IEB Ph.D. Defense | Nicole Adams

Nicole Adams
Ph.D. Candidate, Integrative & Evolutionary Biology Graduate Program
Google Scholar Profile

Genetic diversity and its effect on the scat microbiome in the threatened insular canid, Urocyon littoralis

Tuesday, March 5
1 PM
RRI 121

Abstract: Loss of genetic diversity in wild populations can have profound effects on the ability of a population to respond to a changing environment.  Small populations can have low genetic variation due to inbreeding and strong drift, which may be exacerbated by further declines in population size.  The Channel Island fox, Urocyon littoralis, was delisted/down-listed from the federal endangered species list in 2016 after successful conservation efforts brought them back from a 90-99% population decline in the 1990s. While their demographic recovery has been dramatic, much less is known about their genetic recovery. Therefore, we looked at the “natural” experiment of the Channel Island fox population declines, which varied in bottleneck presence, size, cause, and recovery across multiple islands. To assess their recovery, we conducted the first direct genetic comparison at the population level of pre- and post-bottleneck samples.  In order to understand functional consequences associated with the loss of genetic diversity, we evaluated the relationship between island fox genetics and the bacterial community after characterizing the scat bacterial community using 16S amplicon sequencing.

PI: Drs. Suzanne Edmands and Xiaoming Wang

QCB Colloquium Series | Danny Barash, Ph.D.

Danny Barash, Ph.D.
Professor, Ben-Gurion University, Dept. of Computer Science
Faculty Profile

Inverse RNA Folding and Computational Riboswitch Detection

Thursday, February 28
2 PM
RRI 101

Abstract: The inverse RNA folding problem for designing sequences that fold into a given RNA secondary structure was introduced in the early 1990's in Vienna. Using a coarse-grain tree graph representation of the RNA secondary structure, we extended the inverse RNA folding problem to include constraints such as thermodynamic stability and mutational robustness, developing a program called RNAexinv. In the next step, we formulated a fragment-based design approach of RNA sequences that can be useful to practitioners in a variety of biological applications. In this shape-based design approach, specific RNA structural motifs with known biological functions are strictly enforced while others can possess more flexibility in their structure in favor of preserving physical attributes and additional constraints. Our program is called RNAfbinv (recently extended to incaRNAfbinv by incorporating a weighted sampling approach borrowed from incaRNAtion). Detection of riboswitches in genomic sequences using structure based methods, including the use of incaRNAfbinv, will also be discussed

Host:  Remo Rohs

MCB Colloquium Series | Allison J. Shultz, Ph.D.

Allison J. Shultz, PhD
Assistant Curator, Natural History Museum of Los Angeles County, Dept. of Ornithology
Research Website

Evolution across timescales: comparative and population genomics studies of host-pathogen co-evolution in birds

Friday, March 1, 2019
12 PM
RRI 101

Abstract: Infectious disease produces some of the strongest selective forces on natural populations across the tree of life. The signatures of pathogen-mediated evolution on host genomes have been described for several traditional model organisms, but few studies of more diverse organisms have detected such signatures beyond candidate immune loci. Here, I combine population and comparative genomics to study the dynamics of pathogen-mediated selection at across evolutionary timescales in birds. First, I use alignments of 39 bird genomes to estimate parameters related to positive selection for 11,000 genes conserved across birds. I use functional pathway analyses, transcriptome data, and comparisons with mammals to show that pathogens, particular viruses, consistently target the same genes across divergent clades, and that these genes are hotspots of host-pathogen conflict over deep evolutionary time. Second, I use whole genome resequencing data to estimate parameters of selection at the population level across birds, and investigate if the same genes observed under selection at deep evolutionary timescales are under selection at shallow evolutionary timescales. Finally, I use genomes of a songbird collected across time and space to understand the demographic impacts of two anthropogenic disturbances, an introduction event and a novel pathogen. I find that the demographic history had the largest genomic impact, and that pathogen-mediated selection likely occurred at many different regions of the genome.

MEB Seminar Series | Todd Oakley, Ph.D.

