REPORT The National Institute for Biotechnology in the Negev 5 February 2008 The agreement with the government on the establishment of the NIBN: On the threshold of a new era After months of negotiation with the Government, agreement on the establishment of the NIBN is just around the corner. Indeed, I hope this NIBN report will be the last one before the implementation of the agreement of the NIBN funding by the Government, our principal Donor and the University. Such an agreement will mark a turning point with respect to NIBN activities, the support of its members and the advancing of its goals. This issue of the NIBN report is also being published before the visit of the extended International Advisory Committee. I greatly look forward to this visit which is aimed at exploring the potential of the NIBN and to help us transform the NIBN into a world-class research center, both in terms of its people and its facilities. One of the challenges that the NIBN faces is bringing industry to the Negev. While it is crucial that NIBN members stand behind this goal, I admit that it is not easy to present a clear road-map of how to move forward on this front. There has always been a rather uneasy relationship between the interests of basic science and those of the business world. While biotechnology companies are product-driven, with focus on the immediate, namely developing a product to meet a specific market need, academy is discovery-driven and takes a long-term view of biotechnology development. Over the last months, I have had the opportunity to present the mission and goals of the NIBN to major players in industry and biotechnology, as well as to faculty forums at BGU. While the importance of exposing industrial concerns to the NIBN is obvious, I also believe it is very important to expose the BGU faculty to the NIBN mission, its structural organization, its research focuses and the relationship between the NIBN and the University. Moreover, I have made every effort to highlight the benefits to the university that will result from the establishment of the NIBN. These include the fact that the NIBN attracts and recruits excellent scientists, allowing them to develop their research as well as providing a collaborative research atmosphere as well as establishing industrial contacts. I believe that the exciting research going on in the NIBN will greatly benefit from the new links with industry that have been established but which are too numerous to list here. Finally, as in previous NIBN reports, in this issue we shine the spotlight on some of our members. We introduce you to Dr. Ran Taube, a newly-recruited scientist joining the NIBN and the HIV as a tool for gene delivery and discovery of new antibodies Dr. Ran Taube

Gene therapy is broadly defined as the How can the genetic material get detect in other microbial or cell-free transfer of genetic material into cells into cells? display systems. Moreover, we are currg rently collaborating with researchers and tissues, with the goal of either regg A basic approach for gene therapy invg at Harvard University in a pre-clinicg gaining or inhibiting the function of volves the use of viruses as genetic degl cal study, where we use viral particles a given gene. The approach is mainly livery vectors, capable of efficient and to introduce an intracellular antibody used to cure genetic disorders, or at stable gene transfer, without causing (intrabody) against the HIV-1 Tat progt least improve the clinical condition of any undesired associated pathogenic tein into Rhesus macaque monkeys, a patient. Researchers may use several or immunogenic effects. These enging and analyze the protective effects of techniques for correcting defective neered shuttle vehicles are safe and such intrabodies against viral infectg phenotypes, the most common being cannot replicate, but still maintain tion. to insert a functional gene into the geng their capabilities of delivering new In December, 2007, I joined the nome, where it replaces the non-funcgt genetic material. Both RNA and DNA NIBN and the Department of Virolog tional copy. Additionally, the regulagt viruses can be used as shuttle vectors ogy and Developmental Genetics at tion (i.e. the degree to which a gene is for gene therapy manipulation. Such the Faculty of Health Sciences. I am turned on or off) of a particular gene vectors are based on well-defined retrg certain that this environment will could also be altered. Other agents roviruses, like murine leukemia virus allow me to continue my research in that can inhibit a corrupted gene (MLV), or DNA viruses, such as adeg Schematic diagram illustrating the assay for the screening a competitive manner, and