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Paying It Forward

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The UCSF Student Newspaper

Thursday, January 16, 2014


Clinical Corner: The General Appearance of Patients By Akshay Govind Associate Editor


linicians in training are told that their assessment of a patient should begin the moment they enter a room. In fact, if there are notable sounds or smells that can be appreciated from outside the patient’s room, this assessment can start even earlier. It is often recommended that young clinicians go through a set checklist or fixed routine to ensure nothing is left out during data collection. Then, with all information gathered, one can go back, piece together a problem list, and try to think through all the possible explanations for these problems before narrowing down the most likely causes and deciding how to address them. As clinicians gain experience, these processes happen simultaneously, allowing interviewers to move various disease processes up and down their mental lists, driving the next lines of questioning or examination. A patient’s general appearance is among the first things a clinician should observe, and this can help to guide the entire clinical encounter. This skill, like anything, takes practice. Several pieces may contribute to an individual’s general appearance, including any signs of distress, such as sweating or labored breathing, level of consciousness or ability to interact, height, build, body odors, whether

they appear different from their chronological age, any obvious wounds, or even unusual jewelry or tattoos, to name a few. One remarkably tangible item I find useful is a description of a person’s apparent state of health. From across a room, we really can tell in a fraction of a second if someone looks well, and if not, we can describe them as appearing agitated, ill, in pain or frankly toxic. Developing a rich vocabulary to describe people’s general appearance in just a few words is well worth the effort. I learned my favorite exercise for practicing this from a class I took in dental school that used art to hone students’ skills in physical diagnosis. To do this exercise, go with a friend to your favorite museum, and venture into separate wings that have paintings, photographs or sculptures filled with people. On a notepad, describe seven or eight specific subjects in the works using just a few words. Then find your friend, switch wings of the museum and notepads, and based on each other’s descriptions, find the people your friend picked out. Of course, you can do the same with real people from your social circles or celebrities, but I always enjoy a reason to get out and view some art. B elow are a few quick examples of patients I have seen:

Volume 58, Number 15


Fall Rec League Sports Champions Crowned

Photo courtesy of Fitness & Recreation Centers @ UCSF First-year medical student team, Med '17 or Bust, defeated the School of Dentistry's Flossoraptors to capture the student basketball league crown.

uring my first year in graduate school, I quickly learned that I needed some sort of outside-of-lab activity, or else I would go crazy. I tried a smattering of hobbies, from rock climbing to making wall art out of wire (that didn’t end well), but nothing ever stuck. After TA-ing during my second year, I realized that I enjoy teaching. I like preparing lectures and inventPhoto courtesy of Erin Oswald ing creative ways to explain complex topics. And if I am to be completely honest, I feel encouraged by having people actually listen to what I am saying.

teams of the fall at the Parnassus campus. The student basketball league crown was captured by the first-year medical student squad, Med ’17 or Bust. Comprised of medical students Norver Trinidad, Jackie DesJardin, Jameze James, Stephen Brown, Ranvir Dhillon, John Bonano, Ruiji Jiang, Frank Lu, Dennis Zheng and physical therapy student Dorian Danic, the team won four of its seven regular-season games to enter the one-day playoffs as the second seed. In the post-season semifinals, Med ’17 or Bust defeated its elders, the second-year medical team, We Get Buckets, before squeaking by the previously undefeated Flossoraptors of the dental school for the title. “Stephen (Brown) and John (Bonano), both of whom are former Pac-12 athletes, were key to our ability to dominate the paint,” said team captain Norver Trinidad. The Penetrators, made up of Brandon Chu, Terry Lee, Jun Loayza, Vannor Phan, John Kwon, Emmanuel Igbinosa, Ryan Satcher and Gary Anderson, won the six-feet-andunder basketball league title. After suffering only two losses — both of which came when short-handed — during its seven-game regular season, the group entered the one-day playoffs as the fourth seed of four teams but remained confident. Down big in the first half of the semifinal game, the Penetrators fought back to win that game and the next for its second straight league title. A former Stanford walk-on, Igbinosa led his team by making plays on both ends of the floor.




By Dennis Zheng Staff Writer


or the members of UCSF’s recreational sports leagues, the year 2014 pres ents ne w opp or tunities. Champions will either be toppled or continue their reign. Although the winter quarter leagues began last week, there’s still time to recognize the five winning


Paying It Forward at Cal Academy “Serving the community [is] ingrained in the ethos of UC San Francisco,” proudly proclaims the university website. Indeed, as members of a health sciences university, UCSF students and staff are devoted to improving the lives of people throughout the world. For many, this passion for public service extends beyond their career aspirations. This column highlights these altruistic individuals as well as the organizations they serve. Please email if you would like your organization to be featured in “Paying it Forward.” ~ Jenny Qi Executive Editor

By Erin Oswald Contributing Writer


2 | January 16, 2014 |



Thursday, Jan. 16, 6-8 p.m., Genentech Auditorium, Mission Bay Steve Burrill, founder and CEO of the investment firm Burrill & Company, will deliver his respected annual analysis of the life science industry: opportunities, challenges and trends for the next year. Join us to learn what’s in store for the industry and where you should focus to take advantage of the opportunities.


