Research
at the NIBN
Engineering affinity scaffolds for
cancer imaging and therapy
Itay Cohen and Dr. Niv Papo
Research at the NIBN
B e n - G u r i o n UNI V ER S I T Y O F T H E NE G E V
Contents
NIBN Overview
5
Cancer Research Group
Dr. Eyal Arbely
Dr. Roi Gazit
Dr. Dan Levy
Dr. Niv Papo
Prof. Angel Porgador
Dr. Barak Rotblat
Prof. Varda Shoshan-Barmatz
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7
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Autoimmune and Metabolic Diseases Group
Prof. Amir Aharoni
Prof. Angel Porgador
Prof. Assaf Rudich
Prof. Orian Shirihai
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Neurodegenerative Diseases Group
Dr. Anat Ben-Zvi
Prof. Alon Monsonego
Prof. Israel Sekler
Prof. Varda Shoshan-Barmatz
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Infectious Diseases Group
Dr. Natalie Elia
Dr. Eyal Gur
Dr. Tomer Hertz
Prof. Michael M. Meijler
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Human Genetic Disorders Group
Prof. Ohad Birk
Prof. Ruti Parvari
Dr. Esti Yeger-Lotem
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Applied Biotechnology Group
Prof. Ohad Medalia
Prof. Amir Sagi
Dr. Raz Zarivach
Dr. Stas Engel
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Infra-Structure Supporting Group
Bioinformatics Core Facility
Crystallography Unit
Genetics Unit
Cytometry, Proteomic and Microscopy Unit
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42
Dr. Roee Atlas
43
NIBN Overview
The National Institute for Biotechnology in the Negev
(NIBN) Ltd. is the first, self-organized, independent
scientific research and development (R&D) body in
Israel. It has been established through a tri-lateral
agreement between the government of Israel,
Ben-Gurion University of the Negev (BGU) and
philanthropist, Dr. Edgar de Picciotto. In November
2009, the NIBN became a company and implemented
a detailed, 8 year applicable-orientated R&D program
to specifically allow scientific excellence with a
commercial outlet, funded by the NIBN.
The missions of the NIBN are to bridge the gap
between basic and applied research as well as
forming a major channel between applied science
and industry, resulting in the establishment of a
scientific infrastructure for biotechnology industry in
the Negev. The strengths of the NIBN are derived from
a combination of outstanding scientists, conducting
multi-disciplinary research with both basic and
biotechnological implications, close cooperation
with BGU departments, faculties, and research
centers, all under the umbrella of a state-of-the-art,
scientific infrastructure. Such features coalesce to
permit scientific excellence and create the required
leverage for the emergence of an internationallyacclaimed and successful biotechnology institute in
the Negev and in Israel.
In order to fulfill this ultimate goal, the NIBN
strongly encourages and funds “cutting-edge”,
creative research in the fields of Cancer Research,
Infectious Diseases, Human Genetic Disorders,
Neurodegenerative Diseases, Autoimmune and
Metabolic Diseases and Applied Biotechnology. The
resultant “value through innovation” fuels a plethora
of new biotechnology applications and commercial
opportunities. Such business development outlets
include: a) the creation of “spin-out” companies
through funding bodies; b) joint collaborative efforts
with Big Pharma’; c) exclusive out-licensing of a
technology or product to biotechnology companies.
Using these approaches, NIBN has already succeeded
to generate commercial outlets in the fields of drug
targets for cancer therapy and infectious diseases,
anti-inflammatory drugs as well as major advances
in aquaculture technology. These initial commercial
successes have all been guided by NIBN’s highly
experienced management team.
In December 2014, NIBN members located in several
BGU buildings will relocate to The Edgar de Picciotto
Family National Institute for Biotechnology in the
Negev, a new 5400 sq m building. The building has
been carefully designed to provide state-of-theart scientific infra-structure and to accelerate the
institute’s development and growth, as well as to
host start-up companies, with the aim of leveraging
additional commercial activities.
NIBN’s ultimate goals are primarily driven by two
issues. Firstly, the recruitment of outstanding
scientists as reflected in their academic excellence,
achievements and biotechnological implications of
their research. Secondly, NIBN’s revered international
Scientific Advisory Board (SAB) composed of Nobel
Prize laureate Prof. Sir Aaron Klug, FRS as well as
distinguished scientists Prof. Raymond Dwek, FRS,
Prof. Philip Needleman, Prof. Richard Ulevitch, Prof.
