Black Lives Matter at The Rockefeller University

Natural Selections Editorial Board

The appalling and tragic murder of George Floyd in Minneapolis during a pandemic that was already disproportionately affecting Black communities provoked a global re-awakening for justice for Black people. This seeking of justice has not excluded the realm of academia. 

The Rockefeller Inclusive Science Initiative (RiSI) is a student-run organization formed in 2018 with the support of Erich Jarvis as the faculty advisor. Dr. Jarvis, a Rockefeller alum himself, is the first and only Black full professor in the 119-year history of Rockefeller. RiSI’s mission is “to unify diverse voices and improve our campus and broader scientific community” in terms of diversity and inclusion. In the two short years since its inception, RiSI’s work and passion have already had an impact on the Rockefeller community and the broader scientific community, including their advocacy for contracted custodial workers at the beginning of the shutdown due to COVID-19.

So when no official statement came from Rockefeller for days after the murder of George Floyd and the beginning of protests, RiSI stepped up. On May 31, 2020, they sent an e-mail to the Rockefeller community acknowledging Floyd’s murder and encouraging university members to show their support for the Black community (see RiSI e-mail, page NNN). 

Black Lives Matter signs were subsequently hung around the university, most prominently displayed to the public on the north side of the Kravis Research Building along the East River and in the halls of university housing (shown below). Unfortunately, the sign hung in university housing by Rockefeller graduate students Rachel Leicher and Donovan Phua was removed the next day, according to Leicher. 

Photo courtesy of Rachel Leicher

RiSI also followed up with an e-mail linking to helpful resources including fundraisers, petitions, literature, and organizations related to social justice and the Black Lives Matter movement. After sending a statement of solidarity to the community along with this list of resources, RiSI collaborated with Women in Science at Rockefeller (WISeR) and People at Rockefeller Identifying as Sexual Minorities (PRISM), as well as a group of Rockefeller alumni to send concurrent e-mails to the Rockefeller administration addressing their silence. 

RiSI, WISeR, and PRISM sent a collaborative e-mail to the administration on the evening of June 1 (see RiSI, WISeR, and PRISM e-mail, page NNN). After collecting 116 signatures from alumni belonging to graduating classes ranging from 1969 to 2020, the alumni group sent their e-mail the following afternoon on June 2 (see Rockefeller alumni e-mail, page NNN).

On the afternoon of June 2, the Rockefeller administration broke their silence with an e-mail to the Rockefeller community. After additional prompting by RiSI and others within the Rockefeller community to stand publicly in solidarity with the Black community, the initial e-mail response was made public two days later.

The administration also acknowledged their receipt of the alumni letter and said that they would use their ideas as resources to consider how to move forward and improve the community at Rockefeller. 

RiSI continued to have multiple meetings with the administration and followed up with an additional letter and petition for the administration to commit to taking actionable steps to address racism on campus (see RiSI petition e-mail and petition, pages NNN-NNN). 

Within twenty-four hours, the petition had garnered support from 350 members of the Rockefeller community. This continued effort led by RiSI resulted in the first racial equality Town Hall meeting of academic staff and students with the administration on June 10, which was also the date of #shutdownSTEM, a day used by academia to protest and reflect on social injustice in support of the Black community. As of June 25, RiSI’s petition had the support of 444 members of the Rockefeller community, including sixteen Heads of Laboratory.

The Rockefeller administration is trying to respond to these cries for justice. To show their support, they have provided free COVID-19 testing for those wishing to participate in protests in the city. Statements of solidarity, like the one given by President Rick Lifton at the beginning of the 2020 Virtual Convocation Ceremony, are greatly appreciated as are steps that have already been taken to make the university inclusive. But a response to cries for justice predicates that there is an unmet need in the community and there is clear room for improvement. Continued, consistent, and intentional action and support are required. Our community needs to unequivocally say and show that Black Lives Matter. 

RiSI e-mail:

“Last Monday’s horrific scene in Minneapolis, in which police officer Derek Chauvin kept his knee planted on George Floyd’s neck until his death, has sent shockwaves throughout the US. The frustration and anger towards Mr. Floyd’s death and staggering frequency of injustices on the Black community has culminated in nationwide protests in at least 48 cities. People are tired of the silence and frustrated at the lack of meaningful response to previous movements calling for social change.

Now is the time to show our support to the Black community in any way that we can at Rockefeller University. Though many may take comfort in the claim that science is apolitical, our Black community members are not afforded this privilege. The excellent work of several laboratories and departments at Rockefeller (lab safety, custodial, food, animal facility, etc) are led by people from communities hit the most by police brutality and racism. As Rockefeller begins to reopen, more people from these communities will be on campus and it will be important for their presence to be recognized.

One simple way to do this is by posting signs that reflect our support for the Black Lives Matter movement around the laboratory and other areas on campus that are heavily trafficked. Please refer to the signs in the dropbox link for examples to easily print out and put on windows and doors. If other laboratories/facilities nearby are interested as well please coordinate with each other to make something more visible.

Please ensure that your Head of Laboratory is comfortable and supportive of posting signs prior to doing so.”

 

RiSI, WISeR, and PRISM e-mail:

“Dear Members of the Rockefeller Administration,

Last Monday’s horrific scene in Minneapolis, in which police officer Derek Chauvin kept his knee planted on George Floyd’s neck until his death, has sent shockwaves throughout the US and the world. The frustration and anger towards Mr. Floyd’s death, and the staggering frequency of injustices on the Black community, has culminated in nationwide protests in at least 48 cities. People across the country are tired of the silence, and frustrated at the lack of meaningful responses to previous movements calling for social change.

Though many may take comfort in the claim that science is apolitical, many in the Black community, and other communities of color, are not afforded this privilege. Science and medicine have a long, unfortunate history of exploiting marginalized communities, particularly those of color. Some of the most infamous examples include the Tuskegee Syphilis experiments, the acquisition of HeLa cells from Henrietta Lacks, and the erroneous justification of racism through genetic studies. 

Black individuals and communities most affected by police brutality and racism are an integral part of the Rockefeller community, leading much of the excellent and vital work in several laboratories and departments (lab safety, custodial, food, animal facility, etc.). As Rockefeller begins to reopen, more individuals from these communities will be on campus and it is imperative that their presence be recognized.

This past weekend, we, the Rockefeller Inclusive Science Initiative (RiSI), sent out a call for students and postdocs to speak to their HOLs about posting Black Lives Matter signs around the laboratory. Additionally, we sent a list of funds, organizations, and media to support the cause further. Our emails were met with enthusiasm from both students and the HOLs they’ve contacted. The Rockefeller community is coming together during this time to show that movements for equality can be, and should be, advocated for by scientists.

As leaders of the University, your voice speaks volumes to our community, and those watching us. It would be meaningful to Black members of our Rockefeller community, and the community at large, for the administration to directly address the systemic racism brought to the forefront by recent tragedies, including George Floyd’s death. We ask that you consider joining many universities in expressing support for the Black Lives Matter movement, principles of equity and inclusion, and condemnation of police brutality and systematic racism in our nation. We also ask for your support in a community effort to hang Black Lives Matter signs in places where we can most powerfully show our stance, such as on the pedestrian bridge over 63rd St and Kravis Research Building windows facing the river. 

Best,

César Vargas and Josue Regalado
Rockefeller Inclusive Student Initiative
www.rurisi.com

Stephanie Marcus and Audrey Harnagel
Women in Science at Rockefeller (WISeR)
www.wiseratrockefeller.com

The PRISM Board
People at Rockefeller Identifying as Sexual Minorities (PRISM)
www.ruprism.org” 

 

Rockefeller alumni e-mail:

June 2, 2020

Dear Members of the Rockefeller Administration,

We are writing as alumni of Rockefeller University to express our support for the recent call to action from the graduate community to address racial justice and anti-racism. As you’re aware, there has been a large and appropriate response to the murder of Black Americans across the country. George Floyd, Breonna Taylor, and Tony McDade’s names have all been added to a long list of Black lives lost at the hands of those sworn to protect and serve. We must recognize that our Black colleagues live with the knowledge that it could be them.

Rockefeller’s motto — science for the benefit of humanity — is a fundamentally political statement implying that science has a duty to serve society. Embedded within that motto are political questions, such as: for the benefit of whose humanity? Who is allowed to steer the science for that benefit? Throughout our history, we have seen the biomedical research community make research choices driven by politics and value judgments. When we run a Fisher’s Exact Test, we cannot forget that Ronald Fisher was a pioneer of eugenics. When we pull out a culture of HeLa cells, we cannot forget those cells were extracted from Henrietta Lacks without her consent. When confronted with the devastating statistics surrounding COVID-19, we cannot forget that this virus has taken disproportionately more Black lives because of systemic inequities in healthcare.

As leaders, you have a responsibility to Black trainees, faculty, and staff to openly and loudly affirm that you are aware of our history and that this legacy stops here. Your voice is essential in asserting you are working to ensure that Black members of our community are safe at work from racism and discrimination — that you commit to working for the benefit of their humanity, as well. 

Universities and institutions across the country, including Harvard School of Public Health and Johns Hopkins School of Public Health, have issued statements echoing their commitment to racial justice and anti-racism, as well as concrete actions they can take to ensure their words carry weight. Actions Rockefeller can take, in addition to supporting the community effort to hang a #BlackLivesMatter sign along the pedestrian bridge, include:

  • Join leaders in the biomedical research community and publicly denounce racial injustice and anti-Black racism;
  • Pledge not to call the police for non-violent crimes, while ensuring campus security are trained in methods of de-escalation;
  • Require bystander intervention training;
  • Hire anti-racist educators to educate faculty, staff, postdocs, and trainees on meaningful strategies to dismantle systemic racism;
  • Convene a committee to draft an explicit anti-racism policy for the campus community, bringing in scholars of anti-racism and compensating them appropriately for their time;
  • Hire independent diversity, equity, and inclusion consultants to assess the current atmosphere and university practices and serve as change management officers to transform the workplace culture;
  • Create an anonymous system for members of the Rockefeller community to report acts of discrimination and bias;
  • Recruit and retain students and faculty of color, particularly those who have been historically underrepresented;
  • Create a policy that explicitly describes how faculty will be rewarded for mentorship and outreach in decisions of tenure and promotion, as these responsibilities often fall disproportionately on underrepresented faculty.

We sincerely hope that you use your position to combat the history of racism and violence — both within and outside of science — and stand with the Black community. Supporting Black lives follows in John D Rockefeller’s commitment to the abolition of slavery and his founding of Spelman College, America’s oldest private historically black liberal arts college for women. We must commit to do the learning and transformation necessary to be part of the solution and to develop robust anti-racist practices in science and society. 

Until then, we are left with George Floyd’s last words to fill the silence: ‘I can’t breathe.’

Sincerely,

The Rockefeller Alumni”

 

RiSI petition e-mail:

“Dear Rockefeller community, 

In response to the global outrage at continued systemic racism and police brutality against members of the Black community, President Lifton’s statement last week called for “the beginnings of efforts to bring about lasting change” and a “rigorous inquiry to evaluate our own biases”. We hope that this statement only marks the start of campus-wide steps to address institutionalized racism on our campus. In efforts towards this cause, we at the Rockefeller Inclusive Student Initiative (RiSI) have been working with the Dean’s Office and administration to develop actionable plans for lasting change. 

While we continue this dialogue, we want to ensure that all in our community are heard and that progress be transparent. We ask that everyone respond to a survey/petition to assess which changes are most needed and desired at Rockefeller. This survey also serves the dual role of a petition where everyone’s voices will be collected and sent to the administration as evidence that the broader Rockefeller community stands behind these actions. The longer this list of names is, the more significantly we can push for institutional change.

Within the survey, there is also a field for individual comments which we strongly encourage all to fill out to strengthen our petition with personal testimonies. There is a national movement for science and academia to #Strike4BlackLives planned for tomorrow, Wednesday, June 10th. We ask that on this day of pause, each of you take a moment to complete the survey and submit any personal accounts you feel comfortable sharing of institutionalized racism in education or science and reasons why institutional support for Black and underrepresented scientists is important. These will be collected and presented to the administration (with the option of remaining anonymous). Please respond by 11:59pm Wednesday, June 10th.

SURVEY/PETITION HERE: https://socialchangeatrockefeller.wordpress.com/

We are also currently asking the administration to conduct a campus-wide town-hall on racial equality issues present at Rockefeller. The responses provided in the survey will be an opportunity for you to draft what you’d like to see discussed at a town-hall, with the possibility of either reading it out yourself or by a member of RiSI on your behalf.

Finally, we encourage discussion within your labs and departments, and we ask that heads of labs and departments make space for difficult conversations concerning diversity and inclusion in science. We want to foster serious, empathetic conversations about racial discrimination and its effects on our scientific community campus-wide to show that these issues involve us all. Together we can take the anger, shock, and frustration that so many of us have rightfully felt these past days to take a stand for a campus that listens to and supports our Black and underrepresented minority members. 

We owe it to George Floyd, Breonna Taylor, Ahmaud Arbery, Tony McDade, and countless others whose lives have been taken at the hands of institutionalized racism to fight for a more just and equal future. This begins by calling on the leaders of Rockefeller University to listen to our collective voice and fight with us. This movement will continue to press on because this is how change happens. We thank you for your passion.

