On behalf of the MCB Graduate Program, we’re pleased to share our annual Newsletter filled with insights

about our students, faculty and staff. Dr. Wali Karzai started his fourth year as Director of the MCB Pro-

gram. This program has nearly 100 faculty members, representing 13 different departments on the Stony

Brook campus, in addition to a large number of investigators from Cold Spring Harbor Laboratory and

Brookhaven National Laboratory.

This past Fall we welcomed 9 new incoming MCB graduate students. Our Admission season is now complete

for 2016 and new students are appointed for the Fall.

Here’s our 2015 students:

Molecular & Cellular Biology

2015 - 2016 Newsletter

http://www.stonybrook.edu/mcb/

Jessica Imperato Yixin Hu Julie Bettke

Jialin Sun Wenbo Xu Qian Zhang

Muyang Li Megan Mladinich Padmina Shrestha

Drosophila embryo

(AKA - Fruit Fly Embryo)

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Molecular, Cellular, and Structural Biology

Training Program (MCSB) We’re proud of our training program which was established in 1997 with another renewal just

submitted. The goal of our Molecular, Cellular, and Structural Biology (MCSB) Training Program is

to provide outstanding pre-doctoral training on a wide variety of topics involving basic biological

and biomedical processes at the molecular and cellular level. The training program enhances the

education of students from two interdepartmental Stony Brook Graduate Programs: Molecular

and Cellular Biology (MCB) and Biochemistry and Structural Biology (BSB).

Students currently supported by the MCSB training grant are Matthew Elmes, Eric Paulissen,

Matthew Simons and Gregory Carbonetti from the MCB program. And Johnna St. Clair

and Roger Shek from the BSB program.

Andreyah Pope was chosen to be an affiliate of the training grant (a participant in the training

grant activities but with financial support from other grants).

Jinelle Wint and Andreyah Pope were chosen to participate in IMSD-Merge, an NIH funded

Program for underrepresented minorities.

2015 MCB/BSB Retreat Our annual retreat was a picture perfect day in September on the beautiful waterfront at Lombardi’s

on the Sound. Dr. Karzai was our M.C. and MCB and BSB faculty were invited to speak and present

their research. Our speakers included Brian Sheridan, Dave Matus, Mark Bowen, Jiang Chen, and

Steve Glynn. All 4th year MCB and BSB students presented their posters, which generated much in-

terest among the attendees. Best poster awards were given to Kuan Hu and Anthony Rampello.

Outstanding Service awards were given to Greg Carbonetti, Matt Elmes, Matt Simons and

Johnna St. Clair. Neha Puri won Best Presentation Award.

microscopic fluorescent

image of cells

P A G E 3

“Although there’s

a lot of infor-

mation available

online, it’s so much

better to hear it

from someone who

actually went

through the

process in person.”

2015 MCB and BSB Student Symposium “Life Science Career Choices

Beyond Tenured Track Research”

Our symposium was held at the Hilton Garden Inn. Invited speakers were Dr. Michael Rosconi, Senior Scientist at

Regeneron Pharmaceutical; Dr. Gregory Caputo, Chair Department of Chemistry at Rowan University; Dr. Paul

Meers, Rutgers University; Dr. Franklin Abrams, Patent Attorney at Springut Law; Dr. Susan Malenbaum, Associate

Director at Boehringer Ingelheim, and Dr. Juanita Sharpe, Assistant Vice Provost at Virginia Commonwealth Universi-

ty. This symposium brought together scientists, and their discussions included academic and non-academic career

paths spanning faculty life in the University with an emphasis on teaching to the biotechnology industry, to patent law,

and to University administration. Students had the opportunity for questions and discussions with a reception after

the meeting.

“ It gave me a

glimpse of the

career

possibilities for

someone with a

degree in molecu-

lar biology.”

P A G E 4

2015 Student - Invited Faculty Seminar

This seminar was held at the Hilton Garden Inn with faculty and students. The speaker was Dr. Craig Townsend from Johns Hopkins Uni-

versity. His talk was entitled “Biosynthesis of -Lactam Antibiotics and the Force of Convergent Evolution.” Students had an enriching

interaction with him. This event was organized by Neha Puri and Michael Tramantano and was a huge success!

Student Comments:

“Undertaking research in the area of pathways is increasingly rare and it was nice to see someone who has spent their entire career

focused on elucidating a novel pathway.”

“I learned a great deal about the fundamentals of drug development and chemistry that goes behind designing small molecule inhibitors."

