Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering

Annual Report 2017

10 YRS The Lokey Center 10 YRS

Annual Report 2017 2 Life Sciences and Engineering (LS&E) Infrastructure Center 6 Bioinformatics Knowledge Unit (BKU) 10 Technion Center for Structural Biology (TCSB) 14 General Activities 20 Science Updates

Pictured on cover: SiR-Tubulin Image in Live Human Neuronal Precursor Cells, courtesy of the Meller Lab Lokey Center I Annual Report 2017

Celebrating the 10th Anniversary of the Center

The Interdisciplinary Center celebrated its biology, bioinformatics, across different faculties 10th anniversary in 2017. Ten years ago, metabolomics, nano- to obtain initial results or Nobel Laureate Prof. Aaron Ciechanover optics, molecular/genomics data to prepare for large-scale and the great philanthropist and visionary neuroscience, antibiotic funding opportunities. Mr. Lorry I. Lokey drafted an ambitious resistance, etc. The interface and prospectus for a new “Interdisciplinary convergence between these disciplines As we celebrate the achievements of the Center for Life Sciences and Engineering.” will be lead to the emergence of new past decade, we also dedicate ourselves This initiative received strong support from discoveries that will impact and transform to a more promising future, with our Technion’s Management, whose policy was health care and therapeutics in the future. vision realized. Aiming to prepare and to develop new areas of research where lead the next generation of researchers in basic science combines with engineering The Center has advanced the research the most pressing challenges of the day, principles to tackle biological, biomedical of almost all the Technion faculties’ and consistent with its strategic plan and and medical questions and challenges. researchers. During the last decade, we focus on achieving its goals, this year the organized dozens of conferences, seminars Center launched a new initiative called Four inter-related dimensions and training workshops, inviting specialists “Biomedical Informatics Big Data Science.” have guided the Center’s work: and experts to our Center to share the new The main attraction of using “big data” is Innovative interdisciplinary research - technologies and their knowledge with our that decision-makers will be better able Enhancing the spirit of innovation and staff and students. We assist 120 labs to understand and make decisions about the core belief in the power of new ideas and 500 researchers annually. Our staff huge scale questions and challenges that emerging from collaboration between works closely with universities, research were previously unimaginable. We aim to different disciplines. institutions and industry across the country. turn massive amounts of genomic, imaging and clinical data into health breakthroughs Education – Creating the atmosphere Our infrastructure unit offers cutting edge where we can build better health profiles and the access to knowledge, to foster equipment in the fields of microscopy and better predictive models around collaborative relationships and to share and imaging, flow cytometry and next individual patients in order that we can ideas by organizing international and generation sequencing and structural better diagnose and treat disease. domestic conferences, seminars and biology, providing researchers with workshops. high-end equipment as well as support Ten years on, the Lokey Center has services. The LS&E Infrastructure Center is achieved more than anyone could have Infrastructure – Providing researchers with operated by staff that trains researchers ever imagined. It helped change the Life cutting-edge technologies, equipment and on the various instruments and helps Sciences at Technion for the better and related expertise, education and training. conduct the experiments. has done a great job in lifting up some of the important components needed for Support Systems – Creating systems Our support systems offer bioinformatics academic excellence. to manage and support research and consulting services in applying the tools of its outputs. Bioinformatics and Data Management to Even with all the center’s accomplishments, help drive research, providing researchers our work is still far from finished and we Today the Lokey Center has grown to a with bioinformatics strategies and will continue to strive for excellence! robust, highly interdisciplinary home for a methods. An additional component of wide range of scientific fields: single cell our support system offers seed grants – molecule technology, computational biology internal funds intended to help generate Prof. Roy Kishony, Director and machine learning, biomedical optics more compelling grant submissions, and imaging, systems biology, synthetic initiate and foster new collaborations LIFE SCIENCES AND ENGINEERING (LS&E) INFRASTRUCTURE CENTER

Headed by Dr. Maayan Duvshani-Eshet Lokey Center I Annual Report 2017

The Life Sciences and Engineering (LS&E) Infrastructure Center was established in 2007 under the auspices of the Lorry I. Lokey Center. The LS&E Infrastructure Center provides services on cutting-edge technology installed in its facility, including training and teaching to all researchers throughout the Technion campus and nationwide.

The Center offers state-of-the-art technologies for researchers on the front-line of life sciences and engineering fields. The technology platforms offer services to all Technion researchers, Israeli academia and other Israeli institutes, as well as for hospitals, government research centers and industry. In addition, the Center is active in technology development and teaching to ensure that Technion scientists, and all users, will have access to the latest methodologies and knowledge.

The Center provides service For this reason, the Center has designed manual with three facilities: user guides for each piece of equipment. In addition, the Center organizes special seminars, Bio-Imaging – Light Microscopy Facility workshops and conferences in each of the Flow Cytometry Facility fields of the Center’s facilities. The Center also Advanced Genomics – Technion Genome participates in academic courses in these fields. Center (TGC) The LS&E Infrastructure Center, which is at the Investments in the top equipment and trained forefront of technology, continues to expand for personnel enable the Center to provide efficient the benefit of researchers in life sciences and services to the whole research community. engineering. Plans for the coming years include the addition of more sophisticated systems such In the last 10 years, since its establishment, as High Throughput-High Sensitivity Cell Sorter the Center has been headed by Dr. Maayan (BD-Influx), new imaging technology and new Duvshani-Eshet. The Center is constantly growing sequencing technology. and in 2017 the Center comprised 14 highly trained staff, most of them holding a PhD degree. It is also scheduling an additional academic course in the fields of light microscopy and The Infrastructure Center’s agenda is that flow cytometry. every user should have firm knowledge of the instrumentation and the field they are working in.

3 Major Achievements Bioinformatics pipelines – the TGC in 2017 bioinformatics team developed new pipelines for the Next-Generation-Sequencing analysis, in particular, for the Oxford NanoPore data, CelSeq During 2017, the Center maintained its facilities data and Exome analysis. and professional service to researchers. New protocols were developed and new Imaris Image Analysis Workshop – a full pipelines were implanted. In addition, new day hands-on workshop on the Imaris software. instrumentation was added. A few of the year’s The workshop was given to 16 participants. achievements include the following: Flow Cytometry Symposium – a full day Image Stream – Flow Imager: The Image symposium dedicated to “flow as a research tool” Stream is a flow cytometer equipped with a and application of Flow cytometry in the Life camera, so that the instrument produces multiple Sciences Research. high-resolution images of every cell directly in flow. This allows massive analysis of cells and LS&E User Symposium – this special makes new applications possible. symposium was dedicated to research done with the LS&E Infrastructure Center. The symposium BD Influx cell sorter was purchased and comprised of 11 talks by users from different should arrive in Q1 of 2018. This is a high- faculties on various topics. The symposium sensitivity high-throughput cell sorter. It will be presented advance research taking place at the the first and only BD Influx cell sorter in Israel. Center and was a major success.

CelSeq - A single cell sequencing protocol Continuing to participate in the academic that was developed in Professor Itai Yanai’s lab courses given in collaboration with the Center’s (Hashimshony et al. Genome Biol. 2016), offered at facilities. the Center as a service for all users. The experimental design includes all steps of the protocol: from Increased number of publications were single cell separation and sorting, to the unique published in peer-reviewed papers that utilized sequencing design and bioinformatics analysis. the Infrastructure Center for their research.