In solidarity,

The Rockefeller Inclusive Science Initiative” 

RiSI petition:

“June 9, 2020 

We are disappointed in the administration’s tepid response to the Black Lives Matter movement and a lack of commitment to institutional changes to make the University a more diverse AND inclusive place. We demand that the administration immediately design, circulate, and implement an action plan to make Rockefeller University a supportive environment for all our members of Black and underrepresented minority communities, among our students, postdocs, faculty, and staff. 

This is our opportunity as a community to communicate that issues of diversity and inclusion are fundamentally important and need to be addressed by Rockefeller University’s administration. 

We ask that you stand with us in our efforts to make Rockefeller University more inclusive by becoming a model for these efforts across academia, and sign this petition by the end of the day on Wednesday. 

IN ADDITION to the action items requested in the alumni petition, we demand that the University commit to: 

  1. Administrative position dedicated to diversity and inclusion: Hire a diversity/inclusion officer or similar position that reports to the president. We wholeheartedly agree that promoting diversity and inclusion should be in everyone’s job description, and we will continue championing that goal, but coordinating these long-term efforts takes a significant time commitment. We strongly feel that having a professional solely dedicated to the administrative side of these efforts will shift some of the burden from trainees. 
  2. Public statement on recruiting underrepresented faculty and trainees: Publicly make a commitment to recruit trainees and faculty from communities underrepresented in science on the university website (appropriate locations would be in the Faculty Recruitment and Graduate Program in Biosciences pages). 
  3. Town hall: Organize a town hall (or series of town halls) for community members to discuss incidents of institutional racism experienced at Rockefeller, to brainstorm ways to address these inequities, and for the administration to be transparent with details on how they are enacting institutional change. Recent examples have occurred at other institutions including Weill Cornell, UCSD, Caltech, and an upcoming vigil hosted by Columbia University Medical Center (this Wednesday at 6:30pm over Zoom). 
  4. Climate survey: Administer and publicly disseminate the results of a new, anonymous campus-wide climate survey that specifically addresses issues of racial inclusivity, discrimination, and bias on campus. 
  5. Inviting speakers from diverse backgrounds: Commit to increase the number of invited speakers for lectures and seminars who are from underrepresented backgrounds. Here, we propose to also create an annual Friday lecture that is centered on the issues surrounding diversity and inclusion in science. 
  6. Annual reporting on HOL mentorship: Require HOLs to complete an annual report on mentorship practices and undergo additional training if they do not actively work toward creating a diverse and inclusive work environment. 
  7. Research relationships with minority-serving institutions: Develop a research training relationship with medical schools, Historically Black Colleges and Universities (HBCUs), and other minority-serving institutions (as defined by the Higher Education Act of 1965) across the country. We aim to provide research experiences at Rockefeller laboratories to Black and Native American MD and MD/PhD students, and additionally, retain at least one spot in the SURF program for undergraduate students from HBCUs or other minority-serving institutions. 
  8. Anti-racism, anti-bias in science training: Require a module or class on the implications of race, gender, sexuality, gender identity, and disability on the history and future of bioscience. This could be incorporated as an extension of the Responsible Conduct of Research course. 
  9. Diversity statements from faculty candidates: Require faculty candidates to provide statements on their past, present, and future contributions to promoting equity, inclusion, and diversity in their professional career. 
  10. Increased diversity in executive team: Development of an institutional plan (with milestones) to increase diversity within Rockefeller’s executive leadership and board of trustees. Increasing diversity amongst the administration will push for decisions to be more inclusive on campus. Current executive leadership and board of trustees are listed here.” 

Excerpt from Rockefeller’s Response:

  • Rockefeller does not have a diversity/inclusion officer. We commit to evaluating the models utilized by different institutions to promote diversity and inclusion, concluding with our own plan no later than the end of August.
  • The University has long published our encouragement for applications from communities underrepresented in science for graduate school and faculty appointments. We will immediately put these statements on display on our public web sites as well. 
  • We will provide forums and mechanisms to report and discuss incidents of discrimination, bias, and institutional racism at the University and determine actions to address inequities and prevent bias.
  • We will administer and disseminate results of an anonymous campus climate survey regarding issues of racial inclusivity, discrimination, and bias.
  • We commit to increase the number of invited speakers and seminars from underrepresented backgrounds, and will host a featured annual Friday lecture focused on promoting diversity and inclusion in science.
  • Working with the Academic Council of the faculty, we will establish guidelines for annual reporting on HOL mentorship practices and provide further training as warranted. 
  • We will seek to establish relationships with minority-serving institutions and expand research experiences at Rockefeller labs to BIPOC students from minority-serving institutions.
  • We will require training on anti-racism and anti-bias in science through the Responsible Conduct of Research course and evaluate anti-racism and anti-bias training for the broader campus community, including training and interventions tailored to units on campus in which specific problems are identified. 
  • By the end of August, we will develop a plan to increase diversity at all administrative levels including the executive team and board of trustees.”

Graduating Class of 2020

Megan E. Kelley

On Thursday, June 11, The Rockefeller University held a virtual convocation for the conferring of doctorate degrees upon thirty graduate students. This streamed ceremony was the culmination of years of dedication, hard work, and perseverance by the honorees. Although we were not able to commemorate this occasion with our usual parade and after-party, this in no way diminishes our shared enthusiasm for the accomplishments of these new graduates. Natural Selections would like to acknowledge and celebrate these former students. Congratulations, doctors! We wish you well in your future endeavors.

Sarah Ackerman

Sarah Baker

“Graduate school has been a trek of self-discovery, a lesson in resilience, and a time to reflect on what I want my place in this world to be. I will forever be grateful to Rockefeller for the support, the friendships, and the unforgettable journey.“

Mariel Bartley

Kate Bredbenner

Ian Andrew Eckardt Butler

Daniel Alberto Cabrera

James Chen

Brooke Conti Trousdale

Amelia Dunn

Nicholas Hernandez

Alexis Jaramillo Cartagena

Nathaniel Kastan

Mariya B. London

Emily M. Lorenzen

Paul Andrew Muller

Lisa Brooke Noble

Philip Mojsov Nussenzweig

Sean O’Connor

Benjamin Ostendorf

Luca Parolari

Rudolf Píša

Cristina Santarossa

Stephanie Lena Sarbanes

Aylesse Sordillo

Leonid Alexeevich Timashev

Waring “Buck” Trible

Zikun Wang

Daniel Neil Weinberg

Anna Yoney

Reopening Rockefeller

Natural Selections Editorial Board

At 5 p.m. on March 18th, 2020, The Rockefeller University shut down its campus due to the impact of the SARS-CoV-2 pandemic on the New York City area. A reduced staff maintained the most essential operations, such as security and power, while the vast majority of research was halted. Only research directly related to COVID-19 was permitted to continue. Four days later, Governor Cuomo issued an executive “New York State on PAUSE” order closing all non-essential businesses and canceling all non-essential gatherings in the state. 

For more than two months, the majority of Rockefeller employees and researchers have stayed home in various levels of isolation and quarantine. Our collective efforts to stem the spread of the virus appear to have had an impact. The Regional Monitoring Dashboard, which evaluates COVID-19 spread and pandemic readiness, shows that nine of New York’s ten regions have met the requirements to begin phased reopening. Even though New York City has not yet satisfied the requirements for reopening, it is hard to keep ourselves from projecting into the future and imagining what a new normal will look like for Rockefeller.

On May 4th and 5th, Rockefeller University President Rick Lifton hosted a virtual Town Hall for students and postdocs to discuss the campus shutdown and address questions from the community. While there are few specifics regarding exactly how or when Rockefeller will reopen, Lifton was able to speak to some common concerns. Natural Selections also reached out to others in the administration for comment.

How has the shutdown affected Rockefeller University?

In the midst of the shutdown, a small cohort of Rockefeller scientists have continued their benchwork. These scientists are studying COVID-19, in keeping with Rockefeller’s long-standing tradition of conducting “science for the benefit of humanity.” Although, according to Lifton, there are only about 125 individual researchers physically working on campus, they represent twenty laboratories studying everything from COVID-19 prophylaxis and therapeutics to understanding the course of infection and disease severity.

However, for many scientists, the Rockefeller University shutdown dramatically decreased the amount of research being done. Core facilities are closed and non-COVID-19 bench experiments are prohibited. Graduate students have expressed concerns that the shutdown may impede their progress, delaying their ability to meet milestones for a timely graduation. Lifton addressed these concerns, expressing that the expectations for progress have been adjusted. Sid Strickland, Rockefeller’s Dean of Graduate and Postgraduate Studies, has echoed these sentiments, encouraging students to contact the Dean’s Office to discuss any issues they may have. While there is no blanket policy, it is understood that individual circumstances will vary, and students would not necessarily be expected to meet the same deadlines as were established before the pandemic. “One of the great attributes of Rockefeller is that we are a small institution that can deal with issues on an individual basis,” Strickland said. “We know all of the students personally and care deeply about their well-being. If anything is concerning any student, please reach out to us anytime.” 

Researchers expressed similar concerns regarding the need for extensions in fellowships granted by the National Institutes of Health (NIH). In the Town Hall with students, Lifton said there was a precedent for this kind of support—in 2008 after the financial crisis, billions of dollars were set aside to help NIH funding recipients. Lifton and others in the Rockefeller administration are now advocating for funds to be similarly allocated.

When should Rockefeller reopen?

Before reopening Rockefeller, Lifton said, we would need evidence of a recovering city. This is in line with Governor Cuomo’s orders that regions are to remain shut down until they have met the seven metrics for reopening according to the Regional Monitoring Dashboard. At the time of this writing, New York City had met four of the seven metrics for reopening, with our hospital and ICU capacity still below 30%. The expectation is that New York City will meet the requirements to begin reopening in the first half of June. Rockefeller will begin restarting non-COVID-19 research activities on June 1st.

The newly formed Rockefeller University Research Restart Committee will evaluate the conditions at Rockefeller and determine exactly how to proceed with a phased-reopening of campus. Strategies for reducing risk to employees include staggering work hours, establishing laboratory capacities, and/or encouraging remote work where possible. While the details of each phase of reopening are unclear, we know that it will not be an immediate return to pre-pandemic operations. Reopening will be incremental, guided by the changing conditions and information.

How will we keep the Rockefeller community safe once we reopen?

Frequent testing of all Rockefeller employees for SARS-CoV-2 would be essential for maintaining the safety of Rockefeller employees as asymptomatic carriers can spread COVID-19. In his Town Hall meetings, Lifton emphasized the need to identify emerging infections, trace contacts, and isolate those affected in order to keep the campus healthy. The university currently has an Abbott point of care instrument and an on-campus test site on the tennis courts. Although testing is currently low-throughput, an aspirational goal is to eventually be able to test all Rockefeller employees twice per week. 

In addition to testing, preventative measures such as mask-wearing, social distancing, and diligent hygiene will be necessary to provide a safe work environment. Lifton said the university will insist on social distancing and has already mandated mask-wearing in all areas, with the exception of private offices occupied by a single person. The Office of Research Support has issued safety guidelines to Heads of Laboratories, each of whom will designate a Research Restart Officer within the laboratory responsible for safety training and enforcement. Amy Wilkerson, Associate Vice President of the Office of Research Support, said that in addition to oversight by the Research Restart Officer, “Security, Plant Operations, and [Laboratory Safety and Environmental Health] personnel, who are regularly in the labs to provide service and support, will also report non-compliance. Failure to comply will result in loss of access to campus.” However, Wilkerson said, “Everyone will be responsible for working safely.” Unsafe working conditions can be reported directly to the relevant supervisor or by emailing restart@rockefeller.edu.

A common concern is how we can maintain six feet between one another in spaces designed to facilitate interactions. The River Campus, for example, is designed so that researchers must walk through multiple laboratories in order to reach their individual workspaces, with laboratory benches and desks clustered together within each laboratory. Even in the older buildings, laboratory bays often position researchers back to back, and common areas feature couches and group seating areas. While these designs were appreciated in the time before COVID-19, they may require some reworking to fit with the new social distancing model. 

Alex Kogan, Associate Vice President of Plant Operations, is working with the Rockefeller administration to address these concerns. “There are many means to reduce risk,” Kogan said, including establishing laboratory capacities and staggering work hours to ensure social distancing. And while laboratories are inherently enclosed spaces, Kogan assured us that Rockefeller’s laboratories are supplied with 100% outside air, exchanged eight to twelve times per hour. Kogan also said that Rockefeller is “looking into spreading out common space furniture, limiting the number of people in break rooms, conference rooms, etc.” But, according to Kogan, the most important factor in ensuring employee safety will be community compliance with COVID-19 safety guidelines issued by the university.

What does Rockefeller’s future look like?

Over the past two months, there has been a massive transition to remote work and virtual meetings. Everything from weekly group meetings, to the Friday Lecture Series, to Rockefeller’s convocation are being held virtually. Although the Zoom format may be a little impersonal to some, it has allowed for continued scientific communication during the shutdown and made some seminars more accessible to our community. While working from home and virtual meetings may have been rare in the past, we expect these will become part of the new normal for many at Rockefeller, even as in-person seminars return. Todd Wells, Lead Media and Design Support Specialist of Rockefeller’s Information Technology Department, spoke with Natural Selections about continuing to offer remote options after the campus reopens. Wells said that “both Caspary and Carson Family Auditoriums are equipped with integrated camera systems that are Zoom and webcast ready, as are many of the conference rooms, especially on the River Campus,” and there are plans to similarly upgrade other campus meeting rooms. “We have already broadcast many events in both formats, even before the lockdown, and we expect this to become much more common as we continue to adapt how we host events in response to the pandemic.”