Friday, Jan .17, noon-1 p.m., Graduate Division. CC-310, Mission Bay Synapse is looking for Mission Bay and Parnassus writers, bloggers, photographers and designers. Come to the lunch meeting, share your story ideas and enjoy a free lunch. RSVP to


Friday, Jan. 17, 1-2 p.m., Helen Diller, 160, Mission Bay
 The Muslim Community at UCSF holds regular Friday prayer services (Jum’a) for the UCSF Muslim community every week. Join your fellow brothers and sisters for prayer, lunch and socializing. All are welcome.


Friday, Jan. 17, 4-5 p.m., Genentech Hall, N114, Mission Bay Research In Progress Seminar is a seminar series at which one student and one postdoc present their current research. Talks are 15 minutes in length and are preceded by a 20-minute social. Snacks and beverages are provided.


Tuesday, Jan. 21, 5-6 p.m., Genentech Hall, N114, Mission Bay Meet your Student Regents to see how you can make a difference in the UC system. Enjoy delicious hors d'oeuvres and pick up an application to be the next Student Regent.


Tuesday, Jan. 21, 5:30 p.m., Genentech Hall, N114, Mission Bay Meet your executive board members at the monthly GSA meeting and be a part of the discussion on topics relating to student priorities. Visit the GSA website for more details and to RSVP.


Wednesday, Jan. 22, noon-2 p.m., Rutter Center lobby, Mission Bay More than 35 UCSF and external vendors will give away free information, fresh produce, snacks, free healthy lunch and hundreds of wellness resources. “Know Your Numbers” health assessments will also return, with a chance to earn $35 and chair massages. Please join us to celebrate wellness within the UCSF community. Complete the “Wellness Pledge Card” and turn it in for your free Wellness Lunch. annual_wellness_expo_save_the_date


Wednesday, Jan. 22, 6-9 p.m., Genentech Hall Atrium, Mission Bay

Bring your favorite board games to share. Enjoy free beverages, pizza, and raffle prizes provided by GSA & Student Life.


Thursday, Jan. 16, noon-12:45 p.m. Cole Hall, Parnassus Violinist Melissa Kleinbart, cellist Tanya Tomkins and pianist Eric Zivian perform Schumann’s Piano Trio in D Minor, Op. 63. The Chancellor’s Concert Series on Thursdays is a great place to take a break from classes while listening to classical music. Seating begins at noon. If you are unable to come, you can now listen to the music through live stream. This concert is free.


Thursday, Jan. 16, 5-7 p.m., Multicultural Resource Center, Parnassus Attention artists, writer, singers, filmmakers! The Office of Diversity and Outreach is looking for performers/presenters for the upcoming open mic night. If you would like to sign up to perform at this open mic or have questions about the event, please email sarah.


Thursday, Jan. 16, 5-7:30 p.m., Nursing Mezzanine, Parnassus The Korean American Health Professional Students Association will be preparing the ingredients needed to make pat-bing-su, traditional Korean shaved ice. Participants will get to grind their own ice and customize their toppings, which include red bean, condensed milk, grain powder, fruits, rice cake and jellies.


Thursday, Jan. 16, 5-9 p.m., Cole Hall, Parnassus This annual event, held by the second-year School of Pharmacy class cabinet, brings the School of Pharmacy together through a friendly competition. A nominee from each class will compete for the title of “Mr. Pharmacy,” by presenting their skills and participating in various games.


Friday, Jan. 17, 1-2 p.m. , Medical Sciences, 163, Parnassus The Muslim Community at UCSF holds regular Friday prayer services (Jum’a) for the UCSF Muslim community every week. Come join your fellow brothers and sisters for prayer, lunch and socializing. All are welcome.


Friday, Jan. 17, 7-10:30 p.m., Nursing, 517, Parnassus Join the Campus Evangelistic Fellowship for their weekly meeting with Bible study, hymn singing and fellowship.


Tuesday, Jan. 21, 5:15-7 p.m., Nursing, 225, Parnassus Tim Wise offers an incisive critique of colorblind race logics in U.S. politics. To be

blind to color, he argues, is to be blind to the consequences of color, making it impossible to effectively address racial inequality. After watching the film, students can discuss the consequences of denying the existence of race. Sponsored by the UCSF Multicultural Resource Center.


