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Department of Biochemistry and Cell Biology Annual Newsletter 2013 Frogs of the species Xenopus tropicalis are being used for studies of vertebrate embryonic development in Dr. Jerry Thomsen’s lab (Nakayama et al 2013, Genesis 51:835-843). The origin recognition complex protein "machine” (ORC, yellow), already activated by a DNA replication initiation factor (Cdc6, brown), grabs onto the helicase core (Mcm2-7, purple blue) to load the helicase ring onto the DNA double helix (red). The atomic structure of DNA is modeled on the top and bottom of the cryo-EM 3D structure. This helicaseloading intermediate was captured in vitro by using a slowly hydrolyzable ATP analog (ATP-gamma-S). (Sun et al, NSMB, 2013). (From Dr Huilin Li’s lab) Department of Biochemistry & Cell Biology Annual Newsletter 2013 2013 News & Photos Research collaborators from Stony Brook’s Institute for Chemical Biology & Drug Discovery (ICB&DD) with Benjamin S. Hsiao, PhD, Vice

President for Research at Stony Brook University (second from right). Pictured from left: Robert Rizzo, Iwao Ojima, Dale Deutsch, Martin Kaczocha, and Huilin Li. Not pictured are Stony Brook team members Bill Berger, Brian Ralph, Trent Balius, William Joseph, and Samir Haj-Dahmane of The University of Buffalo. http://medicinestonybrookmedicineedu/newsroom/nida-grant FACULTY HONOR WALL DEDICATION The new Faculty Wall of Honor located in the Melville Library acknowledges the following distinguished faculty in 2013: Drs. Vitaly Citovsky, Rolf Sternglanz, William Lennarz and Masayori Inouye (a former Chairman of the Department). They were honored by Stony Brook University in 2013 and had their names placed on the Faculty Honor Wall located at the Melville Library. Congratulations to Vitaly, Rolf, Bill and Masayori on this honor. STUDENTS IN THE NEWS Samuel Katz – Biochemistry major, Samuel Katz, was awarded a 2013 Fulbright Scholarship and traveled to Germany during the Fall of 2013 to

conduct research on direct cellular reprogramming at the Berlin Institute for Medical Systems Biology. Samuel’s past accomplishments also include research (later published in the Journal of Immunology) under the mentorship of Dr. Bethany Moore at the University of Michigan. Samuel plans to apply to PhD programs after returning to the United States after completing his Fulbright Scholarship year. Brian Ralph – Working for Dale Deutsch’s lab since his freshman year, Brian Ralph, a member of the Honors College and a junior Biology major (with a focus in Quantitative Biology and Bioinformatics) has co-authored a paper in PLOS ONE entitled, “Targeting Fatty Acid Binding Protein (FABP) Anandamide Transporters – A Novel Strategy for Development of AntiInflammatory and Anti-Nociceptive Drugs.” You can read more at http://medicinestonybrookmedicineedu/newsroom/nidagrant Christina Roman - Biochemistry major, Christina Roman, has been working in Dr. Ed Luk’s lab since February 2012

and recently had a 2nd opportunity to attend the Annual Biomedical Research Conference for Minority Students in Nashville. Christina’s research has been funded and supported by URECA and the Minority Access to Research Careers (MARC) program. Christina has an interest in epigenetics and is planning to look for a post-baccalaureate program or research assistant position in the coming year, and then has plans to apply to PhD programs in 2015. Student Recipients of the John Dunn Award for Excellence in Life Sciences – 2013: Brian McGillick, Biochemistry & Structural Biology 3rd Year MD/PhD student; Samema Sarowar, Biochemistry & Structural Biology 3rd Year PhD student. PHOTOS Dr. Yusuf Hannun with Dr Michael Airola. 3 Dr. Ed Luk (top center) and Lab members (left to right), Lu Sun, Michael Tramantano, Karole D’Orazio, Won Kyun Koh. Department of Biochemistry & Cell Biology Annual Newsletter 2013 Center for Science and Mathematics Education (CESAME) The Center

for Science and Mathematics Education (CESAME), which is housed in the Biochemistry Department, was founded by David Bynum in 2007, and has grown to become a national leader in STEM education research, teacher education, and community outreach. CESAME has been an incubator of innovative, interdisciplinary STEM education collaborations with the university and its surrounding communities. CESAME is now directed by Biochemistry and Cell Biology faculty member Keith Sheppard CESAME has made notable contributions to STEM teaching, research, and policy at the university since 2007 including: • • • • Generating over $ 7.5M in external grant funding Hiring three new tenure-track faculty members (Keith Sheppard, Angela Kelly and Ross Nehm) who collectively produce substantial amounts of high-impact discipline-based science education research; additionally, there are 10 affiliated faculty members in 8 STEM departments, 4 instructors and 3 administrative staff. Creating a Ph.D Program

in Science Education in 2010, which currently enrolls 35 students Doctoral courses were offered at Stony Brook Manhattan for the first time this year. Faculty are active in state and national STEM educational policy activities, serving on editorial boards, writing policy statements, serving on advisory panels, meeting with key state leadership staff, and testifying at state-level education commissions. CESAME is a major provider of high quality STEM Teacher Education: • • • Offering a full complement of B.S and MAT programs in all STEM education fields and is one of the major producers of STEM teachers in the state. Developing 24 graduate courses, of which 21 are currently active, and 7 undergraduate courses. CESAME recently became the regional hub for the New York State Science and Mathematics Master Teacher program CESAME is a leading provider of high quality STEM outreach and student support: • • • • • CESAME has awarded $4.4M in fellowships and scholarships to

post-doctoral, graduate, undergraduate, and high school students who have been actively involved in research or teaching in STEM disciplines. Over 5,500 students attend our Teaching Labs annually; 85% of Long Island school districts have participated. Labs are offered in biology, geoscience, chemistry, sustainable chemistry and physics Summer camps are offered in all disciplines of sciences, mathematics, and engineering. CESAME sponsors Science Open Nights for the public and the annual Celebration of Undergraduate Research and Creative Activity. CESAME has established research and professional development partnerships with the wider scientific community at Cold Spring Harbor Laboratories, Brookhaven National Laboratories, STEM Hub, American Museum of Natural History New York Botanical Garden, as well as NYS schools and community colleges. CESAME annually hosts the Protein Modeling Challenge for regional high schools and also North American Computational Linguistics Olympiad. 4

Department of Biochemistry & Cell Biology Annual Newsletter 2013 Master of Science Graduate Program BCB 2013 marked the fourth year of the Biochemistry and Cell Biology MS program, which continues to flourish. Our mission is to provide students with a rigorous theoretical foundation of biochemistry, cell and molecular biology, and the research skills necessary for academic, medical, or biotechnical research careers. We congratulate eight of our students that graduated this year. These students are all on track toward attaining their career goals. Two are going to medical school, three to PhD programs, one back to practicing law, and two will be moving toward the biotechnology sector. This year’s incoming 2013 class of fourteen students promises to be equally successful. All of these incoming students have been placed in outstanding labs of their choosing here at Stony Brook, as well as at Brookhaven National Laboratory and Cold Spring Harbor. The enthusiasm of top-notch

research labs to recruit and train our BCB MS students is a testament to the success of the program and the quality of the students who have been part of it. We congratulate Moises Guardado, Steven Tsotras, and Jinelle Wint, who were each awarded a prestigious National Science Foundation Bridges to Doctorate Fellowship. This award provides a $30,000 annual stipend for two years. We applaud their success in obtaining this fellowship, which will provide an opportunity to achieve their academic goals of continuing studies toward a doctorate program. We hope their achievements will help our efforts to recruit more outstanding underrepresented minority students who are considering advancing their careers in Biochemistry and Cell Biology. BCB MS INCOMING CLASS OF 2013 BCB MS incoming class of 2013: Standing from left to right: Qian Zhang, Pal Jai Inder, Benjamin Rajan, Amanda Russo, Leili Sarrafha, Iva Chitrakar, Laura Dougherty, Jonathan Wyrick, Jinelle Wint, Robert Policastro, Rohan

Ramakrishna, (seated) Kamilla Hussein and Matthew Murray. 5 Neta Dean, Program Director Department of Biochemistry & Cell Biology Annual Newsletter 2013 PhD Program BSB AND MCB The Molecular and Cellular Biology (MCB) and Biochemistry and Structural Biology (BSB) programs continue to prosper. Erwin London started his seventh year as Director of BSB, while Wali Karzai started his second year in MCB. In the Fall 2013 class, we had eight new students entering the MCB program and six new students entering the BSB program. The first group of students was chosen to participate in the newly expanded MCB-BSB training grant. The training grant students for 2013-2014 are MCB students Hana Goto, Anthony Rampello and Beth Harvey and BSB students Raymond Suhandyata and Samema Sarowar. This Year’s Student Invited seminar, organized by Mike Tramantano and Neha Puri, included speaker Frank Pugh (Willaman Chair in Molecular Biology and Professor of Biochemistry and Molecular Biology).