to establg include: RNA-based drugs, such as enoviruses or adeno-associated virusge andisolation of scFv particles from mammalian cells. lish an independent scientific career, siRNA, dominant negative variants, es. Each vector has its own advantagge A diverse scFv non-immune library was inserted into a lentivector as a fusion protein of an Fc domain and a transmembrane moiety. Generated viral particles were used to transduce new cells, leading combining both basic and applied toxins, and intracellular antibodies. es, but all share a major shortcoming, to a stable integration of scFv fusion proteins in the host genome and their expression on the cell research. My group and I will contg Obviously, genetic disorders that arise namely they cannot infect (transduce) surface. The result is a collection of cells, each displaying scFv on the surface. For isolating cells tinue to improve the mammalian- from mutations in a single gene are non-dividing cells. To overcome this displaying specific scFv molecules, cells were sorted based on their binding to a fluorescent-labeled display screening system and isolate the best candidates for gene therapy. problem, novel retroviral vectors derg antigen. Sorted cells were expanded and re-selected or the scFv fragments were directly PCR-rescued new scFvFc particles directed against However, gene manipulation can also rived from lentiviruses - such as hugm from the cells and re-cloned either into the lentivector for a second round of screening or directly into numerous infectious diseases. These be conducted to treat a broad range of man immunodeficiency virus (HIV) an expression vector. can be engineered into highly efficient metabolic and neurologic disorders, – have been developed. These novel agents that will be further utilized for different kinds of cancer, hemophilia, vectors promote high and stable expg caution. Clearly, further understandig chain antibodies (scFvFc), consisting therapeutic applications. We will focg cardiovascular disorders, and numerog pression of the transgene, and also ing of their mechanisms is essential of both the heavy and light variable cus our efforts on HIV targets, mainly ous infectious diseases. offer great advantage for long-term for developing improved gene therapy regions of an antibody. These particg on viral proteins that participate in therapy, in that they efficiently infect technologies. cles, expressing scFvFc fragments on the regulation of transcription elongg embryonic stem cells. their surface, were used to deliver the gation. Additionally, we will continue Still, the ideal delivery vehicle still How can our lab promote the safe library into human cells, resulting in to develop improved and safer lentivg remains to be found. At this time, the transfer of genetic material? stable scFvFc surface expression. This viral vectors. Our recombinant scFv performance and pathogenicity of In our lab, we set out to exploit lentivirg unique mammalian display platform pseudo-typed lentiviral particles will candidate vectors, along with questg ral particles as gene-delivery vehicles. for screening new scFvFc particles is be used as highly efficient gene deliveg tions on safety and ethical parameters, Intracellular antibodies (intrabodies) required to overcome constraints assg ery vehicles to target specific cells via are being considered. Encouraging resg or other agents that can correct the sociated with protein expression and their scFv moiety, while maintaining sults have formed the basis for clinical function of the gene, are delivered into obstacles related to library size, corrg their highly infectious properties. Fing trials addressing numerous disorders. cells for the treatment of infectious rect folding, and protein post- translg nally, our human display platform can However, despite some initial success diseases, mainly Human Immunodefg lational modifications – all of which accommodate other protein libraries in these trials, previous drawbacks ficiency Virus (HIV). In addition, we limit bacterial-dependent antibody that are currently screened in bacterg have halted our progress. Thus, preseg use lentiviral vectors for the developmg selection methods. Upon screening rial systems, allowing the isolation of ent viral vectors are used with great ment of a new display platform for the of these human cells by FACS-sort newly improved variants with unique screening of large-sized protein librargi technologies, improved scFv moieties structural and biochemical propertg Cell-Surface localization of scFv ies in the context of mammalian cells. directed towards the envelope glycopg ties. We hope to take these newly isogl Cells were transfected with a bicistronic