While teleconferencing and remote work can help to reduce the spread of the virus, working from home can be challenging for employees with families, especially those with children. Without childcare, working from home or even returning to work may be untenable. Lifton acknowledged that reopening the Child and Family Center (CFC) would be imperative for allowing employees with families to return to work, but there are significant challenges: the CFC typically follows the public school system, which is closed for the remainder of the academic year. In addition, many CFC teachers have their own children to care for, and no childcare available to them. While unresolved, the issue of childcare at Rockefeller is at the forefront of the administration’s mind.

Very little is certain, and nearly everything is subject to change. Every day we have more information about how COVID-19 is affecting our community, and best practices shift with our understanding of the disease. Communication will be critical for ensuring a safe return to research and a healthy future. Rockefeller has demonstrated its commitment to communicating with the campus community, and we are hopeful that the university will continue to prioritise our collective safety as we reopen our campus.

Musings on a Ph.D.

Sarah Baker

A few weeks ago, I earned the opportunity to defend my thesis, the terminal task in receiving my Ph.D. While everyone’s path is different, the journey for me has been a rollercoaster of both academic and emotional development, and I’d like to reflect on what the process has taught me.

Photos courtesy of Melissa Jarmel

Photo courtesy of Jim Keller

It’s okay to feel lost at times.

I started my graduate school journey knowing that I wanted to study neuroscience, but I had very little experience in the field. Most of my research as an undergraduate was done in a physical inorganic chemistry lab, so I lacked the basic textbook knowledge of the neuroscience field. Getting up-to-speed was daunting, and it felt like many of my colleagues came into graduate school with a much better understanding of these fundamental concepts than I had. I spent my evenings those first couple of months reading textbooks and watching videos online. I wish I had known that what I would learn in the lab in the process of doing research was going to be more valuable than any chapter of a textbook that I had read. 

Graduate school can feel lonely, but you are not alone.

Moving to a new city and starting at a new institution where you don’t know anyone can feel overwhelming. You lose the camaraderie that naturally develops in high school and college when your whole class is studying for the same test and seeing each other regularly. The pressures of graduate school can add another dimension to feelings of isolation. While you interact with lab members and collaborators, the process of working on a Ph.D. is largely supposed to be your ownyour own project, your own body of work. Everyone feels imposter syndrome at one time or another (or maybe even constantly). Once I realized that everyone else was also going through their own unique challenges, or maybe even many of the same ones I was, I stopped thinking of graduate school as a solitary pursuit. I began to reach out to others. Daily coffee breaks with friends and colleagues to talk about our highs and lows became crucial to building a sense of community. 

Self-care is important.

Graduate school is full of pressure, either self-imposed or loaded on by mentors, competitors, and colleagues. For some, this may develop into feelings of having to constantly be in the lab to be productive. But as I have seen both with myself and classmates, this oftentimes leads to burnout. The rest of life does not stop just because you are now a graduate student. Make time to cook yourself a good meal and spend time with your friends and significant other. And don’t be afraid to make time for yourself. For me, I was most productive in the lab around the time that I became involved in more groups on campus and began training for a triathlon. My busier schedule meant that everything I did each day in the lab was more structured, as I needed to make the time for the things I enjoyed outside of the lab. Growth in graduate school is not limited to cognitive and academic growth, but can expand to other aspects of your life, as well. During the course of my Ph.D., some of my new experiences included travelling to three new countries, learning how to play volleyball better than I ever had in high school, teaching myself how to knit, and rekindling my love of reading and writing. I would encourage any other student to expand on an old hobby or something they have always wanted to do simultaneously with progressing on their thesis project.

Thank your people.

Getting good grades in high school and college largely comes from your own study habits and hard work. In graduate school, success not only comes from effort, but also from the insights and advice of colleagues and the support system that gets you through those hard days. Thank the people who help you along the way. And ask for help when you need it. Although no one in my family is in science, they have remained steadfast in their support of all my pursuits. My friends, both at Rockefeller and outside of the university, are the people who lift me up just by being there. Small gestures can show your support system that you are grateful.

You will find a new way to see the world.

It is impossible to complete a Ph.D. without learning something along the way. I have a new appreciation for the complexity of the dysregulation of immune processes that happen in Alzheimer’s disease, the topic of my thesis project. I learned new methodologies and improved my ability to critically evaluate both my own experiments and those published in the scientific literature. But more than that, I have a newfound admiration for the process of sciencethis deeper understanding could only happen by being a part of the process myself. 

I came into my Ph.D. having no career plan in mind, but came out the other end realizing the strengths I could pull together to have a successful career in medical communications. I recognized that my favorite parts of the Ph.D. were the times when I was writing and critically evaluating datadeveloping my thesis research proposal, working on grants, and authoring papers. I feel lucky that these experiences prepared me for an internship and new career at a medical education company. 

Beyond my professional growth, the process of graduate school has made me more confident in speaking up, fighting for what I care about, and being resilient when things do not go as planned. Despite beginning my Ph.D. with so much uncertainty and doubt, I have only become increasingly happy that I followed through with this pursuit. To any new graduate students out there, hang in there. The path is certainly a winding one with many peaks and valleys along the way. But try to savor the journey and keep moving forward. The trek will set you up to better face challenges for the rest of your life.

A Different Kind of Outbreak

Anna Amelianchik

Before the novel coronavirus resulted in travel restrictions, event cancellations, and toilet paper shortages, The Rockefeller University community faced a different kind of outbreak: The Outbreak challenge. The Outbreak is a team-based six-week step and fitness challenge that syncs real-life steps and physical activity data recorded by a fitness tracker and translates them into virtual actions that you can take to survive a zombie outbreak. The app-based game tells an immersive story and offers six scenarios in which players have to reach safehouses to escape the zombie horde and progress through the challenge. Like many other workplace fitness challenges, The Outbreak helps employees build a community around a healthy lifestyle and foster behaviors that improve one’s health and reduce healthcare costs. The Rockefeller University’s leading team—“No Shorz Too Short”—is a great example of what the challenge was set to achieve with the average of 15,176 of team steps per day and the total of 637,395 steps over the six-week period. In addition, No Shorz Too Short put their steps to good use killing 1,055 zombies and reached all six safehouses in time. I had a conversation with the team leader, Zina, a Unit Clerk in The Rockefeller University’s Hospital, about The Outbreak challenge and its impact on her fitness and overall health. 

Can you describe your fitness regimen during the challenge?

My regimen was nothing too crazy to me, just had to go back to my old habits. I used to walk all the time anywhere and everywhere until I started working here. I have been taking transportation anywhere and everywhere and would cry about how thirty minutes was too far of a walk.

On day one of the challenge, I walked to work, then come week three, I walked to AND from work every day. If I had any errands to run, whether it was to return an item to a store, food shopping, pay bills etc., I made sure to walk there rather than hop on a bus or train.

Yeah it’s cold outside but once you get moving, trust me you will be stripping in the middle of the street when it gets hot. Playing Pokémon GO helped me a lot when I needed to get steps in. There were Pokémon I needed, and I would walk all over the city to get them before I headed home.

I went to the gym every day during my lunch break or went for a walk outside, depending on how my body felt that day. Hop on the bike for a few minutes then lift some weights. 

Did you notice any changes in your mood, energy levels, or general health while you were completing the challenge?

I will say after week three, I was exhausted physically, but alert and happy. I had trouble sleeping before. During the challenge I was knocked out at night and had a restful sleep. 

I was pushing my body to the limit every day but I wanted to keep going. So I made some adjustments to still reach my goal but not tire out (lift weights less and less cardio during the week). I felt stronger each day nonetheless and was happy to see the numbers on the scale go down each week, too. My mood improved. I was able to focus on the challenge and I became very competitive. I felt the need to outdo the other team. My team (“No Shorz Too Short”) and I would encourage one another to lead the race. Normally I am very lackadaisical. 

Are you able to keep it up now that the challenge is over?

When the challenge started, I had to tell myself every day, “Got to go to the gym or I got to work out.” Now that the challenge is over I wanted to take a break for a week and start again (don’t recommend it, you get lazy fast).

This challenge created a good habit that I will say I still keep to this day. I am still active and maintain the minimum step goal of 30,000 and daily walks/gym visits. I am going to wear my “short shorz”…eventually. HA!

Sustainability at Multiple Levels

Audrey Goldfarb

Milo Martinovic and Peter Selestrin, the chief engineer and assistant chief engineer of the power house, stand in front of the new boiler. Photo courtesy of Alex Kogan.

A glove recycling system in the Darnell Lab at The Rockefeller University. Photo courtesy of Audrey Goldfarb.

Individual action to fight climate change and habitat destruction is important. Plastic waste from just one person can have devastating consequences on wildlife, as exemplified by viral footage of a sea turtle with a straw stuck in its nose.

However, when considering the big picture, it is easy to feel powerless. How could the actions of one person influence the rampant and pervasive destruction of our planet? That single straw becomes much less meaningful in the context of the entire ocean. To significantly abate climate change at large, top-down policy changes are exceedingly more effective. Universal guidelines and initiatives incite cultural changes, which in turn demand more significant top-down policies. Both components are essential for progress.

Ainhoa Perez, a Research Associate in the Stellar Lab at The Rockefeller University, is an advocate for sustainability and personally leads a zero-waste lifestyle. She supports both individual and campuswide actions, but believes that neither are on pace with what the Earth is demanding. “There are things that can be done, but we are moving much slower than what we could and what we should,” Perez said. “We need support top-down from the university to provide the opportunity to do the right thing.”

Incentives from the government and from the university have been motivational in the past. The New York City Mayor’s Office of Sustainability launched the Carbon Challenge to encourage private institutions, including Rockefeller, to reduce their carbon emissions by 30% in ten years. Rockefeller joined the challenge in 2007, the same year the Sustainability Committee was established, and by 2019 the university had reduced emissions per square foot by 32%. “Some of the most impressive changes happened when the University got into a city-wide competition,” Perez said. “We were one of the first institutions to reduce carbon emissions, I think just because we had a challenge and had that as a goal.”

The success is largely attributed to a switch from oil to gas as a fuel source, in addition to the construction of LEED-certified buildings; in the last ten years, 33% of our campus received LEED silver status certification. The university is now committed to reducing its carbon footprint by 40% by 2025. However, Perez advocates for more ambitious goals. “One of the important things is for the university to commit to be zero waste and carbon-free,” she said. “It would make a huge difference just to have that as a goal.”

Alex Kogan, the Associate Vice President of Plant Operations and Housing Departments since 2001, is the driving force behind Rockefeller’s central sustainability initiatives. His efforts are focused on university-wide, quantifiable initiatives that benefit Rockefeller financially in addition to aiding the planet, such as using less fossil fuels and electricity. “Our approach has always been about carbon footprint reduction,” Kogan said. “We try to achieve this systematically campuswide.   We can control the amount of heat content and cooling content we distribute to all buildings on a macro level.”

Rockefeller’s power house, which contains the heating and cooling plants, sits underneath the Rockefeller Research Building and Hospital Building. It provides heating throughout campus from the President’s house to Faculty House and Scholar’s Residence, and cooling to every building except for housing. Touring the massive facility leaves a lasting impression; slight adjustments to central heating and cooling—i.e. lowering the maximum temperature in the winter and raising the minimum in the summer—is a powerful and quantifiable mechanism to reduce emissions.

However, the practices of individual labs are up to the heads of labs and their lab members. “Laboratories are inherently terrible energy hogs because you can’t recirculate the air,” Kogan said. “For obvious safety reasons, laboratories require a certain amount of ‘air-changes’ in order operate. The best thing a scientist can do is to lower the setpoint in the winter and raise the setpoint in the summer.”

Some Rockefeller lab heads prioritize sustainability more than others. Daniel Mucida is a great example of this. “Daniel has been one of our biggest champions,” Kogan said.

The Mucida lab reuses and recycles wherever possible. Ainsley Lockhart, a graduate fellow in the Mucida Lab, notes that these practices have little impact on the lab’s efficiency. “It probably takes me an additional ten minutes total per week,” she said.

Though these practices have been in place in the Mucida lab for ten years, few have followed suit to the same degree. “Not many labs do this,” Mucida said. “You walk around the labs and you want to have a heart attack because it’s so bad.”

Mucida was inspired to take action as a post doc at La Jolla Institute for Allergy and Immunology after attending a meeting in Japan. He saw how efficiently and conscientiously the labs there functioned, and started advocating for his lab in La Jolla to do the same. However, it wasn’t until Mucida started his own lab that he was able to implement meaningful cultural changes. Now, he wants to fight for sustainable practices campuswide.

The use of disposable containers in the cafeteria is a big issue. Though the bottoms of takeaway containers are compostable, the lids are plastic. Neither are reusable, and both are superfluous. “I’ve been trying to change this for ten years,” Mucida said. “I wish there were zero disposable containers. I think people would adapt very easily.”

