Thursday, October 2, 2014

Tenure Track Plant Evolution Position

The Department of Biological Sciences at California State University, Long Beach (CSULB) is seeking to hire a tenure-track plant evolutionary biologist with research experience in molecular and morphological traits.  We invite broadly-trained scientists committed to excellence in innovative research and teaching at an undergraduate and M.S. degree-awarding university to apply.  CSULB is located three miles from the ocean in the ethnically-diverse greater Southern California area and serves over 35,000 students.

We have a brand new state of the art research facility which includes three new greenhouses and a full-time botany technician.  Major instrumentation supporting faculty research and teaching include confocal, scanning, AFM, and transmission electron microscopes, proteomics facility with MALDI-TOF-TOF mass spectrometer, flow cytometer, quantitative PCR machines, and a Typhoon phosphorimager.

The full job description and application instructions are attached and can also be found at  Please distribute this request to talented postdoctoral researchers with an interest in establishing a research lab and teaching program at a dynamic comprehensive university.

CSULB seeks to recruit faculty who enthusiastically support the University’s strong commitment to the academic success of all of our students, including students of color, students with disabilities, first generation to college, veterans, students with diverse socio-economic backgrounds, and diverse sexual orientations and gender expressions.  CSULB seeks to recruit and retain a diverse workforce as a reflection of our commitment to serve the people of California, to maintain the excellence of the University, and to offer our students a rich variety of expertise, perspectives, and ways of knowing and learning.

Kind regards,

Judy Brusslan
Chair, Plant Evolution Search Committee

Mindful USC

In Memoriam | Richard F. Thompson, 84

A world-leading behavioral neuroscientist who spent a half-century on memory research, University Professor Emeritus Richard F. Thompson developed USC Dornsife’s neuroscience research program.

USC Dornsife’s Richard F. Thompson was the first neuroscientist to identify and map the neural circuits responsible for classical conditioning — a form of learning. Photo by Philip Channing.

Link to article

What is C-DEBI?

The Center for Dark Energy Biosphere Investigations explores life beneath the seafloor, making transformative discoveries that advance science and benefit society.

Link to video 

PhD Fellowships at Oregon State

Attached: position announcement for three Ph.D. fellowships in Systems Biology at Oregon State University.

These fellowships are supported by the USDA National Needs Graduate Fellowship and are available in the Department of Animal and Rangeland Sciences at OSU. Please circulate the announcement with your graduate students. In lieu of circulating the pdf announcement, you are welcome to share the link from our website announcement at

I appreciate your time and effort to help us attract top quality students to Oregon State University. If you have any questions or comments regarding this fellowship announcement or OSU, please let me know.

Thank you again,

Lindsey Hollinger
Department of Animal and Rangeland Sciences
118 Withycombe Hall
Corvallis, OR  97331
(541) 737-5327

Plants and their Stressors

New research identifies a genetic switch that regulates a plant’s internal clock based on temperature, leading to plants that can better adapt to climate change.

Dawn Nagel, a postdoctoral researcher at USC Dornsife and lead author on a new study published in the Proceedings of the National Academy of Science, works in Steve Kay’s laboratory. Photo courtesy of Kay Lab.

Link to article

Grand Computational Challenges in the Metagenomics Era | Computational Biology Colloquium

“Grand Computational Challenges in the Metagenomics Era”

Jizhong Zhou
University of Oklahoma
Dept of Microbiology & Plant Biology
Institute for Environmental Genomics

