Thursday, December 3, 2020

Postdoctoral Opportunity: The Tufts Institutional Research and Academic Career Development Awards Program (IRACDA)

We would like to tell you about an exciting postdoctoral training program that is in place at Tufts University in Boston, Massachusetts. This program, called IRACDA (Institutional Research and Academic Career Development Awards Program), is funded by the IRACDA mechanism of NIH-NIGMS. 

This NIGMS-funded program is designed to prepare talented young scientists for the multiple demands of an academic career in biomedical research. Scholars spend on average 75% of their time conducting bench research and 25% of their time in career development activities. Teaching skills are developed through programs involving mentored classroom assignments at minority-serving institutions in the Boston area. The training is further supplemented by workshops on essential skills such as grant and manuscript writing, mentoring, lab management, scientific presentations, and responsible conduct of research as well as on teaching methods that encourage active learning. The training components are sequenced to allow scholars to balance the activities and to build on previous experiences. The first year of support for IRACDA scholars is provided by the faculty research mentor and then up to three years of support, plus a yearly travel and supply allowance, comes from the IRACDA Program. 

The application deadline for positions beginning in the fall of 2021 is March 1, 2021. Later applications will be considered if positions are available. 

Applicants must be U.S. citizens or permanent residents with no more than two years of postdoctoral training at the time of their appointment to the program. The strongest candidates will have strong academic and research credentials, an interest in teaching, mentoring, and increasing diversity in STEM fields, and a commitment to the goals of the Tufts IRACDA program. 

For additional information on the Tufts IRACDA Program and application procedures, please visit our website, or contact Claire Moore, the Program Director, or Jordan Wilkinson, the Program’s Research Administrator with questions. We have also attached a printable flier describing the program.

Tufts IRACDA Program Flier 21-22 by Adolfo De La Rosa Jr on Scribd

Tuesday, October 6, 2020

Annual BioResearch Product Faire

Please join us for our Annual BioResearch Product Faire Lab Tools and Techniques Event, held virtually for USC Researcher Audiences on October 7, 2020.

USC Researchers: Visit more than 2 exhibitors and receive a $25 Amazon card.

Click link to attend: https://lab.biotech-calendar.com/uschs-2020-vbpf

Stop by the event to meet with Reps from:

Vectorbuilder
Goldbio
Spectrum Chemical
BD Biosciences
Macherey-Nagel
Funakoshi
Science Careers

When: Wednesday, October 7, 2020
Where: Virtual Event
Time: 10:00 AM - 3:00 PM
Cost: No admission fees + free lab door prizes & give-aways

Saturday, September 26, 2020

QCB Special Seminar | Dr. Vsevolod (Seva) Katritch

Dr. Vsevolod Katritch
Assistant Professor, USC Dept. of Biological Sciences, QCB

GPCR modeling: from structure to function to rational design of new receptors and ligands

Thursday, October 1 @ 2 PM

Zoom Meeting ID: 984 8270 9945 | Passcode: 329869

Abstract: Comprising the largest protein superfamily in human, 800 G-protein Coupled Receptors (GPCRs) play key regulatory roles in most physiological processes and serve as a target for about a third of all therapeutic drugs. Over the last few years, a flow of structural information from crystallography and cryo-EM helped to establish a solid framework for computational modelling inquiry into GPCR functional mechanisms and 3D pharmacology of GPCR ligands. The quantitative understanding of atomistic details of GPCR structure-function is also directly applicable to the rational design of both receptors and ligands with new properties. This talk will describe several new approaches to GPCR computational modelling and design developed in my lab. Using sequence-based, structure-based, and machine-learning approaches we developed the CompoMug software for predicting stabilizing mutations in GPCRs, which has already helped to crystallize more than a dozen receptors.  Discovery of new allosteric co-factors, including highly conserved sodium ion in the center of the 7TM bundle in Class A GPCRs, has opened a venue for rational design of highly potent bitopic ligands with unusual signalling properties. This design approach has yielded novel opioid receptor probes and can be applied to many GPCRs.  Finally, we develop a conceptually new Virtual SYNTon Hierarchical Enumeration Screening approach, V SYNTHES, which enables fast and accurate screening in combinatorial REadily AvailabLe (REAL) chemical space as large as 10 Billion compounds and more. Tested in prospective screening for Cannabinoid receptor ligands, V-SYNTHES yielded 20 novel submicromolar ligands, while showing more than 100-fold improved speed and better hit rates than the traditional virtual ligand screening. The approach is scalable to the rapidly growing combinatorial libraries beyond 1010-1013 compounds, yielding better hits and also streamlining their optimization.  We apply these computational tools to the key receptors in inflammation, sleep and pain modulation pathways, facilitating discovery of novel GPCR ligands with desirable functional profiles as molecular probes and lead candidates.