Habits become second nature quite quickly, and sustainable practices demand significantly less effort than most New Year’s resolutions. For most people, carrying a reusable container for lunch is much less challenging than committing to a workout routine. Central guidelines and regulations would expedite these transitions. Once green practices like proper recycling become part of the culture, it will be effortless to comply. “This is very simple,” Mucida said. “It should be like brushing your teeth.”

“Many people believe that those goals are very hard or impossible to achieve,” Perez said. “But that’s just because we got so used to this wasteful, single-use-based lifestyle. It’s so engrained in our routines that we tend to think that there are no alternatives.”

While reducing carbon emissions and other waste helps the environment and is financially advantageous, it is also personally rewarding. “It has a lot of benefits for the people working at the university,” Perez said. “It brings people together. We are the perfect place to be doing this because we already have a sense of community.”

Having Kogan lead central carbon emission policy has proven to be effective. These initiatives are organized, quantifiable, and growing. “We’re on the cutting edge of HVAC and electrical infrastructure, we have a very good idea what our peers are doing, and we’re well connected in the [academic] facilities community,” Kogan said.

However, there is no department at the university dedicated to reducing waste in the cafeteria, ensuring proper recycling, and educating scientists on sustainable lab practices. “The recycling here is a mess,” Perez said. “Nobody even knows how it works. All the bins look exactly the same. It is very poorly organized and advertised.”

There are a multitude of opportunities to improve, but the organized manpower to fight for them is limited. The students and postdocs that compose the Sustainability Committee move away from Rockefeller after several years, making it difficult to establish long-term plans. These members are also dedicated to their own research, which must take priority over membership to the committee. “It is all dependent on who is coming to the meetings and who is able to invest time and effort on these initiatives, which is not very much because we don’t have much extra time,” Perez said. “People come and go from the university. It’s important to have continuity and permanence of initiatives that are started.”

Another issue that many Rockefeller employees may be unaware of concerns the University’s investment options. “Our pension money is invested through a pension plan in fossil fuels, and there is no way to change that,” Perez said. “This is unbelievable. A research institution forcing their employees to give money to companies that are funding climate change denial?”

Though it will require substantial effort and cultural changes, Kogan, Mucida, and Perez are optimistic that Rockefeller can be a leader of sustainable biomedical research. “We need people to engage and to take action,” Perez said. “We can do it! It would be easy, it would be cheap, it would be better, it would be extremely impactful… and we have the responsibility to do it.”

Health: On Mindful Meditation and The Skill of Being Present

Anna Amelianchik

If you are determined to make 2020 your healthiest year yet, now might be the time to add one more item to your list of New Year’s resolutions. While better nutrition and exercise can bring you closer to your fitness goals, your physical health and emotional well-being will most likely further benefit from mindful meditation. Although the practice of meditation dates back to 5000 B.C., meditation as a secular and therapeutic activity in the past several decades brought renewed attention to the ancient practice. In the traditional context, meditation is a mental practice designed to improve concentration, increase awareness of the present moment, and allow for the spiritual exploration of one’s mind. However, a more contemporary definition of meditation refers to the practice of focused attention, mindfulness, and compassion designed, among other things, to reduce stress and promote relaxation.

Meditation has also received a lot of attention in the scientific literature, where its benefits on brain function and cardiovascular health have been extensively studied. Scientific studies focusing on the neuroscience of meditation report both short- and long-term changes in brain electrical activity that occur as a result of dedicated meditation practice. These changes include the activation of the frontal cortex of the brain (associated with meta-awareness), the sensory cortex and the insula (associated with body awareness), the hippocampus (linked to cognitive function and memory), and cortical areas (linked to self- and emotion regulation). Scientific studies have also evaluated the effect of meditation on multiple cardiovascular risk factors, such as physiological response to stress, blood pressure, and smoking and tobacco use. These studies concluded that meditation possibly reduces cardiovascular risk. In fact, in 2017, the American Heart Association stated that meditation is a useful therapeutic tool for cardiovascular risk reduction when used as an adjunct to more traditional medical recommendations.

Although multiple forms of meditation exist, mindful mediation, which originated from Buddhist teachings, has been popularized in Western culture by people like Jon-Kabat Zinn, Ph.D., the creator of the Mindfulness-Based Stress Reduction (MBSR) program, and Sharon Salzberg. Salzberg is a meditation teacher and a New York Times bestselling author who played a major role in bringing meditation and mindfulness to the West in the 1970s. In December 2019, Salzberg visited The Rockefeller University where she gave a public talk on compassion and guided a short meditation practice. Salzberg described meditation as a skills training which is available to everyone, regardless of religious affiliation or worldview. These skills include concentration, mindfulness, and compassion. “Most of us would describe ourselves as fairly scattered or distracted,” said Salzberg, adding that when we let our attention go to the past or the future, the feelings of regret and anxiety cost us energy. This is why the first principle of meditation is gathering—gathering the attention, learning how to settle, and learning how to center. Salzberg defined the second skill acquired through meditation—mindfulness—as a quality of awareness in which our perception is not distorted by biases, like old fears or pain. Finally, the third skill—compassion—is central to mindful meditation, as this form of meditation teaches one to accept all that arises as a consequence of the practice without judgement. Salzberg highlighted the importance of self-compassion and described it as resilience against the pain of not having fulfilled something or having made a mistake.

The foundational technique of mindful meditation taught by Salzberg and other experts involves choosing an object of awareness, resting all of one’s attention on that object, and bringing the attention back when it wanders without self-inflicted judgement. Commonly, the central object of awareness is the feeling of breath. However, many people find it difficult to continuously focus on breathing and eventually fill their mind with thoughts, which causes them to lose their object of awareness. Salzberg teaches that being able to start over is an important part of meditation: “The healing and the empowerment is in being able to come back. Having self-compassion is not the same thing as being lazy—it’s the source of tremendous strength, not a weakness. Self-compassion is the best way to have a sustained effort toward learning something or making a change.”

Whether you are new to meditation or trying to improve your existing practice, consider following these steps to learn concentration, mindfulness, and compassion:

  1. Sit as comfortably as you can.
  2. Close your eyes or keep them open—however you feel most at ease.
  3. See if you can find the place where your breath is strongest and clearest for you: in the nostrils, the chest, or the abdomen.
  4. Unlike in some yoga traditions, in meditation the breath is natural—do not try to make it deeper or different from your normal breath.
  5. When you find the place where the breath is the clearest for you, bring your attention there and rest.
  6. If you like, you can use a quiet mental notation, such as “in-out” or “rise-fall”, to help support the awareness of the breath.
  7. If images, sounds, sensations, or emotions arise, let them flow, unless they cause you to lose the feeling of the breath.
  8. If you lose the feeling of the breath, it is your chance to let go and begin again by bringing your attention back to your object of awareness.

Salzberg recommended finding a formal dedicated time period for meditation practice—ideally about ten minutes a day during which your only goal is to hone your meditation skills. Although some meditation teachers encourage their students to meditate in the morning, Salzberg believes that the best time for meditation should be determined by you. In addition to dedicated practice, the “short moments many times” type of meditation can help you be present when you are under the most pressure and during the most complex times of the day. Consider taking a few mindful breaths before making a phone call, writing an email, or attending an important meeting. However, just like weight training makes your muscles stronger and prevents you from strain-induced injury, dedicated meditation allows you to practice being present to protect your physical and emotional health from the stresses of modern life.

Last March, Ann Campbell, MSN, MPH, an occupational health nurse practitioner at The Rockefeller University and a Nalanda Institute fellow, and the late Dr. Bruce McEwen, the head of Rockefeller’s Harold and Margaret Milliken Hatch Laboratory of Neuroendocrinology, formed an interdisciplinary steering committee which currently includes scientists and non-scientists who are interested in measuring the effect of mindfulness practices on health and expanding the available classes on campus.

McEwen’s research indicated that mindfulness practices might have an impact on public health. Campbell was interested in clinical translation of mindfulness practices as a clinical practitioner. Before the steering committee was formed, there were no free yoga classes on campus. Currently there are five yoga classes and two free 30-minute meditation sessions available to the members of the Rockefeller community for free. In addition to expanding mindfulness practices on campus, the committee is working to develop clinical protocols to measure the effect of mindfulness practices on various health outcomes in patient populations, such as patients with rheumatoid arthritis. In particular, they will focus on the effect of mindfulness practices on the results of blood tests, levels of inflammatory markers, and gene expression. Additionally, they are organizing a journal club and bringing speakers to increase awareness of the benefits of mindful meditation.

It can be advantageous to do mediation in guided sessions versus on your own because when someone guides you, this helps you understand barriers and create an awareness of “inner landscape.” You can attend one of these mindfulness practice sessions on Tuesdays at 12 p.m. or 12:30 p.m. in Rockefeller Research Building 110.

CRISPR In Mycobacterium Tuberculosis Rocks the Boat

Audrey Goldfarb

Photo courtesy of Tony Rinaldo.

Photo courtesy of Alexandra Rowley.

Dr. Jeremy Rock heads the Laboratory of Host-Pathogen Biology located on the south side of the River Campus Research Building. Rock studies Mycobacterium tuberculosis (Mtb), a bacterium that exclusively parasitizes humans. Tuberculosis (TB) is the leading cause of death from infectious disease, but Mtb biology is still poorly understood.

Rock pursued his interest in Mtb after completing his Ph.D. at the Massachusetts Institute of Technology working with yeast, the exhaustively characterized workhorse of genetics. “I did a Ph.D. in yeast genetics, and I loved it,” Rock said. “The rigor and depth with which you can answer a question in this model organism is second to none. But I wanted to move to an area that was more directly medically relevant, and in which there was a lot of big, unanswered questions.”

Immediately, there were challenges. Yeast doubles once every ninety minutes, and E. coli every twenty. To the disadvantage of Rock and his colleagues, Mtb’s doubling time is a full twenty-four hours. “It was not a painless transition,” Rock said. “Everything grows faster than TB. So, if you don’t have sterile technique everything gets contaminated.”

Rock wanted to identify essential genes in Mtb using CRISPR in order to reveal potential therapeutic targets. However, the traditional CRISPR systems used in other organisms did not seem to work in Mtb. It took Rock two years of his postdoctoral fellowship to identify the Cas9 allele that could edit the Mtb genome.

His lab at Rockefeller is now able to identify hundreds of candidate genes from a single CRISPR screen. “We can do 100,000 experiments at once,” Rock said. “We have a lot of very interesting hits, and we’re now trying to figure out the biology. This is what we wanted to do with it, and it’s actually working.”

Using CRISPR guides of different strengths, Rock is able to knock down essential genes to varying degrees. This ranks essential genes by their vulnerability: even slight knockdown of some genes in Mtb is lethal, while others require more robust depletion to kill the bacterium. If a gene product requires minimal inhibition to elicit a therapeutic benefit, it can more easily be targeted by drugs.

Though the lab is less than two years old, Rock is already thrilled with the people he has recruited. “They’re a very hard working, collegial bunch,” he said. “Everyone collaborates and helps each other. These are people I spend a lot of time with, and they’re all people I love being around.”

The lab’s productivity is due in large part to the bioinformatics expertise of computer scientist Dr. Michael DeJesus. “He’s just phenomenal,” Rock said. “The math behind what we’re doing pretty quickly got complicated to the point where we needed someone like him. He was the perfect person to bring in.”

Developing CRISPR in Mtb was a huge hurdle with a huge payoff. “It was slow, it was hard, and it didn’t always work,” Rock said. “But it was clearly a problem that was important, and it was going to open a lot of doors.”

Rock also acknowledged the support he has received throughout his career, especially as a new faculty member at Rockefeller. “When you start a lab, you have to build it from the ground up,” Rock said. “But it’s not like you do that alone. Both junior and senior faculty were very welcoming, and the administration is amazing. They really take care of you and help you in this process.”

Rock is excited to pursue mechanistic studies to nail down the detailed biology of Mtb. Collaborations to elucidate pathways and structures may be on the horizon. “We like screening for genes that contribute to interesting phenotypes, and now that we have lots of hits we’re excited about and zooming in on more mechanistic studies,” Rock said.

Meaningful success in science is usually preceded by myriad failures, making hard work and persistence essential even for talented minds. “A lot of this job is just tenacity,” Rock said. “That goes a really long way. In order to be tenacious, you have to really love your project. Science is never easy, but you’ll figure it out.”

First Year Reflections

Audrey Goldfarb

Unbelievably, less than a month remains in the 2019 fall semester. The last few months have been a whirlwind of rotations, classes, and transitions for the first-year class. Though Rockefeller students tend to present as confident, curious, and well-adjusted people, few painlessly sail through the first year (or subsequent years for that matter). I gathered anonymous reflections from a sample of first-year students, many of which echo each other.

Photo Courtesy of The Rokcefeller University

Photo Courtesy of The Rockefeller University

Though the freedom of the Ph.D. program at Rockefeller was a major draw for members of the 2019 first year class, the unstructured nature of the classes has been an adjustment for some. Rockefeller’s curriculum is advertised to have few mandates and still offer courses instructed by world leaders who genuinely care about teaching. The actual content and structure of the individual courses is not extensively discussed during recruitment, which may contribute to unmet expectations.