During my post-doctoral training at protein of the SARS virus were isogl lated agents a step further, and benefit vector expressing both the scFvFc-TM fusion the Dana-Farber Cancer Institute at lated. Overall, we have demonstrated from their therapeutic properties for protein and ZsGreen. Cells were stained with Harvard University, we established a the advantage of a new lentivirus-megd specific gene delivery applications into a rhodamine-conjugated anti-human Fc for unique system, where high titer functg diated mammalian display platform cells with genetic disorders or against the detection of scFvFc surface expression, as tional lentiviral particles could accomgm for the selection and identification of infections diseases. visualized by a confocal microscope. modate a naïve 1x108 library of single- antibodies that would be difficult to

2 3 From peptide self-assemblies at the nanometer scale to novel multifunctional bone regeneration therapeutic hydrogels Fig. 1 Bottom-to-top Dr. Hanna Rapaport design manifestation of the AAbPs system (left to right) “Humans are attracted by the app- molecular level and by understandig from individual peptides pearance of order from disorder and ing intermolecular interactions that in a b-sheet structure, to Self-assembly is one of the few practic- govern their self-assembly, we will nanometer scale fibrillar cal strategies for making ensembles of successfully develop new well defined assemblies, to cells cultured nanostructures…” (J. Whitesides, Scige and multifunctional peptidic biomatg on matrices of the fibrillar ence, Vol. 295, 2002). terials. assemblies and to peptide We have recently developed hygd hydrogels that can be Living organisms constitute sophisticg drogels composed of amphiphilic and administered by injection cated molecular self-assemblies that acid-rich b-sheet peptides, named into bone tissue. interact through non-covalent intergm AAbP. These peptides, originally desg molecular forces. For example, cells signed in our lab to form two-dimengs shown that our AAbPs mimic bone matrices are designed to provide cells expedite bone healing and regeneratg can be considered as active micromeg sional molecularly ordered assemblies acidic proteins, owing to their unique with a scaffold for adhesion and progl tion. eter scale machines that are being at interfaces, also have the capacity to ability to accelerate calcium phosphate liferation. We have shown that osteogb Dr. Rapaport, a faculty member of maneuvered by bio-molecules, such self-assemble into three-dimensional mineralization and hydroxyapatite blast-like cell lines may be cultured the Department of Biotechnology Engg as proteins, lipids and DNA, that oftg hydrogel structures under physiologicg nucleation under simulated body fluid on two dimensional and three dimengs gineering, graduated from Ben-Gurigo ten self-assemble into functional cal conditions. In-depth structural solution conditions (Fig.2). sional AAbP matrices (Fig. 1). We are on University with a B.Sc. in Chemical nanostructures. In nano-biotechnolgo knowledge, combined with the modulg In normal bone, osteoblasts, the continually developing the AAbP biogm Engineering and a subject minor in ogy, the aim is to acquire full control lar nature of these designed peptides bone-forming cells, and osteoclasts, mimetic scaffolds to also modulate the Biotechnology. She completed a Mastg over the nanometer scale building and the fidelity of the methods used to the bone-resorbing cells, work togethge recruitment of osteoblasts cells, ingh ter’s degree in Chemical Engineering blocks of living matter, i.e. biological create these artificial matrices, render er in a coordinated fashion to form hibit osteoclasts activity and provide at the Technion, received a Ph.D. from molecules, to construct systems with these hydrogels promising candidates and remodel the tissue. The AAbP the various other factors necessary to the Materials and Interfaces Departmg varied biological, chemical and physicg for applications in biotechnology-regl ment at the Weizmann Institute and cal functionalities, inspired by nature, lated fields, such as controlled drug went on to postdoctoral studies at the at the nanometer scale. Biomolecular release and tissue engineering (Fig. 1). California Institute of Technology. self-assembly serves as an alternative In tissue engineering, natural or Dr. Rapaport’s lab is engaged in variog paradigm to the conventional photolg synthetic scaffolds serve as an architg ous other studies related to nanometer lithography technology applied on ingo tectural support onto which cells may scale structural characterizations and organic materials in the semiconducgt