Hosts: Dr. Charles McKenna and Dr. Remo Rohs

Monday, May 11, 2020

GENEWIZ Week Grant Program

The 5th annual GENEWIZ Week Grant Program is now open! Apply for one of six grants valued up to $5,000 in GENEWIZ credit as we recognize excellence in genomics research.

Winners will receive credit toward a GENEWIZ service that applies to their project, including next generation sequencing, synthetic DNA solutions, PCR + Sanger sequencing, Sanger-only sequencing, or 4titude consumables from Brooks Life Sciences. To apply, simply submit a short abstract (up to 250 words) describing your project. See full grant terms and conditions for contest rules and eligibility.

Submit your application by June 1, 2020 for consideration.

Learn more about our GENEWIZ Week activities including webinars about the latest genomic innovations and discoveries, limited-time GENEWIZ promotions, and more. Feel free to contact us with any question. We look forward to celebrating with you!

Ingenuity Pathways Analysis online training

Please join us on Tuesday May 19 for an online training on the Ingenuity Pathways Analysis (IPA).

Learn how you can leverage Ingenuity IPA’s expert curation of the scientific literature from the past 18+ years and the thousands of hours spent to validate and organize NGS data from sources such as the SRA database, GEO, TCGA and more.  Researchers can easily analyze their own NGS data alongside public datasets and manual curation of literature to identify the best testable hypotheses, targets and biomarkers.

Training Agenda 
Time:                 Tuesday, May 19th, 10am-12:30pm Zoom Web Training
Presenter:        Devendra Mistry, PhD, Field Application Scientist

10-10:15am:    Introduction to IPA Database and Applications Supported
       
10:15-11:00am:   Live demo of IPA Analysis Workflow
Format, upload your data, and launch an analysis
Identify pathways associated with your gene/protein/metabolite list
Find causal regulators and their directional effect on genes functions and diseases

11:30 -1pm:     Advanced IPA Analysis Topics
Build pathways, make connections between entities, and overlay multiple dataset
Multi-groups (treatments, time points etc.) and multi-omic comparisons
o How the pathways, biological processes and regulators are regulated across different time points, treatments, disease conditions?
o Generating a list of biomarkers specific to a condition
How to gain insights from public data using Analysis Match and Activity Plot
o Compare user analysis with analyses of public datasets from GEO, SRA, TCGA etc.
o How is the regulator, pathway, biological function of interest behaving across ~60,000 public dataset analyses

Please follow the link below to register for this training:
https://usc.qualtrics.com/jfe/form/SV_0cZIV5DwfXuaOhf

Let us know if you have any questions.

USC Libraries Bioinformatics Services
https://libraries.usc.edu/bioinformatics
nmlbio@usc.edu


Monday, April 27, 2020

Watershed Stewards Program recruiting for Year 27

The California Conservation Corps Watershed Stewards Program in Partnership with AmeriCorp (WSP) is currently recruiting Members to serve in our 10.5 month program.

WSP offers exceptional training and hands-on experience for individuals interested in natural resources and watershed protection. The mission of WSP is to conserve, restore, and enhance anadromous watersheds for future generations by linking education with high quality scientific practices. 

Our Apply To WSP web page contains information about our WSP Corpsmember (Fisheries and Restoration Technician) and Team Leader positions for our 27th program year.

BISC Honors 2019-20



Monday, April 20, 2020

COVID-19 Resources

Face Coverings
http://publichealth.lacounty.gov/media/Coronavirus/GuidanceClothFaceCoverings.pdf

Social Distancing
http://publichealth.lacounty.gov/media/Coronavirus/GuidanceSocialDistancing.pdf

LA County Resources
http://publichealth.lacounty.gov/media/Coronavirus/resources.htm

COVID-19 Cases
https://www.worldometers.info/coronavirus/

Centers for Disease Control and Prevention
The Centers for Disease Control and Prevention is the National Lead Agency for COVID-19.  Visit their COVID-19 site for up-to-date information and guidance, including information for community organizations and community gatherings:  https://www.cdc.gov/coronavirus/2019-ncov/index.html 

World Health Organization
https://www.who.int/emergencies/diseases/novel-coronavirus-2019