“The biggest surprise for me starting grad school at Rockefeller were the classes, or the lack thereof. By lack I don’t necessarily mean like lack of actual classes to take, more like how un-stringent the classes so far actually are.”

“I will admit that part of the draw for me was knowing that I could get to take the classes I was most interested in while circumventing some of the ones I wasn’t. But I didn’t realize that that would also translate into classes that are way less structured than I was used to.”

“I knew beforehand that the classes were very relaxed, but I think this allows us to actually care about learning and not worry about getting a passing grade, which we all know how to do.”

Rockefeller students are allowed the freedom to pursue research in fields in which they have no experience but are generally expected to acquire the fundamental knowledge of that field independently. Classes don’t offer extensive background information before delving into complex concepts and modern research. This proves to be a formidable challenge, especially while balancing classes and productivity in the lab. However, this process is a key part of independent research, and developing a degree of self-sufficiency is valuable in the long run. Some first-year students already feel their hard work paying off.

“I was hoping that the classes I was interested in would’ve started out by giving me that background and then bringing in guest speakers to talk more in depth about their topics and then I would be able to engage with the material better after having that first introduction. …I’m trying to transition into a completely new field from my previous experiences and I was kind of counting on the classes to help ease my way into that transition.”

“I wasn’t able to get as much out of the talks as I could’ve because I didn’t start with a solid foundation of the subject, so many of the seminars I spend just trying to catch up on background.”

“Going into a general bio program after doing research in a pretty specific subfield of biology was challenging at first–I felt like I was often missing something in class and have had to relearn plenty of material. I do think this has been rewarding, because I feel ultimately more prepared to understand all facets of the research in my field.”

“Since I started my PhD program at Rockefeller, I have been experiencing elevated feelings of excitement coupled with huge responsibility. My excitement stems from being at this amazing institution with limitless opportunities to learn and thrive on the academic and personal levels; however, it is up to me really to decide to what extent I will be growing at this new stage. In the first couple weeks, I have been mentally transitioning from being an undergraduate student with a packed schedule of classes and exams to being a graduate student with a more flexible schedule and no rigid requirements for classes and lab work. This flexibility, although very useful, can be scary sometimes if I don’t make use of my time efficiently. I have been also learning to set my own short-term goals and evaluate myself periodically. It is worthwhile to mention that the environment at Rockefeller as an institution and in my lab are very conductive of learning and adjusting at my own pace. “

Textbook discoveries made at Rockefeller laid the foundation for decades of incredible discoveries, and the University’s history continues to inspire this generation of scientists.

“I think the history and the impact of this place keeps hitting me when I least expect it. I’ll be going about my day and remember I’m walking past the same building where Avery, McCarty, and MacLeod figured out DNA was the heritable material.”

“I’ve gotten to hear really incredible scientists give talks in my classes.”

“One of the things I have been enjoying about being at RU is the enriching scientific community between RU, MSKCC, and WCMS. I have the chance to listen to outstanding scientists in different fields from all over the world and learn from them. Also, the organized breakfast and lunch events with some of the speakers at RU are a good chance to hear their perspectives and discuss common issues in the scientific community. These events are also potentially very useful in expanding our network and building connections.”

“So much of textbook biology was written here. The research I spent my entire undergrad on was pioneered here—and I’ll remember that while I’m in sweatpants on the couch, eating an entire tin of Trader Joe’s dolmas straight from the can.”

As with every transition, starting graduate school in a new city comes with many challenges. Building a new support network of friends and colleagues is made easier by the welcoming environment at Rockefeller.

“My biggest fear when moving to New York to start graduate school at Rockefeller was leaving everything that was familiar behind, including friends and family. However, everyone here has been super supportive and the friends that I have made here are like my second family. I was surprised at how well I was able to actually adjust once I got here, and the people at Rockefeller played a huge role in that. Although, I am still incredibly intimidated being at an institution with such a high scientific caliber, I don’t regret my decision coming here.”

“From the first day at RU, the environment has been welcoming at every level. The orientation week was a great time to talk to my colleagues and get to know them more and also to get to know the Dean’s Office and university staff. Also, the various student and science retreats have been a great chance to learn more about the science and the people at RU. I think this gave me a chance to build a close community of colleagues, which is very important to me.”

“I feel fortunate to be friends and colleagues with members of the first year class. Their curiosity, diversity of expertise, and ability to be comfortable with their own ignorance fosters a stimulating and supportive atmosphere. Owing to this class, I am comfortable calling Rockefeller my home. I am looking forward to seeing where their interests take them and to celebrate their successes in and out of the lab.”

“The transition back to research and into the PhD after clinical rotations in med school was a welcome break in the pace of my daily life. But what surprised me the most about trying to re-integrate into the research world was how afraid I had become [of] asking questions. The hierarchy and intense grading schemes of clinical rotations had now taught me to be afraid of seeming stupid when asking questions in the hospital. However, this fear had integrated much more deeply than I ever suspected. Luckily, the more I’m around my peers and lab members at Rockefeller, the more I’m realizing there is nothing to be afraid of. I’m consistently in awe of the research ideas that develop from questions asked in casual conversations or in lab meetings. As I work on slowly getting back to being a confident question-asker, I feel really lucky to be in the intellectually curious environment fostered by the community here at Rockefeller.”

“Overall, I am pretty happy with the experience and the program. I feel that our year has a good mixture of people from different backgrounds and whenever they voice their opinion on data and experiments, I’m learning too.”

Of course, there are exceptions, and word travels fast about the hostile reputations of some labs.

“…I’m not rotating with them because I know this from fellow students, so I think there should be something done about it since their research is pretty cool and keeps away many students (I’m sure it’s not only me).”

The amenities Rockefeller offers to its graduate students are the cherry on top. As advised by older students, we are enjoying the free bagels and coffee while they last.

“In addition to the science seminars, I am really enjoying the Peggy concerts hosted at RU. I view these concerts as a chance to enjoy the taste of music and just relax after a long lab day.” 

“When I started graduate school at Rockefeller, I knew it was the place for me. Not really because of the fabulous community within my first year cohort, or the wonderful community of driven and excellent scientists, but because of the plentiful and bountiful opportunities to eat free food. There have been weeks where I was able to get gourmet lunch 4/5 days, without spending a penny. What a luxury!”

Tim Blanchfield, Rockefeller’s Fitness Guru

Sarah Baker

Photo credit: Evan Davis

“Don’t put anything off. Do it today. Don’t wait.” This is the advice that Timothy Blanchfield, the Fitness Manager of The Rockefeller University, has for the Rockefeller community. If you have been to Rockefeller’s gym in Founders Hall, you have most likely run into Blanchfield. Since he was hired in the spring of 2014, it has been his main goal to keep Rockefeller fit—he manages the gym and its equipment, runs free fitness classes for the campus community, and is in charge of Rockefeller’s participation in the Virgin Pulse Global Challenge every summer. I sat down with him at Rockefeller’s Faculty and Student’s Club to discuss his job and the path that led him to fitness.

Blanchfield grew up in Beacon, New York, about an hour north of New York City. When Blanchfield was living in Beacon, the Breakneck Ridge trail was not well known, but now it is a popular hike due to a challenging rock scramble and nearly vertical climb in the first mile, as well as its stunning views of the Hudson River and neighboring mountains. However, in those days, the Mount Beacon Railway was a popular tourist destination. This trolley followed the steep mountain face, had sweeping views of the valley, and led to a casino at the top called the Beaconcrest Hotel. In 1978, after several fires and financial issues, the railway closed.

In college, Blanchfield began doing some fitness training with his friends. He was completely self-taught, but he realized that he could help people get into shape at the gym. A few years later, Blanchfield joined Teach for America in the Bronx, where he was teaching for five years. Although he was teaching history, he also helped with some of the physical education programs and found that many people would come to him for fitness advice. Blanchfield used his free time to begin personal training after school and when he left teaching, he was a full-time fitness trainer until Rockefeller hired him as part of Human Resources’ initiative to increase the wellness offerings at Rockefeller. Now he works part-time for Rockefeller and manages his own personal training business on the side.

When Blanchfield first started at Rockefeller, many people did not know about his free fitness class offerings. In fact, initially, only people from Human Resources attended his classes, but this worked to get the ball rolling. Through word-of-mouth and increased advertising of the fitness classes, a diverse array of Rockefeller community members of all ages and fitness levels now attend his classes. Classes are always being added and adapted. One of the most popular classes is Blanchfield’s strength and conditioning class on Mondays at 7:30 a.m. and Wednesdays and Fridays at 12 and 1 p.m.

Blanchfield also organizes Rockefeller’s annual participation in The Virgin Pulse Global Challenge. There is space for 210 people (30 teams) to participate. Participants receive a fitness tracker at the beginning of the challenge to track their steps and other physical activity online for 100 days each summer. The program aims to improve physical activity, mental wellness, nutrition, and sleep; this contributes to improvement in all-around wellness of the participants. In addition, the Global Challenge provides both a sense of comradery and competitiveness to campus as participants work harder to get in steps and climb the leaderboard, visible on the Virgin Pulse app.

Blanchfield says that he loves every part of his job. He finds satisfaction in helping people improve themselves and enjoys working at an institution like Rockefeller where there is a constant flux of students, postdoctoral fellows, research technicians, and other employees—there are always new people with whom he gets to work. To make the most of the limited space for equipment, Tim is continually working on replacing old machines and putting in new and improved equipment. He is excited about adding an upright rower to the gym soon. A cardio intervals class will also be added with a focus on high-intensity interval training. Blanchfield’s biggest pet peeve is when people do not return their weights to the rack after they finish using them. No one wants to spend half of their workout looking all over the gym for the weights they need!

Blanchfield’s advice for anyone at Rockefeller who wants to get into fitness is to start slow and find something you can enjoy and can handle. It is okay to modify anything as needed. The biggest mistake people make when they decide to start working out is that they go too hard at first, especially if they are working out with a friend who has been working out for years. So ease into everything to avoid injury and fatigue. The goal is to find a way to include fitness in your lifestyle in a way that will be maintainable for you.

Motivation can be hard to find and to sustain. Even incredibly fit people like Blanchfield burn out sometimes. This past year, Blanchfield realized that this was happening to him. He had completed six full Ironman races in four years. (That’s six long-distance triathlons where he swam 2.4 miles, biked 112 miles, and ran 26.2 miles!) Plus, he had done about ten half Ironman races in that same four-year period. So this past year he has been taking a bit of a break from intensive training and has allowed his proclivities for pizza to creep up on him. Everyone needs a break sometimes. However, Blanchfield is still very active—he discovered a love for mountain biking about three years ago, and now, he goes up to his condo on Hunter Mountain to ride his bike through the mountains almost every weekend. Not only is it fun and a beautiful place to bike, but this can also get him up to 90,000 steps for the Global Challenge.

Since Blanchfield’s advice to us is not to put anything off, I asked him what is one thing he would to do that he has not yet done. He has no plans to leave New York anytime soon, but eventually he does want to move somewhere more south or somewhere more west. Some options are North Carolina, Jackson Hole, or Park City—anywhere beautiful with plenty of places to go mountain biking. He says he’s been in the city too long, but we are thankful he has been here because he is doing a wonderful job of helping members of the Rockefeller community lead happy and healthy lives.

A description of the Rockefeller University fitness center can be found here and you can check out the full fitness class schedule here.

New Member Guide to Campus

The Natural Selections Editorial Board

We welcome all of the new members of our community to The Rockefeller University! Here are resources you may find of interest:

Markus Library

Located in Welch Hall (enter the Founder’s Hall lobby and walk down the stairs), the library provides resources for scientific research at the university. In addition to providing access to scientific articles, the library has public computers, meeting spaces, a lounge with current magazines and newspapers, and Kindles loaded with popular books that are available for checkout.

Classifieds

Classifieds are posted by members of the community looking for scientific items, selling items, searching for housing, or submitting announcements. You can subscribe to receive RU classifieds alerts here: https://inside.rockefeller.edu/classifieds/.

The Faculty and Students Club

Located on the B level of Abby Aldrich Rockefeller Hall and open from 4-11 p.m. Monday through Friday, the Faculty and Students Club is a place for social interaction, thesis celebrations, barbecues, parties, and meetings. The club provides discounted drinks to members of the Rockefeller community who have an account. To set-up an account, contact Human Resources.

Resource Centers

Rockefeller has many collaborative resources centers with specialized equipment and expertise. Find the complete list here: http://inside.rockefeller.edu/rc/.

Information Technology

IT maintains a safe and secure campus technology network and aids in technical support for computer issues. Their website can be found here: http://it.rockefeller.edu/.

Occupational Health Services

Located in Room 118 of the Hospital Building, OHS provides free health care services to Rockefeller employees covering physical, mental, and emotional wellness. Services provided can be found here: http://inside.rockefeller.edu/hr/occupationalHealthServices.

Office of Sponsored Programs Administration

OSPA aids with the compilation of research grants in compliance with the correct policies and regulations, the identification of available funding, and any issues with obtaining funding (http://www2.rockefeller.edu/sr-pd/homepage.php).

Athletic Facilities

There is a tennis court, squash court, and gym on campus. To access the gym (6th floor of Founder’s Hall), you must sign a waiver at the security desk in Founder’s Hall. The tennis and squash court must be reserved at https://appintpl.rockefeller.edu/tennis/t_logins and https://appintpl.rockefeller.edu/squash/s_logins.