attach, proliferate, and synthesize new the design of new peptidic biomateriag tor industry for preparing functional tissue. Bone repair or replacement is als for therapeutic and diagnostic apgp organic nanostructures with diverse a viable consideration in clinical indg plications. shapes, sizes and functions. dications, such as osteoporosis, bone In our lab, we are exploiting the tumors, spinal fusion, fractures, traumg bottom-to-top molecular design appg ma cases and in procedures related to proach in seeking to build functional teeth implants. Current trends in tissg Figure 2. TEM images of amorphous protein biomaterials from self-assg sue engineering transform the clinigc calcium phosphate particulates sembled and well defined nanometer cal focus in orthopedics and dentistry adhered to AAbP hydrogel fibers. a) scale peptides. Peptides and proteins from traditional metal implants to Unstained sample showing dark dots are particularly attractive as models biologically-based products for mineg that appear more abundant on the for hierarchical molecular systems becg eralized tissue regeneration. Bone tisgs peptide fibers than in the background. cause many of the fundamental rules sue engineering presents unique chalgl b) - c) Negatively-stained hydrogel that govern the association between lenges. This organ is an exceptional fibers ~30 nm wide decorated amino acid sequences and their folding organic/inorganic composite material by calcium phosphate spherical and stability are continuously being that constitutes around 70% calcium particulates. d) An optical microscope unraveled. The design of our peptidic phosphate, mainly in the form of hydg image of peptide fibers decorated systems is based on known structural droxyapatite mineral, with the rest with spherical calcium phosphate principles, together with new insights being bone cells, extracellular matrix particulates. The fiber marked by the that we acquire by in-depth structural collagen and other proteins. Biomineg white arrow reaches more than 1 mm characterizations. We believe that by eralization in nature is controlled by in length and 30 mm in width. describing the very fine detailed structg acidic residue-rich proteins and other tures of our designed peptides at the macromolecules. We have recently

4 5 DNA microarrays and sequencing: Assessing gene expression and genetic variations with advanced technologies Dr. Micha Volokita

The idea that every cell of the body compared. These ‘genomic comparisg II. SNP detection – This applicagt in the cell. Using the same methods, contains a full set of chromosomes, sons’ showed that genomes differ from tion of DNA microarray technology arrays containing DNA sequences of containing identical genes, and that person to person and implied that allows for the identification of SNPs known SNPs are hybridized to labeled only a fraction of these genes are such variation can be exploited for degc among alleles within or between popugl genomic small fragments, thus revealig turned on, or ’expressed’, in each cell ciphering the genetics of complex diseg lations. This approach enables scientg ing the SNP profile of an individual. type to confer upon it unique propergt eases and personal traits. There are an tists, for instance, to perform genome- The DNA microarrays core laborg ties, was raised well before the completg estimated 15 million positions along wide association studies to compare ratory at the NIBN was established at tion of the Human Genome Project. our DNA sequence where one base can the distribution of SNPs in hundreds, the beginning of 2004. It includes a In according with this premise, it was differ from one person or population or even thousands, of people with and dedicated scanner and computer-contg suggested that studying which genes to the next. Individual genomes can without a particular disease. By scoring trolled fluidic center for the hybridizatg are active and which are inactive in difgf also differ in many other ways. Small which SNPs co-occur with symptoms, tion, scanning and analysis of high- ferent cell types would help researcheg sections of DNA, ranging from a few to researchers can determine how much density arrays. Since its establishment, ers to understand both how these cells many thousands, and even millions of increased risk is associated with each the laboratory has performed numerog function normally and how they are bases, can get lost, added, or inverted SNP. Eventually, SNP profiles that are ous analyses for investigators at the affected when various genes do not in an individual>s genome. Such revigs characteristic of a variety of diseases NIBN, at BGU and outside the univg perform properly, as occurs