FEMA COVID-19 Best Practices
FEMA has created a page for Emergency Management Best Practices for COVID-19:  https://www.fema.gov/coronavirus/best-practices

Additional websites with useful information
The following includes a list of websites with useful information on COVID-19
Workplace, School, and Home Guidance
People at Risk for Serious Illness from COVID-19
How COVID-19 Spreads
Symptoms
Steps to Prevent Illness
Testing
Frequently Asked Questions
What You Need to Know
Facts about COVID-19
Information for People at Higher Risk and Special Populations
Communication Resources

COVID-19 Emergency Assistance Fund

OVERVIEW
USC will be receiving funds under the CARES Act to provide emergency financial aid grants to students for COVID-related expenses, such as food, housing, course materials, technology, health care, and child care. The Financial Aid Office is working closely with Student Affairs and Campus Support and Intervention to coordinate providing financial assistance to students.

WHAT YOU SHOULD KNOW
Students facing extraordinary one-time costs as a result of the COVID-19 pandemic should complete the COVID-19 Emergency Assistance for Currently Enrolled Students application. The application identifies common costs that are eligible for emergency grant funding. The current funding limit is $3,000. Students can access the form in the Document Library on the Financial Aid Summary and Tasks (FAST) page. A copy is also attached.

This funding is available to continuing undergraduates and graduate students, regardless of whether they are financial aid recipients. Newly admitted undergraduates and undergraduates facing a change in income that may affect their expected family contribution should upload a separate Appeal Concerning Expected Contribution through FAST, which may result in additional financial aid.

The Financial Aid Office, Student Affairs, and Campus Support and Intervention are working in collaboration to respond to student needs related to COVID-19. We are sharing information and providing referrals so that students may obtain appropriate assistance. Our goal is to assist the maximum number of students possible with financial assistance to meet their needs throughout the duration of the COVID-19 emergency.

WHAT YOU NEED TO DO
Students should be advised to complete and upload the COVID-19 application to their FAST page. We are aware that departments may be establishing their own emergency grants as well and are supportive of those efforts. In some cases, we may contact your department to determine if further assistance is available for a student. Please note that departmental grants are institutional funds that will need to be coordinated into a student’s financial aid package, although we will make every effort to preserve all existing sources of financial aid.

WE ARE HERE TO HELP
Please contact Diane Anchundia, Associate Dean, Outreach and Loans, or me if you have any questions about this funding or have a specific student situation that requires special attention.

Thank you for your support during this extraordinary time.

Thomas McWhorter
Dean of Financial Aid
University of Southern California
John Hubbard Hall  MC 0914
Los Angeles, CA 90089-0914
T: (213) 740-5445   F: (213) 821-3796
Email: faodean@usc.edu
Web: financialaid.usc.edu



Monday, April 13, 2020

Stem Cell Challenge Grants 2020-21


Phi Beta Kappa Alumni Scholarship 2020

The graduate school is delighted to announce that the nomination site for the Phi Beta Kappa Alumni Awards is now open. The scholarship recognizes international students pursuing graduate degrees in the U.S. Recipients of the PBK award must be about to begin the final year of their program and be seeking a degree that is considered “terminal” in their field (i.e. PhD).

One award in the amount of $1,000 will be given to a graduate student at USC

Students should complete the attached Phi Beta Kappa Alumni Awards application and upload it to https://provost.sma.usc.edu/prog/gs_pbk by Friday, May 8, 2020.

Two letters of reference should uploaded to the application site by Sunday, May 10, 2020.  One of these letters should be from the student’s faculty advisor.  Students will be able to send a request to their recommenders to upload letters directly through the application site.

Please let me know if you have any questions.

Kate Tegmeyer
Assistant Director of Graduate Programs
The Graduate School
Office of the Provost
University of Southern California
Tel: (213) 740-9037 | Fax: (213) 740-9048
gradfllw@usc.edu



Bioinformatics Self-learning Resources Guide

The USC Libraries Bioinformatics Services is pleased to announce the availability of the Bioinformatics Self-learning Resources Guide as part of our ongoing efforts to support the COVID-19 Research Continuity Plan by the university as well as by the Keck School of Medicine.

This Bioinformatics Self-learning Resources Guide has been compiled for students and researchers who are interested in learning how to carry out some of the most common bioinformatics tasks.  This resource provides links to our previous workshops and training on our licensed commercial bioinformatics software.  It also includes the links to our hand-picked list of high-quality publicly accessible bioinformatics tutorials and webinars from other institutions, focusing on open-source tools.