People at Rockefeller Identifying as Sexual/Gender Minorities

PRISM fosters a community of support for LGBTQ+ individuals at Rockefeller. PRISM co-hosts Friday breakfasts with seminar speakers, organizes talks and social events, and provides resources for the Rockefeller community. Find out more here: http://ruprism.org/.

Women in Science at Rockefeller

WISeR is a professional development and advocacy group for women scientists at Rockefeller. WISeR co-hosts Friday breakfasts with PRISM, organises lectures, outreach and a mentorship programme. Check out their activities and resources here: https://www.wiseratrockefeller.com/ and sign up to join.

Science Education and Policy Association

SEPA gives scientists the ability to be engaged in policy-making and see how scientists affect policy and policy affects science. SEPA provides training, hosts career panels, and allows for engagement with policy at local and national levels. Check out the website here: https://sepanyc.org/.

Rockefeller Inclusive Science Initiative

RISI is a student-run group that serves as a support system for Underrepresented Minorities on campus. RISI organizes seminars, mentoring programs, and training. Follow RISI on Twitter here: https://twitter.com/ru_risi?lang=en.

Science Communication and Media Group

The SCM team (http://scicommandmedia.rockefeller.edu/) is comprised of a group of students and postdocs who bring interesting lectures and film screenings to campus throughout the year. If you are interested in bridging the gap between scientists and the public, you can consider joining the SCM group by emailing scienceandmedia@rockefeller.edu.

Postdoc Association

The PDA provides social and career development resources for postdocs and research associates at Rockefeller. In addition, the PDA holds a retreat every year, communicates with the administration about the needs of the group, and hosts seminar series and social events throughout the year. You can learn more here: http://pda.rockefeller.edu/.

RockEdu Science Outreach

RockEdu is Rockefeller’s outreach initiative aimed at students K-12 in the New York City community to foster awareness of science and hands on lab experiences. If you are interested in volunteering through RockEdu, you can sign up here: https://www.rockefeller.edu/outreach/volunteers/.

Tri-I Biotech Club

The Tri-I Biotech Club is for members with a shared interest in biotechnology. Find out more here: https://wcbiotechclub.org/.

Tri-I Consulting Club

The Tri-I Consulting Club is for members with a shared interest in consulting. Find out more here: https://triiconsulting.wordpress.com/.

Art Studio

There is an art studio available on campus for community use. If interested, contact Zachary Mirman (zmirman@rockefeller.edu).

Weill Cornell Music and Medicine

The Weill Cornell Music and Medicine group fosters balance between medical and musical interests of the Tri-I community. For more info, go here: https://music.weill.cornell.edu/recruitment. Also, of note, there are 2 music rooms on campus in Scholars and the Abby. Contact the Founder’s Hall security desk for access.

Bronk Fund

The Bronk Fund is available to students in their first through fifth years on campus. Students can be reimbursed half of receipts for fitness activities, language/art class, or theater/concert/sporting events, up to $125 total per year. The fund also provides a lottery of free tickets to students for various events throughout the year.

Graduating Class 2019

Sarah Baker

On June 13, 2019, The Rockefeller University will add thirty new alumni to its community, each with a freshly obtained Ph.D. The road to a Ph.D. is not an easy one and requires a combination of hard work, resilience, creativity, motivation, and probably some luck. Some of the graduating class have moved on to new jobs or postdocs elsewhere, whereas others are continuing their work at Rockefeller. This month, the Natural Selections editorial board honors them for their determination and accomplishments. Congrats to our new doctors!

Intimately tied to my time at Rockefeller are my greatest accomplishments, my deepest disappointments, and my fondest friendships—it’s been a ride I feel fortunate to have taken. – Annie Handler

 

RuPaul’s Drag Race All Stars, Season 2, Episode 1, 52:10 – Robert Heler

 

I knew I would get to indulge in creative and exciting science during my time here, but I’m equally grateful for the time I had to enjoy so much of what NYC has to offer from brunch to Broadway and new best friends. – Melissa Jarmel

 

Rockefeller is the best! – Kouki Touhara

 

I didn’t realize how strong people’s feelings could be about free cookies. –Anonymous Graduate

 

Natural Selections Interviews Rockefeller’s Viviana Risca

Natural Selections Interviews Rockefeller’s Viviana Risca, Principal Investigator of the Laboratory of Genome Architecture and Dynamics

Alice Gadau

Viviana Risca, photo by Alice Gadau.

At the age of fourteen, Viviana Risca spent her summer break unlike most teenagers. Every morning, she took the train from Long Island to work in Dr. Daniel Eichinger’s parasitology laboratory at New York University. Despite the cabinet full of dead worms in formaldehyde she had to pass every morning, this first exposure to biological research was highly influential in propelling her into a lifetime of research. Since then she has been excited about using molecular techniques to understand the processes that occur in cells.

Viviana has now joined the Rockefeller community as one of the two new tenure-track assistant professors hired in 2018. After completing her Ph.D. in Biophysics at the University of California, Berkeley, she continued her scientific career as a postdoctoral scholar at Stanford University with Professor William J. Greenleaf. Viviana is interested in the biophysical rules that contribute to the dynamics and stability of the genome. In addition, she wants to understand how the three-dimensional genome architecture can regulate DNA-based processes.

Alice Gadau: What is the central question you are trying to address in your lab, and how is this an expansion from your past work?

Viviana Risca: The three-dimensional structure of the genome is controlled by its association with a variety of proteins, together making up a DNA-protein complex we call chromatin. Through the efforts of large-scale sequencing projects, we now know much of the linear sequence of bases that make up the human genome, but we are still far from fully understanding the mechanisms that control how and when the information encoded in DNA sequence is read out by transcription. A skin cell and a muscle cell contain the same genome, but they express different sets of genes that give rise to their unique identities.

My lab seeks to understand how three-dimensional chromatin structure controls the ways in which various proteins, including those involved in transcription, access their binding sites on DNA in order to perform their biological functions. One of the driving hypotheses of our work is that chromatin structure acts as an integrator of many molecular inputs to modulate access to DNA. I am particularly interested in how chromatin modifications, inter-molecular interactions, and polymer effects give rise to specialized parts of the cell’s nucleus that stably repress transcription and help maintain cell identity and normal cell function. Both chromatin structure and the processes that shape it are often perturbed in cancer, as well as during aging, and I hope that our work on these fundamental processes will provide useful leads toward better cancer therapies and diagnostics.

As a postdoc at Stanford, I worked on exploring how the landscape of enzyme-accessible chromatin can give us insights into the regulatory networks that control gene expression in several cell types, including a cancer model, using a popular method called ATAC-seq. I also did a lot of technology development, which resulted in RICC-seq, a method for mapping chromatin fiber structure at high resolution, and ChAR-seq, a method for mapping contacts between RNA and DNA genome-wide. In my own lab, we will continue to use and develop these technologies, applying them toward the goal of understanding the basic biophysical and molecular mechanisms responsible for stable transcriptional repression and overall control of access to genomic DNA.

AG: How does three-dimensional genome architecture contribute to DNA regulatory processes?

VR: Since the 1920s when Emil Heitz coined the terms euchromatin and heterochromatin, we have known that the cell nucleus is divided between regions of high and low chromatin density. Since then, we have learned that organization of chromatin is far from random—it is in fact organized at multiple length scales.

At short length scales, every 150-200 bp of eukaryotic genomes is wrapped around roughly 10 nm-wide histone complexes called nucleosomes. Regions of DNA that are depleted of nucleosomes tend to be hyper-accessible to exogenous enzymes we use to probe them, and we interpret these regions to be also accessible to endogenous proteins like transcription factors, chromatin remodelers and polymerases. Indeed, many of these proteins seem to localize to nucleosome-depleted DNA. We also know that some histone modifications, like lysine acetylation, is associated with low-density, euchromatic regions of the genome that tend to be more accessible to protein binding. The high-density, heterochromatic parts of the genome are less well understood, from a structural standpoint, and many labs, including my own, are currently trying to decipher the mechanisms that drive the exclusion of transcriptional machinery from these silent genomic regions. Candidate mechanisms that have been proposed include occlusion of binding sites by DNA buried in compacted chromatin, chemical exclusion by phase-separated liquid domains, and simple volume exclusion from high density regions.

We also know that there is functional communication between genomic regions at much longer length scales spanning tens of thousands and sometimes hundreds of thousands of kilobases. Enhancer elements in the genome, which are acetylated, hyperaccessible, and bound by transcription factors when active, somehow must communicate with gene promoter regions because they regulate these promoters. This is thought to happen via DNA looping interactions in three dimensions, but the exact nature and dynamics of these contacts are an active area of research and not yet understood. Lastly, we also know that the cell nucleus is divided up into regions with different functional profiles, through associations with the nuclear lamina or self-association of potentially phase-separated domains like the nucleolus. How this long-range organization relates to short-range chromatin folding is also an area that my lab plans to explore.

AG: What is RICC-seq and how can it accurately examine short range DNA contacts?

VR: RICC-seq stands for ionizing Radiation-Induced Correlated Cleavage. In the 1990s, it was shown that the pattern of DNA damage induced by X-rays or gamma-rays on a cell’s genome is shaped by the way the DNA is folded into chromatin. RICC-seq takes advantage of this convenient property of chromatin. We irradiate cells with X-rays or gamma rays, carefully extract the short pieces of resulting single-stranded DNA, and then sequence those pieces. Their ends tell us about the pattern of DNA damage and consequently, about the way the DNA was folded in the original cell. This method works well for mapping high-resolution DNA-DNA contacts on the order of less than 10 nm and less than a thousand base pairs, making it complementary to other three-dimensional structure mapping methods like Hi-C, which work better for contacts spanning thousands of kilobases.

AG: What makes RICC-seq novel from other sequencing techniques?

VR: RICC-seq has two unique advantages. First, it can be performed on living cells that are not fixed or permeabilized. Therefore, we can probe chromatin structure in its native state. Second, it uses hydroxyl radicals generated by radiation as its probe. The radiation can penetrate all areas of the nucleus, no matter how dense, and the radicals are smaller than water and can easily diffuse. Therefore, we can get data from not only the low-density euchromatin in the nucleus, but also from highly compacted, dense heterochromatin.

AG: What other tools are you incorporating in your lab to understand genome architecture?

VR: RICC-seq is not a single-cell method and requires quite a bit of input material, so we will be combining it with lower-input methods like single cell or bulk ATAC-seq and RNA-seq, as well new cutting-edge technologies as they emerge. We will also be complementing this work with protein binding measurements like ChIP-seq or CUT&RUN, and microscopy that can tell us about the long-range organization of the nucleus. Lastly, we will also be collaborating with chromatin engineers to develop perturbations that will help us dissect causal and functional relationships between molecular factors and chromatin structure.

AG: Are there other hobbies you have that incorporate science?

VR: I’ve long loved incorporating skills that I pick up in the lab into my other hobbies. When I learned microscopy and optics, I also took up photography in my spare time, because the basic concepts are the same. I love art in general and see a lot of parallels between the lives of scientists and artists. We are both seeking fundamental truths, and both need to continually find ways to nurture our creativity. I also love to cook. I often use it to relax because it uses many of the same skills as biochemistry or molecular biology, but you can usually determine failure or success more rapidly than at the bench, and it is also easier to share your successes with your friends.

Lastly, I love science outreach and communications, but I would not call those hobbies. I think all of us as scientists have a responsibility to share our work with the public that, after all, supports our work through taxes and donations, to advocate for the societal benefits of basic research, and to equitably educate the next generation.

Rockefeller’s Campus Gets an Upgrade

Sarah Baker

The Natural Selections Editorial Board in front of the new President’s Office and Dean’s Office building.

Excitement abounds at The Rockefeller University as we prepare for the grand opening of the new $500 million Stavros Niarchos Foundation—David Rockefeller River Campus, a four-year construction project to add two acres and a new research building to Rockefeller’s fourteen-acre campus. Construction began during the summer of 2015, right when I arrived at Rockefeller as a first year graduate student. Since then, I have gotten a chance to follow the progress of the new building, mainly through glimpses of the roof from my lab’s conference room in the Hospital Building, whilst crossing the Queensboro bridge, or from viewing the outside of the building from the esplanade. But these piecemeal looks never gave me a real understanding of the full scale of the project. In early February, Alex Kogan, Associate Vice President of Plant Operations and Housing at Rockefeller, agreed to give the Natural Selections Editorial Board a tour of the building, where we got a more comprehensive idea of what a massive undertaking this project has been.

If you walk anywhere on Rockefeller’s campus, it is easy to miss the massive river building completely (barring the constant construction that has been taking place for the past couple of years). In fact, the architects designed it this way in order for it to blend into the preexisting campus. Limited to the space between the Franklin D. Roosevelt Drive and York Avenue between 62nd Street and 68th Street, the university had to take a highly creative approach to expand the campus. The university was able to take advantage of the air rights over the FDR that it has owned since 1973 to expand into a long horizontal structure over the highway. In the summer of 2016, nineteen modular metal structures were installed from the East River using a marine crane to lift them over the FDR onto columns that had previously been built. The FDR was closed nineteen nights that summer as the modules were transported on a barge from New Jersey and lifted one-by-one into place.