under sions can change the number of copies will be established. versity. Some of these analyses, for certain pathological conditions. In the of a gene or of regulatory DNA, fuse III. Comparative Genomic Hybb instance, assisted in studies aimed past, researchers have only been able to two genes together, change their prodgu bridization – This application is suitag at identifying genes involved in neurg conduct such genetic analyses on a few ucts or shut them down. In fact, this able for the identification of genomic rogenesis, important for neural tube genes at once. Today, this is no longer year (2007), researchers became aware gains and losses or changes in the closure in mouse embryos; identifying the case. that these changes, which can alter a number of copies of a particular gene. genes specific to petals of the Arabidg Since the completion of the first genome in just a few generations, afgf Such differences do matter, as was dopsis flowers and identifying narrow draft of the Human Genome Projge fect more bases than single nucleotide demonstrated by several studies. One homozygous regions in DNA of indivg ect almost seven years ago, there has polymorphisms (SNPs). Altogether, survey concluded that in some popugl viduals from Bedouin family membg been an explosion in human DNA individual genomes differ in size by as lations, almost 20% of differences in bers affected by hereditary disease. sequence information available. This many as 9 million bases. gene activity are due to copy-number At the end of 2006, the BGU DNA avalanche of information includes the The development of the DNA micg variants; SNPs account for the rest. For sequencing services were merged identification of many novel genes, as croarray technology during the last example, people with high-starch dige with those of the DNA microarrays well as their physical mapping. Morego decade has allowed us to follow the ets, such as in Japan, have extra copies core laboratory. Efforts were made to over, since 2001, genomes of several expression level of numerous genes of a gene for a starch-digesting protein, improve the performance of the seqg individuals have been sequenced and simultaneously, offering, for example, as compared with members of huntgi quencing unit and to offer additional insight into how gene expression patgt ing-gathering societies. By scanning services. Today, the unit can provide terns vary in various malignant cells. the genomes of autistic and healthy sequence reads of up to approximately Today, three major applications of children and their parents for copy- 700 bases with high accuracy and repg DNA microarrays are common: number variation, other geneticists producibility. In addition, a new servg I. Gene expression profiling – Regl have found that newly-appeared DNA vice, i.e. genotyping, using the ABI lying on this approach, it is possible to alterations pose a risk for autism. prism 3100 Genetic Analyzer, is availag monitor the expression levels of thougs A microarray works by exploiting able and is already being used by seveg sands of genes simultaneously and thus the ability of a given single strand of eral laboratories at BGU. study the effects of certain treatments, nucleic acids (RNA or DNA) molecule Future developments: diseases, and developmental stages on to bind specifically, or hybridize, to New technologies, such as DNA micg gene expression. One such example its complementary sequence. By usgi croarrays printing and mega-base seqg of microarray research is the study of ing an array containing many known quencing and genotyping, will soon cancer. In the past, researchers classigf DNA sequences, the expression levels be acquired. Rapid improvements in fied different types of cancers based on of hundreds or thousands of genes sequencing technologies, such as DNA the organs in which tumors developed. within a cell can be determined, in a sequencing-by-synthesis, will make With the help of microarray technolgo single experiment, by measuring the the sequencing of chromosomes or ogy, we will be able to further classify amount of labeled mRNA bound to even whole genomes a real possibility. cancers based on the patterns of gene each site on the array. With the aid This sequencing technology enables activity in tumor cells. As a result, regs of a computer, the amount of labeled large-scale sequence comparisons to searchers will be able to design treatgm nucleic acids bound to the spots on detect genetic variations along the ment strategies targeted directly to the microarray is precisely measured, whole genome (or a long portion of it) each specific type of cancer. generating a profile of gene expression within or between populations.