Nathan Nelson and Prof. Hermona Soreq. The SAB
sets a gold standard of scientific excellence, longterm scientific goals and major guidance concerning
commercial efforts.
This booklet presents the current members of the
NIBN, their selected research projects as well as the
Institute's core service facilities. It is our hope that
the information in this booklet will serve as a major
stepping stone in solidifying the NIBN as a World-Class
Research Institute in biotechnology and fostering
commercial opportunities with industry. David BenGurion wrote that “the ultimate test for Israel in our
generation is to prevail, through the power of science
and a pioneering spirit over the wide expanses of the
south and the Negev”. At the NIBN, we are translating
this vision into reality.
5
Cancer Research Group
An estimated 14 million cancer cases occurred world-wide
during 2012 which is expected to increase to about 24 million
by 2035. While having a wide diversity of cancer types and
characterizations, all cancer types involve several hallmarks
include sustaining proliferative signaling, evading growth
suppressors and resisting cell death. NIBN’s cancer research group
focuses on multi-disciplinary themes including understanding
cancer biology through epigenetic modifications (eg. DNA and
protein methylation changes), metabolic re-programing, the
role of dysregulated cell growth, evading apoptotic cell death
and mitochondrial involvement (via voltage-dependent anion
channels), the development of appropriate immune-stimulatory
strategies by targeting Proliferating Cell Nuclear Antigen (PCNA),
the development of innovative animal models to simulate human
leukemias and solid cancers, development of innovative diagnostic
tools and the rationale design of small molecules, siRNA’s, peptides
and protein-based anti-cancer therapeutics including bispecific
molecules.
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6
Dr. Eyal Arbely
Dr. Roi Gazit
Dr. Dan Levy
Dr. Niv Papo
Prof. Angel Porgador
Dr. Barak Rotblat
Prof. Varda Shoshan-Barmatz
Dr. Eyal Arbely
Expanding the repertoire of
ribosomally-synthesized proteins
Background
Ph.D.: The Hebrew University of
Jerusalem, Israel
Post-doctorate: MRC Center for
Protein Engineering and Laboratory of
Molecular Biology, Cambridge, UK
Position: Senior Lecturer
Department of Chemistry
Faculty of Natural Sciences
E-mail: [email protected]
Selected publications
Arbely E. and Arkin I.T. (2004). Experimental Measurement
of The Strength of a Cα- H…O Bond in a Lipid Bilayer. J. Am.
Chem. Soc. 126:5362-5363.
Arkin I.T., Xu H., Jensen M.O., Arbely E., Bennett E.R., Bowers K.J.,
Chow E., Dror R.O., Eastwood M.P., Flitman-Tene R., Gregersen
B.A., Klepeis J.L., Kolossváry I., Shan Y. and Shaw D.E. (2007).
Mechanism of Na+/H+ Antiporting. Science 317:799-803.
Arbely E., Rutherford J.T., Sharpe D.T., Ferguson N. and Fersht
A.R. (2009). Downhill versus Barrier-Limited Folding of BBL 1:
Energetic and Structural Perturbation Effects upon Protonation
of a Histidine of Unusually Low pKa. J. Mol. Bio. 387:986-992.
Arbely E., Rutherford J.T., Neuweiler H., Sharpe D.T., Ferguson
N. and Fersht A.R. (2010). Carboxyl pKa-Values and Acid
Denaturation of BBL. J. Mol. Bio. 403:313-327.
Arbely E., Natan E., Brandt T., Allen M.D., Veprintsev D.B.,
Robinson C.V., Chin J. W., Joerger A.C. and Fersht A.R. (2011).
Acetylation of Lysine 120 of p53 endows DNA binding
specificity at effective physiological salt concentration. Proc.
Natl. Acad. Sci. USA. 108:8251-8256.
Arbely E., Torres-Kolbus J., Deiters, A., Chin J.W. (2012).
Photocontrol of tyrosine phosphorylation in mammalian cells
via genetic encoding of photocaged tyrosine. J. Am. Chem.
Soc. 134:11912-11915.
The translation mechanism has been evolved over hundreds
of millions of years to translate 64 triple-nucleotide codons,
each encoding either one of the common 20 amino acids, or
the termination of translation. Yet, this machinery is far from
exploiting its full potential – proteins with expanded chemistry
can be ribosomally synthesized by site-specific incorporation of
non-proteinogenic amino acids, using the amber stop codon
(UAG) and an orthogonal aminoacyl-tRNA synthetase/tRNA pair.