The MCB program inaugurated its annual second year symposium in June 2013 at the Hilton Garden Inn. Students were given their opportunity to showcase the research work to their colleagues and MCB program faculty. Wali Karzai, MCB Program Director & Erwin London, BSB Program Director MCB-BSB RETREAT The annual MCB-BSB retreat was held in October at the very scenic Lombardi’s on the Sound. New MCB and BSB faculty were invited to speak and present their work. Speakers included Ando van der Velden, Sasha Levy, Liang Gao, Jarrod French, David Matus, and Martin Kaczocha (previous MCB student who is now Assistant Professor in the Department of Anesthesiology). All 4th and 5th year students presented their posters, which generated much interest among the attendees. Best poster awards at the retreat were given to Jennifer DeLeon and Junwei Shi. Students Nadia Jaber, Samema Sarowar, and Angad Garg received awards for outstanding service in the MCB and BSB graduate programs. Andrew

Fesler, Mike Tramantano, Evelyn Prugar. Dr. Sasha Levy Achraf Shamseddine, Benjamin Newcomb, Justin Snider, Mohamad Adada, Chih-Li Lin, Jae Kyo Yi. 6 Department of Biochemistry & Cell Biology ! 7 Annual Newsletter 2013 Department of Biochemistry & Cell Biology Annual Newsletter 2013 FACULTY UPDATES & NEWS VITALY CITOVSKY Vitaly Citovsky received the F1000 Faculty Member of the Year Award, and his name was inscribed on the Faculty Honor Wall in Melville Library. Vitaly was a recipient of competitive continuation grants from the US Department of Agriculture/National Institute of Food and Agriculture (USDA/NIFA) and from the US-Israel Binational Agricultural Research and Development Fund (BARD), and an administrative supplement from NIH/NIGMS, and he continues to be funded by NIH/NIGMS, NSF, and US-Israel Binational Science Foundation (BSF). Vitaly Citovsky joined the Editorial Board of Scientific Reports by Nature Publishing Group, and continues to serve on

Editorial Boards of F1000 Research, Virology, Plant Physiology, Frontiers in Plant-Microbe Interactions, Frontiers in Plant Physiology, Plant Signaling & Behavior, Communicative and Integrative Biology, The Open Plant Science Journal, and Gene Regulation and Systems Biology, and is a member of the Cell Biology section of Faculty 1000 Biology. Finally, Vitaly Citovsky co-organized International Conference “Plant Transformation Technologies III“ to be held in February 12-15, 2014 in Vienna, Austria. OUTREACH SEMINAR: Seminar at the Biology Colloquium Series, Millersville University, PA Lab members include undergraduate students: Dianyi Liu, Vishwaja Muppa, Harleen Singh, Kevin Singh, Abe Williams, Gyeongsuk Yu and Graduate student Lisa King. Lab Postdocs include Elena Garcia-Cano, Ido Keren, Benoit Lacroix, Renhong Wu, Cheng Yuan, and Research Assistant Professor Adi Zaltsman. Sabbatical faculty include: Yedidya Gafni (Volcani Institute, Israel), Sondra Lazarowitz (Cornell

University, Ithaca, NY), Xianchao Sun (Southwest University, Chongqing, China). KEVIN CZAPLINSKI Kevin Czaplinski’s Ph.D, student John R Sinnamon (Program in Neuroscience) successfully defended his thesis in September Daniel Catt graduated with a Masters Degree from the Biochemistry and Cell Biology Masters program. Kevin received an NSF CAREER award for studies on the mechanism of mRNA trafficking in the cytoplasm and was invited to be a panelist for an NSF grant review panel as well. Kevin presented seminars of his lab’s research at the Hunter College Department of Biology and at the University of Albany to the Hudson Valley RNA club. Kevin’s lab published two manuscripts, the work described in one of these resulted in a new technology disclosure filing for the development of a new method for RNA fluorescence in situ hybridization (RNA-FISH). Kevin was invited to supply a review for the “Seminars in Cell and Molecular Biology” series for 2014. Undergraduate Ariana Levin

(SBU, Biology, 2014) was awarded a NYSTEM summer stem cell research fellowship for her work in the lab and received a URECA researcher of the month honor for March 2013. Undergraduate Cassandra Dix (SBU, Biochemistry 2015) joined the lab in the fall Clodagh Rose Czaplinski joined the family in May. DALE DEUTSCH Dale Deutsch was the PI on a 5 year 3.7 million dollar NIH grant for the discovery of drugs that raise "the natural THC levels (marijuana)" levels in the body. The grant involved investigators from Chemistry, Applied Math, Biochemistry, and Anesthesiology Dale is particularly happy that one of his former students, Martin Kaczocha, was appointed as an assistant professor in Anesthesiology at Stony Brook Medicine and that he will be collaborating on this new grant. Another student, Brian Ralph received a scholarship for his research over the summer. Although he is an undergraduate, he has taken graduate courses in computational biology and according to the instructors,

is an A student. JARROD FRENCH Although we have encountered many challenges setting up a new lab, this process has been significantly facilitated by the tremendous outpouring of support and guidance provided by the office staff and all of the faculty members in the department. The construction in the French lab is nearing completion and we will soon be able to occupy our new space. Equipment purchases continue as the halls throughout the department fill with fridges and incubators that will end up in the lab. We have been fortunate to be able to utilize the space previously occupied by the Lennarz lab in order to begin some experiments in the interim. Two new graduate students from the Chemistry department (Yue Yin and Weijie Zhou) have joined the lab and will be working together to characterize the structure and function of the first three enzymes involved in the human de novo purine biosynthetic pathway and the role that they play in the purinosome. In addition, Weijie will be

helping with a longstanding collaboration with an engineering group at Penn State to optimize an acoustic device that is used to manipulate tiny protein crystals. We also have a Masters student joining us (Ben Rajan) who will be working to understand how a short isoform of the enzyme adenylosuccinate lyase may mediate the interaction between purinosomes and mitochondria. It is an exciting time as we begin our first experiments and look forward to many exciting breakthroughs 8 Department of Biochemistry & Cell Biology ! Annual Newsletter 2013 "#$%&(!%)*#+,!-!.+/,! STEVEN GLYNN Steven Glynn’s lab welcomed 2 new graduate students in 2013; Anthony Rampello (MCB) and Bojian Ding (BSB). Faiza Sheikh became the first student to graduate from the lab in the BCB Masters Program. ROBERT HALTIWANGER Bob continues to serve as Chair of the Department of Biochemistry and Cell Biology and is very excited about the continued growth of the Department! Together with Dr. Peter

Tonge (Chemistry), he serves as co-chair of the search committee for the Biomolecular Imaging Cluster. This is three-year initiative to hire 5 faculty, two of whom were hired last year (Jarrod French and Liang Gao, both joint hires with Chemistry). The search continues this year Bob also continues as Editor-in-Chief for the journal, Glycobiology, and serves on the Board of Directors for the Society for Glycobiology. Bob organized the Institute for Chemical Biology and Drug Discovery (ICB&DD) Symposium in October with the theme, “Frontiers in Glycosciences and Chemical Biology”, with a number of world-class glycobiologists. The symposium was very well received Bob’s NIH grant on the O-Glycosylation of Epidermal Growth Factor-like Motifs was renewed for another four years. Bob was invited to speak at the ASBMB meeting in Boston, the Eppley Short Course in Cancer Biology at the Eppley Institute in Omaha, Nebraska, the Notch Meeting in Athens, Greece, the annual Society for

Glycobiology meeting in St. Petersburg, Florida, and the Complex Carbohydrate Research Center at the University of Georgia in Athens, Georgia. Deepika Vasudevan successfully defended her doctoral dissertation entitled, “A Role for O-Fucosylation in the folding of Thrombospondin Type-1 Repeats”, and Usman Aslam successfully defended his Master’s thesis entitled, “Does Lunatic Fringe modify itself?” Two high school students, Justin Cooper and Caroline Miller, both from Ward Melville High School, worked with Beth Harvey during the summer on the glycosylation of Drosophila Notch. YUSUF HANNUN From Stony Brook News: “Stony Brook University Cancer Center Director Yusuf A. Hannun, MD, received the Kuwait Prize in the category of Basic Sciences for 2012. Dr Hannun, a native of Jordan, received the honor for his research on a class of lipids implicated in the cancer disease process. An internationally recognized cancer researcher and physician-scientist, Dr Hannun is also the Vice

Dean for Cancer Medicine and Joel Kenny Professor of Medicine at Stony Brook. For the past 30 years, he has investigated how lipid metabolites serve as regulators of cell function. Dr Hannun and colleagues discovered that a specific class of lipids, called bioactive sphingolipids, plays a vital role in the development of cancer and in other human disease processes, such as neurodegeneration, inflammation, diabetes and infectious diseases. The KFAS awarded the Kuwait Prize to Dr Hannun for his entire research effort on bioactive sphingolipids, and because discoveries from his laboratory have advanced basic science research in the area of molecular biology. Lab members are Michael Airola, Daniel Canals, Christopher Clarke, Monica Garcia-Barros, Nabil Matmati, Masayuki Wada, Nicolas Coant, Nadia Rana, Janet Allopenna, Mengling Liu, Benjamin J. Newcomb, Achraf Ali Shamseddine, Justin Snider, Vinodh Rajagopalan, Saroja Kolluru, Nara Jeong, Joseph Jacob, Ashwin Kelkar, Baasil Sharif, Noemi