Nanopore Technology - The Oxford NanoPore The number of labs and research groups sequencing technology was implanted at the TGC. using the Infrastructure Center has grown from This technology enables sequencing of ultra-long 204 in 2016 to more than 223 in 2017. Of these, 66 reads (hundreds of KB) using a direct (PCR free) DNA labs are from Israeli academia (non-Technion) sequencing method. These unique features have and 29 labs are from industry, hospitals and multiple advantages in a variety of applications government centers. including de novo assemblies, detection of genomic rearrangements, duplications and splicing junctions. Lokey Center I Annual Report 2017

Research at LS&E on the front lines of scientific research: Infrastructure Center > Upgrade the Light-Sheet microscopy system for clearing techniques. > High sensitivity flow cytometer sorter The LS&E staff is constantly participating in > New sequencer – for long reads courses, conferences and workshops in Israel > High throughput fluidics system for single and worldwide to study new technologies and cell sequencing genomics. become familiar with the newest technologies and equipment. Computerizing and automating the whole workflow at the Technion Genome Center: a new The LS&E Infrastructure Center promotes research Internet site will control all orderings and will in a large range of fields, including medicine, follow all samples as they go through the biology, biotechnology and food engineering, sequencing and bioinformatics pipelines. biomedical engineering, physics, chemistry and chemical and mechanical engineering. Continuing to organize special seminars, conferences, workshops and education training The Center provides services from designing the in the fields of microscopy, flow cytometry and experiments to working on the instruments and genomics. data analysis. Attending international conferences, Selected examples of research projects that workshops, tutorials and courses to keep all staff utilized the LS&E Infrastructure Center and updated in cutting-edge scientific technology. acknowledged it in high impact journals include: In 2018 – the LS&E Infrastructure Center will L. Levy, L. Anavy, O. Solomon, R. Cohen, M. enlarge its space and will encompass an Brunwasser-Meirom, S. Ohayon, O. Atar, S. additional wing on the first floor of the Emerson Goldberg, Z. Yakhini, R. Amit, A Synthetic Oligo building. The microscopy facility will then have Library and Sequencing Approach Reveals an more space and the Genome Center will take Insulation Mechanism Encoded within Bacterial over a whole wing of the building. s54 Promoters. Cell Reports 2017 K.

Krinsky, M. Kaduri, A. Zinger, J. Shainsky- Staff (2017) Roitman, M. Goldfeder, I. Benhar, D. Hershkovitz, I. Schroeder, Synthetic Cells Synthesize Inbal Adir Therapeutic Proteins inside Tumors. Adv Dr. Efrat Barak Health Mater. 2017. Lavi Bar-Ziv Dr. Nitsan Dahan Anastasia Diviatis Objectives for 2018 Dr. Ma’ayan Duvshani-Eshet Dr. Tamar Gettengo In 2018, the Center will continue to provide Dr. Tamar Hashimshony service, support and training on the various Dr. Tal Katz-Ezov instrumentations located at the Center. Julia Kelman Dr. Shay Kirzner Purchasing new cutting-edge equipment to Dr. Efrat Kligun enable high level academic research and thus Dr. Yael Lupu-Haber position the LS&E Infrastructure Center facility Ahinoam Perl 5 BIOINFORMATICS KNOWLEDGE UNIT (BKU)

Headed by Prof. Yael Mandel-Gutfreund Lokey Center I Annual Report 2017

The mission of the Technion Bioinformatics Knowledge Unit (BKU) is to empower life sciences researchers at the Technion and its affiliated hospitals by providing bioinformatics consulting and assisting researcher in bioinformatics and statistical analyses of their data, specifically data coming from high throughput experiments.

The BKU’s activity is closely tied to the dynamic development of biological and biomedical research as reflected in its main research topics:

Genomics, Transcriptomics and Proteomics Data Integration and Data Mining Structural Bioinformatics: Protein and Small Molecule Docking, Molecular Dynamics and Molecular Moldeling

7 Main Objectives of the BKU M. Truman-Rosentsvit, D. Berenbaum, L. Spektor, LA. Cohen, S. Belizowsky-Moshe, Service: Continue to provide bioinformatics L. Lifshitz, J. Ma, W. Li, E. Kesselman, I. Abutbul- consulting, computational methods and tools to Ionita, D. Danino, L. Gutierrez, H. Li, K. Li, H. Lou, researchers and medical doctors. M. Regoni, M. Poli, F. Glaser, TA. Rouault, EG. Meyron-Holtz. Ferritin is secreted via 2 distinct Research and Development: Expand the nonclassical vesicular pathways. Blood Epub expertise of the unit by acquiring new skills in 2017 Oct 26 Jan 18; 131(3):342-352. state-of-the-art bioinformatics strategies and methods to ensure the best consulting and M. Chojnacki, W. Mansour, DS. Hameed, useful results. RK. Singh, F. El Oualid, R. Rosenzweig, MA. Nakasone, Z. Yu, F. Glaser, LE. Kay, D. Education: Organize bioinformatics courses Fushman, H. Ovaa, MH. Glickman. Polyubiquitin- and workshops to introduce cutting edge Photoactivatable Crosslinking Reagents for technologies and research, new bioinformatics Mapping Ubiquitin Interactome Identify Rpn1 as approaches, tools and algorithms. a Proteasome Ubiquitin-Associating Subunit. Cell Chem Biol. 2017 Apr 20; 24(4):443-457.

Major Achievements M. Romero-Durana, C. Pallara, F. Glaser, J. Fernández-Recio. Modeling Binding Affinity of in 2017 Pathological Mutations for Computational Protein Design. Methods Mol Biol. 2017; 1529:139-159. Research Projects S. Chornyy, A. Parnis, M. Shmoish, D. Cassel. During 2017 the BKU participated/initiated High abundance of ArfGAP1 found in the mossy 36 different research projects, of which 12 fibers in hilus of the dentate gyrus region of the have been completed. The projects are in mouse brain. PLoS One. 2017 Dec 14; 12(12). collaboration with Technion researchers from a variety of faculties, including the Faculty of Grant Awards Biology, Faculty of Biotechnology and Food Engineering, Faculty of Medicine, Faculty of In 2017 the BKU joined the international Biomedicine, Faculty of Computer Sciences consortium of universities & hospitals from and Faculty of Civil Engineering. These projects Poland, Turkey, Germany, Italy and Israel which resulted in 4 publications that have been granted the prestigious ESPE Research Grant, published in high impact factor journals (see awarded by the European Society of Paediatric below) and 3 papers submitted. Endocrinology. The aim of the research plan of the consortium is to extract medical records from obese children (including steroidal Lokey Center I Annual Report 2017

signature, genomic and chemical features) An advanced R-Bioconductor workshop will and to integrate the data in order to learn the take place in July 2018. This follows on from the dynamics of weight changes in obese children. very successful workshop that took place in 2016. As part of this project, the BKU will contribute in The new workshop is planned to be an advanced developing computational tools to predict who course, concentrating on different methods of will develop liver diseases and help provide statistical analysis to analize and interpret NGS recommendations to the medical teams. data. In addition the BKU is planning to organize an advanced molecular dynamics course which will follow up on the very successful Objectives for 2018 international AMBER course organized by the BKU and hosted at the Technion in 2015. Organization of workshops, courses and tutorials Other Activities