Todd Oakley, Ph.D.
Professor, University of California, Santa Barbara, Ecology, Evolution and Marine Biology
Lab Website

Origin Stories: The unexpected history of an aesthetic radiation of bioluminescent crustaceans

Tuesday, February 19
12 PM
AHF 153 (Torrey Webb Room)

Abstract: Bioluminescence is an ecologically impactful phenotype often used in communication, including courtship signals whose origins increase rates of speciation. Because bioluminescence is strongly influenced by few or even single genes, learning how those genes originate is critical for understanding how genetic changes impact diversification. One origin of bioluminescence occurred in cypridinid ostracods (Crustacea), which employ complex courtship displays that differ among dozens of species from the Caribbean. Cypridinid bioluminescence involves c- luciferase enzymes , which contain only two deeply conserved sequences. I will discuss the unexpected history of this gene, including a proliferation of its constituent domains, which predates the inferred origin of cypridinid bioluminescence. Although we still have much t o learn about gene function , this mode of gene origin may be similar to Innovation Amplification Duplication (IAD), but with different timing . In this case, Amplification began before functional Innovation and gene Duplication events (AID). This order of events has implications for mechanisms of molecular evolution. These results illustrate how contingent, unpredictable genetic histories might contribute to ecologically impactful phenotypes.

PhD Achievement Award Applications

Nominations for the USC Graduate School PhD Achievement Award are due to Doug Burleson (burleson@usc.edu) by Wednesday, March 6th at 5:00pm.  This award is intended for students who will be graduating this spring or summer.  The attached document outlines the requirements for the award.  I am also including the signature page for the award.  Please collect signatures from your advisor and the Department Chair prior to submitting your application materials.  I will get the Dean’s signature for you. If you have any questions, please let me know.

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HOWARD UNIVERSITY Summer Programming for Students interested in healthcare and/or STEM

Greetings from Howard University, College of Pharmacy’s Pipeline Programs!

Our Advance College Summer Enrichment Program Tier I and Tier II application is now open.  We are contacting you to share the attached information with students that are interested in pursuing careers in healthcare and/or STEM fields. Students are highly encouraged to apply and submit all documentation as soon as possible for consideration. The application closes on February 15th and is very competitive. ACSEP Tier I and Tier II programs are FREE to those that participate. Here is a summary of what our program has to offer along with requirements:

Advanced College Summer Enrichment Program (ACSEP)
ACSEP is a five-week summer enrichment program for undergraduate level students who have an interest in careers in healthcare and STEM.  Twenty students, per tier, will be selected. Tier 1 students should be freshman and sophomore students with at least 15 semester credits. Tier II students should have at least 60 semester credits or more (see website for required prerequisites). The overall goal of the program is to encourage, expose and increase under-represented minority students in the pursuit of careers in healthcare and STEM. This is achieved through relevant academic curriculum, professional mentor pairing, workshop presentations, and shadowing opportunities.   We are looking for students with at least a 2.75 GPA or higher. A complete application includes an official transcript, two letters of recommendation, resume, 250-word essay, and an interview by the committee.

Please contact our offices using the below contact information or visit us on the web by clicking here For more detailed information.   To start the application, please Click Here or go to: https://howard.az1.qualtrics.com/jfe/form/SV_005a8SZH0TZPa2V.   When applying, please use the code (SCR19) in the “how did you hear about us” section by selecting other.

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USC's Young Research Program

USC's Young Research Program is recruiting new mentors for the summer of 2019. For the past 10 years, YRP has mentored over 100 high school students to successfully conduct research in a collegiate setting. We welcome mentors from all backgrounds in STEM. Our mission statement is: “To provide motivated high school students from neighborhoods around USC the opportunity to learn about STEM fields and complete their own scientific research project.”