We will continue to update this resources guide and we welcome any comments and suggestions.

Stay safe and healthy!

USC Libraries Bioinformatics Services
nmlbio@usc.edu
https://libraries.usc.edu/bioinformatics

CET Teaching Online Tip Sheet

Monday, March 30, 2020

Lessons learned from cancer tracking helps fight coronavirus

Peter Kuhn, Dean’s Professor of Biological Sciences and professor of medicine, biomedical engineering and aerospace and mechanical engineering and a founding member of the USC Michelson Center for Convergent Biosciences.

“We’ve teamed with a Bay Area company to make a phone app to record and analyze coughs and symptoms and compare it to an individual’s social interactions using GPS,” Kuhn said. “It’s all about using data from individuals that becomes a source we can use to help stop the spread of coronavirus.”

He added:
Work at USC’s Convergent Science Institute in Cancer (CSI-Cancer) laid a foundation for tracking health performance across populations.
CSI-Cancer is partnering with San Francisco-based HealthMode to develop the app.
The app would work by linking an individual’s symptoms to their previous locations and contacts.
The data can help identify sick people and prevent the spread of disease.
Privacy protection measures will be included in the app.

Stay tuned!

Move! It will help your mental health and boost immunity

David Raichlen, a USC expert on exercise and human evolution, is in the same boat as anyone whose county or state have enacted a stay-at-home mandate to reduce the spread of infection. It can make you feel trapped. He has this advice for boosting both mental and physical health:

"These are highly stressful times, with anxiety levels increasing, and few outlets to help us maintain our mental health. One thing we can do, even when we are housebound, is to engage in physical activity and exercise. Exercise is not only good for your physical health and immune system, but exercise can play a key role in improving mental health. In fact, recent work has shown that exercise can be an effective treatment option for mild depression and anxiety disorders.

"Why does exercise affect your psychological state? One possibility is that exercise increases the activity of neurotransmitters like endorphins and endocannabinoids which are associated with reductions in stress and improvements in mood. These neurotransmitters activate the same receptors as drugs like opioids and marijuana, but with milder effects that can lead to more general feelings of well-being in most people.

"How can you take advantage of these effects? Moderate intensity aerobic exercise is the most commonly studied activity shown to activate these systems. A brisk walk or jog will do it, and will get you outside (while keeping a safe 6 feet of distance from others). You know you’re at a moderate intensity if you can talk but not sing. If you can only manage a few words without having to catch your breath, you are going too hard."

Analyzing single-cell RNAseq data in Partek Flow--Webinar on Thursday April 2nd

Partek Flow has a powerful workflow for single-cell RNAseq data analysis.  If you have or will have single-cell RNA-seq data soon, we strongly recommend that you sign up for next Thursday April 2nd webinar, select the Boston session, which starts at 11:15 AM LA time.

Three Sessions to Choose From:
April 1, 2020, 2:15 p.m. SGT (Singapore)
April 2, 2020, 2:15 p.m. BST (London)
April 2, 2020, 2:15 p.m. EDT (Boston)

Same content in all sessions

Tissue transcriptomics is a family of techniques designed to allow transcriptomic profiling of cells within a tissue. It has gained a lot of attention over the past two years and is paralleling and extending advances made in single cell RNA-Seq technology.

Join us for a webinar where we will demonstrate the analysis of 10x Visium data in Partek Flow software. You will learn how to leverage its statistical power to answer your biological questions and see exciting new features in the Partek Flow Data Viewer.

What you will learn:
Import 10x Genomics spatial transcriptomics data
Combine gene expression data with histological information
Identify clusters of spots based on gene expression profiles
Perform differential gene expression

Monday, March 23, 2020

An important update on our bioinformatics services

As part of USC Libraries’ COVID-19 responses, our offices on both HSC and UPC will be closed starting Monday March 16 and possibly 'til April 13.  However, the USC Libraries Bioinformatics Services will continue to deliver the quality bioinformatics support you have come to expect during this period of time as we will be working from home.  While the in-person consultation will not be available, all of your questions and requests will be addressed in a timely manner via emails and online platforms such as the Zoom.  All our bioinformatics computing resources will be operating as usual to support your sequencing data analysis needs. 

1. For general inquiries and request, email nmlbio@usc.edu.
2. For consultation request: https://uschsl.co1.qualtrics.com/jfe/form/SV_di1fbQJYL4QsxXD
3. For NGS data analysis request: https://uschsl.co1.qualtrics.com/jfe/form/SV_8GHy25wi20UsL2Z
4. Whenever necessary, Zoom meeting will be arranged between 10 am and 4 pm, Monday to Friday.