Wednesday, Jan 22, 10 a.m.-3 p.m., ACC, 400 Parnassus Ave.
 Shop the Farmers’ Markets on Wednesdays to pick up locally grown produce and more. Sponsor: Pacific Coast Farmers’ Market Association.


Wednesday, Jan. 22, noon-1 p.m., Millbery Union 123W, Parnassus Synapse is looking for Mission Bay and Parnassus writers, bloggers, photographers and designers. Come to the lunch meeting, share your story ideas and enjoy a free lunch. Email for more information and to RSVP:


Wednesday, Jan. 22, noon-1 p.m., Nursing, 217, Parnassus Take a mid-week break and join Student Health and Counseling for the Winter Hump Day Student Wellness Series. Topics focus on staying well throughout the year. Talks will occur every Wednesday at Parnassus in N-217, with the exception of the March 12 talk, which will be held at Mission Bay in Rock Hall 102. Free lunch at all talks for students with RSVP. Led by Felicia De La Garza Mercer, Ph.D. For more information or to RSVP, contact


Wednesday, Jan. 22, 5:30-6:30 p.m., Millberry Union Central Desk, Parnassus Please drop by and join UCSF Fit & Rec for a run. Each Wednesday night, the Run Club runs various distances (from 3-6 miles) at 9 to 11 minutes per mile.


Wednesday, Jan. 22, 6-8:30 p.m., Clinical Sciences, 130, Parnassus English Corner is an informal conversational English class given as a free community service and provided on a voluntary basis by both people born and raised in the United States as well as many people who have, at one time in their lives, experienced life as a new immigrant to the United States.

SAY CHEESE! SYNAPSE WANTS YOUR BEST PHOTOS FOR OUR PHOTOGRAPHY ISSUE! Submit photos and captions to Synapse by February 7.


The Center for Science Education and Opportunity is looking for 20 UCSF students to serve as mentors to small groups of 10thgraders from San Francisco's Burton High School. The Burton students will be doing the research on health topics with your guidance, developing an interactive activity/ discussion that will be presented to the school community and families. The students will also design an educational brochure and create a large informational poster. Please contact Anthea Lim for more information.


The Human Rights Center at UC Berkeley and the UC Berkeley Art Museum and Pacific Film Archive (BAM/PFA) are sponsoring a juried exhibition of student artwork. Students from all University of California campuses are invited to submit their works to be considered for the exhibition, addressing critical human rights issues. festivals_unique_info.php?ID=1671


Saturday, Jan. 25, 9 p.m-1 a.m., Westin St. Francis, SF
 Purchase your tickets today and get ready to enjoy a night of dancing, desserts and photo booths.



Thursday, Jan. 9, 5-9 p.m., Stanyan and Waller Streets, SF Off the Grid is a roaming mobile food extravaganza that travels to different locations daily to serve delicious food, with a free side of amazing music, craft and soul.

The Student Regent is a voting member of the Regents of the University of California, attends all meetings of the Board and its Committees and serves for two years (one year as a designate and one year as a voting member) commencing July 1. All mandatory University fees and tuition are waived for the Student Regent during the academic years in which he or she serves as a Regent-designate and as a member of the Board. Submit applications by Feb. 20 at 5 p.m. regents.




Thursday, Jan. 16, 6-10 p.m., Cal Academy, Golden Gate Park Immerse yourself in cerebral science this week as NightLife gets inside your head. In the Planetarium, join a guided meditation led by neuroscience guru Dr. Philippe Goldin of Stanford University and get a closer perspective on human brains (even your own!) with a special fulldome audiovisual presentation at 6:30 p.m., 7:30 p.m. and 8:30 pm. Use your brain to power the sights and sounds of NeuroDisco, a mind-controlled music, light and sculpture installation. Catch a special set by turntable master and hiphop pioneer DJ Qbert, hailed as one of the most prolific DJs of all time. NightLifeTickets,

Wednesday, Jan. 29, 5- 6:30 p.m., RSVP for location, Parnassus
 Are you of the first generation in your family to attend college? You are not alone! Please join fellow UCSF first-generation-to-college students, residents, postdocs, fellows, faculty and alumni at this community reception. Refreshments and opportunities to connect with first-gen role models included. Registration:


UCSF students and staff can now post online classified ads for free on the Synapse website. All you need is an email account. Try it out! | January 16, 2014 | 3