Thursday, October 2, 2014
2:00 pm
RRI 101
Host:  Ting Chen

Microorganisms constitute the most abundant life forms on Earth’s biosphere, and play integral and unique roles in ecosystem functioning, such as biogeochemical cycling of carbon (C), nitrogen (N), sulfur (S), phosphorous (P) and various metals. Understanding the functional diversity, composition, structure, and interactions of microbial communities across different spatial and temporal scales is a critical issue in microbial community ecology. However, analyzing microbial community structure and linking community structure to functions are very difficult. Metagenomics and associated genomics technologies such as high throughput sequencing and functional gene arrays have been demonstrated to be powerful tools for understanding microbial community composition, structure, function, and dynamics and linking microbial communities with environmental factors and ecosystem functioning. With recent advance in metganomics technologies, massive experimental data can be produced, but one of the greatest difficulties is how to handle, analyze and synthesize such massive metagenomics data. In this talk, I will first briefly highlight the current status and most recent development of metagenomics technologies. Then I will describe some great challenges in handling sequencing-based soil metagenomics data. Also, I will describe mathematical prediction of random sampling problems, which results in artifacts in overestimating microbial community diversity across different samples. In addition, I will introduce a new random matrix theory-based mathematical framework to describe ecological network interactions based on metagenomics data, their challenges, and future directions.

Tuesday, September 23, 2014

Academic Careers Week sponsored by USC Center for Excellence in Teaching

Writing Your Cover Letter & CV - Monday, Oct. 6th, Noon - 1:00 pm
Doheny Memorial Library (DML) 240
Presented by: CET Faculty Fellow Erin Moore, Associate Professor (Teaching) of Anthropology, and CET Distinguished Faculty Fellow Geoff Spedding, Profesor of Aerospace and Mechanical Engineering
Lunch Provided
More Information
RSVP here

Negotiating an Academic Job Offer - Tuesday, Oct. 7th, 12:30 - 1:30 pm
Doheny Memorial Library (DML) 240
Presented by: CET Distinguished Faculty Fellow and Executive Vice Provost Michael Quick, CET Distinguished Fellow Bruce Zuckerman, Professor of Religion, and Jessica Cantiello, Lecturer, The Writing Program
Lunch Provided
More Information
RSVP here

Instant Contact: How to Shine on Your Interview Day - Wednesday, Oct. 8th, Noon - 1:00 pm
Doheny Memorial Library (DML) 240
Presented by: CET Faculty Fellow Krishna Nayak, Associate Professor of Electrical Engineering
Lunch Provided
More Information
RSVP here

Drafting Your Teaching Philosophy / Research Statement - Thursday, Oct. 9th, 12:30 - 2:00 pm
Doheny Memorial Library (DML) 240
Presented by: CET Distinguished Fellow Armand Tanguay, Jr., Professor of Electrical Engineering/Electrophysics
Lunch Provided
More Information
RSVP here

Oxygen & the Ecology of Upwelling Margins In a Changing Ocean - An MEB Thursday Noon Seminar

UC San Diego

Sept. 25 @ 12 PM
AHF Torrey Webb Room

Persistent hypoxia (low oxygen) alters both structural and functional aspects of benthic communities, with major consequences for ecosystems services at shallow and bathyal depths. Continental margins subject to upwelling exhibit strong gradients in oxygen, CO2 and temperature, and can serve as ideal natural laboratories for the study of environmental stressors.  Several decades of study of open ocean oxygen minimum zones (OMZs) reveal massive influence of oxygen on benthic abundance, biomass, body size, species composition, species distributions, lifestyles and biodiversity. Differing low-oxygen sensitivities exist among taxa as a function of phylogeny, body size and exposure history, leading to very different oxygen thresholds and responses. Functional consequences of the structural changes include shifts in trophic pathways and efficiency, enhanced roles for chemosynthesis, altered predator and prey encounter dynamics, changing pathways of carbon processing and burial, reduced ecosystem resilience, connectivity and a host of other emergent properties.

As a result of rising CO2 in the atmosphere, upwelling margins are experiencing increased coastal hypoxia and hypercapnia (high CO2).  The strong natural variability of O2 and CO2 on multiple time scales poses a challenge for understanding population and ecosystem responses to OMZ expansion. Approaches for resolving the effects of declining oxygen and pH on margin ecosystems and their services include the use of natural environmental gradients, laboratory manipulations, geochemical proxies and time series data. Scientists today are faced with a need to integrate the influence of natural variability, climate-driven change and direct human activities in management of continental margin ecosystems and resources. The US West coast is increasingly becoming a testbed for ways to address this challenge.