Jimenez, Diana Choe, Eunmi Jeong, John Mendis. You can read more about Dr Hannun at: http://sbccstonybrookedu/news/medical/131218hannunphp BERNADETTE HOLDENER Bernadette continues to study mouse mutations that disrupt gastrulation, and has established a successful collaboration with Dr. Robert Haltiwanger at SBU and Dr. Suneel Apte at the Cleveland Clinic to investigate the role of O-fucose modification on mesoderm differentiation. Bernadette served on the Biochemistry and Cell Biology Executive committee, is assisting the Director of Undergraduate Biochemistry Majors, and served as a reviewer for several journals. Lance Lee, a former PhD student in the lab and now assistant professor at the Stanford School of Medicine of the University of South Dakota was part of a team that obtained a NIH COBRE grant that will fund five labs and three core facilities in the under-funded state of South Dakota. Andrew Taibi, former MS student in the lab, has moved to the University of Utah, where he

is completing his first semester of a PhD program in Molecular biology. A portion of his thesis work was recently published in PlosOne 9 Department of Biochemistry & Cell Biology Annual Newsletter 2013 FACULTY UPDATES & NEWS NANCY HOLLINGSWORTH Nancy Hollingsworth gave seminars at the Wesleyan University in Middletown, CT and the Institut Curie in Paris, France. In addition, she presented a talk at the EMBO Meiosis Conference in Dresden, Germany and at the New York Academy of Sciences sponsored Genome Integrity in Manhattan, New York. She was a co-organizer of the “Symposium for Rolf Sternglanz” which was held to celebrate Rolf’s illustrious scientific career. Nancy continues to serve as an Associate Editor for Genetics and has also acted as a Guest Editor for PLoS Genetics. Ezra Margono, who received an Honors Thesis in Biochemistry based on experiments he did in the Hollingsworth lab was the recipient of the Irwin Oster Award in Genetics. Ezra is currently doing

research in a lab at the National Institute of Health. Nancy was very fortunate in that the competitive renewal of her NIH grant was funded Nancy’s lab members include graduate students Matt Murray (BCB Master’s student), Evelyn Prugar (PhD student), Ray Suhandynata (PhD student), postdocs Tracy Callendar and Xiangyu Chen, undergraduates David Chen and Min Jung and lab technician Allison Marullo. SASHA LEVY Sasha Levy develops technologies using random DNA barcodes and next-generation sequencing to simultaneously study the behavior of millions of small lineages in large cell populations. He uses these tools to understand how cell populations, such as microbial pathogens or cancer, evolve; how environmental fluctuations shape evolutionary strategies; how genetic and protein-protein interaction networks change across environments; and how genetic architecture constrains the adaptive process. Sasha is a Marsha Laufer Endowed Assistant Professor of Quantitative and Physical Biology

and an Assistant Professor in the Department of Biochemistry and Cellular Biology. HUILIN LI In September 2013, Huilin presented a platform talk at the biannual CSHL meeting on EUKARYOTIC DNA REPLICATION & GENOME MAINTENANCE. He presented the group’s cryo-EM research on several yeast DNA replication initiation complexes This is a collaborative work with Dr. Bruce Stillman at CSHL and Dr Christian Speck at UK MRC Clinical Sciences Center The cryo-EM work was done by Dr. Jingchuan Sun, a talented research scientist in the group The group was very happy to see that one of Jingchuans cryo-EM structures was featured on the cover of the abstract book of the 2013 replication meeting. 2013 was also a good year for Samema Sarowar, a third year graduate student. Samema successfully defended her thesis proposal and won the inaugural "John Dunn Award for Excellence in Life Sciences”, a Stony Brook graduate school award presented to excellent graduate students doing thesis research at

BNL. She also won the best poster award at the 2013 Young Investigator Symposium organized by Brookhaven National Laboratory. Lab members are undergraduate student Shuanglu Zhang, MS student Won Kyun Koh (BCB program; co-advised by Huilin and Ed Luk), Ph.D student Samema Sarowar (BSB program), rotation student Zuanning Yuan (BSB), postdoctoral scholars Lin Bai, Tong Wang, Shaoqing Yang, and Hongjun Yu, and research scientists Hao-Chi Hsu and Jingchuan Sun. ERWIN LONDON Erwin London presented seminars at the Membrane Structure and Assembly Subgroup meeting during the Biophysical Society annual meeting, Philadelphia, PA. Feb 2013, at Indiana University Purdue University Indianapolis (IUPUI) Indianapolis, IN, Depts of Chemistry and Physics, April 2013, and gave an informal talk at Oak Ridge National Laboratory, Oak Ridge TN, April 2013. Erwin continues to serve as the Director of the Biochemistry and Structural Biology Graduate Program, as a member of the Editorial Advisory Board for the

journal Biochemistry and as a member of the Editorial Board for the Journal of Membrane Biology. He also continues to be a member of the Postdoctoral Fellowship Award Committee for the Life Sciences Research Foundation. An article published at the end of 2012 on the topic of “Acyl chain length and saturation modulate interleaflet coupling in asymmetric bilayers: effects on dynamics and structural order” with former postdoc Dr. Salvatore Chiantia was discussed as a “New and Notable” article in Biophys. J (Dec 19, 2012) and in “Research Highlights” in Nature Chemical Biology (Feb 2013) It was also selected as a notable article on the Faculty of 1000 site. Lab members at the end of 2013 included postdoctoral scientists Guangtao Li, Mi Jin Son, Qingging Lin (the latter two recent Ph.D graduates from the lab); PhD students were JiHyun Kim, James LeBarron and Zhen Huang. Zhen Huang, who carried out MS degree research in the lab, received her MS degree from the Chemistry Dept this

year 10 Department of Biochemistry & Cell Biology Annual Newsletter 2013 FACULTY UPDATES & NEWS ED LUK Ed Luk welcomes Lu Sun to join his laboratory. Lu is a second year MCB student and is working on a project studying how histone modifiers and chromatin remodelers remove histones from promoters to facilitate the assembly of the transcription machinery. Michael Tramantano is now a third-year MCB student in Ed’s lab. Mike has made great progress with his research project He found that the transcription machinery is playing an active role in ejecting histones from the promoters in preparation for transcription. His abstract was selected for a poster presentation at the Keystone Conference on Transcription in New Mexico in February 2014. Karole D’Orazio finished her thesis project and graduated with a Master’s degree from the BCB program. In December, Karole joined Elissa Lei’s laboratory at the NIH to study chromatin regulation in flies. Lihong Wan, a postdoctoral

fellow in the Luk Lab, is working on a project to elucidate the structure of a chromatin remodeling enzyme. In collaboration with Won Kyun Koh and Jingchuan Sun in Huilin Li’s laboratory, they have generated 3-D images that will ultimately help reveal the molecular function of this enzyme. Finally, Ed received an R01 project research grant from the NIGMS and was invited to give a seminar at the Cell Biology of Yeast Meeting at Cold Spring Harbor in November. Undergraduate Program News: Christina Roman was selected to the Exceptional Research Opportunities Program (EXROP) funded by the Howard Hughes Medical Institute and conducted a summer research project in Cynthia Wolberger’s Laboratory at Johns Hopkins University. In the Wolberger lab, she studied the structure and function of Sirtuins In the Fall, she returned to Stony Brook and restarted her honors thesis project in the Luk lab. She will continue to study how a chromatin remodeling enzyme modulates the stability of

nucleosomes. Currently, she is purifying a component of the chromatin remodeling enzyme. She wants to apply X-ray crystallography, which she learned in the Wolberger lab, to study the structure of this protein. HARVARD LYMAN Harvey Lyman continues as the Director of Undergraduate Studies for the Biochemistry Department, Chair of the Faculty Committee on Health Professions, Member of the Admissions Committee of the Stony Brook University School of Medicine, Co-Director of the Post Baccalaureate Pre-Health Program and an elected member of the Council of the School of Professional Development. In the lab, Malak Hamade graduated and entered the Stony Brook School of Medicine, and Hamna Zafar graduated and entered medical school. Ann Job and Earvine Eugene continue in the lab looking at the regulation of phototaxis. Their work is aided by two new Motic cameras, which allow rapid recording and analysis of phototaxis. Professor Lyman was awarded the 2013-2014 Chancellor’s Award for