Clinical Corner » FROM HOME PAGE

1. Caucasian man in his 40s with leathery skin, smelling strongly of body odor and alcohol, devil horns tattooed on forehead. Lying in bed with eyes closed. 2. Pale, elderly Caucasian woman, looking unwell, lying in bed, trembling but alert. Blood splattered on her ankles and shoes. 3. Young Middle Eastern man of college age, appearing healthy, talkative and friendly but visibly anxious. Fidgets and paces occasionally. 4. Elderly Asian-American woman, finely dressed and neatly made up, quietly sitting in a chair, knitting. 5. Indian man in his 60s, lying in bed intubated, opens eyes to voice and makes eye contact before falling back asleep. In the above examples, I might prioritize a mental status exam and a toxin screen in Patient 1 and a vascular exam and blood counts in Patient 2. Patient 3 may need reassurance

UCSF and Quest Diagnostics Collaborate to Advance Field of Precision Medicine

David Hockney's current collection at the de Young Museum includes decades worth of portraits on which to practice descriptions of people's general appearance.

before being interviewed, while Patient 4 may require close attention to detail with each recommendation. Patient 5 will likely not participate much in his examination, but he can hear and comprehend and will benefit from


QB3 Registration for Small Business Grant Workshops Is Open Staff Report


ife-science startup companies face unique challenges compared to tech startups. For instance, they need initial access to capital for obtaining proof-of-concept data or for developing a prototype. Their dependence on space and facilities increases the initial financial commitment, and entrepreneurs have little control over the scientific phenomena driving success or failure. For these reasons, a logical first step for scientist-entrepreneurs starting a company is an SBIR (Small Business Innovation Research grant) application. SBIRs are grants awarded by government agencies, and have frequently become the funds that bring new science-based businesses to life as an important part of a successful “lean biotech” startup strategy. However, the logistical and mechanical challenges of the application often put some of these new teams at a disadvantage.


For example, familiarity with the mechanical aspects of the application is necessary to make sure that an application does not land on the pile of the 20 percent of applications that are rejected for technical reasons before even being reviewed. For over three years, QB3 has been running 15-hour workshops focused on helping entrepreneurs file successful applications. These workshops focus on crafting a wellstructured research plan, getting persuasive letters of support, crafting an efficient budget and helping teams anticipate reviewers’ comments. Students who have participated in the workshop obtain grants with twice as much success than the national average. Teams filing these applications are commonly graduate students or postdocs who join their venture full-time upon funding, so this makes a nice way to line up a job. The spring session for the course starts on January 22. For more information, please visit

500 Parnassus Ave. Millberry Union 108W San Francisco, CA 94143 tel: (415) 476-2211 | fax: (415) 502-4537

The UCSF Student Newspaper STAFF

Yi Lu | EDITOR Jenny Qi | EXECUTIVE EDITOR Alexandra Greer | SCIENCE EDITOR Angela Castanieto | ASSOCIATE EDITOR Akshay Govind | ASSOCIATE EDITOR Steven Chin | MANAGING EDITOR Victoria Elliott | COPY EDITOR


Synapse is the UCSF student-run weekly newspaper, which runs on Thursdays during the academic year and monthly during the summer. Synapse seeks to serve as a forum for the campus community. Articles and columns represent the views of the authors and not necessarily those of the Board of Publications or the University of California.


Announcements and letters should be submitted six days before publication. All submissions can be either emailed or mailed. All material is subject to editing. Letters to the Editor must be signed by the author.

Subscriptions Subscriptions cost $20/year ($40/outside US).


Paid advertisements do not necessarily reflect the views of Synapse. Synapse and its editorial board reserve the right to decline advertisements promoting false or misleading claims, known health risks, or content deemed by the editors to be antithetical to the interests of UCSF students or the UCSF community. Synapse does not accept advertisements from tobacco or alcohol manufacturers, or sexually oriented personal ads. Synapse reserves the right to run any ad with a disclaimer.

being told out loud what is happening. When communicating about patients verbally, describing the general appearance allows listeners to get a mental picture of the patient as a whole before going into the system-by-system details. In an ideal world, we ask every patient every question under the sun and closely examine every part of the body, but limited time and resources require clinicians to use their time with patients wisely. Noting a patient’s general appearance allows a clinician to be thoughtful and directed about each encounter, and developing this skill can be fun and gratifying. Perhaps I’ll see you this weekend at the De Young’s David Hockney exhibit.

Akshay Govind is a third-year resident in the Department of Oral and Maxillofacial Surgery.