Friday, September 19, 2014

Travel Awards available to Graduate School funded fellows

Who's eligible: PhD students who were funded by Provost’s, Annenberg, Rose Hills Foundation and Global Fellowships who have passed departmental screening or completed 24 units in their USC PhD program

Link to Signature Page

Thursday, September 18, 2014

13 Dishes to Eat to Call Yourself an Angeleno

Whether you were born here or you're a recent transplant, you can't call yourself an Angeleno until you've tried all of these at least once.

Photo by Philippe, the Original

Link to Zagat article

Genome-wide Studies of DNA Structure, Function, and Evolution - BISC Intersection Seminar

BISC Inter-Section Seminar

A series of presentations highlighting ongoing research by your colleagues in
Molecular & Computational Biology, Human & Evolutionary Biology, Neurobiology, and Marine & Environmental Biology, as well as guest lecturers that span sectional interests.

"Genome-wide Studies of DNA Structure, Function, and Evolution"

Remo Rohs
Molecular & Computational Biology
Faculty profile

Where? Hedco Neurosciences (HNB) 107
When? Thursday 18 September 2014 @ 4:00 PM
Social hour to follow in the HNB Conference room


survey services

The Secret Life of Bacteria

Get to know the tiny beings that live all around us—and how USC researchers are understanding and harnessing their powers.

Link to story

The Rise of Troy

USC Village will reshape how generations of Trojans live and learn on campus.

Link to story

Synergy Corporate Housing's September 2014 Newsletter (Issue 5)

Link to Newsletter

ChIP-seq: unleashing its full potential through data integration - Computational Biology Colloquium

Computational Biology Colloquium

“ChIP-seq: unleashing its full potential through data integration”

Hongkai Ji
Department of Biostatistics
Johns Hopkins University
Bloomberg School of Public Health

Thursday, September 18, 2014
2:00 PM
RRI 101
Hosts:  Ting Chen

One major goal of functional genomics is to comprehensively characterize the regulatory circuitry behind coordinated spatial and temporal gene activities. With the ability to map genome-wide transcription factor binding sites and histone modifications, ChIP-seq has quickly become an indispensable tool for studying gene regulation. Despite its unprecedented power, a number of challenges must be overcome before one can take full advantage of this high-throughput technology. First, ChIP-seq is increasingly used for analyzing dynamic changes of regulatory circuitry across different biological contexts (i.e., different cell types, time points, etc.). The conventional methods for analyzing data for one protein in one cell type cannot meet the emerging needs for characterizing quantitative and synergistic changes of DNA binding of multiple proteins between different conditions. New methods are required for dealing with the exponentially growing number of multi-protein combinatorial patterns, and for evaluating the statistical significance given the background biological and technical variation. Second, ChIP-seq is high-throughput with respect to analyzing the whole genome, but low-throughput with respect to analyzing gene regulation in a large number of biological contexts. New strategies need to be developed to better utilize ChIP-seq data originally collected from one biological system to gain insight into gene regulation in other biological systems or diseases. Third, ChIP-seq data also contain information on allele-specific binding (ASB). However, applying ChIP-seq to study ASB often suffers from low statistical power due to the limited number of reads mapped to heterozygote SNPs. In this talk, I will demonstrate that the problems above may be approached computationally by developing new statistical methods for jointly analyzing multiple ChIP-seq datasets and methods for integrating ChIP-seq data with enormous amounts of gene expression data in Gene Expression Omnibus (GEO).

Trader Joe’s Coming to USC Village

The Trader Joe's in Silver Lake. A 12,700-square-foot Trader Joe's will open in USC Village in fall 2017. Photo by Gary Leonard

Link to story

Wednesday, September 17, 2014

Dissertation Defense | The Influence of Diet of the Gut Microbial Community in Ring-Tailed Lemurs and Verreaux's Sifaka

From Correlative to 3D – Recent Advances in Bio Scanning Electron Microscopy

Imaging Users:  We have a great seminar for you as we continue build nano-imaging at University Park Campus!  Please bring your questions!