Over the past couple of weeks, equipment and scaffolding blocking views of the new walkways to the River Campus have been cleared, showing off the beautiful staircases and many entrances to the new building. Take one of the two new outdoor staircases between Founder’s Hall and the Nurses Residence, or between Founder’s Hall and Smith Hall, and you will find yourself on the top of the new Marie-Josée and Henry R. Kravis Research Building where there are two acres of open space containing a beautiful garden with many benches, an amphitheater of seats facing inward towards Welch Hall, and a lovely unobstructed view of the East River. The garden is strikingly devoid of noise from the FDR and looks to be the perfect place to watch fireworks on the Fourth of July or to hang out on a nice day. On the south side of the green space is the new cafeteria, which will replace Weiss Café. With state-of-the-art kitchen equipment and a full glass window looking out at the river, the dining services staff are eager to move into the new space and away from the undesirable conditions in Weiss, where the kitchen is far removed from the cafeteria. There is plenty of seating in a large open room adjacent to the cafeteria and I can see this becoming a big hang-out spot on campus. On the other side of the roof, as you walk north along the river atop the Kravis Research Building, are the President’s and Dean’s Offices with two large conference rooms that will be available for reservation by campus members as needed.

The Kravis Research Building below aims to provide Rockefeller scientists with a cutting edge research facility, and will replace many existing labs on campus that have desperately needed an upgrade in the modern bioscience world. Spanning three New York City blocks, the building has rows and rows of benches, tissue culture rooms, and chemical hoods. By the windows sit individual desk spaces for all researchers that will ultimately be separated from the main lab spaces by a glass panel, which will allow scientists to enjoy a coffee or snack at their desk. All Head of Lab offices are exactly the same size, meaning nobody has a bigger office than anyone else. All of the lab spaces are designed to be completely flexible, making it easy to adjust where benches and equipment will be set-up and allow for a space tailored to the unique needs of each group of scientists. There are four main wings of the building, each to be shared by six labs, which include north and south wings on each of the two floors of the building. The quadrants each share a common conference room and kitchen. All faculty were offered a chance to move to the new building, and so far eighteen labs will be moving into the new space, with the first labs set to move in March. No lab was given preference to particular locations in the building, but they have tried to put labs that collaborate closely near one another. I cannot help but be envious of the labs that received corner spaces with large windows—these seem like the perfect locale for bouts of deep pondering whilst doing science.

In the middle of each floor are two common spaces where there will be plenty of seating to meet for coffee or get away from the lab. There is also another large common kitchen that will be open to all of the labs on the floor. The bottom floor also has a lactation room for breastfeeding mothers. Bathrooms have been put in in the center of each floor as well, meaning everyone working in the building will be converging in the middle of the building at least a couple of times a day. The whole design of the building is open, which the architects hope will foster more cross-talk between people from different labs. In fact, I think it is going to be difficult to distinguish where one lab ends and the other begins.

At the end of the north side of the building, in front of the President’s House, will be a new large lawn that will serve as a backyard, and further, past the lawn by the 68th Street gate is a new conference center. This conference center will be open to Rockefeller labs and rentable by members of the public in order to generate some revenue for the university. With full glass windows facing the river, I think it will be highly desirable for meetings. It is completely separate from the rest of campus (meaning you will have to walk outside to get to it) and was designed to be sort of a retreat space to get away from the main interconnected research buildings. It will be accessible by the 68th Street turnstile, which will reopen soon, after having been closed for the past couple of years.

Campus has been under construction for four years now and I can fully say that it has been worth the wait. Although my lab is not moving to the new building, I will definitely be spending a lot of time there enjoying the gorgeous architecture, relaxing in the open space over coffee and lunch, and strolling in the lovely gardens above. The beautiful and highly innovative design of the expansion will be a refreshing addition to campus—the official opening cannot come soon enough! You can follow installed cameras with time-lapse views of the new building here.

Alex Kogan excitedly discusses the expansion of Rockefeller and the construction of the new river campus.

View of the new amphitheater facing Welch Hall from the green space above the research building.

The finishing touches are being put on the Marie-Josée and Henry R. Kravis Research Building, which must be prepared for the move of eighteen Rockefeller labs starting in March.

All photos courtesy of Megan Elizabeth Kelley. Follow her on Twitter @MeganEKelley.

Rockefeller’s Resolutions for 2019

Sarah Baker

The Ancient Babylonians are thought to be the first people to make the equivalent of what we think of as a New Year’s resolution. Four millennia ago, they would make promises to the gods that they would pay their debts in the upcoming year. This happened at the beginning of the Babylonian new year, in March, during an eleven-day festival called Akitu, or the Festival of the Sowing of Barley. The Babylonians believed that if they kept these promises, the gods would bless them with good luck throughout the year.

This trend persisted thousands of years later, picked up by individuals mostly for religious reasons, and ancient Romans and early Christians continued to make promises to their deities or deity on the first day of the new year, which became January 1 after Julius Casear moved it to this date to honor the Roman god of beginnings, Janus. People normally used this as an opportunity to promise that they would atone for past mistakes and be better in the future. Today, New Year’s resolutions are common in the Western world and are generally individual goals for self-improvement. About 45% of Americans make New Year’s resolutions, but the success rate for keeping these goals is a measly 8%, according to a poll conducted in December 2018.

Now, at the start of 2019, we have reached a time when we all reflect on what we have or have not accomplished in 2018 and how we would like to improve ourselves this upcoming year. My own resolutions include seriously starting to plan my wedding, running my first half marathon, and being able to do ten pull-ups in a row. Maybe writing it down for you all to see will make me feel more accountable, and I can be in that 8% of people who actually achieve their goals.

Here is a glimpse of the resolutions that other members of the Rockefeller community have for 2019:

“My resolution is to survive toward end of the year, while 1) raising three kids, 2) taking care of a house 3) commuting between New York and Richmond, 4) doing my Ph.D., and 5) running two businesses at the same time. Steps taken so far: I have tried to fill every minute of my day with something.”

– Du Cheng

Du with his partner and three kids.

“My resolution is to lose weight by eating less burgers and more chicken and to become an “Intermediate+” volleyball player so that I can play with the Tri-I on Wednesday nights.”

– Shigeru Kaneki

Shigeru eating chicken he cooked for himself in his new InstantPot.

“My resolution is to figure out my career plan and to break out of this quarter-life crisis. I would also like to more seriously consider learning how to cook an adult meal.”

– Jyen Yiee Wong

Jyen trying to figure out her next life steps.

“My resolution is to cook healthier and eat in more moderation!”

– Steven Cajamarca

Chicken that Steven cooked for himself.

“My New Year’s Resolution is to travel more. So I decided to start the year right and spent a day in Moscow on my way back to NYC. It was so cold, but so beautiful!”

– Anna Amelianchik

Anna embracing the beautiful cold in Moscow.

Science (Policy) for the Benefit of Humanity

Sarah Ackerman

Science policy is a broad subject, which is vitally important to all scientists and members of society. It encompasses many topics ranging from NIH grant funding, to restrictions on new technologies, such as CRISPR or stem cells, to how data and science should be used when making policies about health care or the environment. These policies greatly impact scientific research and it is essential for scientists to understand these policies and to advocate for their research with society in mind.

The Science and Education Policy Association (SEPA) is a Tri-Institutional group led by graduate students and postdoctoral fellows who recognize the importance of science policy.  To bring these topics to light, SEPA organizes speakers on policy issues, discussion groups, career panels, and writing workshops to educate our academic community about science policy and potential career options in the field.

On November 10, SEPA hosted the Second Annual Science Policy Symposium at the Rockefeller University. The day was sponsored by The Schmidt Foundation, The Moore Foundation, The Rockefeller University, and Weill Cornell Medicine.  The goal of the symposium was to expose early career scientists to the world of science policy, provide training workshops to acquire skills used in science policy, and create a networking opportunity for like-minded scientists. The symposium attracted over 200 attendees, predominately graduate students, from all over the country.

The event was kickstarted in Caspary auditorium by Dr. Jennifer Pearl, the director of the American Association for the Advancement of Science (AAAS) Science and Technology Policy Fellowship.  Throughout the day we heard talks by Erin Heath, an AAAS Federal Budget expert, Dr. Frances Colon, the former Deputy Science and Technology Advisor for the State Department, and Dr. Dalal Najib, the senior program officer in the Policy and Global Affairs Division of the U.S. National Academy of Sciences. The day also included a panel titled Rebuilding a Sustainable and Resilient Puerto Rico through Science and a panel with representatives from different science policy fellowship programs. Six workshops throughout the day also trained attendees in skills pertaining to science advocacy, working with non-profit organizations, science communication, scientists in political office, and changes to STEM education. More than thirty students/student groups also participated as presenters in a poster session. The day’s schedule ended with a keynote talk given by Dr. Kerri-Ann Jones, the Vice President of the Pew Charitable Trusts and the former United States Assistant Secretary of the State for Oceans and International Environmental and Scientific Affairs at the U.S. State Department.  She discussed her invaluable experience serving as a scientific advisor in the White House.

This jam-packed symposium schedule allowed attendees to tailor the day to their interests, interact with and ask questions of high-level scientists working in the policy field, and build relationships with other early career scientists interested in science policy. The event has fostered connections and training opportunities for symposium attendees from around the country and particularly for SEPA members who organized and volunteered for the event. The magnitude of interest curated from the event encouraged attendees that there are other like-minded scientists passionate about science policy and that these interests are possible to pursue as a career. In a follow-up survey given to our attendees, 85% said that after attending the symposium they are more likely to contact someone they met at the symposium and 90% said they would attend another conference like ours in the future. For more coverage of the day, check out our twitter hashtag #NSPNsymposium18!

For those who are interested in science policy there is more exciting news—SEPA, in collaboration with the Science Policy Initiative (SPI) from the University of Virginia, has launched the new National Science Policy Network (NSPN). The organization aims to connect science policy groups all over the country and come together on new initiatives. One initiative is the microgrant project. The first round of grants have been given out to science policy groups around the country for specific projects or to launch their own group at their university. NSPN’s second initiative is the memo writing competition. Memo writing is a critical component for influencing policy and knowing how to write one is crucial for a successful science policy career. At the Symposium on November 10, NSPN announced the start of the memo writing competition. Winners will receive a reward and be published in the Journal of Science Policy and Governance.

If you are interested in being part of our memo writing team or just want to get involved please email SEPA (nyc.sepa@gmail.com).  SEPA is working hard to educate our community about science policy issues and provide unique educational opportunities for scientists to be competitive for policy fellowships and jobs. Come join us!

Rockefeller Mutant Takeover

Alice Gadau

“What about ‘Spooktacular’?”, “I like spooky scientists!”, “What about something with CRISPR?”, “Oh! I got it ‘CRISPR Gone Wrong’!”—and that is how, in the back of yellow cab, Donovan Phua came up with the theme for this year’s Halloween party. Each year, the first year graduate student class organizes the Rockefeller University Halloween party. A group of highly qualified party planners (wink!) were chosen from the first year class to organize, plan, order, and set up for the party. Just as every other year, the party took place in the famous Faculty Club with a chill bar set on the patio outside. The party planners created fun activities for kids and adults alike, including pumpkin DNA extractions during the kids’ hour, and a costume contest for adults. Beautiful, original pumpkin carvings designed by the first years were on display during the Halloween party, which took place on October 26. Hopefully you didn’t miss it! In the words of one party planner, Mari Soula, “It [was] lit!”

Mental Health Awareness

Sarah Baker

Mental Illness Awareness Week (MIAW) falls on the first full week of October, meaning that this year it will occur October 7-13. MIAW was established by Congress in 1990 after the National Alliance on Mental Illness (NAMI) pushed to increase public awareness about mental health and illness and to reduce stigma in talking about mental health issues. In 2018, NAMI is promoting the theme of CureStigma to get rid of the environment of shame or fear that prevents individuals from seeking help. There are several other days in October further dedicated to the focus on mental health in our society. World Mental Health Day falls on October 10 with the emphasis this year on young people and mental health in a changing world. Recent previous themes include mental health in the workplace (2017), psychological first aid (2016), dignity in mental health (2015), and living with schizophrenia (2014). Furthermore, October 11 is National Depression Screening Day, and October 9 is National Day Without Stigma.

The goal of these October events is to increase awareness about mental illness, promote community outreach and public education, advocate for treatment and recovery, and fight stigma that prevents people from seeking help for mental illness. At the Rockefeller University, we have the chance to do that too. Rockefeller has many resources available to those struggling with mental health, if one just knows where to look. One common complaint I have heard from the campus community is that these resources may be hard to find, so I have worked with Human Resources to compile this list below:

Psychiatry

  1. Dr. Nisha Mehta-Naik

Private confidential sessions on-site in OHS, HOS118.

Tuesday and Thursday, 9 a.m. – 5 p.m.

Call x8414 for an appointment.

No copay

 

  1. Weill Cornell Psychiatric Center

(646)962-2820

315 East 62nd Street, 5th Floor

Monday – Friday, 9 a.m. – 5 p.m.