Paying It Forward » FROM HOME PAGE After the quarter was over, I saw that the California Academy of Sciences was looking for new volunteer docents. After a few quick interviews, I was accepted into the program, given a huge binder of reading materials and enrolled in a series of training lectures. The lectures covered a wide range of topics, from the history of the Academy to how fossils are dated. Even with a science background, I learned a lot of new information, including ways to engage visitors in scientific conversations without being overbearing or over-boring.After the training, I was able to work on the floor as a docent. New docents are asked to volunteer for 10.5 hours per month (split into three shifts). During a shift, my duties include helping guests understand the exhibits and encouraging them to think about how they relate to the animal or information they are observing. Many docents refer to themselves as “interactive signs” that assist in making the museum more relatable. I claim I am there to make guests actively think, instead of mindlessly wandering around looking at dead things. Whether or not I actually accomplish this goal, or just annoy people, is an entirely different story. I would highly recommend the docent program to any creative individuals who have an interest in improving the way they teach to both scientists and non-scientists. Perks of being a volunteer docent include access to a tremendous community of nature enthusiasts with a lot of great life advice (most of them are retirees from quite successful careers), invites to all the fancy parties held at the Academy (as a guest, not a volunteer!) and a plethora of fun facts to impress your friends with. More information on being a docent and other volunteer opportunities at the Academy can be found under the “Get Involved” tab on the California Academy of Sciences website (

Erin Oswald is a third-year graduate student in the Biomedical Sciences.

UCSF and Quest Diagnostics, the world’s leading provider of diagnostic information services, have formed a collaboration to accelerate the translation of biomedical research into advanced diagnostics in the field of precision medicine, for improved patient care, treatment and outcomes. Initial clinical areas of focus include autism, oncology, neurology and women’s health. The collaboration, which combines the research discoveries and capabilities of UCSF with the national testing database and technical and clinical development capability of Quest Diagnostics, has an overarching aim of enabling holistic and integrated diagnostic solutions that close gaps in care or enable new clinical value.Under the terms of the agreement, scientists will jointly research, develop and validate diagnostic innovations to solve specific clinical problems and provide actionable information to improve patient care.

Research Shows How Household Dogs Protect Against Asthma, Infection Children’s risk for developing allergies and asthma is reduced when they are exposed in early infancy to a dog in the household, and now researchers have discovered a reason why. Exposure of mice to dust from houses where canine pets are permitted both indoors and outdoors can reshape the community of microbes that live in the mouse gut — collectively known as the gastrointestinal microbiome — and also diminish immune system reactivity to common allergens, according to a new study by researchers led by Susan Lynch, PhD, associate professor with the Division of Gastroenterology at UCSF, and Nicholas Lukacs, PhD, professor with the Department of Pathology at the University of Michigan. The scientists also identified a specific bacterial species within the gut that is critical to protecting the airways against both allergens and viral respiratory infection. The study, funded by the National Institute of Allergy and Infectious Diseases (NIAID), is published online in the Proceedings of the National Academy of Sciences (PNAS).

Stem Cells Used to Model Disease that Causes Abnormal Bone Growth Researchers have developed a new way to study bone disorders and bone growth, using stem cells from patients afflicted with a rare genetic bone disease. The approach, based on Nobel-Prize winning techniques, could help shed light on a disorder in which muscles and tendons progressively turn into bone. It also addresses a similar destructive process that afflicts a growing number of veterans who have suffered blast injuries — including traumatic amputations or injuries to the brain and nervous system. The disease model, described in a new study by a UCSF-led team, involves taking skin cells from patients with the bone disease, reprogramming them in a lab dish to their embryonic state, and deriving stem cells from them. Once the team derived the stem cells, they identified a cellular mechanism that drives abnormal bone growth in the thus far untreatable bone disease, called fibrodysplasiaossificans progressiva (FOP). Furthermore, they found that certain chemicals could slow abnormal bone growth in the stem cells, a discovery that might help guide future drug development.

4 | January 16, 2014 |

Come and see the results of biomedical research 1-2 February 2014

1-2 February 2014

The Moscone Center · San Francisco, California, USA


Technical Conference



BiOS Expo, 1 - 2 February 2014, is the world’s largest biomedical optics and biophotonics exhibition. Come walk the floor and see the latest technologies for your lab, clinic, or research project. The future of healthcare is on the floor at BiOS Expo.

Attend BiOS 2014, the world’s largest biomedical optics conference, and learn the latest results in bioscience, diagnostics and therapeutics, biophotonics, new imaging modalities, optical coherence tomography, neurophotonics, optogenetics, tissue optics, biomedical optics, biomedicine, and translational research. More than 2,000 presentation on the results of biomedical research.

Financing Life Sciences and Healthcare Ventures

Saturday Hot Topics · 7:00 to 9:00 pm

The Moscone Center, Room 130, Exhibit Level Saturday 1 February 2014 · 3:30 to 5:00 pm Panel Moderator Linda Smith Ceres Tech Advisors

Symposium Chairs James Fujimoto Massachusetts Institute of Technology (USA)

R. Rox Anderson, M.D. Wellman Center for Photomedicine, Massachusetts General Hospital and Harvard School of Medicine (USA)

Part of

SPIE Photonics West 2014 1–2 February 2014 SPIE Photonics West is the most influential conference for biophotonics and biomedical optics, highpower laser manufacturing, optoelectronics, and microfabrication.