6 7 Dr. Alon Monsonego received the Zehava and Chezy Vered Career Development Chair for the study of Alzheimer’s and Neurodegenerative Diseases

Recent Special Events | May - December 2007 Visits at the NIBN Upcoming Conferences Special Seminars NIBN International Advisory Committee (IAC) The second Ein-Gedi International ISF Tha SardiNIA Project: Gene-finding and longit- members Prof. Sir Aaron Klug and Prof. Philip workshop ‘Mitochondria: Function and tudinal studies for age-associated conditions Needleman - May 13-15, 2007 Dysfunction’ in a Sardinian population cohort, Prof. David Mr. Morris Kahn, Chairman, Mrs. Molly Globus, Organizers: Abdussalam Azem, Orly Elpeleg, Schlessinger, National Institute on Aging, NIH President, Mr. Dan Gelvan, and Mr. Hanan Ophry Pines, Breitbart Haim, Atan Gross, Gadi - June 6, 2007 Meiron, CEO, Kahn Family Foundations Aurum Schuster and Varda Shoshan-Barmatz Beyond Expression – New Applications of Ventures M.K.I Ltd. - July 29, 2007 February 13-15, 2008 Affymetrix GeneChip Technology, Amos Grundwag, Eisenberg Bros. - October 15, 2007 IAC member, Prof. Raymond Dwek - Industry Contacts and Visits to NIBN October 9-10, 2007 On-going meetings with business develop-m NIBN Kahn Foundation grants Mr. Lorry Lokey - November 4, 2007. ment consultants: Dr. D’vora Greaser, Dr. Giora A total of 20 research proposals were Agam, Dr. Smadar Shavit, Dr. Avi Reinhartz submitted of which 9 proposals were Towards the Establishment and Sari Alajem awarded: of the NIBN Sigal Weisswasser, CEO, Technology Business Prof. Amir Sagi and Dr. Amir Berman A series of meetings were held between repr- Network Group (TBN Group) - May 24, 2007 Dr. Eitan Rubin and Dr. Dan Mishmar resentatives of BGU and Government officials Prof. Ruti Parvari and Dr. Vered Caspi to discuss the establishment of the NIBN, Dr. Liora Tavron, Dr. Rafi Nudelman and Dr. Dr. Amir Aharoni, Dr. Michael M. Meijler, including a meeting with Mr. Gaby Maimon, Yaacov Herzig, Teva Pharmaceutical Dept. of Chemistry Director General of the Ministry of Industry, Industries - May 29, 2007 Dr. Hanna Rapaport and Dr. Levi Gheber Trade & Labor, Mr. Avi Feldman, Adv., Head of Dr. David Rosen, Development and Commer-c Prof. Ruti Parvari and Prof. Dina Raveh Investment & Development Department and cial Head, Strategic Alliances, Pfizer, USA - Dept. Of Life Sciences Mr. Ran yehezkel, Budget and Control Direct- June 4, 2007 Dr. Alon Monsonego and Dr. Eitan Rubin Dr.Uri Abdu and Dr. Ohad Medalia tor, Office of the Chief Scientist. Inotek Pharmaceuticals representatives Dr. R.S. Marks, Dr. Zeevi Ben-Yosef and On November 28, 2007, Dr. Alon Monsonego Dr. Andy Salzman, June 14, 2007, and Dr. Paul Dr. A. Kushmaro received the Zehava and Chezy Vered Career Salama - October 29, 2007 Development Chair for the study of Alzheim-e Dr. Kobi Cohen, TEVA Pharmaceutical er’s and Neurodegenerative Diseases in an Industries - June 14, 2007 inauguration ceremony. Dr. Elai Davicioni, President and CEO, Genome Workshop Diagnostics - USA, July 16, 2007 RGCA Scampi strain selection and monosex Dr. Eyal Neria, Peptera - July 19, 2007 The National Institute for Biotechnology on the Negev project - BGU, July 25-30, 2007 Prof. Haim Aviv and Dr. Silvia Noiman - Organized by Prof. Amir Sagi Beer-Sheva, 84105, Israel October 29, 2007 Tel: 972-8-6461912 Protalix Biotherapeutics, representative Fax: 972-8-6272983 Website: nibn.bgu.ac.il Dr. Yoseph Shaaltiel, Executive Vice President E-mail: [email protected] R&D, Dr. Daniel Bartfeld, Director of Protein Chemistry and Dr. Dudu Merrero - November 27, 2007