From Correlative to 3D – Recent Advances in Bio Scanning Electron Microscopy
September 25,12.30
Irani Hall  RRI 101

Kirk J. Czymmek, Ph.D.
Director of North American Applications & Labs
Carl Zeiss Microscopy, LLC

Biological structures, such as organelles, bacteria, somatic cell layers, tissues and model organisms are inherently three-dimensional (3D) and technologies that aid visualization and analysis of 3D biological samples is growing rapidly. Specifically, recent developments in Bio Scanning Electron Microscopy allow high-resolution imaging of samples embedded in resin, then physically sliced and the resulting sections collected in a serial ribbon on tape, glass slide or slotted grid. Each approach has unique benefits and allows access to antibody and other affinity probes for interrogation of specific molecules.  Alternatively, 3D tomograms of entire sliced volumes can be automated with serial block face imaging, where an ultramicrotome is either integrated directly into the electron microscope chamber or a focused ion beam (FIB) is used to mill away the specimen. Block face images have significantly lower distortions associated with material removal than the compression seen in thin sections, thus final 3D EM reconstructions from this approach align closely with the 3D LM volume image. Furthermore, a far greater understanding of the structure-function relationship in cells and tissues is now achievable via high resolution correlation of chemical markers and structural components in both 2D and 3D dimension. This presentation will focus on contemporary methods and probes, methods and workflow for array tomography, serial block face imaging and correlative light and electron microscopy (CLEM) and demonstrate with practical examples how these tools can provide  powerful and novel  insights into biological problems.

If you have any questions and to RSVP please contact your Zeiss Electron Microscopy Specialist, KD Derr, at

Refreshments will be served.

3 Steps for Eliminating Your Bad Habits

Derail, replace, incorporate: habits are based in cues. Here's how to change them for the better. (Based on research by USC Provost Professor of Psychology and Business & Vice Dean for Social Sciences, Wendy Wood)

Link to story

Manahan Named Honorary Fellow

For his contributions to science and his pioneering work in the Antarctic, Donal Manahan becomes an Honorary Fellow of the Welsh university where he earned his doctorate.

USC Dornsife's Donal Manahan (left), who served as chief scientist for many research expeditions to the Antarctic, has been awarded an honorary fellowship by Bangor University in Wales. Here, he stands with Bangor University Vice Chancellor John Hughes during the ceremony. Photo courtesy of Bangor University.

Link to story

World's Most Influential Scientists

Ranking among the top one percent most cited for their subject field and year of publication, four USC Dornsife researchers earn the mark of exceptional impact.

USC Dornsife Dean Steve Kay, Hashem Pesaran, Kenneth Nealson and Ray Stevens are among those deemed by Thomson Reuters to have the most scientifically influential minds in the world.

Link to story

Jim Dines | Whale Mating: In the Hips

A new study turns a long-accepted evolutionary assumption on its head, finding that whale pelvic bones play a key role in mating.

Matthew Dean of biological sciences, (left), and Jim Dines searched through more than 10,000 boxes of unsorted cetacean bones in search of pelvic bones. Photo by Gus Ruelas.

Link to story

Tropical forests in the Anthropocene - Special Seminar

Please consider attending the following special seminar. It should be an overview from a leading forest ecologist that would appeal to anyone with a general interest in historical and contemporary environmental change (from megafaunal extinctions to climate change).

Tropical forests in the Anthropocene
Dr. Yadvinder Malhi, Professor of Ecosystem Science, Oxford
Wednesday, September 24th, 2014 at 4pm
ZHS (Zumberge Hall) 159

Abstract: The Anthropocene is characterized as an epoch when human influence has begun to fundamentally alter many aspects of the Earth system, and many of the planet¹s biomes. Here I review and synthesize our understanding of Anthropocene change in tropical forests, in the context of the long-term environmental history of humanity in the tropics from the Pleistocene to the present. I explore possible reactions and responses to change in the tropics. Key facets of Anthropocene change in tropical include deforestation, timber and wood extraction, the loss of fauna that maintain critical ecological connections, the spread of fire, landscape fragmentation and the spread of second-growth forests, invasion and pathogen spread, and increasing CO2 and climate change. The patterns of change are spatially heterogeneous, often have strong interactions among them, can have both large-scale and remote effects and play out through ecological cascades over long time scales. As a consequence, most tropical forests are on a trajectory to becoming altered ecosystems, and many are becoming novel ecosystems. I explore strategies for shaping the transition of tropical forests through the early Anthropocene, as well as highlight opportunities and challenges for the tropical forest science and conservation community.