· · · · · · ·

20,000 attendees 2 free exhibitions 1,225 exhibiting companies 4,600 technical sessions 17 plenary presentations 40 technical and networking events 70 courses, and more | January 16, 2014 | 5




Recent research by UCSF scientists By Taylor LaFlam Staff Writer

Photos courtesy of Fitness & Recreation Centers @ UCSF The Penetrators won the "6' and under" basketball title.

“He’s six feet, so that helps,” captain Chu best volleyball of the season and cruised said. “He might be 6’1 or 6’2, but every team to their fifth championship in six tries. in this league has at least one person pushing “Every team that we’ve played has said the limits.” we’re very consistent,” said first-time captain Finally, the champions of the Monday in- Koga. “Without good team passing and determediate basketball league were the Threat fense, our hitting and offense wouldn’t be as Matrix, led by captain Christopher Knight. effective.” The volleyball league at Parnassus was won by Joyce Lin, Kristen Honma, Helen Lam, Carl Arevalo, Alvin Woo and Brian Koga, who collectively made up the Giant Warriors, a team of former pharmacy students and nonUCSF affiliates. The Giant Warriors are the volleyball league champions. They entered the playoffs with a 6-1 record, havTeam D2, featuring Zach Lee, Conrad ing lost only to the overall No. 1 seed, Two Drinkwater, Sean Silvereo, Randy Rosales, Dink Minimum, during the regular sea- Reina Kawazoe, Ricardo Jara, Fernando Varson. But once they were in the playoffs, the gas and Ricardo Vargas, took home the title Warriors, whose core has been together in the futsal recreational league. It was the since 2008, found themselves playing their group’s fourth consecutive championship, according to captain Ricardo Vargas. “We tend to slack a bit in the beginning of the season and then turn it on and really click as a team toward the end of the season and during playoffs,” he said.

Team D2 are the champions of the futsal recreational league for the fourth consecutive time.

Dennis Zheng is a first-year medical student.

BIOCHEMISTRY: Heat shock transcription factor σ³² co-opts the signal recognition particle to regulate protein homeostasis in E. coli. Lim, B., et al. (Gross). PLoS Biol. 2013. 11(12):e1001735. Stressful conditions that threaten protein stability, such as a rapid increase in temperature, lead to activation of the heat shock response (HSR), which features increased expression of proteins such as chaperones, which help other proteins fold. In E. coli, the protein σ³² plays a critical role in the HSR by targeting RNA polymerase to HSR genes. Although many aspects of the regulation of σ³² have been determined, questions remain, including over the role of an essential piece of σ³² and how σ³² regulates intramembrane proteins. In this report, members of the Gross laboratory answered both questions. They showed that the signal recognition particle and its receptor, previously known to direct proteins to the plasma membrane, regulate σ³². The signal recognition particle binds σ³² and leads it to the membrane, allowing for it to respond to membrane-associated triggers. CELL SIGNALING: Cytoneme-mediated contact-dependent transport of the Drosophila decapentaplegic signaling protein. Roy, S., Huang, H., Liu, S., Kornberg, T.B. Science. 2014 Jan 2. [Epub ahead of print] More than a decade ago, the Kornberg lab observed thin, lengthy projections of certain cells of the developing fruit fly wing that extended towards cells that produce factors regulating their development. They hypothesized that these projections, which they called cytonemes, were important for this regulation. In this paper, researchers presented data supporting this hypothesis, showing the transfer of an important signaling protein, Dpp, from the producing cell to the cytoneme and transport of Dpp back along the cytoneme. They further showed that several mutations that interfere with cytoneme development also result in disruptions in Dpp signaling. Cytonemes have been observed in a variety of cell types in various species, and the authors suggest cytonemes may facilitate cell-cell communication in many settings. ONCOLOGY: Mutational analysis reveals the origin and therapy-driven evolution of recurrent glioma. Johnson, B.E., Mazor, T., et al. (Costello). Science. 2014. 343(6167):189-193. Tumors show both genetic heterogeneity and evolution. Previous research has explored this in hematological malignancies and solid tumor metastases but not in local recurrence in the brain. In this study, the authors compared the exomes (the expressed portion of the genome) of low-grade gliomas and their eventual recurrences. These included some tumors from patients treated with temozolomide (TMZ), a chemotherapeutic that is a known mutagen. Surprisingly, they found that in nearly half of 23 cases, at least half of the mutations observed in the initial tumor were absent in the recurrence, suggesting that the originating cell of the recurrence originated early in the tumor’s evolution. They also found that the recurrences of patients treated with TMZ showed evidence of TMZ-induced mutagenesis and an alternative path to becoming high-grade tumors. NEUROSCIENCE: Mutant LRRK2 toxicity in neurons depends on LRRK2 levels and synuclein but not kinase activity or inclusion bodies. Skibinski, G., Nakamura, K., Cookson, M.R., Finkbeiner, S. J Neurosci. 2014. 34(2):418-433. Most instances of Parkinson’s disease have no identifiable cause, but a minority are genetic, most commonly from mutations in leucine-rich repeat kinase 2 (LRRK2). The prevailing explanation for disease in these patients has been that mutant LRRK2 is toxic through its increased activity and aggregation into inclusion bodies. In this paper, the authors challenged this hypothesis. They used a microscope that allows the tracking of thousands of individual neurons to monitor over time neurons induced from cells from human patients and rats with mutant LRRK2. They found that inhibition of LRRK2 kinase activity appears to prevent toxicity to a degree that corresponds with the degree of reduction in the amount of LRRK2 protein present. They also unexpectedly found that reducing α-synuclein, another protein associated with Parkinson’s disease, decreased LRR2-mediated toxicity.