Visualization of Muscle Actin and Satellite Cell Nuclei in Two Day Old Zebrafish

A Digitized "Brainbow”

2015 MCB 2nd Year Student Symposium Second year students had a full day with breakfast and lunch as they presented their research to their colleagues and MCB faculty. Also

in attendance were a few of our newly entered 2015 students: Julie Bettke, Jessica Imperato and Padmina Shrestha.

Jaber N, Pratt CP, Chen M, Zong WX, Marks MS, Joshua-Tor L, Pappin DJ, Trotman LC. PTEN functions by recruit-ment to cytoplasmic vesicles. Mol Cell. 2015 Apr 16;58(2):255-68. doi: 10.1016/j.molcel.2015.03.011. Epub 2015 Apr 9. PubMed PMID: 25866245; PubMed Central PMCID: PMC4423730 Jaber, N, Mohd-Naim, N, DeLeon, JL, Sheshadri, N, Chen, J, Edinger, A, Braga, V, Zong, WX. Class III PI3-kinase Vps34 regulates Rab7 through recruitment of the GTPase activation protein Armus. Submitted 2016. Bott AJ, Peng IC, Fan Y, Faubert B, Zhao L, Li J, Neidler S, Sun Y, Jaber N, Krokowski D, Lu W, Pan JA, Powers S, Rabinowitz J, Hatzoglou M, Murphy DJ, Jones R, Wu S, Girnun G, Zong WX. Oncogenic Myc Induces Expression of Glutamine Synthetase through Promoter Demethylation. Cell Metab. 2015 Dec 1;22(6):1068-77. doi: 10.1016/j.cmet.2015.09.025. Epub 2015 Oct 23. PubMed PMID: 26603296; PubMed Friedlander LR, Puri N, Schoonen MA, Wali Karzai A. The effect of pyrite on Escherichia coli in water: proof-of-concept for the elimination of waterborne bacteria by reactive minerals. J Water Health. 2015 Mar;13(1):42-53. doi: 10.2166/wh.2014.013. PubMed PMID: 25719464 Fesler A, Xu X, Zheng X, Li X, Jiang J, Russo JJ, Ju J. Identification of miR-215 mediated targets/pathways via trans-lational immunoprecipitation expression analysis (TrIP-chip). Oncotarget. 2015 Sep 15;6(27):24463-73. PubMed PMID: 26287603 Zhai H, Fesler A, Ba Y, Wu S, Ju J. Inhibition of colorectal cancer stem cell survival and invasive potential by hsa-miR-140-5p mediated suppression of Smad2 and autophagy. Oncotarget. 2015 Aug 14;6(23):19735-46. PubMed PMID: 25980495;PubMed Central PMCID: PMC4637317. Newcomb, B. and Hannun, Y. A. (2015) A new twist to the emerging functions of ceramides in cancer: Novel role for platelet acid sphingomyelinase in cancer metastasis. EMBO Molecular Medicine 7: 692- 694. PMCID: PMC4459812 Jae Kyo Yi, Ruijuan Xu, Eunmi Jeong, Izolda Mileva, Jean-Philip Truman, Chih-li Lin, Kai Wang, Justin Snider, Sally Wen, Lina M. Obeid, Yusuf A. Hannun and Cungui Mao. Aging-related elevation of sphingoid bases shortens yeast chronological life span by compromising mitochondrial function. Oncotarget, Mar, 2016 Simon Edvardson, Jae Kyo Yi (Co-First author), Chaim Jalas, Ruijuan Xu, Bryn D Webb, Justin Snider, Anastasia Fedick, Elisheva Kleinman, Nathan R Treff, Cungui Mao, Orly Elpeleg. Deficiency of the alkaline ceramidase ACER3 manifests in early childhood by progressive leukodystrophy. Journal of Medical Genetics. Jan 2016 María José Hernández-Corbacho, Daniel Canals, Mohamad M Adada, Mengling Liu, Can E Senkal, Jae Kyo Yi, Cungui Mao, Chiara Luberto, Yusuf A Hannun, Lina M Obeid. Tumor Necrosis Factor-α (TNFα)-induced Ceramide Generation via Ceramide Synthases Regulates Loss of Focal Adhesion Kinase (FAK) and Programmed Cell Death. Journal of Bio-logical Chemistry. Oct 2015 Kai Wang, Ruijuan Xu, Jennifer Schrandt, Prithvi Shah, Yong Z Gong, Chet Preston, Louis Wang, Jae Kyo Yi, Chih-Li Lin, Wei Sun, Demetri D Spyropoulos, Soyoung Rhee, Mingsong Li, Jie Zhou, Shaoyu Ge, Guofeng Zhang, Ashley J Snider, Yusuf A Hannun, Lina M Obeid, Cungui Mao. Alkaline Ceramidase 3 Deficiency Results in Purkinje Cell Degen-eration and Cerebellar Ataxia Due to Dyshomeostasis of Sphingolipids in the Brain.PLoS Genet. Oct 2015 Liang Jin, Aaron M. Neiman. Post-transcriptional regulation in meiosis. Current Genetics. 2015, doi: 10.1007/s00294-015-0546-2. Liang Jin, Kai Zhang, Yifeng Xu, Rolf Sternglanz, Aaron M. Neiman. Sequestration of mRNAs modulates the timing of translation during meiosis in budding yeast. Molecular and Cellular Biology. 2015, 35(20): 3448-3458. JiHyun Kim and Erwin London. "Using Sterol Substitution to Probe the Role of Membrane Domains in Membrane Functions." Lipids 50. 8 (2015): 721-34. Elmes, M. W., Kaczocha, M., Berger, W. T., Leung, K., Ralph, B. P., Wang, L., Sweeney, L.M., Miyauchi, J.T., Tsirka, S.E., Ojiama, I., & Deutsch, D. G. (2015). Fatty Acid Binding Proteins (FABPs) are Intracellular Carriers for Δ9-Tetrahydrocannabinol (THC) and Can nabidiol (CBD). Journal of Biological Chemistry, 290(14):8711-21.