$15 copay (RU Choice and RU Managed Care Plans)

20% coinsurance after deductible (Oxford Plan)

 

  1. Employee Assistance Program Consortium

(212)746-5890

409 East 60th Street, Room 3-305

Monday – Friday, 9 a.m. – 5 p.m.

On-call therapist available after hours

No copay

 

Occupational Health Services

OHS serves to promote a culture of physical, mental, and emotional wellness.  Two nurse practitioners and an occupational health nurse are available to help with any stress you may find yourself dealing with. The office is located in HOS 118 for drop-ins, or call x8414 to schedule an appointment.

http://inside.rockefeller.edu/hr/occupationalHealthServices

 

Mindfulness Practices for Stress Reduction

Tuesdays, 12pm or 12:30pm, RRB110; September – May

Stress is one of the biggest contributors to poor health. Its effects can cause physical illness, damage relationships, and negatively impact work performance. Mindfulness meditation is a means to reduce stress, boost the immune system, improve attention, and promote well-being.

 

Nutrition Series

To help manage stress through healthy eating habits, the University offers a nine-month lecture series and one-on-one nutrition counseling sessions. The series begins in the fall.

 

Yoga

This is a seven-week series throughout the year designed to focus on different parts of the body.  The fall series begins September 10, 2018 in the Great Hall, Welch Hall.

Beginner Class at 12 p.m.; Intermediate Class at 1 p.m.

Must register at x7788.

 

Run/Walk Club

Tuesdays 12pm – 1pm. Meet at Security booth at 66th Street.

Step away from the stresses of your day and walk or run with a group or solo at your own pace.  See Tim Blanchfield, Fitness Manager, for more information.

 

Fitness Center

Exercise is also vital for maintaining mental fitness, and it can reduce stress.

Located on the 6th floor of Founders Hall, from free weights to cardio equipment and classes, the gym contains several options to fit everyone’s fitness needs. For more information and to find classes you may be interested in, click here:  http://inside.rockefeller.edu/hr/aboutGym.

 

Stressed over childcare?

Bright Horizons offers backup daycare for when your regular arrangements are unavailable.  They have center based and at-home care available. Call 877-BH-CARES for more information.

 

Stressed over Eldercare?

Bright Horizons offers assistance in finding a home health care provider.  Call 877-BH-CARES for more information.

 

Financial Well-Being

Retirement Planning – A TIAA representative is available on-site to discuss your personal financial situation.  This includes discussions about saving for college, purchasing a home, etc. while continuing to save for retirement.

Saving for College – Applying for college can be stressful, but what about paying for college?  The University offers you the option of payroll deductions for the NY State 529 plan.  Find out more at www.NYsaves.org.  Additionally, the University offers tuition reimbursement for fulltime staff employees.

 

While most of these resources are available to students, post-docs, faculty, and employees at Rockefeller, the options may differ based on your position or immediate needs, so please reach out to Human Resources if you are unsure which option would be best for you.

We do have fantastic resources available at Rockefeller, but from my experience, some students are hesitant to use them. Cost should not be a factor, as the psychiatry services available are either free or a small co-pay. Some people are afraid of their mentor or peers finding out that they are struggling, as this may affect the perception of them as a scientist. As a community, let’s break the stigma of being able to talk about mental health. Mental health is just as important as physical health and Rockefeller is working hard to foster an environment of overall well-being for its community. Academia can be a highly stressful place in which to work, especially if one lacks encouragement from a superior or peers. The university is a place where support can come from many levels that all contribute to the current and future success of its trainees. One of the most protective things that I have found for my own mental health is feeling a sense of community, both inside and outside of the lab. So look out for each other, find things to engage in that you are passionate about, and take advantage of the resources Rockefeller has to offer. This is how we will set up trainees to be successful, productive, and satisfied.

 

A Special Obituary: Günter Blobel

 

Joseph Luna

Editor’s note: This article was originally published as Twenty-four visits to Stockholm: a concise history of the Rockefeller Nobel Prizes by Joseph Luna in June 2016.

 

Günter Blobel (May 21, 1936 – February 18, 2018)

Let’s start with a fantastical scene: picture a band of Neolithic humans in a hot air balloon overlooking modern New York City. What would they see and experience? Lacking a vocabulary and a mental model of twenty-first century life, our ancient friends would be awestruck at seeing miniscule specks and strangely ordered structures, lines and squares, in green and gray. Perhaps the occasional yellow rectangle from which specks would enter and exit would catch their attention. Or they might ponder a box with flashing lights, speeding its way across a grid. It’s near impossible to imagine being in their shoes, but it’s easy to envision the excitement as they try to describe and make sense of what they saw.

This totally novel experience wasn’t far off from what early cell biologists encountered, as they used the electron microscope (EM) as a sort of hot-air balloon to discover the cities inside cells. By the mid-1960s, they had plotted the geography of all sorts of cellular worlds, had given names to energy-making blobs and recycling vesicles, and with the help of radioactive amino acid labeling, had a basic sense of where proteins were made and where they ended up. But big questions remained such as how did a protein know where it needed to go? For a discipline built on EM observations from high above, this was a challenging question to answer, but it captivated a young German post-doc enough to dream as if he landed his hot air balloon and walked among molecules, where the view was much clearer.

Günter Blobel arrived in George Palade’s laboratory in 1967, shortly after completing his PhD at the University of Wisconsin at Madison. He joined a dynamic group of researchers who had stumbled upon an odd observation concerning the protein factories of the cell, its ribosomes: proteins destined to remain inside the cell were often made from a pool of freely cytoplasmic ribosomes, whereas proteins meant to be exported from the cell quickly associated with ribosomes attached to the endoplasmic reticulum (ER). How a new protein made this decision to stay in the cytoplasm or go to the ER was a mystery.

Within a few years, and overwhelmingly without much evidence, Blobel and a colleague (and Rockefeller University alum) named David Sabatini formulated what became known as “the signal hypothesis” that might explain how proteins got sorted to their proper locations. It represented a truly imaginative and startlingly precise leap, as if one could envision a five digit postal code and a stamp authentication system simply by watching mail trucks from space. Blobel and Sabatini proposed that ER destined proteins contained a special stretch of amino acids that acted like a signal that became apparent the moment the protein was being made at a ribosome. This signal sequence, located at the head of a protein, would be recognized by a factor (or factors) that would, in turn guide the synthesizing ribosome to the ER, where the protein in question could finish being born as it translocated across the ER membrane. Once properly sorted into the ER, the signal sequence was no longer needed and could be removed by an enzyme, even while the protein was still being made. Once finished, the protein could then go and do its job.

For many, this all sounded needlessly baroque. One attractive alternative was to consider different types of ribosomes, where each type was responsible for ferrying a nascent protein to a particular location. Another idea postulated that the mRNAs encoding proteins somehow got to the correct place before undergoing translation from any nearby ribosome. The signal hypothesis was one of many possible models, and a far-fetched one at that. But it made very precise predictions that could be tested, the first of which was the existence of a transient signal sequence.

Myeloma cells provided the first toe-hold for testing the signal hypotheses, since they secreted lots of IgG antibody light chains that could be readily detected. Using cell-free translation systems, based on these cells, other laboratories had observed slightly heftier IgG molecules than those secreted from intact cells, suggesting that a larger precursor was made and pruned to a final, smaller form. Yet, worries of an in vitro artifact abound. Blobel first repeated this experiment, and once confirmed, tinkered with his cell free system to uncover the order of events. Using detergent, he separated ribosomes from bits of ER (called microsomes) and added a drug that blocked new IgG production. He then let the ribosomes that had already started making an IgG to finish, keeping track of what they produced and when. Early in the experiment, only the smaller form emerged, which made sense if these ribosomes had already been at the ER and were nearly finished making IgG when Blobel had isolated them. But later in the experiment, a mixture of larger and smaller forms showed up: ribosomes that had just started making IgG indeed made a larger version. But lacking sufficient ER targeting, the signal sequence wasn’t pruned efficiently. Blobel had glimpsed a totally new feature in the early lives of proteins.

This was just the start. Over the ensuing years, Blobel and his team devised ways of recapitulating numerous aspects of protein targeting in the cell, from isolating the complex that ferried a signal sequence bearing protein to the ER (the aptly named “signal recognition particle”) to later confirming and characterizing the protein channel at the ER (the translocon) that nascent proteins traversed for proper processing. In part because of Blobel’s efforts, the hot air balloon view gave way to detailed explorations from the ground. A dream, as all good hypotheses are, turned out to be true.

 

This month Natural Selections interviews Jazz Weisman of the Scientific Computing Users Group

Juliette Wipf

Picture: Jason Banfelder, Director of the RU High Performance Computing Systems, talking about the most commonly used computing tools at the inaugural meeting of the SciComp group.

On April 12, Scientific Computing Users Group (SciComp) of The Rockefeller University’s (RU) held its inaugural meeting in CRC 406. The founders of the group, Jason Banfelder, Director of the RU High Performance Computing Systems (HPC), and first year graduate student Jazz Weisman, led the meeting. I caught up with Jazz Weisman about this new group on our campus.

NS: How did you and Jason come up with the idea to start the SciComp group?

I attended Jason’s Quantitative Understanding in Biology course at Cornell University and wanted to learn more. When I asked him about opportunities he said that starting a group is always a good, as well as a feasible idea. In fact, he had thought about starting something for a while as well. I actually recommend Jason’s lecture, or a similar intro level data analysis class, to everybody. A lot is already going on in that area, and we tried to create something in this pool. The future is definitely more computed, and we have to start somewhere.

NS: What do you think is the biggest plus of the SciComp group?

Painful and repetitive work should be reduced as much as possible. So many things can be done a lot easier with the help of computing, which will make repetitive tasks in science a lot less painful. But there are a lot of side benefits to our group. People get to know Jason as a representative of the IT department, which will make communication between the scientists in the lab and IT easier. People tend to be a bit shy about their computer skills, and we hope to make the IT department more accessible. Finally, we want to get interested people together. Labs can sometimes be a bit insulated; however, their computational interests would be similar.

NS: Researchers (myself included) can sometimes be a bit scared of using new programs, even though we use computer programs daily. Why do you think that is?

I think most are afraid of messing up their data. We also don’t want the design of our results to change, since we have long chains of experiments, sometimes generated over years, and a change in the output can sometimes make it hard to represent data neatly. But, as I said, most of our experiments come in long chains. Programming languages, such as R, Python or MATLAB, can simplify such tasks, and are actually a lot faster and easier to use than, for example, Microsoft Excel. Most importantly however, they make things repeatable, which is always better. If we use code to perform a string of tasks, this code can be given to a new student for example, and everybody can be sure the desired analysis was executed exactly the same way as usual. The student, on the other hand, can also study the string of code in peace and quiet, which will make understanding of the method easier for the new student as well.

NS: What can people expect from those meetings? Are there exercises that you do on computers together, or is it more of a discussion round?

Our group meetings usually start with a short talk of approximately 15-25 minutes on a chosen topic. For example, in our second meeting on May 18, we chose to talk about the data visualization tool ggplot2. After the presentation, we hope to get an open discussion going where everybody can ask questions. You can bring your laptop because it can help showing others the actual problem you are experiencing. It is not necessary that you attend the whole meeting; you can also just come for one part of it. We want our meeting to be an open thing. Also, we understand that everybody is busy and that you might have limited time for stuff.

NS: Who can attend the SciComp meetings? What skill level is expected from participants?

Absolutely everybody can attend our meetings and no previous experience is required. If you want to learn more on the discussed topic, please come. We expect nothing and are simply happy you are interested. If we talk about an R-based tool like ggplot2, for example, it will all make a bit more sense to you if you know some of the programming language R already. But it is not expected at all. We want the group to be widely accessible. Everybody who wants to should come!

NS: What do you expect from the participants (ask questions, prepare, etc.)?

People shouldn’t be afraid to get a discussion going. We are happy to answer the most basic questions! This is exactly why we thought the group environment would be nice, just to make everything more laid-back and relaxed. Ultimately we hope to also see group members helping each other out, with me or Jason only assisting when needed.

NS: What topics will be discussed in the meetings?

People can actually vote on which topic will be discussed. In this Google group, people should add their requested topics. If you and your colleagues want to learn about a specific program your lab is using, you should individually log onto the Google group and vote, so we can see how big the demand is. With this approach, reruns of hot topics are also possible if needed; just reenter the topic into the Google group. We hope to soon talk about DNA or RNA sequencing, which I definitely think is the topic most people are interested in at the moment. In addition, we will use the Google group for general updates as well as a place for people to ask questions.

NS: In your inaugural meeting, you talked about the most successful tools currently available to get a feel for the needs and interests of the attendees. In the last meeting you discussed the R plotting tool ggplot2, which makes all kinds of beautiful plots and graphs. When will the next SciComp meeting take place and what topic will be discussed?

We’ve decided to have the next meeting on August 3 in CRC 506 from 5:30 – 6:30. We will discuss Dynamic documents in R, presented by Thomas Carroll, head of the new bioinformatics resource center​. Finally, if anyone is interested in becoming a co-organizer they should contact me via email at jweisman@rockefeller.edu. I think that one or two more people to plan and put the word out could be a good thing for the SciComp group.

Jason Banfelder, Director of the RU High Performance Computing Systems, talking about the most commonly used computing tools at the inaugural meeting of the SciComp group.