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

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).

   How to Schedule a Virtual Appointment by uscbiscgrad on Scribd

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

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.

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.

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.