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 NFB 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.

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.

Spring 2020 PhD Pathways Career Planning and Preparation Workshops

   PhD Pathways Career Series_Spring 2020 by uscbiscgrad on Scribd

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

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.

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.