With the help of a graduate students, post-doc / faculty supervisors, high school students near the greater USC-area are mentored for about 5 weeks. The goal is to complete a small project (designed by the mentor) to be presented among other students. If you are interested in mentoring a student here is some important information:
•  High school students will be supervised for ~15 hours per week; how that time is split in the lab, is up to the supervising mentor
•  Mentors must decide if they would like to participate in the program by March 14th and sign the proper documents.
•  The program will begin the last week of June and Poster presentations will take place the first week of August. 
•  Mentors receive a personal $300 stipend and $200 lab-supply stipend for participating in the program.
•  All mentors MUST have a signature of agreement to participate as a mentor from their Lab's Principal Investigator. no exceptions.  
•  All mentors must complete an online mandate reporter training for working with minors.
•  There is one mandatory orientation in mid June for mentors.
If you would like to participate please email: Porat@USC.edu

If you would like to attend an informational session please arrive by 1:30pm for a brief presentation at McKibben Hall (MCH) room 149 in Health Sciences Campus on February 21st.

A second info session will take place at UPC sometime in early March.

PIZZA PROVIDED AT INFO SESSION.

Call for Nominations: 2019 Student Recognition Awards

Call for Nominations by on Scribd

Nominations are available online at http://studentrecognition.usc.edu/.

MCB Colloquium Series | David Gilbert, Ph.D.

David Gilbert Seminar 2-22-... by on Scribd

In Memoriam - Dr. John Petruska

The following piece was written and based mostly from an e-mail conversation with Dr. Petruska's long-time colleague and friend, Dr. Robert Baker...

Dr. John A. Petruska was born in 1933 and "grew up in poverty in rural northeastern Canada." It was a fascination for science, in particular physics and chemistry, that brought him to the University of Chicago, where he received his Doctorate in 1961. He would make several stops, among them a Post-Doc at Caltech with Nobel laureate Dr. Linus Pauling, before joining the Faculty at USC in 1968, along with Dr. Baker.

The two of them would spend many lunches together, tossing around questions and ideas like youngsters out playing catch with a football. John "marveled at the universality of the genetic code and the ways that higher biological cells differentiate into [other] kinds of cells, [all within] the same organism." And though he saw what everyone else was seeing in the natural and physical world, he seemed to always come up with ideas that were entirely different and new.

For John, being an educator was just as important as being a scientist; "they went hand in hand." In fact, he never stopped doing either (Dr. Petruska taught parts of BISC-435, 493 and 494 this Spring). He also was the advisor for the Alpha Alpha chapter of Phi Sigma, an honor society for biology students. John was always willing to impart his knowledge and speak on topics that were of great interest to him. At his best, students noted his passion and enthusiasm. His love for science simply poured out of his lecture slides and into detailed explanations of various subject matter like zinc fingers and mutagenesis.

And though it would seem his mind was always on work, John "truly cared for his [late] wife, Marti, and his children, David and Mark." He and Marti lived in San Marino, where she was a docent at The Huntington. When she passed in 2008, John remained “optimistic and looked to the bright side.” Perhaps, it was his duty to the university who welcomed him more than 50 years ago and all the relationships he had formed over that span that kept him going. Sadly, we must now go on without him. There is no denying that his presence will surely be missed.

To a great man, scientist, father, and friend.

MEB Seminar Series | Ben Tully, Ph.D.

Benjamin Tully, Ph.D.
Post-Doc Research Associate, USC, C-DEBI
Research Website

Exploration of metagenome-assembled genomes sheds light on enigmatic Bacteria and Archaea

Monday, February 11, 2019
12 PM
AHF 153 (Torrey Webb Room)

Abstract: The vast majority of microbial life belongs to uncultured groups, for which we have limited knowledge about their metabolisms and the role they may play in biogeochemical cycles. A concerted global effort to apply metagenomic techniques to the marine environment through the Tara Oceans expedition has provided an opportunity to explore metabolic diversity in cultured and uncultured organisms a like. Combined with recent computational advances, metagenomic datasets can be utilized to reconstruct high-quality, near-complete microbial genomes directly from the environment. We have been analyzing the microbial genomes generated from four studies that applied binning techniques to the Tara Oceans metagenomic datasets in effort to expand our understanding of uncultured microbes in the oceans. This effort has led to the description, identification, and characterization of several known and unknown microbial groups, including a novel lineage of phototrophic Alphaproteobacteria, Candidatus Luxescamonaceae, and the Marine Group II Euryarchaea. Combined with the Tara Oceans metagenomic datasets, we can provide a snapshot of global ecology and abundance for each genome. The observed ecological distributions for these genomes provide insight into their metabolic potential and their contribution to global geochemical cycles.