Please take a good care of yourself, everyone!

Fight on!

Yibu, Meng, and Eddie

USC Libraries Bioinformatics Services
nmlbio@usc.edu
libraries.usc.edu/bioinformatics

Graduate Housing Update

Graduate students living in USC Housing on the year-long contract must complete the survey you received via email to request an exception to stay in housing.

We do not plan on asking those students to move out, but we need them to still follow our process to request the exception so we can track true occupancy numbers right now.

Please follow the instructions above if relevant to your housing situation.

If you have any questions, please reach out to USC Housing Services at (213) 740-8488 or via email at housing@usc.edu or to my office at graduatedean@dornsife.usc.edu.

- Dr. Steve Finkel
College Dean of Graduate and Professional Education

The Writing Center has moved online

The Writing Center has transitioned to online consultations for the remainder of the Spring 2020 semester and will reopen for appointments on Wednesday, March 25 at 9am.

The appointments will be "synchronous," meaning that students and consultants can video chat and work on a document in real time.  The schedule remains the same, and all appointments will be held in PST.

Instructions are provided below on how to schedule and attend an online appointment at the Writing Center.

If you have questions, please e-mail or call Cory Nelson (213-740-0231).

COVID-19 Updates for BISC Graduate Students (3/17)

Graduate Advising

All advising staff will be working from home until at least Tuesday, April 14th.  Ashley, Paloma, Adolfo, and I will be available by email for any questions.  Should you need to talk to us, we can also arrange for phone calls or zoom meetings. 

Summer Support Forms

Please email us your summer support forms, if you have not already done so.  Despite the current situation, or deadlines for entering your summer support to ensure timely payment have not changed.  Your forms were due to your advisor on Friday, March 20th.  Scans are preferred.  You may obtain e-signatures from your advisor, if necessary.

Spring Classes

All Spring classes will continue to be offered remotely for the remainder of the semester, including laboratory courses.  You will be able to complete your courses via Zoom and this decision will have no impact on your academic progress. 

Graduation and Commencement

Students will be able to complete the semester and graduate. International students with specific concerns about travel, visas, and online capability should contact the Office of International Services at (213) 740-2666 or ois@usc.edu; other students concerned about online capability should contact (213) 740-6291 or covid19@usc.edu.

The university is postponing commencement activities originally scheduled for May 15th. An in-person, on-campus celebration that will take place once travel and large group events become safe and permitted.

Qualifying Exams and Dissertation Defenses

All oral qualifying exams and dissertation defenses may now be conducted remotely, if desired.  Permission of the department and Dean are required.  If you intend to complete your oral qualifying exam or dissertation defense remotely between today and the end of the spring semester, please email me to request approval.  I will coordinate departmental and Dean’s approval for you. 

Research Continuity

You should have all received a detailed email from the USC Graduate School last week detailing the expectations related to your continuing research in the labs.  Please review this email carefully and work with your PI to set a plan that works best for you.  The university is asking for you to complete as much of your lab work from home as possible and to adhere to good hygiene and social distancing practices when in the lab. If you did not receive the email from the graduate school, please let me know and I will forward it to you. 

>>

If you have questions related to this information or if I can be of assistance to you in any way, please feel free to contact me.

- Douglas Burleson

Monday, March 16, 2020

COVID-19 Updates for BISC Graduate Students

Spring Semester Classes

Beginning today, March 11th and continuing through Sunday, March 29th, all USC lecture, quiz, and discussion sections will be moved online.  Lab courses will meet as scheduled through March 13th.  The current assumption is that lab courses will also move online beginning on March 14th and continuing through March 29th.  Should this change, we will update as soon as possible.  We currently are working with university officials to determine how the move to online course instruction will impact those of you who are currently Teaching Assistants.  As soon as any decision has been made in this regard, I will update you on your responsibilities.

Research

All research staff and graduate students should continue to work in their labs at this time, while following recommended USC practices related to minimizing the impact of COVID 19.  These practices include things such as staying home if you are sick, not shaking hands, practicing good hygiene and practicing social distancing.  More detailed information regarding research practices may be found here.