Excellence in Faculty Service. KEN MARCU Ken Marcu continues to work with his colleagues and collaborators at Stony Brook and several other institutions in Europe and the States on the impact of NF-kappaB signaling in different disease-related settings. Together with his colleagues at The Hospital for Special Surgery in Manhattan and the Rizzoli Orthopedic Research Institute (Bologna, Italy), Ken continues to work on deciphering the functional and mechanistic roles of IKKbeta and IKKalpha in the onset and progression of osteoarthritic (OA) disease employing primary human OA derived articular chondrocytes and mice harboring articular cartilage specific inducible IKK KO genes. With his colleagues Dr. Vangelis Kolettas (Forth Basic Research Institute, Ioannina Medical School, Ioannina, Greece) and Dr Apostolos Klinakis (Biomedical Research Foundation Academy, Athens, Greece), Ken has generated lung epithelial cell inducible IKK KO mice to begin to decipher the intrinsic functional roles

of IKKalpha and IKKbeta in lung cancer models. With his colleague Dr Roland Wolkowicz (Biological Sciences Dept. of San Diego State University), work is on-going to define the functional contributions of canonical NF- kappaB signaling in human hepatitis C virus infections. Together with Dr Richard Kew (Pathology Dept, Stony Brook), new work is planned (grants pending) to define the functional contributions of IKKalpha-dependent non-canonical NF-kappaB signaling in cell migration response to mediators of tissue damage. Ken gave a seminar at San Diego State University on his recent work on the kinase-independent functions of IKKalpha in human and murine primary chondrocyte differentiation towards terminal hypertrophy, and also became a PLOS ONE academic editor. 11 Department of Biochemistry & Cell Biology ! Annual Newsletter 2013 "#$%&(!%)*#+,!-!.+/,! BEN MARTIN The Martin Lab continued to grow in 2013. We welcomed PhD students Hana Goto (MCB) and Brian Kinney

(Genetics), master’s students Steve Tsotras and Lily Sarrafha (BCB), and research technician Neal Bhattacharji. They joined postdoctoral fellow Richard Row and undergraduate Sam Kimmey. Sam received an URECA-Biology Alumni Award that allowed his to spend the summer working in the lab, and Steve was awarded a Bridge to the Doctorate Fellowship. Ben was invited to present his research to the Department of Biological Sciences at St. John’s University The lab continues to study endothelial cell fate specification in the zebrafish embryo, funded by the American Heart Association. We have several other active projects examining neural/mesodermal fate decisions and stem cell maintenance during early embryogenesis. DAVID MATUS David joined the department and was happy to continue the funding on his Howard Temin Pathway to Independence career development award from the National Cancer Institute at the NIH, following the transition from post-doctoral researcher at Duke University to

Assistant Professor here at Stony Brook University. David uses a combination of evolutionary, cell and developmental biological approaches to understand how cells are programmed to invade through the basement membrane. This is a critical process that occurs during development, immune surveillance and is mis-regulated during cancer metastasis. The Matus lab uses the roundworm nematode, Caenorhabdtitis elegans, to examine cell invasive behavior utilizing high-resolution live cell imaging approaches combined with genetic and genomic analyses. Renovations on his new space are nearly complete on the fourth floor of the Life Sciences Building. He is looking forward to setting up the new lab and excited to begin training new students AARON NEIMAN Aaron Neimans lab continues to focus on spore formation in budding yeast as a model system of cellular differentiation. Aaron presented the labs recent work on the activity of the Vps13 protein at the Molecular Membrane Biology Gordon Conference.

Aaron also continues to oversee the University’s Microscopy Imaging Center core facility. The facility received NIH funding and University support this year that has allowed the acquisition of two new super-resolution microscopes. Two longtime members of the Neiman lab moved on this year. Chien Lam, a technician, left for Dental School at Temple University and Coney Lin, a graduate student in the BSB program, completed her Ph.D studies Coney has begun postdoctoral work at NIH Lab members include Jae-Sook Park (Research Scientist), Reuben Hoffman (grad student), Esma Ucisik-Akkaya (grad student), Sai Zhou (grad student, joint with Rolf Sternglanz), Liang Jin (grad student, joint with Rolf Sternglanz), Leor Needleman (technician), Robert Policastro (masters student), and Iqra Syed (undergraduate). STEVEN SMITH Steven Smith was an invited speaker at the Protein and Antibody Engineering Summit in Boston in April and at an NMR symposium at the National Magnet Laboratory in Tallahassee in

December. He continues as the Director of Structural Biology at Stony Brook Three Ph.D students (Darryl Aucoin, Tzu-Chun Tang and Yi Hu) graduated from his group in 2013 ROLF STERNGLANZ Rolf has been retired for more than a year now but he continues doing research with a small group and is an active participant in departmental activities. He co-directs two graduate students with Aaron Neiman as part of an NIH Program Project Grant on yeast meiosis. 12 Department of Biochemistry & Cell Biology ! Annual Newsletter 2013 "#$%&(!%)*#+,!-!.+/,! GERALD THOMSEN The Thomsen lab continues to pursue cellular and molecular mechanisms of early development and regeneration in the frog Xenopus and the sea anemone Nematostella vectensis. We also have branched out a bit to investigate a new regulator of signaling in breast cancer cells, supported by a grant from the Carol Baldwin Foundation. We published our first sea anemone regeneration paper this year, and the “we” are

Research Scientist Pat Bossert and Postdoctoral Fellow Matt Dunn (along with Dr. T) The paper was published and featured on the cover of the journal Developmental Dynamics. On the Xenopus side of things, we collaborated with Rob Grainger’s lab to show one of the first applications in Xenopus of a mutagenesis technique called CRISPRCas, and published a paper in the journal Genesis, which also was featured as a cover story (the “we” in this case are graduate student Jamina Oomen-Hajagos and Dr. T, with longtime colleagues Dr Rob Grainger and Dr Takuya Nakagawa, and their associates at the University of Virginia) Jerry published his first scientific paper with Rob Grainger back in 1983 (“been a while”). Lab members also have a couple of papers submitted and others in the works that should make 2014 very exciting. The lab bid a big congrats (!) to student (now “Dr”) DongHyuk Ki, who defended his PhD thesis in the summer and is now doing a postdoctoral research at Children’s

Hospital of Harvard Medical School. Undergraduate Jaclynn Chen graduated with honors in the WISE program (Women in Science and Engineering) this past summer and is now in a Masters Program at Stony Brook University School of Medicine (Congrats Jaclynn!). Researchers in the lab during 2013 included Research Scientist Dr. Patricia Bossert and Postdoctoral Fellow Dr Matthew Dunn, working on sea anemone regeneration and stem cells. IRACDA Postdoctoral Fellow Dr William (Bill) Gillis and MCB graduate student (now Dr.) DongHyuk Ki, were working on signaling and developmental regulation by GTPases Molecular Pharmacology graduate student Francesca Nakagawa and undergraduate Sara Supriyatno, are working on the regulation of BMP and nodal signaling. Research Scientist Dr. Yasuno Iwasaki (who was a full-time lab member but is now in Peter Gergen’s lab), who together with Genetics graduate student Jamina Oomen-Hajagos and undergraduate Biochemistry major Jaclynn Chen, have been working on RNA

splicing regulation. We welcome a new BCB Masters student (and Stony Brook undergrad alumnus) Jonathan Wyrick to the lab We also had two summer guest researchers this year, Steve Cincotta of Boston University, who was an undergraduate NYSTEM Fellow (working on sea anemone regeneration), and Giselle Feliciano, a summer intern from Brentwood High School. Besides Jerry’s academic and home lab duties, he is also the Co-Director of the Cold Spring Harbor Lab course, Cell and Developmental Biology of Xenopus. The lab is supported by grants from the New York Department of Public Health (NYSTEM) to study sea anemone regeneration and stem cells, the Stony Brook School of Medicine (Carol Baldwin Breast Cancer TRO award) for the new cancer investigations, and residual fumes from NIH grants to support the frog developmental research (better get cracking on new grants – and donations are welcome). 13 Department of Biochemistry & Cell Biology ! Annual Newsletter 2013

"#$%&(!%)*#+,!-!.+/,! RESEARCH FACULTY UPDATES NURIT BALLAS Nurit Ballas was promoted to the rank of Research Professor as a dual appointment with the School of Medicine. She was a recipient of Carol Baldwin Breast Cancer Award. She served on the graduate student committee She also served on NIH/NICHD/CHHD-C Developmental Biology Study Section. The two summer students, Taylor Medwig (SBU) and Rileigh Darby-Mcclure (OU) in the Ballas lab were recipients of URECA and NYSTEM fellowship awards. Lab members include Postdocs: Dr Fang Du, Dr Yasuno Iwasaki, Research Technician Christy Felice, and undergrads Taylor Medwig (Stony Brook University) and Rileigh Darby-Mcclure (University of Oklahoma). ALISON LIU Alison Liu has published one high-impact research paper and one high-impact review article; its significance was highlighted in the news of Stony Brook University, National Science Foundation, and Times Beacon Record Newspaper. This is the first genome-wide profiling of microRNA

expression in plants that are exposed to the climate conditions predicted to occur within this century. It was shown that small RNA- and RNA-sequencing methods, when combined with phenotypic analysis, can lead to the identification of biological pathways or networks affected by climate conditions. This work confirms that plants can react rapidly to elevated greenhouse gas concentrations similarly to temperature and other physical factors through non-coding small RNAs, and demonstrates a new perspective for climate research. Alison presented a poster in Plant Biology 2013, sponsored by America Society of Plant Biologists, and gave an invited seminar in the Department of Ecology and Evolution at Stony Brook, and was subsequently accepted in its Graduate Program. She is on the editorial board of JMS Cell, and has reviewed the papers for the journals: Plant Sciences, Plant Physiology, Bioscience, Biotechnology, and Biochemistry (Japan society of Bioscience, Biotechnology, and