Short Bio: Ben received his Ph.D. from the University of Southern California in 2013. In 2014, he joined the Center for Dark Energy Biosphere Investigations as their Bioinformatic Specialist. He works with the community to provide the bioinformatic resources required by researchers of the Center and expertise on bioinformatic problems/questions/concerns.

MCB Faculty Candidate Special Seminar | Katharina Schlacher, Ph.D.

Katharina Schlacher Seminar... by on Scribd

MCB Colloquium Series | Brandon Gaut, Ph.D.

Brandon Gaut Seminar 2-15-2019 by on Scribd

QCB Faculty Candidate Special Seminar | Sangeet Lamichhaney, Ph.D.

Sangeet Lamichhaney, Ph.D.
Wenner-Gren Post-Doc Fellow, Harvard University
Research Profile

Exploring adaptive evolution through the lens of modern 'omics

Tuesday, February 12, 2019
2 PM
RRI 101

Abstract: These are now exciting times in the field of evolutionary biology as rapid
technological advancements is allowing us to analyze genomes, transcriptomes, proteomes and diverse range of phenotypes in any species of interest relatively easily in a cost-effective manner. This provides us an unique opportunity to study adaptive evolution through the lens of modern 'omics. Motivated by this fact, my current work studies multiple vertebrate systems ranging from fish (Atlantic herring), reptiles (Squamates) and birds (Darwin’s finches & Ruff) and integrate genomic methods with the traditional knowledge about ecology and evolutionary history to reveal insights into adaptive traits that have amazed evolutionary biologists for decades. My work primarily focus on the interrelated avenues of (a) Parallel evolution of adaptive traits in geographically isolated populations (b) Genetic basis of adaptive radiation and rapid speciation (c) Impact of interspecies gene flow on trait evolution and hybrid speciation (d) Role of structural variants in adaptation and diversification (e) and understanding evolutionary processes underlying adaptive evolution at micro and macro evolutionary scales. My future work will build up on the groundwork of my current findings and ideally aim to set up a multi-disciplinary research program on “integrative genomics” that would bridge concepts and skills from several research areas and involve integrated analysis of multi-level ‘omics’ data, an approach that can contribute to providing mechanistic explanations for classical questions in evolutionary biology.

Host: Fengzhu Sun

Neurobiology Seminar Series | Zachary Knight, Ph.D.

Zachary Knight Seminar Flier by on Scribd

MCB Faculty Candidate Special Seminar | Daniel Wagner, Ph.D.

Dan Wagner Seminar 2-04-2019 by on Scribd

Dan Wagner CV by on Scribd

Dornsife Endowed Fellowships Announcement

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QCB Faculty Candidate Special Seminar | Christian Huber, Ph.D.

Christian Huber
ARC DECRA Fellow, University of Adelaide
Research Profile

Population genomics of selection in natural populations

Thursday February 7, 2019
2 PM
RRI 101

Abstract: Natural selection is one of the cornerstones of modern biology and remains the primary explanation for how species adapt. Population genetic methods have been highly successful in using genetic variation data to quantify the amount and type of natural selection in the genome. However, the main factors that lead to differences in selection strength between species are still unclear. Further, complex demographic history often leads to biased estimates of the rate and strength of selection across the genome. In this talk, I first discuss how modelling population structure is key for quantifying positive selection in the genome. I present a new method for detecting positive selection that is both robust to demography and more powerful than previous approaches. Next, I present a comparative population genomic approach that suggests that amino acid changing mutations in humans are, on average, more deleterious than mutations in Drosophila. More generally, species complexity, as well as the distance of the population to the fitness optimum, are found to be the key drivers of the deleteriousness of new amino-acid mutations. Finally, I present a first estimate of dominance from natural population data and find that mutations are predominantly recessive. Contrary to classical models of the evolution of dominance I suggest that variation in dominance between genes is a consequence of the cost of gene expression.