Travel

All non-essential travel for faculty, staff, and graduate students is suspended until further notice.  Essential travel must be approved in advance to be reimbursed.  If you have incurred costs related to the cancellation of travel due to cancellations of conferences or meetings, you may still be able to be reimbursed.  Details on what will be considered essential travel and how to be reimbursed for any incurred expenses may be found here

Qualifying Exams, Dissertation Defenses, and Graduate School Petitions

The USC Graduate School has issued temporary policy related to oral qualifying exams and dissertation defenses.  Both may now take place remotely, with prior approval from the student, committee chair, and dean of the school.  Here is the specific language related to this policy from the Graduate School:

How can I defend my dissertation if COVID-19 affects my ability to meet with my dissertation committee in person?
Remote participation in a dissertation or thesis defense is always an option for a limited number of committee members.  With the approval of the student, committee chair, and the dean of the school, the defense can be conducted entirely through Zoom or other videoconferencing tool.  The standard rules apply to the defense.  This means that all committee members must be part of the same defense “meeting,” whether they are on campus or remote.

How can I submit my dissertation if COVID-19 affects my ability to function on campus?
Dissertation checklists and manuscripts are submitted electronically via Thesis Center (http://graduateschool.usc.edu/current-students/thesis-dissertation-submission/) and are not affected by the location of the student.

How can I take the oral portion of my qualifying exam if COVID-19 affects my ability to meet with my exam committee?
Remote participation in the oral portion of a qualifying exam is always an option for a limited number of committee members.  With the approval of the student, committee chair, and the dean of the school, the defense can be conducted entirely through Zoom or other videoconferencing tool.  The standard rules apply to the exam.  This means that all committee members must be part of the same exam “meeting,” whether they are on campus or remote.

How can my advisor submit an academic petition on my behalf to the Graduate School if COVID-19 affects the university’s functions on campus?
Petitions are submitted by advisors online and are not affected by the location of the student or the advisor.

Student-Organized Events

Effective immediately and until further notice (at least through March 29th), all university-sponsored events, including any event organized by a Registered Student Organization, are suspended.  We ask that you cancel any events currently scheduled and plan to reschedule them, if desired, sometime later in the semester, after March 29th.

We will continue to monitor the situation as it develops and share with you any updates that are impactful to you, your classes, your TA/RAships, and your research.

Monday, March 9, 2020

Vice Provost for Graduate Programs Student Luncheons

USC Graduate School’s Vice Provost for Graduate Programs, Sally Pratt, invites you to attend one of the upcoming Spring 2020 Graduate Student Luncheons. 

The luncheon will be an opportunity to create an inclusive community for graduate students from the University Park Campus and the Health Science Campus. You have the opportunity to talk with the Vice Provost about a variety of university-wide graduate and professional student topics Vice Provost Pratt is interested in hearing your news, updates, and concerns  and in soliciting feedback on aspects of the Graduate School that work well and how the Graduate School can improve its relationships with graduate students. 

The event is open to all USC graduate students, and attendance will be capped at 15 students per luncheon. Space is limited; please note that your RSVP does not guarantee you a seat at the luncheon. The exact location of each luncheon will be communicated through a confirmation email sent to the first 15 students, per event, who have expressed interest in the particular meeting date.

Our Spring 2020 Graduate Student Luncheons will take place on the following dates:
UPC: March 25, 12-1:30 PM
UPC: April 6, 12-1:30 PM
UPC, International Student Topics: April 8, 12-1:30 PM
HSC: April 14, 12-1:30 PM

Reserve your space for one of the luncheons by filling out this form.

MCB Colloquium | Dr. Yang Yang

   Yang Yang Flyer by uscbiscgrad on Scribd

MEB Seminar | Dr. Nicole Ratib

Dr. Nicole Ratib
Post-Doc, USC, MEB (PI: Dr. Cameron Thrash)
Research Profile

Genomic and physiological characterization of Escherichia coli evolving in long-term batch culture

Tuesday, March 10, 12 PM, AHF 153 (Torrey Webb Room)

Abstract: In most natural environments, bacteria spend much of their time under conditions of starvation and stress. Long-term batch cultures are an excellent laboratory system to study adaptation during nutrient stress because cells are incubated for relatively long periods of time, months to years, without the addition of nutrients. During long-term batch culture cells adapt to acquire energy from cellular detritus creating a complex and dynamic environment for mutants of increased relative fitness to exploit. To characterize the population dynamics and identify beneficial alleles, we analyzed the genomes of 1117 clones isolated from a single long-term batch culture inoculated with a single clone and incubated for 1200 days. A total of 679 mutations were identified including single nucleotide polymorphisms, indels, movement of mobile genetic elements, large deletions up to 64kbp and amplifications up to ~500kbp. During the 3.3-year incubation, two main lineages diverge and continuously evolve. There is evidence of at least two instances of a fixed mutation reverting back to the wild type allele, suggesting beneficial mutations may later become maladaptive. Most of the mutated genes encode proteins involved in metabolism, transport, or transcriptional regulation. Clones from the two lineages are physiologically distinct based on outgrowth in fresh medium and competition against the parental strain. Similar population dynamics and mutated genes were detected in three parallel populations sequenced through day 60 providing evidence for positive selection. These data provide new insight into the population structure and mutations that may be beneficial during periods of starvation in evolving bacterial communities.