Agrochemistry). She has worked with graduate students, Cindy Lee, Will Liao, Chongli Wan, and Yijin Wu in the Department of Applied Mathematics and Statistics at Stony Brook; Will and Yijin earned the second and third authorships in our Nature Communications paper for their contribution to computational analysis of small RNA-seq and RNA-seq datasets. HIDEYUKI TAKEUCHI Hideyuki Takeuchi continues to work with Dr. Haltiwanger on biological significance of O-glycosylation of Notch They published one paper entitled “Enzymatic analysis of the protein O-glycosyltransferase0, Rumi, acting toward epidermal growth factor-like (EGF) repeats” in Methods in Molecular Biology in 2013. In November 2013, Dr Takeuchi participated in the Annual Meeting of the Society for Glycobiology held in St. Petersburg, Florida XIAO-HONG YU Xiao-Hong Yu was promoted to Research Assistant Professor in May of 2013. 14 Department of Biochemistry & Cell Biology Annual Newsletter 2013 2013 Departmental

Roster Faculty Members Research Faculty Administrative Staff Paul Bingham, Associate Professor Nurit Ballas, Research Professor Dianna Berger, Secretary I Deborah Brown, Professor Markus Eilers, Research Assistant Professor Caroline Burns, Office Assistant R. David Bynum, Professor Deniz Erezyilmaz, Research Assistant Professor Lydia Dedora, Secretary I Vitaly Citovsky, Professor Martin Kaczocha, Research Assistant Professor Joann DeLucia-Conlon, Graduate Program Kevin Czaplinski, Assistant Professor Alison (Qiong) Liu, Research Assistant Professor Neta Dean, Professor Daniel Moloney, Research Assistant Professor Dale Deutsch, Professor Jorg Schwender, Research Assistant Professor Faiqa Mirzai, Clerk II M. Raafat El-Maghrabi, Research Associate Stefan Tafrov, Research Assistant Professor Judy Nimmo, CESAME Administrator Coordinator Carol Juliano, Department Administrator Hideyuki Takeuchi, Research Assistant Professor Debra Pelio, CESAME Staff Assistant

Jarrod French, Assistant Professor Changcheng Xu, Research Assistant Professor Beverly Piazza, Administrative Assistant I Liang Gao, Assistant Professor Xiao-Hong Yu, Research Assistant Professor Diane Riccardo, Administrative Assistant II J. Peter Gergen, Professor Zuzana Zachar, Research Assistant Professor Diane Rodriguez, Staff Assistant Steven Glynn, Assistant Professor Adi Zaltsman, Research Assistant Professor Professor (Primary Appt. Physiology & Biophysics) Robert Haltiwanger, Professor and Chairman Postdoctorals & Research Scientists Yusuf Hannun, Professor, Director of Cancer Center Lecturers Tracy Callender Ian Hitchcock, Assistant Professor (Primary appointment, Medicine) Susan Erster, Lecturer Xiangyu Chen Bernadette Holdener, Associate Professor Caren Gough, Lecturer Matthew Covey Nancy Hollingsworth, Professor Mike Lake, Lecturer Fang Du Wali Karzai, Associate Professor Linda Padwa, Lecturer Matthew Dunn Sasha Levy, Assistant

Professor Joanne Souza, Lecturer William Gillis Huilin Li, Professor Stephen Wefer, Lecturer Sunita Gupta Chengdong Huang Erwin London, Professor Edward Luk, Assistant Professor Educators Yasuno Iwasaki Harvard Lyman, Associate Professor Kristen LaMagna, Educator Shinako Kakuda Yakov Ido Keren Kenneth Marcu, Professor Benjamin Martin, Assistant Professor Other Faculty Appointments David Matus, Assistant Professor Aaron Neiman, Professor Angela Kelly, Assistant Professor in Physics and Astronomy with a joint appointment in CESAME Nisson Schechter, Professor (Primary Joan Kiely, Director Biotech. Teaching Lab Appt. Psychiatry) Matthew Schmidt, Adjunct Visiting Asst. Professor Keith Sheppard, Associate Professor Sanford Simon, Professor Steven Smith, Professor Gerald Thomsen, Professor Adjunct Faculty Members Chang-Jun Liu, Adjunct Professor Herman Schindelin, Adjunct Professor Richard Setlow, Adjunct Professor John Shanklin, Adjunct Professor F. William Studier,

Adjunct Professor 15 Faculty Emeritus Naoki Kimata Benoit Lacroix Guangtao Li Qingqing Lin Preeti Mehta Anne Ostermeyer-Fay Jae-Sook Park Richard Row Elof Carlson, Professor Soumya Roy Chowdhury Vincent Cirillo, Professor Mi Jin Son Bernard Dudock, Professor Jing Sun Martin Freundlich, Professor Deepika Vasudevan Abraham Krikorian, Professor Lihong Wan William J. Lennarz, Distinguished Professor Zhaoyang Wei Carl Moos, Professor Renhong Wu Rolf Sternglanz, Distinguished Professor Xiaohang Yu Raghupathy Sarma, Professor Cheng Yuan Melvin Simpson, Professor Martine Ziliox Department of Biochemistry & Cell Biology Annual Newsletter 2013 2013 Departmental Roster Technical Staff Volunteers Gregory Rudomen, Director of Laboratories Allie Cohen Teddy Betts Evangeline Giannopoulos Richard Bennett Sharon Huang Neal Bhattacharji Amanda Hutchins Delon Callender Caroline Miller Jun Chang Kevin Chen ` Justin Cooper Nallamai Muthiah Karole D’Orazio

Christy Felice Ziao Fu Rich Grady Hao Chi Hsu Yan Huang Zhen Huang Jane Joseph Min Jung Arthur Korman Chien Lam Priya Mallikarjuna Allison Marullo Leor Needleman Caitlin Pozmanter Brian Ralph Danielle Scarano Alexandria Schauble Tia Sparrow Jing Sun Megumi Takeuchi Namratha Vasudevan Liqun Wang Erika Wunderlich Huijun Yang Visiting Scholars/Scientists Patricia Bossert Richard Elinson Yedidya Gafni Elena Garcia-Cano Sondra Lazarowitz Youngja Lee Min-Vu-Coung Nguyen Miguel Otero Sylvia Samaniejo Guilia M. Stellari Xianchao Sun Michael Yoder 16 Department of Biochemistry & Cell Biology Annual Newsletter 2013 Publications in 2013   NURIT BALLAS  -­‐ Nguyen, M.V, Felice, CA, Du, F, Robinson, JK, Mandel, G and Ballas, N (2013) Oligodendrocyte lineage cells contribute to RTT neuropathology. J Neurosci In press VITALY CITOVSKY - Zaltsman, A., Lacroix, B, Gafni, Y, & Citovsky, V (2013) Disassembly of synthetic Agrobacterium T-DNA-protein VBF complexes via the host SCF

ubiquitin-ligase complex pathway. Proc Natl Acad Sci USA 110, 169-174 Lacroix, B. & Citovsky, V (2013) Characterization of VIP1 activity as a transcriptional regulator in vitro and in planta Sci Rep 3, 2440 Lisa King-Zalepa, L. & Citovsky, V (2013) A plasmodesmal glycosyltransferase-like protein PLOS ONE 8, e58025 Lacroix, B. & Citovsky, V (2013) Agrobacterium In Brenner’s Encyclopedia of Genetics Second Edition (S Maloy & K Hughes, eds), Elsevier, pp. 52-54 Lacroix, B. & Citovsky, V (2013) Crown Gall Tumors In Brenner’s Encyclopedia of Genetics Second Edition (S Maloy & K Hughes, eds.), Elsevier, pp 236-239 Lacroix, B. & Citovsky, V (2013) The roles of host plant factors in Agrobacterium-mediated genetic transformation Int J Dev Biol 57, 467-481. Lacroix, B. & Citovsky, V (2013) A mutation in negative regulator of basal resistance WRKY17 of Arabidopsis increases susceptibility to Agrobacterium-mediated genetic transformation. F1000 Research 2, 33