An advanced AMBER course will take place in Continue to provide support and consulting March 4-8, 2018. This will be the second five-day to current and future projects. course on Amber, a biomolecular simulation package. This course will be led by three leading Attend international conferences, workshops, world experts in the MD field, Prof. Adrian Roitberg tutorials and educational programs to be kept (Department of Chemistry, University of Florida, updated on scientific frontline progression. USA), Prof. Carlos Simmerling (Stony Brook University and Prof. Tom Kurtzman (Lehman College, City University of New York). Staff

The workshop will consist of a combination of Dr. Hagay Enav lectures and hands-on tutorials that will provide Dr. Fabian Glaser a comprehensive introduction to the field of Dr. Guy Horev molecular dynamics simulation and molecular Prof. Yael Mandel-Gutfreund (academic advisor) simulation focusing on practical application of the Dr. Michael Shmoish AMBER MD software. The workshop consists of a series of short lectures followed by hands-on lab Students working as assistants: sessions that cover the use of AMBER and Amber Gur Hevron and Rina Ben-El Tools and the theory behind it. Currently there are 25 participants registered; 15 from different universities and institutes in Europe and 10 from different universities in Israel.

9 TECHNION CENTER FOR STRUCTURAL BIOLOGY (TCSB)

Headed by Dr. Yael Pazy Benhar Lokey Center I Annual Report 2017

During the last year, the TCSB has continued to expand its work with research groups from both the Technion and the broader Israeli scientific community. The TCSB has contributed greatly in conducting extensive crystallization experiments, biophysical analyses of various macromolecules, and in many successful data collections, both in-house and during five trips to the European Synchrotron Radiation Facility. Our staff assisted multiple projects leading to discovery of new protein structures. TSCB also provided assistance in structure-function related projects. These different projects yielded at least four new publications and five submitted papers, acknowledging our work.

Furthermore, the TCSB has expanded its role Outreaching in education. TCSB staff participated in several courses to give an introduction to structural During 2017, the TCSB staff actively biology and protein crystallography in addition participated in several courses, aiming to to conducting hands-on laboratory classes at educate and expose young researchers, the TCSB. graduate students and youth, to the significance of research in the field of protein Currently we are working with more than crystallography. Our work included introduction twenty different scientific groups on a wide to the services given by the TCSB, an range of structural related projects, spanning introduction seminar and tours of our facility. from biophysics of macromolecules through We participated as guest lecturers in the crystallization, data collection and structure Advanced Protein Course and in the Genetic determination. The TCSB has broadened its Engineering Laboratory at the Technion. users beyond the Technion scientific community to labs from other universities, research Furthermore, we conducted a hands-on institutes and industry. crystallization laboratory at the TCSB for Tel-Hai College students.

In addition, we contributed to the community by providing lectures to high-school students, through the Sydney Warren Academic Youth Center at Tel-Hai, about the importance of structural biology.

11 Expanding the capabilities of the TCSB and staff training

The Biophysical unit at the TCSB employs In May we participated in a course at the the Microscale Thermophoresis (MST), the Macromolecular Crystallography School in sensitive Isothermal Titration Calorimeter (Nano Madrid, Spain (MCS2017). During this course we ITC) and our newly purchased Differential were exposed to new programs and technologies Scanning Flourimetry technology (nanoDSF). assisting in three dimensional structure With these instruments, TCSB provides our solutions of macromolecules. Soon after, we users with a wide range of biophysical analysis installed new programs and updated older data regarding their protein stability and ability programs on our computers at the TCSB to bind other small molecules or proteins. In Graphics unit. These updates have contributed June we conducted a nanoDSF-MST workshop greatly to our ability to assist users with their which helped spark new and exciting experiments work in solving structures after data collection that provided new insights and new ideas for and attracted students to work and collaborate better understanding of protein properties. with us at the TCSB.

Furthermore, we have implemented new Currently, we are working on a proposal to protocols and guidelines for researchers that further expand the capabilities of the TCSB for bring new projects to the TCSB. We currently protein production and purification. We believe conduct several preliminary tests and we require that the addition of such a unit will assist the researchers to provide us with basic information scientific community at large and will provide regarding the purity of their proteins, prior to much needed expertise and equipment. initiating crystallization and binding experiments at the TCSB. With this data in hand, we are gradually gaining experience and we are now able to better correlate DSF results and pre-crystallization tests with successful future experiments. As a result, we can guide users how to better prepare their samples.

Lokey Center I Annual Report 2017

Major Objectives Plans for 2018 In addition to our previous objectives, namely: We will continue to work to achieve our major goal in highlighting the benefits of incorporating to provide support and assistance to all and conducting structural biology research TCSB users in all stages of structure in any biological or biomedical project. This determination, three dimensional analysis and year we hope to expand our staff, which macromolecular structural projects; will enable us to better plan and conduct professional workshops and courses that will to establish teaching programs, targeted bring the knowledge and “know how” of protein workshops and training for students of all levels crystallography techniques and the importance at the TCSB; of protein research, on a molecular level, to students and researchers at all levels. to reach out to new users and promote research in the field of structural biology, Furthermore, we would like to conduct a survey particularly using macromolecular of various scientific laboratories and expose crystallography techniques; them to the capabilities of the TCSB. We believe that many labs are not aware of the wide We intend to further expand our collaborations capabilities of the TCSB, on the one hand, and with other structural biology units in Israel, the possible benefits of advancing their research such as the close collaboration with the by providing three dimensional and biophysical Macromolecular Crystallography Research data, on the other. Center at Ben-Gurion University. We also plan to enhance our interaction with other We will continue to reach out to other protein facilities within the Technion, such as the BKU related units and form a network of services (Bioinformatics Knowledge Unit) in order to for users to expand their studies using diverse prepare working strategies that will advance methods such as bioinformatics, genomics, various projects and scientific research. and proteomics, and assist users with protein expression and purification.

Staff

Dr. Efimov Vera Dikla Hiya Dr. Yael Pazy Benhar

13 GENERAL ACTIVITIES

Headed by Shira Sagee

Applying deep learning to medical data makes it possible to address a large variety of biomedical issues in a much more efficient and inexpensive manner Lokey Center I Annual Report 2017

manner. The conference was well organized by Dr. Kira Radinsky and Prof. Roy Kishony, whose unique synergy resulted in a precise mix of speakers who covered a wide range of topics – from practical applications of data science in 1ST International Conference medical care to ethical precision medicine and next generation healthcare. In the course of two on Biomedical Informatics days, 24 eminent speakers from around the world shared their latest research findings with the For two days in December 2017, researchers international audience. and students converged on the Technion to hear from the world’s foremost experts on one Technion President Prof. Peretz Lavie of the most dynamic and groundbreaking fields emphasized the significance of the conference’s today: using deep learning and big data to venue: “We’re living in a fascinating era for improve healthcare scientific research, an era where extensive data is used to improve diagnoses and treatment. The “Biomedical Informatics – Big Data Science There is no doubt that Israel in general, and the – Vision, Promises and Challenges” Conference Technion in particular, is an excellent location for hosted by the Technion drew a large audience such a pioneering conference, since the Technion eager to hear about the latest developments is one of the only technological institutions in in this fascinating field, which is increasingly the world that comprises a medical school.” becoming the focus of research in the academic, public and private sectors worldwide. Applying The conference kicked off with a captivating deep learning to medical data makes it possible keynote lecture by Jonathan Adiri, a serial to address a large variety of biomedical issues entrepreneur and former Chief Technology in a much more efficient and inexpensive Adviser to President Shimon Peres. His most