Monday, March 2, 2020

QCB Faculty Candidate Seminar | Dr. Geoffrey Fudenberg

Dr. Geoffrey Fudenberg
Bioinformatics Fellow, UCSF, Gladstone Institute
Research Profile

Genomes in 3D: connecting structure and function

Thursday, March 5, 2 PM, RRI 101

Abstract: How are micron-long chromosomes spatially organized by molecular interactions between proteins at the nanometer scale? Acting as a molecular microscope, genome-wide chromosome conformation capture (Hi-C) reveals that genomes are intricately folded in 3D. Here I describe how biophysical simulations and machine learning approaches enable interpretation of these large-scale genomic datasets. First, I describe converging theoretical and experimental evidence arguing that Cohesin-mediated loop extrusion with CTCF-defined barriers plays a crucial role in interphase. Second, I describe how convolutional neural networks enable accurate predictions of genome folding from DNA sequence alone. Together, these advance our understanding of the proteins driving and the sequences underpinning 3D genome folding.

Sunday, February 23, 2020

2020 Student Recognition Awards: Call for Nominations

Dear USC Faculty and Staff,
.
On behalf of the 2020 Student Recognition Committee, we invite you to nominate undergraduate, graduate and professional students whose dedication and notable contributions have enriched the quality of campus life and in the local, national and international community.

We are asking your support to identify and nominate outstanding students deserving of this special recognition. To be eligible, nominees must be scheduled for graduation in either May 2020 or August 2020. Recent graduates from December 2019 are also eligible. Faculty and staff may nominate as many students as they deem worthy of consideration; however, not all nominees will receive a Student Recognition award.

By honoring these students, USC continues to celebrate the values of leadership, service and engagement. Nominated students may be eligible to receive one of the following awards:
Undergraduate Students:

• The Order of the Torch: Awarded to outstanding undergraduate students whose dedication to leadership and community service go beyond that of their peers.
• The Order of Troy: Awarded to graduating undergraduate students whose leadership, in conjunction with academic excellence, has provided significant value to the USC community.
• The Order of the Laurel and the Palm: Awarded to less than 1% of graduating undergraduate students who have distinguished themselves from their peers in the fields of leadership, scholarship, and service both on and off campus.

Graduate/Professional Students:

• The Order of the Torch: Awarded to outstanding graduate students whose dedication to leadership and community service go beyond that of their peers.
• The Order of Areté: Awarded to graduating graduate students who have demonstrated significant depth and scope of responsibility in leadership roles benefiting their peers and their broader communities.

The nomination and selection process is as follows:
• Nominations are available online starting Feb. 21, 2020 at http://studentrecognition.usc.edu/ and close on Friday, March 6, 2020 (Only complete nominations will be considered.)
• Faculty and staff nominators must provide all information about each nominee’s involvement and justify their excellence in leadership, scholarship, and service.
• Nominators are responsible for the completion of nomination forms for students,which they nominate.

Student nominees will not be involved in the selection process.
• At least three members from the Student Recognition Review Committee will review completed nominations.
• The committee will select based on academic achievement, leadership, and service including those who have enhanced their academics with a variety of co-curricular activities (including paid positions) and have positively contributed to USC.
• The committee will notify award recipients and their nominators via email to attend the USC Student Recognition Ceremony taking place on Thursday, May 14, 2020 at Bovard Auditorium at 1 p.m.

More information about the awards are located on the Student Recognition Awards.

Please direct any specific questions to 2020 Student Recognition Committee Chair, Cynthia Tucker at uscsrc@usc.edu.

Thank you for helping us recognize and honor our outstanding students.