Taylor LaFlam is a fifth-year MSTP student. For comments or paper suggestions, email Taylor.

FOOD 6 | January 16, 2014 |

The Best Coffee — Home Brew Edition By Yi Lu Editor


ack in my high school, making coffee was simple. I had a small Mr. Coffee machine on the far corner of my desk, a gallon of generic bottled water under my chair and a bag of Maxwell Blend in my middle drawer. This setup ensured that didn’t even have to get out of my chair to make myself a cup of coffee, a convenience that may have played a role in my four-cup-a-day habit, which I am still recovering from. To my credit, high school was also the time when I stopped adding milk and sugar to my coffee, although this was entirely due to laziness, rather than my refined tastes. Why get out of your chair to get milk from the fridge when you can just drink your coffee straight from the carafe? Now that I’m living in San Francisco, I’ve noticed that there are two topics of conversation that will inevitably pop up as party conversation starters and awkward first-date fillers. The first is to complain about how expensive it is to live in San Francisco. “You think your place is expensive? My friend’s friend pays $2,000 a month to live in an outhouse in the Marina!”

The second is to talk about the obsession to find the “best of ” in The City: the best ice cream, the best breakfast pastry, the best notary public/bar mitzvah promoter. In the quest to find the best coffee in San Francisco, I couldn’t ignore the burgeoning interest among the city’s elite (the big three — Mission unicyclists, English majors now working for tech companies and Tendernob gentrifiers) to make that perfect cup of coffee at home. I completely sympathize — if I’m paying $30 a pound for organic fair-trade single- origin coffee made in a women’s co-op in Guatemala, I’m sure as Fell Street not going to be using my Mr. Coffee. But with the glut of different methods, from the swirl-and-chug to the $11,000 Clover Coffee machine, what’s a discerning coffeelitist to do? This column is devoted to my exhaustive quest to determine the best way to prepare coffee at home. I decided to test three different methods: the French Press, the Hario V60 and the Chemex. For those of you not among the coffee 1 percent, the Hario V60 is a cone used for pour-over coffee that has become the Ford Model T among San Francisco’s sizable population of young bourgeois coffee snobs.

Photo by Yi Lu/MS2 The tools of the trade. Top right: French press. Middle right: Hario V60. Bottom right: Chemex.

The Chemex is a popular alternative, an hour-glass-shaped contraption that can double as an Erlenmeyer flask in a pinch. Because money is short (this ain’t the New York Times circa 1960), I only had the opportunity to test one type of coffee, so no promises on the applicability of these results if you’re not making a cup of Coava Kochere from the Coffee Commissary in Los Angeles. A short note on the methods — the coffee was precisely prepared according to the man-

ufacturer’s instructions and blind taste-tested in unadulterated form by three independent reviewers, who have a combined 50 years of coffee snobbery between them. The winner? Two of the reviewers chose the Hario V60 as their favorite, noting how the coffee retained most of the notes that the bag told us we should note. In addition, the coffee had a full-bodied flavor



starts with our scholarship.