15 recent start-up designed a smartphone app that makes it possible to and Engineering at the Technion, lectured perform simple medical tests from home. about the evolution of antibiotic resistance and Adiri’s lecture, “The Era of Permanent new ways to combine drugs that can slow down Revolution,” provided a brilliant overview on or even reverse this evolution. He explained how the pace of technological change in recent recent studies will hopefully enable genome- years from a global perspective. He contended based diagnostics that will guide more resilient that the ‘big story’ is not only that processing patient-specific multi-drug treatments. capacity is growing exponentially, but that at the same time costs are plummeting – and Prof. Shai Shen-Orr of the Technion’s Faculty of these parallel trends together account for the Medicine addressed the ongoing efforts to build current ‘tech tsunami.’ a cell-centered view of genomic data that can be integrated with primary immunology literature. He focused on the subject of leveraging Lectures by Technion public data to improve the translation from Professors mice modeling to humans. According to Prof. Shen-Orr, variability is key to understanding Many interesting lectures at complex systems and a new paradigm is needed the conference were delivered for studying data, and combining data and by Technion professors. Prof. knowledge in a cell-centered framework. Kira Radinsky, the highly- esteemed Technion prodigy Experts from Around the World who is now a Visiting Professor at the Technion The conference also featured distinguished as well as chief scientist of researchers from around the world. Dr. Nigam eBay Israel, gave a riveting talk about predicting Shah, an Associate Professor of Medicine at the future of medicine using data science. Stanford University, described the initiative he She explained how the system she developed leads, which takes data from electronic health is capable of predicting cholera epidemics records and uses machine learning to help with 92% accuracy, among other things. Her doctors answer clinical questions, generate prediction system is based on an algorithm that insights and make predictions. Dr. Hannah identifies patterns culled from large amounts of Bayer, who is a neuroscientist from New York internet query logs. University, spoke about the HUMAN Project, of which she is Chief Scientist. This project Prof. Roy Kishony, who is the Director of the Lorry studies 10,000 New York City residents over I. Lokey Interdisciplinary Center for Life Sciences a period of 20 years, tracking everything from Lokey Center I Annual Report 2017

financial and social data to environmental and Breakthrough in Inhibiting Tumor Growth health factors, mainly using a phone app that gathers the data passively. Dr. Soren Brunak, a Prof. Ze’ev Ronai of the Technion’s Rappaport medical informatics expert from the University of Faculty of Medicine, lectured about the important Copenhagen, Denmark, lectured about disease role of gut microbiome in the context of immune trajectories from population-wide data in the system interactions in the development of context of underdiagnosed diseases. melanoma tumors. He described his research on the RNF5 protein in mice, and the discovery John Wilbanks, Chief Commons Officer at that it affects their gut microbiome as well as the Sage Bionetworks, opened the second day of inhibition of tumors. the conference. He presented The Consent to Research (CtR) platform focused on putting the Prof. Ronai, who is the head of the Technion participant at the center of the data collection Integrated Cancer Center, has conducted a number procedure: specifically by acknowledging of groundbreaking studies related to tumor growth. possible risks to both individual participants His group also recently revealed the critical role as well as sub-populations of participants, of the Sharpin protein in controlling the PRMT5 providing opt-in settings for broad data sharing, enzyme, which is an important factor in the and the development of an open research development of cancer tumors. The new discovery, ecosystem built upon a social contract between which confirms the role of Sharpin in controlling researchers and research participants. PRMT5, makes it possible to identify cancer patients for whom inhibiting PRMT5 is expected to Dr. Ran Balicer, Director of the Clalit Research be a more efficient therapy. Institute, spoke about the future challenges in medicine from the point of view of the service Prof. Ronai’s research group discovered that many provider. “We have had several successes in types of cancer are associated with high levels of predicting diseases and adapting treatment to Sharpin, including melanoma, prostate cancer, breast specific patients, and we do everything in order cancer and lung cancer. They found that inhibiting to improve our use of technology for the patient’s this protein blocks the paths that accelerate tumor benefit,” he revealed.Dr. Varda Shalev, Director growth. According to Prof. Ronai, “Our analysis makes of Maccabi Health Care Services’ Institute for it possible to estimate the patient’s level of future Research and Innovation, lectured about how response to being treated with PRMT5 inhibitors: Maccabi is expending a great deal of effort in when the Sharpin level is low, the treatment is using innovative technology to analyze data in expected to be more productive.” This remarkable the most effective ways. She cited as an example research was carried out at the Technion in Maccabi’s cooperation with conference organizer cooperation with scientists at the Sanford Burnham Prof. Kishony, analyzing urine tests carried out Prebys Medical Discovery Institute in La Jolla, all over Israel. California and Shantou University in China. 17 Lokey Distinguished of C. elegans. As a recognition of her outstanding contribution to science, Prof. Dernburg received Lecture Series 2017 the Scholar Award in 2006, the Edward Novitski Prize in in 2011 and was selected as On May 15 we held a mini-symposium on HHMI Investigator in 2008. She is also a member “Genetics and Biophysics of Chromatin of the “Genetics Society of America” and the Dynamics and Recombination” delivered by “American Society for ” Prof Abby Dernburg from the Department of Molecular and Cell Biology at University of California, Berkeley, CA and Prof. Gary Karpen from the Department of Molecular and Cell Biology, University of California, Berkeley, CA.

Prof. Karpen talked about “Biophysics meets chromatin: Is just a phase?” Prof. Karpen obtained his Ph.D. in Genetics in 1987, where he worked on the role of nucleolus organization on rDNA function in in the lab of Charles Laird at Prof. Dernburg talked about “A liquid Washington University. He continued to work with crystalline compartment between meiotic Drosophila during his postdoc in the lab of Allan regulates .” Spradling at the Carnegie Institute. Prof. Karpen Prof. Dernburg did her Ph.D. with John Sedat at started his own lab at the Salk Institute, La Jolla in the University of California in San Francisco; 1991. After being in San Diego for 12 years, during Dernburg explored diverse aspects of which he obtained his professorship at The Salk biology in Drosophila, leading to Institute for Biological Studies, he moved to the major discoveries in the field including special Lawrence Berkeley National Lab (LBNL) in 2003. regions of each chromosome, called pairing Prof. Karpen became director of the LBNL Life centers, that help the homologous chromosomes Sciences Division in 2011. recognize one another. Prof. Dernburg pursued her efforts in developing high-resolution The Karpen lab has a long-standing interest in cytological tools to study meiotic chromosomes chromatin structure and function, with a special behavior during her post-doctoral work on C. emphasis on heterochromatic DNA regions. The elegans in Anne Villeneuve’s lab at Stanford. current projects in the lab range from centromere Next, Prof. Dernburg established her own lab in formation and function, to the role of lncRNAs, Berkeley and continued to investigate how ageing, and DNA repair in heterochromatin chromosomes find and synapse with their formation and maintenance. Prof. Karpen’s homologs during by combining discoveries were published in top journals and high-resolution imaging of chromosomes in situ earned him many prestigious awards and honors. and in vivo with the molecular genetic advantages Lokey Center I Annual Report 2017