2020 PhD Achievement Award



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QCB Faculty Candidate Seminar | Dr. Assaf Amitai

Dr. Assaf Amitai
Post-Doctoral Researcher, MIT
Research Website

Geometry and stochastic dynamics in biological systems

Thursday, February 27, 2 PM, RRI 101

Abstract: The interaction of proteins with chromatin regulates many cellular functions. Most DNA-binding proteins interact both non-specifically and transiently with many chromatin sites, as well as specifically and more stably with cognate binding sites. These interactions and chromatin structure are important in governing protein dynamics. By analyzing the motion of CTCF, a DNA binding protein responsible for chromosomal organization, we inferred that it interacts with a new type of small nuclear domains. These domains, composed of RNA, are central in guiding CTCF to find its cognate binding site. Hence, weak transient interactions govern chromatin organization and dynamics. In the second part of the talk, I will describe recent advances in the development of a universal vaccine for the influenza virus. Using coarse-grained molecular dynamics simulations and a population scale models of the adaptive immune system, we study the immune response to nanoparticles presenting flu proteins at unique geometries and compositions. We show that these nanoparticles can direct the immune response in distinct evolutionary paths, and elicit the creation of antibodies of high breadth - capable of neutralizing multiple flu strains.

MCB Colloquium | Dr. Cornelius Gati

   Gati Flyer by uscbiscgrad on Scribd

MCB Colloquium | Dr. Xinghong Dai

   Xinghong Dai Flyer by uscbiscgrad on Scribd

Monday, February 17, 2020

USC Student Health - Program expansion for students

QCB Faculty Candidate Seminar | Dr. David Zeevi

Dr. David Zeevi
Independent Fellow, Rockerfeller University, Center for Studies in Physics & Biology
Research Website

Mining the marine microbiome for remediation targets: lessons from the human microbiome

Thursday, February 20, 2 PM, RRI 101

Abstract: Microbial communities can have an immense effect on their environment and are strongly affected by it. Using new methods for metagenomic sequencing analysis, we systematically identified microbial genomic structural variants and found them to be highly prevalent in the gut microbiome and to correlate with disease risk factors (Zeevi et al., Nature 2019). Our results suggest that these variants facilitate adaptation to environmental stress. Exploring genes that are clustered in the same variant, we uncovered potential mechanistic links between microbiome and its host. Inspired by our discovery of potential microbial adaptation to host pressures, I developed a strategy for mining marine microbiome samples for novel bioremediation genes. To this end, we devised a high-throughput evolutionary analysis, and revealed an unexpected insight into the structure of our genetic code (Shenhav and Zeevi, bioRxiv 2019). Our primary analyses uncovered overwhelmingly strong purifying selective pressure across marine microbial life. This selection was highly correlated with nutrient concentrations and has led us to explore robustness in the genetic code, common to nearly all life forms. We show that the structure of the genetic code, along with amino acid choices across all kingdoms of Life, confers robustness to mutations that incorporate additional nitrogen and carbon into protein sequences. By accounting for this nutrient-conservation-driven purifying selection, we will be able to expose a new layer of selection associated with marine pollution.

MCB Colloquium | Dr. Xianrui Cheng

   Xianrui Cheng Flyer by uscbiscgrad on Scribd

Sunday, February 2, 2020

Wrigley Sonosky Sustainability summer fellowship

The USC Wrigley Institute is now accepting applications for the 2020 Sonosky Sustainability Summer Fellowship. Applications due March 11. Notice is attached.

MCB Colloquium | Dr. Joseph Nadeau

MEB Seminar | Dr. Leslie Babonis

Dr. Leslie Babonis
Research Assistant Scientist, University of Florida, Whitney Lab for Marine Bioscience
Research Profile

Understanding biodiversity, one cell at a time

Thursday, February 6, 12 PM, AHF 153 (Torrey Webb Room)

Abstract: I study novelty. Specifically, I am interested in understanding the factors that drive the origin and diversification of novel cell types. More than just taxon-specific oddities, novel cell types can promote niche specialization and facilitate speciation events; thus, studying novelty is critical for understanding the evolution of biodiversity. One of my favorite projects focuses on understanding the mechanisms driving morphological and functional specialization of cnidocytes (stinging cells) across cnidarians (corals, jellyfish, and their kin). Using a combination of observational and functional techniques, I have constructed a cnidocyte gene regulatory network that I use to test hypotheses about the evolutionary origin of this truly bizarre lineage of cells. Surprisingly, the fate of this novel cell lineage seems to have been acquired through recycling and reorganization of an old gene regulatory network, rather that the origin of a novel regulation strategy.

MCB Colloquium | Dr. Jake Harris

   Harris Flyer Flyer by uscbiscgrad on Scribd

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

USC Housing for 2020-21

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.



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.

MCB Colloquium | Dr. Bushra Raj

   Bushra Raj Flyer by uscbiscgrad on Scribd