Lacroix, B., Gizatullina, DI, Babst, BA, Gifford, AN, & Citovsky, V (2013) Agrobacterium T-DNA-encoded protein Atu6002 interferes with the host auxin response. Mol Plant Pathol, in press, doi: 101111/mpp12088 Garcia-Cano, E., Zaltsman, A, & Citovsky, V (2013) Assaying proteasomal degradation in a cell-free system in plants J Vis Exp, in press. KEVIN CZAPLINSKI – Fukuda, N., Fukuda, T, Sinnamon, J R, Hernandez-Hernandez, A, Izadi, M, Raju, C S, Czaplinski, K and Percipalle P. (2013) The transacting factor CBF-A/Hnmpab binds to the A2RE/RTS element of protamine 2 mRNA and contributes to its translational regulation during mouse spermatogenesis. PLoS Genet 2013 Oct;9(10):e1003858 Sinnamon, J. R and Czaplinski, K (2013) RNA detection in situ with FISH-STICs RNA in press DALE DEUTSCH - Leung, K., M W Elmes, S T Glaser, D G Deutsch and M Kaczocha (2013) "Role of FAAH-Like Anandamide Transporter in Anandamide Inactivation." PLoS One 8(11): e79355 Tsuboi, K., N Ikematsu, T

Uyama, D G Deutsch, A Tokumura and N Ueda (2013) "Biosynthetic pathways of bioactive Nacylethanolamines in brain" CNS Neurol Disord Drug Targets 12(1): 7-16 STEVEN GLYNN - Stinson, B.M, Nager, AR, Glynn, SE, Schmitz, KR, Baker, TA and Sauer, RT (2013) Nucleotide binding and conformational switching in the hexameric ring of a AAA+ machine. Cell, 153, 628-639 ROBERT HALTIWANGER – Al-Shareffi, E., Chaubard, J-L, Leonhard-Melief, C, Wang, S-K, Wong, C-H, and Haltiwanger, RS (2013) 6-Alkynyl Fucose is a bioorthogonal analogue for O-fucosylation of Epidermal Growth Factor-like repeats and Thrombospondin Type-1 repeats by Protein O-Fucosyltransferases 1 and 2. Glycobiology 23, 188-198 PMCID: PMC3531295 Lee, T.V, Sethi, MK, Leonardi, J, Rana, NA, Buettner, FFR, Haltiwanger, RS, Bakker, H, and Jafar-Nejad, H (2013) Negative Regulation of Notch Signaling by Xylose. PLoS Genetics, 9(6), e1003547 PMCID: PMC3675014 Takeuchi, H. and Haltiwanger, RS (2013) Enzymatic Analysis of the

Protein O-Glucosyltransferase, Rumi, Acting Toward Epidermal Growth Factor-Like (EGF) Repeats, in Methods in Molecular Biology, vol. 1022, Glycosyltransferases: Methods and Protocols (I Brockhausen, ed.) Humana Press, New York, pp 119-128 17 Department of Biochemistry & Cell Biology Annual Newsletter 2013 Publications in 2013 YUSUF HANNUN - Furuya, H., Wada, M, Shimizu, Y, Yamada, P M Hannun, Y A, Obeid, L M, and Kawamori, T (2013) Effect of Sphingosine kinase 1 inhibition on blood pressure. FASEB J 27: 656-64 PMCID: PMC3545530 Orr Gandy, K. A, Canals, D, Adada, M M, Wada, M, Roddy, P L, Snider, A, Hannun, Y A, and Obeid, L M (2013) Sphingosine 1-Phosphate induces filopodia formation through S1P2R activation of ERM proteins. Biochem J 449: 661-672 PMCID: PMC3623934 Airola, M. V and Hannun, Y A (2013) Sphingolipid Metabolism and Neutral Sphingomyelinases Chapter 3 in Sphingolipids: Basic Science and Drug Development. E Gulbins and I Petrache (eds) Handbook of Experimental

Pharmacology 215: 57-76 Canals, D. and Hannun, Y A (2013) Novel Chemotherapeutic Drugs in Sphingolipid Cancer Research Chapter 12 in Sphingolipids: Basic Science and Drug Development. E Gulbins and I Petrache (eds) Handbook of Experimental Pharmacology 215: 211-238. Orr Gandy, K. A, Adada, M M, Canals, D, Carroll, B, Roddy, P, Hannun, Y A, and Obeid, L M (2013) Epidermal growth factor (EGF)-induced cellular invasion requires sphingosine1-phosphate (S1P)/sphingosine 1-phosphate 2 receptor (S1P2R)-mediated ezrin activation. FASEB J 8:3155-3166 PMCID: PMC3714586 , Chen P-W, Fonseca, L. L, Hannun, Y A, and Voit, E O (2013) Coordination of Rapid Sphingolipid Responses to Heat Stress in Yeast. PLOS Computational Biology Vol 9 e1003078 PMCID: PMC3667767 Matmati, N., Matelli, A, Tripathi, K, Yan, S, Mohanty, B K and Hannun, Y A (2013) Identification Of C-18:1 Phytoceramide As The Candidate Lipid Mediator For Hydroxyurea Resistance In Yeast. J Biol Chem 28817272-17284 PMCID: PMC3682531

Cinq-Frais, C., Coatrieux, C, Grazide, MH, Hannun, YA, Nègre-Salvayre, A, Salvayre, R, Augé, N (2013) A signaling cascade mediated by ceramide, src and PDGFRb coordinates the activation of the redox-sensitive neutral sphingomyelinase-2 and sphingosine kinase-1. Biochim Biophys Acta 1831:1344-1356 Kajimura, D., Lee, HW Riley, K J, Arteaga-Solis, E Ferron, M, Zhou, B, Clarke, C J,, Hannun, Y A, DePinho, R A, Guo, E X, Mann, J. J, and Karsenty, (2013) Adiponectin Regulates Bone Mass via Opposite Central and Peripheral Mechanisms through FoxO1 G. Cell Metabolism 17:901-915 PMCID: PMC3679303 Adada, M., Canals, D, Hannun, Y A, and Obeid, L M (2013) Sphingolipid regulation of ezrin, radixin, and moesin protein families: implications for cell dynamics. Biochimica et Biophysica Acta - Molecular and Cell Biology of Lipids (in press) Jenkins R.W, Clarke CJ, Lucas JT Jr, Shabbir M, Wu BX, Simbari F, Mueller J, Hannun YA, Lazarchick J, Shirai K (2013) Evaluation of the role of secretory

sphingomyelinase and bioactive sphingolipids as biomarkers in hemophagocytic lymphohistiocytosis. Am J Hematol (in press) Adada, M., Canals, D, Hannun, Y A, Obeid, L (2013) Sphingosine-1-phosphate receptor 2: A Review FEBS journal in press Jin J., Zhang X, Lu Z, Perry DM, Li Y, Brice Russo, S, Cowart, L A, Hannun, YA, Huang Y (2013) Acid Sphingomyelinase Plays a Key Role in Palmitic Acid-Amplified Inflammatory Signaling Triggered by Lipopolysaccharide at Low Concentration in Macrophages. American Journal of Physiology - Endocrinology and Metabolism 305: E853-E867 Adada, M. M, Orr Gandy, K A, Snider, A J, Canals, D, Hannun, Y A, Obeid, L M and Clarke, C J (2013) Sphingosine Kinase 1 (SK1) regulates Tumor Necrosis Factor (TNF)-mediated RANTES Induction Through p38 MAPK but Independently of NF-&[kappa]B Activation. J Biol Chem 288: 27667-27679 18 Department of Biochemistry & Cell Biology Annual Newsletter 2013 Publications in 2013 YUSUF HANNUN (cont’d) Garcia-Barros,

M., Coant, N, Truman, J-P Snider, A J and Hannun, Y A (2013) Sphingolipids in Colon Cancer BBA - Molecular and Cell Biology of Lipids (in press) http://dx.doiorg/101016/jbbalip201309007 El-Osta, M. A*, Liu, M.*, Senkal, C. E, Adada, M M, Idkowiak-Baldys, J, Obeid, L M, Clarke, C J, and Hannun, Y A Sustained PKC-&[beta]II activity confers oncogenic properties in a phospholipase D and mTOR-dependent manner. (2013) FASEB J (in press). * These two authors contributed equally to this work Liu, M., Idkowiak-Baldys, J, Roddy, P L, Baldys, A, Raymond, R, Clarke, C J, and Hannun, Y A (2013) Sustained Activation of Protein Kinase C Induces Delayed Phosphorylation and Regulates the Fate of Epidermal Growth Factor Receptor. PLOS ONE Montefusco, D. J, Chen, L, Matmati1, N, Lu, S, Newcomb, B, Cooper, G F, Hannun*, Y. A, Lu*, X. (2013) Distinct Signaling Roles of Ceramide Species in Yeast Revealed Through Systematic Perturbation and Systems Biology Analyses. Science Signaling (in press). •