Capt. Ana Morgan, M.D., HPSP Medical Recipient Brooke Army Medical Center, Texas

You can begin training for the career you’ve always dreamed of with financial assistance from the U.S. Army. Through the Health Professions Scholarship Program (HPSP)*, you could be eligible to receive a full tuition scholarship for an accredited medical program. The HPSP provides reimbursement for books, laboratory equipment and academic fees. You’ll also receive a sign-on bonus of $20,000 and a monthly stipend of $2,157. During breaks, you’ll have the opportunity to train alongside other members of our health care organization. To learn more, call (650)347-3967 or visit San Mateo Medical Recruiting Center 400 S. El Camino Real, STE 450 San Mateo, CA 94402 Email:

*Certain requirements and eligibility criteria apply. ©2013. Paid for by the United States Army. All rights reserved. Information subject to change. | January 16, 2014 | 7

PUZZLES The Weekly Crossword

ACROSS 1 High, pricewise 6 Clothed 12 Saharan sight 14 Pertaining to flight technology 16 Insatiable greed 17 Non-spiritual 18 Tiny amount 19 Carpenter's tool 21 Oklahoma tribe 22 Cold-shoulder 24 Send payment 26 Drops the ball 27 Open, as a bottle 29 ____ as rain 31 Hood's weapon 32 Spanish rice dish 34 Something to prove, in math 36 Lacking, in Lyon 38 Fork feature 39 Continent carver 42 Public standing 46 Mined find 47 Kind of address 49 Brake part 50 Pond dweller 52 Wrapped up 54 Mambo's Puente 55 Turnstile feeder 57 June birthstone 59 Young fellow 60 Flow out 62 Childish 64 Treatment plan 65 Nodded off 66 Humiliate 67 Struck with a patella




by Margie E. Burke 4













16 19

18 22


25 29




38 41



50 55

48 52






54 58







31 35













59 63


64 66


Copyright 2014 by The Puzzle Syndicate

DOWN 1 African plain 23 Modeler's wood 2 Slander 25 1992 film, "A 3 Place for a plug League of ____ 4 Sermon subject Own" 5 Indiana hoopster 28 Come in second 6 Old street 30 Office supply fixture 33 Japanese 7 Hail, to Caesar cartoons 8 Puerto ____ 35 Transplant a Week of 1/13/14 - 1/19/14 plant 9 Haul with tackle 10 Supersize, say 37 "Milk" star 11 Floor plan, e.g. 39 Ready for the dog show 12 Diner bottle 13 Emphatic refusal 40 Pipe problem 15 Colgate 41 Carnival alternative attraction 20 Give off 43 Draw on


44 Ready for the junkyard 45 Weathered away 46 Playful swimmer 48 ____ and bounds 51 Wrangler material 53 Plastered 56 Blow the whistle on 58 Boxer Spinks 61 Tetley product 63 Seafood delicacy

Home Brew » FROM PAGE 6

Edited by Margie E. Burke

Difficulty : Medium

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HOW TO SOLVE:         (Answer appears elsewhere in this issue)

Copyright 2014 by The Puzzle Syndicate

Photo by Yi Lu/MS2 Second-year medical students Eric Rider and Ethan Hua evaluate the three different brews.

that managed to hold up even as it cooled. The third reviewer chose the Chemex, noting its clean taste and its ability to accentuate the acidity of the brew without making it overpowering. The French press ended up last in our rankings, a surprise to one of the reviewers, who exclusively prepares coffee using this method. While the French press produced the fullest body, the bitterness overwhelmed the notes of the beans and became even more pronounced as the cup cooled, which didn’t do it any favors. For those of you interested in following along at home, I should note that coffee snobbery doesn’t come cheap. A three-cup Chemex will run you $34, while a four-cup Bodum French press will set you back $38.

Piled Higher  and  Deeper  by  Jorge  Cham

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Solution to Sudoku

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The Hario V60 is the cheapest among the options, costing about $20 for a ceramic or glass model. Of course, any self-respecting member of the coffeegentsia would not be caught dead pouring out hot water out of any old kettle, so make sure to set aside $48 for the Hario Buono water kettle, with its swan-neck design, which maximizes control over the pour when using the Chemex or V60. Finally, don’t even think about using regular filters from Costco — both Hario and Chemex produce filters specifically for their products. Sounds like too much? Would you rather eyeball your coffee grounds than pull out your calibrated kitchen scale to maintain that 1 gram:16 millileters coffee-to-water ratio? Have you decided that paying $100 for coffee equipment isn’t the best use of your student loans? After rereading this column, I don’t blame you.

Yi Lu is a second-year medical student.

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Parnassus Poets St. John's blue scrubs, bowed heads, hands hold offerings for the sick atheists and faithful alike Muni train rattles stained glass light falls on the Virgin of Guadalupe ~ Sarah Paris title: "Taking  stock"  -­  originally  published  12/16/2013

8 | January 16, 2014 |


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Solution to Sudoku

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Synapse (01.16.14)  

Volume 58, Number 15

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