iGEM Recap

Nine students from different backgrounds and faculties met, united by their drive to change the world. In iGEM, young scientists are called upon to create a multidisciplinary overwhelmed and inspired by the sheer team, come up with an original idea, perform magnitude of the conference. Each team was independent and high quality research, and in unique in their project and background, but, in a the end, present their findings to the scientific larger sense, all the teams were unified by their community in an international conference while motivation and by the joint experience they had competing with over 300 teams. undergone. After an intense weekend the judges submitted their votes, winners were announced, In hindsight, it is difficult to summarize the and medals were given out. While we did not tremendous journey our team has made. We win the overall competition, we were awarded discussed countless ideas, reviewed hundreds a gold medal, and we are very proud of this of papers, conducted dozens of experiments achievement. and spent many sleepless nights in the lab. We experienced heart wrenching failures and Looking back on this whole experience, we blissful moments of success, and after months are thrilled with our accomplishments and of hard work, we finally flew to Boston for the simultaneously humbled by the scope and final competition. nature of modern science. None of this would have been possible without our dedicated The final scientific conference, also known as mentors and professors, and without our the “Giant Jamboree,” held in September 2017, generous sponsors. We owe them both a was a surreal experience. Over 5,000 students tremendous debt of gratitude for allowing us to and scientists, from all corners of the earth, pursue our ideas and for providing us with this gathered for three days of presentations, posters incredible opportunity. and demonstrations. The delegation was

19 SCIENCE UPDATES

Lokey Center Researchers

KAPLAN LAB

BRIK LAB FUCHS LAB LADANIEL LAB B S Lokey Center I Annual Report 2016

KISHONY LAB SHECHTMAN LAB

MELLER LAB SHLOMI LAB

21

Lokey Center I Annual Report 2017

Total Chemical Synthesis of Ester-Linked 1. Suman Kumar Maity, Muhammad Jbara, Ubiquitinated Proteins Unravels their Guy Mann, Guy Kamnesky and Ashraf Behavior with Deubiquitinases Brik*,Total Chemical Synthesis of Histones and their Analogues Assisted by Native Chemical BRIK LAB Ubiquitination is a posttranslational modification Ligation and Palladium Complexes, Nature (PTM) which targets proteins for a variety of Protocols, 2017, 12(11):2293-2322. processes, such as proteasomal degradation, ER-associated degradation and intracellular 2. Pushparathinam Gopinath, Atif Mahammed, trafficking. The ubiquitin (Ub) monomers form a Tal Eilon-Shaffer, Mickal Nawatha, Shimrit chain in which its C-terminal Gly can be linked Ohayon, Doron Shabat*, Zeev Gross* and Ashraf to any of the seven available Lys side chains Brik*, Switching Futile para-Quinone to Efficient or the N-terminus of the preceding Ub, yielding ROS Generator: Ubiquitin Specific Protease-2 a large diversity of polyUb chains. Ub or any Inhibition, Electrocatalysis and Quantification, of the polyUb chains can be linked to a protein ChemBioChem, 2017, 18,1683 –1687, Highlighted in substrate through a Lys residue of a protein via Cover Page. an isopeptide bond. In addition, unusual ester or thioester linkages through Ser/Thr and Cys, 3. Muhammad Jbara, Noga Guttmann-Raviv, respectively, can be formed. Like many PTMs, Suman Kumar Maity, Nabieh Ayoub* and Ashraf ubiquitination is a reversible process where Brik*, Total Chemical Synthesis of Methylated deubiquitinases (DUBs) disassemble the Ub Analogues of Histone 3 Revealed KDM4D as a chains or the ubiquitinated proteins, therefore Potential Regulator of H3K79me3, Bioorganic and playing crucial roles in Ub signalling. Medicinal Chemistry, 2017, 25(18):4966-4970.

Due to the lack of suitable tools to 4. Muhammad Jbara, Suman Kumar Maity, homogeneously produce ester linked Ashraf Brik*, Palladium in the Chemical Synthesis ubiquitinated proteins, their exact physiological and Modification of Proteins, Angewandte Chemie, roles and biochemical behavior remained 2017, International Edition, 56,10644 –10655. enigmatic. We reported (Chemical Science, 2018), for the first time, on the development 5. Somasekhar Bondalapati#, Emad Eid#, of a novel synthetic strategy based on total Sachitanand M. Mali, Cynthia Wolberger, Ashraf chemical synthesis of proteins to construct Brik*, Total Chemical Synthesis of SUMO-2- ubiquitinated proteins, where ubiquitin is linked Lys63-linked Diubiquitin Hybrid Chains Assisted to the substrate via an ester bond. In this study, by Removable Solubilizing Tags (# these authors we prepared ester- and isopeptide-linked contributed equally), Chemical Science, 2017, 8, ubiquitinated α-globin and examined its relative 4027-4034. behavior with various deubiquitinases. We found that deubiquitinases are able to cleave the ester 6. Sachitanand M. Mali, Sumeet K. Singh, Emad linkage with different efficiency relative to the Eid, and Ashraf Brik*, Ubiquitin Signaling: isopeptide-linked substrate. These results may Chemistry Comes to the Rescue, Journal of indicate that ester-linked ubiquitinated proteins American Chemical Society, 2017, 139, 4971−4986. are natural substrates for deubiquitinases. This (Highlighted in Spotlights on Recent JACS novel platform opens the door to investigate in Publications). more detailed analysis the effect of the ester connectivity on various aspects of Ub signaling (like Ub location and specific type of ester bond) and whether such a linkage could be another layer of regulation.

23 DANIEL LAB DANIEL

The Laboratory for Synthetic Ongoing Projects: Biology and Bioelectronics Molecular and Adaptive Genetic The central goal of research at the lab is to use Networks for Intelligent Computation and principles inspired by electrical engineering Bio-Inspired Technology (analog circuit design and logic gates) and The construction of synthetic gene networks and neural networks (supervised learning) to build biological systems are receiving widespread adaptive systems with emergent collective attention as a novel engineering field that parallel computational abilities in living cells applies design principles of electrical and and integrate them with nano-electronic computer engineering into living cells, for circuits. We build our own genetic networks biomedical and biotechnological applications. and study their functions and performance in Yet, the dominant digital design-based several types of organisms. Our work has wide computational paradigm has failed to both applications in medicine, biotechnology, and scale-up the architecture of synthetic gene biomedical electronics. networks beyond a few gates and build adaptive biological systems. This failure primarily stems Important Scientific Achievements: from the fact that biology is not purely digital, and combines analog signals for processing > Established the analog synthetic biology field and actuation (e.g., neural networks). In our lab, (Daniel et. al. 2013). We built the first analog we propose a novel cognitive neural biology- computer in bacteria using a minimum motivated framework, inherently present number of proteins. in evolutionary biological systems, to build > Mapped biological systems to analog adaptive gene networks with emergent collective electronic circuits (Daniel et.al. BIOCAS 2011). parallel computational abilities. This framework We defined a set of design principles of is based on an abstract mathematical morphing biological networks into electronics. transformation that maps architecture of neural > Developed low-cost whole-cell biosensors networks onto molecular biological networks. based on a single photon avalanche diode (Daniel et. al. 2008). Lokey Center I Annual Report 2017