Corresponding authors Montefusco, D. J, Matmati1, and Hannun, Y A (2013) The Yeast Sphingolipid Signaling Landscape Chemistry and Physics of Lipids 177: 26-40. http://authorselseviercom/sd/article/S0009308413001345 Swninnen, E., Wilms, T, Idkowiak-Baldys, J, Smets, B, De Snijder, P, Accardo, S, Ghillebert, R, Thevissen, K, CAmmue, B, De Vox, D., Bielawaki, J, Hannun, Y A, and Windericks, J (2013) The protein kinase Sch9 is a key regulator of sphingolipid metabolism in Saccharomyces cerevisiae. Journal Molecular Biology of the Cell (in press) Vilaça, R., Silva, E, Nadals A, Teixeira, V, Matmati, N, Gaifém, J, Hannun, Y A,, Sá Miranda, M C, Costa, V (2013) Sphingolipid signaling mediates mitochondrial dysfunctions and reduced chronological lifespan in the yeast model of Niemann-Pick type C1. Molecular Microbiology (in press) BERNADETTE HOLDENER - Taibi, A.V, Lighthouse, JK, Grady, RC, Shroyer, KR, and Holdener, BC (2013) Development of a Conditional Mesd (Mesoderm Development) Allele

for Functional Analysis of the Low-Density Lipoprotein Receptor-Related Family in Defined Tissues. Plos One 8:e75782 PMID: 24124512 NANCY HOLLINGSWORTH - Liu, Y., W Gaines, T Callender, V Busygina, A Oke, P Sung, J Fung and N M Hollingsworth (2013) Down-regulation of Rad51 activity during meiosis in yeast prevents competition with Dmc1 for repair of double-strand breaks. PLoS Genet. (in press) HUILIN LI - Rath P, Huang C, Wang T, Wang T, Li H, Prados-Rosales R, Elemento O, Casadevall A, Nathan CF. Genetic regulation of vesiculogenesis and immunomodulation in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 2013 Dec 3;110(49):E4790-7 doi: 10.1073/pnas1320118110 Epub 2013 Nov 18 Riera A, Li H, Speck C. Seeing is believing: the MCM2-7 helicase trapped in complex with its DNA loader Cell Cycle 2013 Sep 15;12(18):2917-8. doi: 104161/cc26132 Sun J, Evrin C, Samel SA, Fernández-Cid A, Riera A, Kawakami H, Stillman B, Speck C, Li H. Cryo-EM structure of a helicase loading intermediate

containing ORC-Cdc6-Cdt1-MCM2-7 bound to DNA. Nat Struct Mol Biol 2013 Aug;20 (8):944-51 doi: 01038/nsmb2629 Epub 2013 Jul 14. Samanovic MI, Li H, Darwin KH. The Pup-Proteasome System of Mycobacterium tuberculosis Subcell Biochem 2013;66:267-95 doi: 10.1007/978-94-007-5940-4 10 QIONG LIU - May P, Liao W, Wu YJ, Shuai B, McCombie R, Zhang MQ, Liu QA. (2013) The Effects of CO2 and temperature on microRNA Expression in Arabidopsis development. Nat Commun 4: 2145 Liu QA. (2013) The impact of climate change on plant epigenomes (Spotlight) Trends Genet 29(9): 503-5 19 Department of Biochemistry & Cell Biology Annual Newsletter 2013 Publications in 2013 ERWIN LONDON - Son, M., and London, E (2013) “The Dependence of Lipid Asymmetry Upon Phosphatidylcholine Acyl Chain Structure” J. Lipid Res 54, 223-231 Lin, Q. and London E (2013) “Altering hydrophobic sequence lengths shows that hydrophobic mismatch controls affinity for ordered lipid domains (rafts) in the

multi-transmembrane strand protein perfringolysin O”, J. Biol Chem, 288, 1340–1352 Chiantia, S. and London, E (2013) “Lipid Bilayer Asymmetry” in Encyclopedia of Biophysics 2nd ed (Roberts GCK Ed) SpringerVerlag Heidelberg: Berlin, pp 1250-1253 Caputo, G.A and London, E (2013) “Analyzing transmembrane protei and hydrophobic helix topography by dual fluorescence quenching” in Methods in Molecular Biology series Volume 974, Lipid-Protein Interactions: Methods and Protocols (Kleinschmidt, J.H Ed.) Humana Press/Springer, New York, pp 279-295 Crowley, J.T Toledo, AM, LaRocca, TJ, Coleman, JL, London, E, and Benach, JL (2013) “Lipid Exchange between Borrelia burgdorferi and host cells” PLoS Pathogens, 9, e1003109. Chiantia, S., and London, E (2013) “Sphingolipids and Membrane Domains: Recent Advances” in Handbook of Experimental Pharmacology: Sphingolipids in Health and Disease (Gulbins, E., and Petrache, I Eds) Volume 215, pp 33-55 Springer, New York LaRocca, T.J,

Pathak, P, Chiantia, S, Toledo, A, Silvius, JR, Benach, JL and London, E (2013) “Proving Lipid Rafts Exist: Membrane Domains in the Prokaryote Borrelia burgdorferi Have the Same Properties as Eukaryotic Lipid Rafts” PLoS Pathogens, 9, e1003353. Su, C.-Y, London, E, and Sampson, NS (2013) “Mapping peptide thiol accessibility in membranes using a quarternary ammonium isotope-coded mass tag (ICMT)” Bioconjugate Chemistry 24, 1235-1247. Son, M., and London, E (2013) “The Dependence of Lipid Asymmetry Upon Polar Headgroup Structure” J Lipid Res, 54, 3385-3393 Huang, Z., and London, E (2013) “Effect of Cyclodextrin and Membrane Lipid Structure upon Cyclodextrin-Lipid Interaction” Langmuir, 29, 14631-14638. Lin, Q., and London, E (2013) “Transmembrane Protein (Perfringolysin O) Association with Ordered Membrane Domains (Rafts) Depends Upon the Raft-Associating Properties of the Protein-Bound Sterol” Biophys. J 105, 2733-2742 KEN MARCU - Samaniego S, Marcu KB. (2013) IKKβ

in Myeloid Cells Controls the Host Response to Lethal and Sublethal Francisella tularensis LVS Infection. PLOS ONE 8(1): e54124 , , , Hashimoto K., Otero M, Imagawa K, de Andrés, MC, Coico JM, Roach, HI Oreffo ROC, Marcu, KB and Goldring, MB 2013 Regulated transcription of human matrix metalloproteinase 13 (MMP13) and interleukin-1 beta (IL1B) genes in chondrocytes depends on methylation of specific proximal promoter CpG sites. J Biol Chem 288: 10061-10072 PMID 23417678 Olivotto, E., Miguel Otero, M, Astolfi, A Platano, D, Facchini, A Pagani, S, Flamigni, F, Facchini, A, Goldring, MB, Borzì, RM, and Marcu, K.B 2013 IKKalpha/CHUK regulates extracellular matrix remodeling independent of its kinase activity to facilitate articular chondrocyte differentiation. PLOS ONE 8(9): e73024 BEN MARTIN - So J., Martin BL, Kimelman D, Shin D Wnt/b-catenin signaling cell-autonomously induces endodermal cells to a liver fate. Biol Open 2013 Jan 15; 2(1): 30-6 Veldman M.B, Zhao C, Gomez GA,

Lindgren AG, Huang H, Yang H, Yao S, Martin BL, Kimelman D, Lin S Transdifferentiation of fast skeletal muscle into functional endothelium in vivo by transcription factor Etv2. PLoS Biol Jun; 11(6): e1001590. Taibi A., Mandavawala KP, Noel J, Okoye EV, Milano CR, Martin BL, Sirotkin HI Zebrafish churchill regulates developmental gene expression and cell migration. Dev Dyn 2013 Jun; 242(6): 614-21 AARON NEIMAN - Park, J.-S, Okumura, Y, Tachikawa, H, and Neiman, A M (2013) SPO71 encodes a developmental stagespecific partner for Vps13 in Saccharomyces cerevisiae Euk Cell 12:1530-1537 Lin, C. P, Kim, C, Smith, S O, and Neiman, A M (2013) A Highly Redundant Gene Network Controls Assembly of the Outer Spore Wall in S. cerevisiae PLoS Gen 9:e1003700 20 Department of Biochemistry & Cell Biology Annual Newsletter 2013 Publications in 2013 STEVEN SMITH - Matsushita, C., Tamagaki, H, Miyazawa, Y, Aimoto, S, Smith, SO and Sato, T (2013) Transmembrane helix orientation influences

membrane binding of the intracellular juxtamembrane domain in Neu receptor peptides. Proc Natl Acad Sci USA 110:1646-51. Defour, J.P, Itaya, M, Gryshkova, V, Brett, IC, Pecquet, C, Sato, T, Smith, SO, and Constantinescu, SA (2013) A tryptophan at the transmembrane-cytosolic junction modulates thrombopoietin receptor dimerization and activation. Proc Natl Acad Sci USA, 110:2540-5. Kotarba AE, Aucoin D, Hoos MD, Smith SO, Van Nostrand WE. (2013) Fine mapping of the amyloid β-protein binding site on myelin basic protein. Biochemistry 2013 52(15): 2565-73 Opefi, C.A, South, K, Reynolds, C, Smith, SO and Reeves, PJ (2013) Retinitis pigmentosa mutants provide insight into the role of the N-terminal cap in rhodopsin folding, structure, and function, J. Biol Chem, 288:33912-26 Xu, B., Chakrabory, R, Eilers, M, Dakshinamurti, S, O’Neil, JD, Smith, SO, Bhullar, RP, and Chelikani, P (2013) High level expression, purification and characterization of a constitutively active thromboxane A2

receptor polymorphic variant. PLoS ONE, 8(9):e76481. Lin C.P, Kim C, Smith SO and Neiman AM (2013) A highly redundant gene network controls assembly of the outer spore wall in S cerevisiae. PLoS Genetics, 9(8):e1003700 Pope, A, Eilers, M., Reeves, P, and Smith, SO (2013) Amino acid conservation and interactions in rhodopsin: Probing receptor activation by NMR spectroscopy. Biochim Biophys Acta, in press ROLF STERNGLANZ - Hsu, H.C, Wang, CL, Wang, M, Yang, N, Chen, Z, Sternglanz, R and Xu, RM (2013) Structural basis for allosteric stimulation of Sir2 activity by Sir4 binding. Genes & Development 27: 64-73 Sampath, V., Liu, B, Tafrov, S, Srinivasan, M, Rieger, R, Chen, E and Sternglanz, R (2013) Biochemical characterization of Hpa2 and Hpa3, two small closely related acetyltransferases from Saccharomyces cerevisiae. J Biol Chem 288: 21506-21513 GERALD THOMSEN - Nakayama T, Fish MB, Fisher M, Oomen-Hajagos J, Thomsen GH and Grainger RM. (2013) Simple and efficient

CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis. Genesis† (in press) PMID 24123613 http://dx.doiorg/101002/dvg22720 Featured on journal cover Bossert PE, Dunn MP and Thomsen GH. (2013) Staging system for the regeneration of a polyp from the aboral physa of the Anthozoan Cnidarian Nematostella vectensis. Developmental Dynamics 242:132031 PMID23913838 http://dx.doiorg/101002/dvdy24021 Featured on journal cover HIDEYUKI TAKEUCHI - Takeuchi, H. and Haltiwanger, RS (2013) Enzymatic analysis of the protein O-glycosyltransferase, Rumi, acting toward epidermal growth factor-like (EGF) repeats. Methods Mol Biol 1022, 119-128 PMID: 23765658 XIAO-HONG YU - XH Yu, R Prekash, M Sweet and J Shanklin. Coexpressing E coli cyclopropane synthase with Sterculia foetida lysophosphatidic acid acyltransferase enhances cyclopropane fatty acid accumulation. Plant Physiology, 2013 doi:10.1104/pp113230953 A Cheng, JY Gou, XH Yu, HJ Yang, X Fang, XY Chen and CJ Liu. Characterization and

Ectopic Expression of a Populus Hydroxyacid Hydroxycinnamoyltransferase. Molecular Plant, 2013; doi: 101093/mp/sst085 C Andre, SW Kim, XH Yu, J Shanklin. Fusing catalase to an alkane-producing enzyme maintains enzymatic activity by converting the inhibitory byproduct H2O2 to the cosubstrate O2. Proceedings of the National Academy of Sciences, 2013, 110(8): 3191-3196 21 Stony Brook University Medical Center - Office of Scientific Affairs, Select Core Facility Services Guide www.osasunysbedu Biostatistical Consulting Core The BCC provides biostatistical guidance and data analysis support for all aspects of a research endeavor. Besides general biostatistical consultations, the BCC statisticians also serve as biostatistical coinvestigators on grants and provide short statistics course/workshops for faculty and staff of the Stony Brook School of Medicine. For additional information, services and fees please link to: http://www.stonybrookmedicalcenterorg/prevm ed/biostatistical CMIC

Facility The Central Microscopy Facility provides light and electron microscopy services under ISO Cl. 7 clean rooms The facility houses two confocal microscopes, both being two-photon capable. One instrument is excellent for both fixed and live-cell imaging. The second instrument is specially constructed to allow imaging of cells within whole organisms. The facility also has an FEI BioTwin transmission electron microscope for thin section or diffraction imaging of samples. Preparation and sectioning of samples for the electron microscope is available. Both the confocal and electron microscopes are overseen by full-time professional staff who are available to train users on the instruments and provide advice on techniques and sample preparation. For additional information, services and fees please link to: http://multiphoton.biosunysbedu/ Genomics Core Facility The Genomics Core Facility is charged with the mission of facilitating all aspects of research related to genetics/genomics

at Stony Brook University. The faculty is well versed in all modern methods of genetic/genomic analysis. The facility aims to provide scientists at Stony Brook University with the tools required to maximize their research. In the longer term, it is hoped that this facility will pave the way for Stony Brook to become a center of excellence in translational medicine, with particular emphasis on human genetics. Multiple technologies are available by way of Microarray, Q-PCR, and Sequencing. For additional information, services and fees please link to: http://www.osasunysbedu/genomics/ Bioinformatics Facility The bioinformatics facility provides a broad spectrum of bioinformatics and IT support to our customers. Services include: general bioinformatics consultation; high throughput sequence, microarray, and pathway analysis; custom software development, etc. For additional information, services and fees please link to: http://www.osasunysbedu/bioinformatics/i ndex.html Proteomics Facility

The Proteomics Center analyzes protein/peptide/small molecule samples with the help of mass spectrometry. The Proteomics technical staff measure intact masses of proteins/peptides/small molecules, identify peptides based on their sequence, and discover post-translational modifications. Comparisons of protein expressions between different samples are conducted. The center has four different mass spectrometers: a Matrix-assisted laser desorption/ionization time-of-flight mass spectrometer; a triple quadrupole mass spectrometer; a linear ion-trap mass spectrometer; and a high-resolution, high mass accuracy hybrid mass spectrometer with four different activation methods (Thermo LTQ Orbitrap XL with ETD). In addition, equipment for running 2D gel electrophoresis and analysis are also present. For additional information, services and fees please link to: http://www.osasunysbedu/Proteomics/ Translational Experimental Therapeutics Laboratory (PK) The Translational Experimental Therapeutics

Laboratory (TETL) has been established to facilitate translational medicine by providing in vivo data on compound absorption, distribution, metabolism, excretion and toxicity (ADME/T). Compounds identified in the initial phase of drug discovery invariably lack one or more biological properties, such as potency, oral bioavailability, selectivity or toxicity, that are essential for use as a diagnostic or therapeutic in humans. The TETL thus seeks to overcome a major hurdle in academic drug discovery pipeline by providing a mechanism for integrating chemical synthesis with methods to assess compound ADME/T. For additional information, services and fees please link to: http://www.osasunysbedu/tetl/ 22 Department of Biochemistry & Cell Biology Annual Newsletter 2013 IN CLOSING: Please write to us and send any news of your current activities. The financial assistance and donations we receive from our alumni and benefactors are essential, especially during these difficult economic

times. We are grateful to all who have donated in the past. With your financial support, we are able to advance our research, educational and scientific missions and offer students scholarship award opportunities. Here is a list of present funds and scholarship programs that are available: Account 266620 - General Biochemistry Account - To help advance the educational and scientific missions of the Department. Account 227060 - Biochemistry and Cell Biology Funds for Excellence - To help advance the educational and scientific missions of the Biochemistry and Cell Biology Department. Account 361160 - Evelyn Bonner Fund – In honor of Ms. Bonner, a former departmental administrator, this fund supports the research of students who have not identified a permanent laboratory during their first academic year. Account 362870 - King and Miller Travel Scholarship Awards – An Endowed Scholarship fund was established in 2000 in memory of Kevin King and John Miller, two PhD students involved in

research with departmental faculty, who lost their lives suddenly in a tragic accident. The funds in this endowment provide Travel Scholarship Awards to graduate students to attend professional meetings Kevin King/John Miller Travel Scholarship Awards totaling nearly $10,000 have been given to thirty-three different students from our Graduate Programs over the last eleven years. In 2012, the following students (in their respective graduate programs) were awarded Travel Scholarship Awards: Gulcan Akgul (Molecular and Cellular Biology), Luisa Escobar-Hoyos (Molecular and Cellular Pharmacology), Daniel Moen (Ecology and Evolution), Cindy Thomas-Charles (Genetics) and Kai Wu (Molecular Genetics and Microbiology). Account 363890 - Melvin Simpson Lecture Fund - To bring top scientists to Stony Brook University to discuss a broad range of topics related to biochemistry and cell biology, which keeps scientists at the forefront of current research and allows faculty from various universities to

interact and collaborate. Account 860065 – Center for Science and Mathematics Education (CESAME) - To help advance the mission of CESAME to attract, inspire and educate students and teachers in the areas of science and mathematics. You can donate online at http://www.stonybrookedu/sb/giving/waystogiveshtml or you can send your check by mail Please make your gift by check payable to the “Stony Brook Foundation”. Please note appropriate account # (from list above) on your check and mail to: The Stony Brook Foundation, Inc. PO Box 1511 Stony Brook, NY 11790-0590 “Making a gift to the Stony Brook Foundation is a highly effective way to realize your transforming philanthropic power. You can feel confident about investing in a world-class institution while creating tax benefits for yourself and your family, or for your organization.” Stony Brook University Department of Biochemistry & Cell Biology 450 Life Sciences Building Stony Brook, New York 11794-5215 !