Recent Student Publications P A G E 5

Ramkumar N, Harvey BM, Lee JD, Alcorn HL, Silva-Gagliardi NF, McGlade CJ, Bestor TH, Wijnholds J, Haltiwanger RS, Anderson KV. (2015). Protein O-glucosyltransferase 1 (POGLUT1) Promotes Mouse Gastrulation through Modification of the Apical Polarity Protein CRUMBS2. PLoS Genetics. 2015 11(10): e1005551. Harvey BM, Eschbach M, Glynn EA, Kotha S, Darre M, Adams DJ, Ramanathan R, Mancini R, Govoni KE. (2015). Effect of Daily lithium chloride administration on bone mass and strength in growing broiler chickens. Poultry Science. 94 (2): 296-301. Shamseddine, A.A., Clarke, C.J., Carroll, B., Airola, M.V., Mohammed, S., Rella, A., Obeid, L.M., and Hannun Y.A. 2015) p53-dependent upregulation of neutral sphingomyelinase-2: role in doxorubicin-induced growth arrest. Cell Death Dis. 6(10), e1947. Sirrs S, Van Karnebeek C, Peng X, Shyr C, Graovac M, Mandal R, Testa D, Dubin D, Carbonetti G, Glynn S, Sayson B, Robinson W, Han B, Wishart D, Ross C, Wasserman W, Hurwitz T, Sinclair G, Kaczocha M. Defects in Fatty Acid Amide Hydrolase 2 in a Male with Neurologic and Psychiatric Symptoms. Orphanet Journal of Rare Diseases 2015. Carbonetti G, Liu X. Liquid Pot Still Requires More Testing. Newsday Opinion-Editorial 2015. Appelmann I, Rillahan CD, de Stanchina E, Carbonetti G, Chen C, Lowe SW, Sherr CJ. Janus Kinase Inhibition by Ruxolitinib Extends Dasatinib and Dexamethasone-Induced Remissions in a Mouse Model of Ph+ ALL. Blood 2015. Yang, M., Lu, R., Guja, K.E., Wipperman, M.F., St. Clair, J.R., Bonds, A.C., Garcia-Diaz, M. and Sampson, N.S., 2015. Unraveling cholesterol catabolism in Mycobacterium tuberculosis: ChsE4-ChsE5 α2β2 acyl-CoA dehydrogenase initiates β-oxidation of 3-oxo-cholest-4-en-26-oyl CoA. ACS infectious diseases, 1(2), pp.110-125. Friedlander LR, Puri N, Schoonen MA, Wali Karzai A. The effect of pyrite on Escherichia coli in water: proof-of-concept for the elimi nation of waterborne bacteria by reactive minerals. J Water Health. 2015 Mar Leiton CV, Aranmolate A, Eyermann C, Menezes MJ, Escobar-Hoyos LF, Husain S, Winder SJ, Colognato H, J Neuro-chem. Laminin Promotes Metalloproteinase Mediated Dystroglycan Processing to Regulate Oligodendrocyte Progenitor Cell Proliferation. 2015 Jul 14. doi: 10.1111/jnc.13241. PMID: 26171643