Synthetic Robust and Large-Scale Gene Integrated Genetics and Memristors Networks: Towards Next-Generation Living Breaking through the Scaling Limits of Bio-Computers Moore’s Law One of the main aspects of synthetic biology “Cytomorphic electronics” is a novel field that research is the study of the design principles was introduced recently in the design of bio- of biological systems by applying forward inspired, ultra-low power, analog-digital circuits engineering. Scaling the architecture of synthetic with parallel computational abilities (beyond gene networks and the construction of robust Von-Neumann architecture) and in the study biological systems are expected to provide new of biological systems. Cytomorphic electronics insights into the fundamental mechanisms that aims to (1) simulate cells, organs, and tissues, cells utilize to make decisions via genetically including the stochastic behaviors of single cells encoded molecular networks. This work aims and their cell-to-cell variations, distortions and (1) to delineate the fundamental principles cross-talks, using supercomputer-integrated required to engineer robust gene networks in electronics. Such simulations are extremely living cells that can reliably function in changing computationally intensive, e.g., solving 4000 environments and (2) to define the biophysical gene regulation stochastic reactions in fundamental elements needed for engineering Escherichia coli bacteria using digital computer large-scale gene networks in living cells. These can take weeks or even several months. objectives will be the first step towards creating (2) Design of novel large-scale synthetic living bio-computers equipped with biological biological systems by providing a fast and knowledge that can interact with our bodies and simple simulation/emulation framework. (3) environments to execute complex tasks under Design of molecular biology-inspired electronic specific activation conditions. circuits and networks with uniquely emergent characteristics and concepts, to be adopted to realize energy efficient hardware, just as neuroscience has led to biologically inspired electronic circuits.

25 FUCHS LAB critical questions: During thisyear we have focused onseveral of stem cell biology, regeneration andcancer. to conduct ground breaking work inthefields the world. Theseresearchers have beenable exceptional scientistswhocome from allover grown significantly andisnow comprised of10 During thecourse of2017ourlaboratory has decreases cell numberandreduces sebaceous of caspase-3 diminishescell proliferation, cell elimination.Deletionorchemical inhibition cells oftheepidermis,butdoesnotinstruct is specifically activated intheproliferating of cell proliferation andorgan size. Caspase-3 apoptotic role ofcaspase-3 asakey regulator program. However, we revealed asurprisingnon- roleimportant inimplementingthecell death in theactivation ofcaspase-3, whichplays an Normally isperceived to culminate regulate proliferation andorgan size. that thekey apoptotic protein caspase-3 can vivo, Dr. Yosefzon andhercolleagues have shown grafting studiesas well aschemical inhibitionin genetically modifiedmice, Lentiviral vectors, both organ size andskinregeneration. Utilizing anovelunearthed mechanismthatregulates Pioneering work ledby Dr. Yahav Yosefzon has in biology:How isorgan size controlled? In thisproject we setoutto answer akey question How isorgan size regulated? regulation affect thesesignalingpathways. now seeks to understand how different layers of Roi Ankawa, adirect track PhDstudentinthelab journal MolecularCell. accepted for publication intheprestigious findingshaveThese important recently been proliferation andorchestrate organ size. machinery can berefocused to regulate cell molecular mechanismshows how theapoptotic organ size augmentation.Thisimportant activation ofcaspase-3 leadsto YAP-dependent a vitalregulator oforgan size. Accordingly, activation andnucleartranslocation ofYAP, is cleaved by caspase-3, thusfacilitating the mechanism, we demonstrate thatα-Catenin gland size invivo. Exploringtheunderlying remarkable that even thoughSCsare featured elimination relatively untouched. Itisquite differentiation, leaving mechanisms for SC cell (SC)field focus onself-renewal and Currently, many investigations inthestem in epidermalhomeostasisandregeneration. HFs uponinjury, indicating they play acrucialrole epidermal repopulation andtheneogenesisof Furthermore,the IFE. thesecells contribute to that thesemultipotent SCsare key inmaintaining time. Multicolor lineagetracing analysis reveals be easily expanded invitro for extended periodsof state, express auniquegene signature andcan These uniquecells are retained inaquiescent located inthelabelretaining zone ofthetailskin. basal layer ofthemousedorsalskin andare These SCsare homogenously distributed inthe of SCsthatresides inthebasallayer oftheIFE. has revealed theexistence ofanovel population Alona Feldman, agifted Ph.D. studentinourlab, replenishes theIFE. known regarding theexact SCpopulationwhich lineage have beenwell described,very littleis While thestem cells (SCs)committing to theHF gland (SG)andtheinterfollicular epidermis(IFE). compartments: thehairfollicle (HF),sebaceous The epidermisconsists ofthree main How doStem Cells Commit Suicide? A Novel Stem Cell Population Lokey Center I Annual Report 2017

heavily in the scientific spotlight as critical to affect stem cell function and led to a drivers of tumorigenesis, and resistance to dramatic improvement in tissue regeneration. apoptosis is considered a hallmark of cancer, we Furthermore, the wounds of the genetically know incredibly little regarding the mechanisms manipulated mice display striking regeneration utilized for SC elimination and their influence on of hair follicles and significantly smaller scars. SC-dependent processes. During the past year These findings have great scientific impact, we have published a perspective piece regarding demonstrating the importance of stem cell the importance of apoptosis in regulating SC- expansion in tissue regeneration. Furthermore, dependent regeneration and cancer development these results also highlight novel targets which in the high impact journal Nature Reviews Cancer. may have therapeutic benefits, such as promoting wound healing and regeneration. Intestinal Stem Cells: Work led by an outstanding PhD student, Elle Koren, reveals that inactivation of Generation of Organoid Models the pro-apoptotic Sept4/ARTS gene has profound An important model for studying stem cell behavior effects on intestinal regeneration. In particular, is organoid formation. In this model, SCs are we find that ARTS and XIAP, a direct biochemical isolated and instructed using specific cues to target for the pro-apoptotic activity of ARTS, generate a mini organ (organoid) in vitro. Alona are important for the regulation of cell death Feldman has decided to pick up the scientific in the intestinal SC (ISC) niche. Loss of ARTS gauntlet of generating sebaceous gland organoids. function protects ISCs and Paneth cells against These organoids have never been generated before apoptosis, increases their numbers and leads to and thanks to Alona, who has been successful dramatic improvement in intestinal regeneration. in her efforts, we are now in a position where we Furthermore, the Sept4/ARTS-/- SC niche displays can shed fresh new light on the development and elevated Wnt/β-catenin activation and augmented homeostasis of this unique mini organ. cellular proliferation. Taking an ex vivo approach, we find that seededSept4 /ARTS-/- crypts often Stem Cells and Cancer give rise to massive cystic-like organoids, which Our lab has made major advances in understanding typically develop from tumorigenic ISCs as a result skin cancer progression. We have focused on how of Wnt pathway overactivity. In contrast, deletion of stem cells contribute to cancer formation as well XIAP impairs intestinal repair and abrogates Sept4/ as the intricate signaling pathways that regulate ARTS dependent phenotypes. These findings are these unique cells. Work led by Egor Sedov and very exciting and are of broad interest for several Dr. Despina Soteriou reveals how stem cells give reasons. First, to the best of our knowledge, this rise and maintain skin tumors, and how these is the first study to demonstrate the importance cancer stem cells can be targeted. Additionally, of apoptosis in restricting ISC expansion, enabling Despina has made important discoveries into the proper and precise repair while serving as a progression of melanoma development. Important defense mechanism against irreparably damaged ways of inhibiting the progression of this deadly SCs and cancer. Our results also suggest that disease have been found. targeting apoptotic pathways in ISCs may have therapeutic benefits to promote intestinal Our lab has been running for three years now regeneration. and we are thrilled about this incredible work environment and the advances we have made. Skin Stem Cells : Work of 3 PhD students: Of great importance we want to emphasize that Lana Kostić, Egor Sedov and Roi Ankawa this work couldn’t have been performed without has shed light on genes crucial for stem cell the use of state of the art resource centers at the death and tissue regeneration. Manipulation Lokey Interdisciplinary Center for Life Sciences and of the apoptotic pathway in mice was found Engineering and its truly incredible staff.

