequences and produce rich research level data including T and B cell receptor sequences, microbiome, genome-wide germline genotypes, and rDNA and mtDNA copy number. We have applied our methods to GTEx multi-tissue RNA-Seq data (n=8,555) and Profile OncoPanel cancer sequencing data (n=20,000). We validated the accuracy of our methods and showed their utility through replication of known genetic associations. The presented systematic atlas of immunological sequences data contains one of the largest collections of immune receptor sequencing across a broad range of tissue. Additionally, we investigated the functional mechanisms underlying connections between the immune system, microbiome, and disease.
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