Ching-Jung Lin, Peter Smibert, Xiaoyu Zhao, Jennifer F. Hu, Johnny Ramroop, Stefanie M. Kellner, Matthew A. Benton, Shubha Govind, Peter C. Dedon, Rolf Sternglanz, and Eric C. Lai. "An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis." RNA. 2015 Dec;21(12):2103-18.

Escobar-Hoyos LF, Shah R, Roa-Peña L, Vanner EA, Najafian N, Banach A, Nielsen E, Al-Khalil R, Akalin A, Talmage D, Shroyer KR. Keratin-17 Promotes p27KIP1 Nuclear Export and Degradation and Offers Potential Prognostic Utility. Cancer Res. 2015 Sep 1;75(17):3650-62. doi: 10.1158/0008-5472.CAN-15-0293. Epub 2015 Jun 24. PubMed PMID: 26109559. Evensen NA, Li Y, Kuscu C, Liu J, Cathcart J, Banach A, Zhang Q, Li E, Joshi S, Yang J, Denoya PI, Pastorekova S, Zucker S, Shroyer KR, Cao J. Hypoxia promotes colon cancer dissemination through up-regulation of cell migration-inducing pro-tein (CEMIP). Oncotarget. 2015 Aug 21;6(24):20723-39. PubMed PMID: 26009875; PubMed Central PMCID: PMC4653038. Li Y, Kuscu C, Banach A, Zhang Q, Pulkoski-Gross A, Kim D, Liu J, Roth E, Li E, Shroyer KR, Denoya PI, Zhu X, Chen L, Cao J. miR-181a-5p Inhibits Cancer Cell Migration and Angiogenesis via Downregulation of Matrix Metalloproteinase-14. Cancer Res. 2015 Jul 1;75(13):2674-85. doi: 10.1158/0008-5472.CAN-14-2875. Epub 2015 May 14. PubMed PMID: 25977338; PubMed Central PMCID: PMC4489986.

Row RH, Tsotras SR, Goto H, Martin BL. The zebrafish tailbud contains two independent populations of midline progeni-tor cells that maintain long-term germ layer plasticity and differentiate based on local signaling cues. Development. 2015 Dec 16. pii: dev.129015. PubMed PMID: 26674311

P A G E 6

Recent Student Publications (continued)

Aleem SU, Craddock BP, Miller WT. Constitutive Activity in an Ancestral Form of Abl Tyrosine Kinase. PLoS One. 2015 Jun 19;10(6):e0131062. doi: 10.1371/journal.pone.0131062. eCollection 2015. PubMed PMID: 26090675; PubMed Central PMCID: PMC4474922. Fan G, Aleem S, Yang M, Miller WT, Tonks NK. Protein-tyrosine Phosphatase and Kinase Specificity in Regulation of SRC and Breast Tumor Kinase. J Biol Chem. 2015 Jun 26;290(26):15934-47. doi: 10.1074/jbc.M115.651703. Epub 2015 Apr 20. PubMed PMID: 25897081; PubMed Central PMCID: PMC4481198. Hanes WM, Olofsson PS, Kwan K, Hudson LK, Chavan SS, Pavlov VA, Tracey KJ. Galantamine Attenuates Type 1 Diabe-tes and Inhibits Anti-Insulin Antibodies in Non-Obese Diabetic Mice. Mol Med. 2015 Aug 17. doi: 10.2119/molmed.2015.00142. [Epub ahead of print] PubMed PMID: 26322849. Cieniewicz B, Dong Q, Li G, Forrest JC, Mounce BC, Tarakanova VL, van der Velden A, Krug LT. Murine Gammaherpesvi-rus 68 Pathogenesis Is Independent of Caspase-1 and Caspase-11 in Mice and Impairs Interleukin-1β Production upon Ex-trinsic Stimulation in Culture. J Virol. 2015 Jul;89(13):6562-74. doi: 10.1128/JVI.00658-15. Epub 2015 Apr 8. PubMed PMID: 25855746; PubMed Central PMCID: PMC4468508. Escobar-Hoyos LF, Shah R, Roa-Peña L, Vanner EA, Najafian N, Banach A, Nielsen E, Al-Khalil R, Akalin A, Talmage D, Shroyer KR. Keratin-17 Promotes p27KIP1 Nuclear Export and Degradation and Offers Potential Prognostic Utility. Cancer Res. 2015 Sep 1;75(17):3650-62. doi: 10.1158/0008-5472.CAN-15-0293. Epub 2015 Jun 24. PubMed PMID: 26109559. Evensen NA, Li Y, Kuscu C, Liu J, Cathcart J, Banach A, Zhang Q, Li E, Joshi S, Yang J, Denoya PI, Pastorekova S, Zucker S, Shroyer KR, Cao J. Hypoxia promotes colon cancer dissemination through up-regulation of cell migration-inducing pro-tein (CEMIP). Oncotarget. 2015 Aug 21;6(24):20723-39. PubMed PMID: 26009875; PubMed Central PMCID: PMC4653038. Li Y, Kuscu C, Banach A, Zhang Q, Pulkoski-Gross A, Kim D, Liu J, Roth E, Li E, Shroyer KR, Denoya PI, Zhu X, Chen L, Cao J. miR-181a-5p Inhibits Cancer Cell Migration and Angiogenesis via Downregulation of Matrix Metalloproteinase-14. Cancer Res. 2015 Jul 1;75(13):2674-85. doi: 10.1158/0008-5472.CAN-14-2875. Epub 2015 May 14. PubMed PMID: 25977338; PubMed Central PMCID: PMC4489986.