27 KAPLAN LAB

The process of reverse-, in which a Immunodeficiency Syndrome (AIDS), a pandemic single-stranded RNA (ssRNA) is copied into a that has taken the lives of millions, and for which double-stranded DNA (dsDNA) is an obligatory there is currently no vaccine or cure. step in the life cycle of retroviruses, and is catalyzed by a single enzyme, the Reverse Major advances toward a molecular level Transcriptase (RT). Of particular importance understanding of reverse transcription have are the RTs of the Human Immunodeficiency been achieved from the structures of HIV-1 RT, Virus (HIV), responsible for the Acquired complemented by a variety of chemical and Lokey Center I Annual Report 2017

enzymatic probing methods. However, such studies provide a picture of a “static” enzyme, revealing little information on the process of translocation, i.e., the stepwise movement of the enzyme during polymerization.

To overcome the limitations of these classical methods, graduate students Omri Malik and Hadeel Khamis, under the supervision of Ass. Prof. Ariel Kaplan, used an “optical tweezers” setup, a method that uses laser beams to apply mechanical forces on single molecules. With this transcriptase is a relatively passive enzyme, approach, they studied RT’s strand-displacement able to polymerize on structures templates by DNA-directed DNA synthesis by following the exploiting their thermal breathing. unwinding of a DNA hairpin under tension. Finally, their experiments indicate that the They showed [1] that strand-displacement enzyme enters the backtracking states from the polymerization is frequently interrupted. pre-translocation complex. Taken together, these Abundant pauses are modulated by the strength results emphasize the potential regulatory role of the DNA duplex ~8 bp ahead, indicating of conserved structural motifs, and may provide the existence of uncharacterized RT/DNA useful information for the development of potent interactions, and correspond to backtracking of and specific inhibitors. the enzyme, whose recovery is also modulated by the duplex strength. Dissociation and reinitiation events, which induce long periods 1. O. Malik, H. Khamis, S. Rudnizky, A. Marx, and of inactivity and are likely the rate-limiting A. Kaplan, Nucleic Acids Res. 45, 10190 (2017). step in the synthesis of the genome in vivo, are modulated by the template structure and the 2. O. Malik, H. Khamis, S. Rudnizky, and A. viral protein Nucleocapsid. Kaplan, Nucleic Acids Res. 45, 12954 (2017).

In a subsequent work [2], they also showed that reverse transcriptase functions as a Brownian ratchet, with dNTP binding as the rectifying reaction of the ratchet. They found that reverse

29 Evolution of Bacteria within Human Host

The human body is inhabited by a variety of

KISHONY LAB KISHONY bacterial species. Although stable for long times, these bacterial populations are dynamic and respond to changes in their environment: physico-chemical conditions, host factors such as the immune system and other bacterial populations. We track the changes accumulating in the genomes of these bacteria over time and from these changes we deduce the key challenges they are facing which drive their evolution within the host. We use several models in which we sample the bacterial populations bacterium may grow unrestrictedly on the body over a long period of time (anywhere between of premature babies, causing severe infections. one month and two years), and clinical isolates Comparing the patterns of dispersal of this are phenotyped by automated in-house robotic bacterium on the bodies of neonates and system and genotyped at the whole-genome adults alike, we track its routes of transmission level at the Technion Genomic Center. Genetic and infection. changes are identified using an in-house This work is carried out in collaboration with Prof. developed bioinformatic toolbox. We focus on 2 Imad Kassis and Dr. Ori Hochwald, Neonatal different model systems: Intensive Care Unit at Rambam Medical Center.

(1) How does Staphylococcus aureus adapt following its transmission from mothers The Ecology of Antibiotic Resistance to their newborns? This pathogenic bacterium is in Natural Habitat carried asymptomatically by ~30% of the population. Interestingly, infants often carry the The antibiotics we use in the clinic are often same strain carried by their mothers. We derivatives of natural products originally compare the genetic changes occurring in the produced by soil microbes as part of an intricate bacteria carried by the newly colonized infants network of warfare and communications within with the ones occurring at the mother borne complex microbial consortia. An unsolved population. Different evolutionary paths between question in the field is how so many species them suggest different environmental coexist in natural communities without a single constraints applied on the bacteria. or several species taking over. Recently, we This work is carried out in collaboration with the have revealed key factors that help explain how lab of Dr. Gili Regev-Yochay, Sheba Medical Center. species coexist: (a) We have shown that species that degrade (2) Does colonization of Staphylococcus antibiotics can dramatically change the epidermidis require its niche-specific adaption dynamics of the community, introducing to different human body parts? This ecological stability into an otherwise inherently commensal non-pathogenic bacterium colonizes unstable community (Kelsic et al, Nature 2015). neonates immediately after birth and is found on (b) We show that high order interactions may the skin of each and every one of us. However, explain sustained diversity. While, pairwise due to a dysfunctioning immune system, this interactions between species are known to Lokey Center I Annual Report 2017

introduce an upper threshold on diversity, metagenomics sequencing of the phylogenetic interactions that go beyond pairwise, i.e. the marker 16S from single grains. way two species interact is affected by a third species, can help maintain diversity without Predicting Antibiotic Resistance and the any member of the community taking over. Potential for Evolution of Resistance from These results suggest a lower threshold, rather Pathogen’s Genome than upper, on diversity. (Bairey et al,Nature Communications, 2016). In the clinic, current approaches to diagnosis and tracking of pathogens are based on These results were founded on theoretical culturing clinical samples. These approaches analysis and modeling. Moving forward, we have are inherently slow and, more importantly, started to test some of these predictions in the analyze the current state of the pathogen, lab, and to analyze the actual composition of but cannot predict its future evolution and microbes and their interactions in situ in the soil spread and the impact of antibiotic use on natural environment. In particular, we focus on resistance. An effective strategy to combat the coexistence of antibiotic producers, bacteria microbial infectious disease requires therefore resistant to the produced antibiotic and bacteria “anticipatory diagnostics” that can predict the sensitive to it. We believe that studying this pathogenicity of the microbe, its immediate multi-species ecology may unveil natural forces response to different antimicrobial treatments, that counter antibiotic resistance spread in the its longer-term capacity to evolve resistance, environment. The specific ecological questions and its likelihood of epidemic spread. Such we are trying to answer are: a strategy is now possible through high- throughput genome sequencing, recent (1) What is the fitness advantage of advances in predictive analysis of microbial antibiotic resistance in the soil? Although rich in evolution, and big-data science. We envision antibiotic producing bacteria, bulk soil contains a future for clinical microbiology in which a very low concentration of antibiotic, if any. treatment is guided by such predictive genome- Accordingly, selection for antibiotic resistance is based diagnosis. Pathogenic microbes will be not seen in the bulk. This observation led us to routinely sequenced at the genome-scale. The try and find markers of selection on small resulting data will be sent for analysis in centers confined volumes of soil – such as single grains. holding large genome sequence databases of To that end, we inoculate bulk soil with both individual clinical isolates and their associated antibiotic resistant and sensitive bacterial clinical indications, treatments, and outcomes. strains used as probes, and measure the fitness differences between the two, both on the bulk As a first step towards this future, we are and the single grain level. collaborating with clinical laboratories in hospitals and health maintenance organizations (2) How variable is the microbial in Israel, as well as with the Central Laboratories community occupying distinct grains of soil? of the Ministry of Health. Together, we are Since the soil is a structured environment, collecting and sequencing bacterial pathogens co-existence of bacteria in small, confined areas from the clinic, including the relevant clinical can point to relatedness between them. To study patient data. the correlation between bacterial existences we wish to characterize the bacterial communities occupying single grains of soil. To that end we developed a method for amplicon-based 31 MELLER LAB