Visualizing and Ablating Endogenous Synaptic Proteins In Vivo - A ZNI Seminar Series Event

Please join us for Fall semester’s very first ZNI Seminar Series event with Don Arnold PhD.

Title: “Visualizing and Ablating Endogenous Synaptic Proteins In Vivo”
Date: Wednesday, September 17, 2014
Time: 12 PM to 1 PM
Location: Herklotz Seminar Room (ZNI 112)

Tuesday, July 8, 2014

Upcoming Fulbright U.S. Student Program Information Sessions

Undergraduate, graduate students are welcome to attend. Must have U.S. citizenship to apply for Fulbright.  

Fulbright U.S. Student Program Information Sessions

Thursday, July 17, 2014
12-1pm, VKC 109

Monday, July 28, 2014
4-5pm, VKC 109

During these sessions staff from the Office of Academic & International Fellowships will cover Fulbright U.S. Student Grant Programs including Research/Study, ETA, Fulbright-Clinton and Nat-Geo.  You must be a U.S. citizen to apply. No RSVP needed.  **The 7/28 event will also be a Google Hangout. If you cannot attend in person, go to:​​

USC Deadline: September 15, 2014
Instructions can be found on our website:
Office of Academic & International Fellowships * * 213-740-9116

Tuesday, May 27, 2014


Tuesday May 27th
NRT LG 503/504  (across the lobby from Aresty) - Health Sciences Campus

1:45-2  meet and greet
2-5 presentations
5:15-6 mingling and questions

2:00   Jim Knowles   “Single Cell RNA Sequencing of Neurons”

2:25  Charles Nicolet  “Overview of the Next Gen Sequencing Core”

2:40  Lora Barsky  “Overview of the Flow Cytometry Core”

3:10  Fluidigm  “Defy the law of averages:  Fluidigm’s Biomark* and C1 single cell auto prep systems”

2:55 Daniel Campo “Single Cell Sequencing Experiences at UPC”

3:45 Clontech, Rachel Fish “V3 SMARTer for Single Cell RNA Seq”

4:00 NuGen “Target Enrichment and sequencing of captured circulating tumor cells”

4:15 Qiagen

4:30 Nanostring*

4:45  Fluidigm CyTOF

*Technologies currently available in the Molecular Genomics Core

Refreshments Generously Provided by Fluidigm

Note that there are a few minutes before and more time afterwards to ask questions, gather materials and speak to the vendors and application scientists, and snack.

To all MEB, GeoBio and Earth Sci

When: 1100 am Monday 2 June 2014
Where: Torrey Webb Room/ AHF


Microbialite genetic diversity and N cycling
Luisa I Falcón
Bacterial Ecology Lab., Institute of Ecology, UNAM

Microbialites have played an important role in the early history of life on Earth with fossilized forms representing the oldest evidence of life on our planet dating back to 3500 Ma. Extant microbialites have been suggested to be highly productive and diverse communities with an evident role in the cycling of major elements, and in contributing to carbonate precipitation. We have analyzed microbial genetic diversity of microbialites living in different types of environments throughout Mexico, including desert ponds, coastal lagoons and crater-lakes. Microbialite communities are very diverse (H = 6–7) and show geographic variation in composition, as well as an environmental effect related to pH and conductivity, which together explain 33% of the genetic variation. N cycle pathways including N2 fixation, nitrification, denitrification and anammox are evident in the potential community, but only N2 fixation by heterocyst-forming Cyanobacteria within Nostocales are actively transcribed. Our studies suggest that N limitation in the environment strongly favors autotrophy and diazotrophy and restricts remineralization pathways via denitrification and anammox. Cyanobacteria that form heterocysts and are actively transcribing for N2 fixation, are fundamental players in microbialites since they are responsible for providing reduced N –amides, C in lipids and carbohydrates, and host in their external cell membranes the main sites of carbonate mineral precipitation.