P A G E 7

Predicted binding poses of tetrahydrocannabinol (THC) and cannabidiol (CBD) within human

Recent Student Publications (continued)

Aaron Neiman, Professor and Chair, was elected to Fellowship in the American Academy of Microbiology.

James Konopka, Professor of Molecular Genetics and Microbiology, was also elected to Fellowship in the American Academy of

Microbiology.

2015 Dr. W. Burghardt Turner Fellowship - Megan Mladinich, 1st year graduate student

2016 Dean's Award for Excellence in Service to Graduate Education by a Graduate Program Coordinator

We’re proud to report, our very own Joann Delucia, Graduate Program Coordinator for MCB & BSB.

Jinelle Wint, 2nd year graduate student – participated in the introduction and conclusion of the video highlighting “Pathways to

Undergraduate Research.” She explained the different opportunities for undergrads to be engaged in research.

Jinelle also participated in the 48-Hour Imagine Science Film Festival Competition. Her team won first place!

Hana Goto, 4th year graduate student – won 1st place award for Best Poster at NESDB (North Eastern Society of Developmen-

tal Biology)

Beth Harvey - recipient of UPenn Postdoctoral Fellowship for Academic Diversity

Kenneth Marcu - retired

Jorge Benach - retired

Welcome to our new MCB faculty: Ashley Snider – Assistant Professor, Department of Medicine; Luis Martinez - Associate

Professor, Stony Brook Medicine, Department of Pathology; Patricia Thompson-Carino - Professor, School of Medicine,

Department of Pathology; Jun Chung – Associate Professor, School of Medicine, Department of Pathology; Bruce Demple –

Professor, School of Medicine, Pharmacological Sciences

August 2015:

Jennifer Martinez – Visiting Faculty Member at Evergreen State College, Washington

Nadia Jaber – Health Communications Fellow at National Cancer Institute, Maryland

Shriya Sahu – Scientist at Prosetta Biosciences, California

Achraf Shamseddine – Returned to Medical School

Saadat Aleem – Returned to Medical School

December 2015:

Brandon Cieniewicz – Post-doc Scholar at Stanford University, California

William Haynes – Technology Commercialization Fellow at the Center for Biotechnology, Stony Brook

Xin Zhou – Postdoctoral Fellow at Integrated Cardio Metabolic Center (ICMC), Sweden

P A G E 8

Second Year Student Symposium – June 17th

New Student Orientation – Week of August 22nd

MCB, BSB, BCB and Genetics BBQ – August 25th (tentative)

Retreat – September 6th

Annual Christmas Party – December TBA

Please contact Lauretta with any news (awards, publications, etc.) to keep us all informed!

Lauretta Viteritti, MCB/BSB Admissions Coordinator

Lauretta.passanant@stonybrook.edu

May 2016

P A G E 9

Genome wide Copy Number Alteration analysis, performed at

single cell resolution