A Modular Super-Resolved Imaging System Neurobiology Under the Microscope

In 2014, the Nobel Prize in Chemistry was Translation is the biological term used to awarded to three distinguished researchers for describe the synthesis of proteins, which are the development of super-resolved fluorescence the biomolecules that carry out every function microscopy. Nowadays, this technology stands in cells. This process is highly complex and out as an excellent tool for studying elaborate involves the orchestrated action of multiple biomolecular processes in real-time. In order to machineries, which ‘read’ the recipe for each image dynamic processes in live single cells, protein from a different mRNA molecule. super-resolution fluorescence microscopy has to Neuronal cells, which quickly carry information meet demanding requirements. These include from and to the brain, require that the initiation high spatiotemporal resolution, a wide of protein translation is tightly regulated. In spectral range available for imaging, as well as fact, deregulation of translation initiation at minimal perturbation of the biological system the neuronal synapses, is strongly correlated under investigation. with a large spectrum of autistic disorders. Furthermore, translation initiation was shown to To meet these challenging technical play a major role in controlling synaptic strength. requirements, we are developing an advanced microscope, capable of ultra-high spatial and Using our custom-made super-resolution STED temporal resolutions in multiple colors, which microscope, as well as a confocal microscope, will reconcile previously incompatible ‘super- we are studying the mechanisms underlying resolution imaging’ modalities. This modular synaptic plasticity in human neuronal networks optical system most notably incorporates by imaging its key biomolecular effectors. To this a novel variant of three-color Parallel STED end, we implement protocols, which allow us to microscopy, in addition to providing STORM, culture and differentiate immature cell lines into SOFI, and TIRF imaging. neural networks. Our main goal is to characterize the mRNA closed-loop formation in live cells, required for translation initiation. In addition, we aim to image the dynamic processes occurring during translation initiation in dendritic spines. Lokey Center I Annual Report 2017

Our multidisciplinary lab develops and Four-Dimensional (Spatio-Temporal) applies microscopy methods for observing the Visualization of DNA Organization and dynamics of life on the nanoscale. Specifically Dynamics in Live Cells. we are interested in applying novel optical Beyond the genetic information encoded in the design, signal processing and machine linear DNA sequence, the spatial conformation learning techniques to extract a maximal of chromatin, namely the genome and its amount of information from challenging live- associated biomolecules, plays an important cell microscopy. Specific projects include: role in a variety of processes, such as gene SHECHTMAN LAB SHECHTMAN expression and regulation, DNA repair, nuclear Optimal Optical System Design for transport, and more. We are currently applying Super-Resolution Microscopy in 3D and in our imaging techniques to observe DNA Multiple Colors. organization in two model systems: homologous What is the optimal way to encode the color recombination in yeast, and enhancer-promoter and the depth of a particle in its microscopic dynamics in human disease-model cells. image? We explore this question using statistical information theory, and employing Relevant reference: Y. Shechtman, A-K Gustavsson, novel algorithmic and fabrication materials and P. N. Petrov, E. Dultz, M.Y. Lee, K. Weis, and W.E. methods for diffractive optical elements. Moerner, “Observation of live chromatin dynamics in cells via 3D localization microscopy using Relevant reference: Y. Shechtman, L.E. Weiss, Tetrapod point spread functions“, Biomedical A.S. Backer, M.Y. Lee, and W.E. Moerner, Optics Express 8, 5735-5748 (2017). “Multicolour localization microscopy by point- spread-function engineering“, Nature Photonics Quantifying Transcriptional Behavior in 10, (2016). Bacterial Promoters by Single Molecule Microscopy. Application of Deep-Learning for The process of gene expression is comprised Super-Resolution Microscopy. of many successive stochastic events, all Deep learning algorithms have dramatically of which depend on a multitude of cellular improved the state-of-the-art in numerous components (promoters, polymerases, etc.). One disciplines in recent years, including in speech key source of variability in gene expression is recognition, visual object recognition, visual fluctuations in promoter activity. We are applying object detection, drug discovery and genomics. single-molecule microscopy to measure and We have introduced deep-learning techniques characterize transcriptional behavior and noise to super-resolution localization microscopy, and from different bacterial promoters, each with its shown their usefulness for fast, precise and own distinct architecture. robust image reconstruction.

Relevant reference: E. Nehme, L.E. Weiss, T. Michaeli, and Y. Shechtman, “Deep-STORM: Super Resolution Single Molecule Microscopy by Deep Learning“, arXiv:1801.09631 (2018).

33 SHLOMI LAB SHLOMI

Our research during the year 2017 focused Developing an Approach for Quantifying on developing integrated experimental and Oscillations in Metabolic Activity Throughout computational methods for studying cellular the Cell Cycle in Proliferating Cancer Cells. metabolism at a spatio-temporal resolution and This work integrates experimental and the application of these methods to studying computational cell synchronization, advanced metabolic alterations in cancer. Specifically, we mass-spectrometry, and metabolic flux work on the following research projects: modelling. We find major oscillations between glucose and glutamine oxidation in the TCA Developing a Rapid Cell Fractionation cycle, providing a first dynamics view of Method that when Coupled with Lc-Ms Based TCA cycle activity in cancer cells. Our paper Metabolomics and Isotope Tracing Enables to describing this research has recently been Infer Subcellular Compartmentalized Metabolic published in Molecular Systems Biology. Fluxes, Focusing on Mitochondrial Versus Cytosolic Fluxes. Inferring the Metabolic Adaptation of Applied to study metabolic alterations in cancer Cancer Cells to Clinically Used Drugs and cells with a defective mitochondrial function due Somatic Mutations in Enzyme Coding Genes. to a loss-of-function mutation in a TCA cycle The goal of this project is to identify metabolic enzyme, we identify a novel target for selective adaptations in cancer cells that can be exploited killing of these cancer cells. A paper describing for selective eradication of cancer cells. We focus this research has been submitted to Nature on metabolic alterations due to the common Communications. deletion of MTAP in pancreatic cancer. In another project we study metabolic changes due to emergent resistance to antifolates. Lokey Center I Annual Report 2017

35 10 The Lokey Center YRS

The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering Technion - Israel Institute of Technology