The chemical and structural diversity of such proteins can be
expanded even further by exploiting the unique chemistry of
bacteriocins - ribosomally synthesized peptides, transformed into
biologically active compounds by a series of unique structural
and chemical post-translational modifications. Our laboratory
is interested in developing and applying different methods for
ribosomal expression of chemically and structurally-modified
proteins for basic biochemical or biophysical research and as a
platform for developing peptide-based, bioactive molecules in
general and particularly for novel antibiotics.
Current research
1. Developing and applying methods for in-vivo
incorporation of non-proteinogenic amino acids: Genetic
code engineering allows the site-specific incorporation of
tailor-made amino acids into recombinant proteins. Equipped
with a unique biophysical or chemical property, such amino
acids may aid in studying the structure and cellular function
of proteins. For example, the incorporation of modified
amino acids carrying a naturally occurring post-translational
modification such as acetylation or phosphorylation. Using
genetic code engineering and directed evolution, we aim
to develop and apply novel methods for in vivo and in vitro
studies of post-translationally modified proteins. Specifically,
we are interested in studying the effect of acetylation on the
structure, subcellular localization and DNA binding affinity of
transcription factors such as NF-κB and p53. In recent years
a direct link was found between acetylation and cellular
metabolism. In light of the high frequency of metabolic
disorders associated with diseases ranging from cancer to
obesity, we aim at understanding how cellular metabolism
and acetylation level are correlated with acetylation and
transcription activity of key transcription factors.
2. Bacteriocin engineering and DNA directed peptide synthesis:
Bacteriocins are ribosomally-synthesized and heavily
posttranslationally modified bioactive (usually antimicrobial)
peptides. In general, the biosynthesis of bacteriocins
includes a series of chemical and structural modifications of
the C-terminal part of a ribosomally synthesized precursor
peptide. Typically, the enzymes that catalyze the biosynthetic
transformations are directed by the N-terminal part of the
precursor peptide, which is usually cleaved off, leaving behind
the modified and bioactive version of the C-terminal peptide.
Consequently, the biosynthetic enzymes show a high
level of promiscuity allowing the biosynthesis of different
natural products using the same biosynthetic pathway. Our
laboratory is studying the biosynthetic pathways of different
bacteriocins aiming at exploiting the high level of promiscuity
for the production of DNA encoded libraries of cyclized and
chemically modified peptides.
7
Dr. Roi Gazit
Hematopoietic stem cells during
health and disease
Background
Hematopoietic Stem Cells (HSCs), the source of blood and immune
cells throughout life, are already clinically-proven in saving thousands
of livesin bone marrow transplants. Nevertheless, despite their critical
importance in the field of adult stem cells, little is known about the
molecular mechanisms underlying HSCs’ functions. Today, bone
marrow transplants are still limited by the availability of stem cells and
a much deeper understanding is required to generate and expand
adequate cells for regenerative medicine. The connection between
HSCs, the immune system and cancer, suggest that advanced
research of the basic underlying mechanisms will provide new insight
and suggest novel treatments by guiding our own adult stem cells.
Current research
Ph.D.: The Hebrew University of
Jerusalem, Hadassah Ein-Kerem, Israel
Post-doctorate: Immune Disease
Institute, Harvard Medical School, USA
Position: Senior Lecturer
The Shraga Segal Department of
Microbiology, Immunology and
Genetics
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Gazit R., Krizhanovsky V. and Ben-Arie N. (2004). Math1
controls cerebellar granule cell differentiation by regulating
multiple components of the Notch signaling pathway.
Development 131:903-913.
Gazit R., Gruda R., Elboim M., Arnon T.I., Katz G., Achdout H.,
Hanna J., Qimron U., Landau G., Greenbaum E., Zakay-Rones
Z., Porgador A. and Mandelboim O. (2006). Lethal influenza
infection in the absence of the natural killer cell receptor
gene Ncr1. Nat. Immunol. 7:517-523.
Gazit R., Weissman I.L. and Rossi D.J. (2008). Hematopoietic
stem cells and the aging hematopoietic system. Semin.
Hematol. 45:218-224.
Gur C., Porgador A., Elboim M., Gazit R., Mizrahi S., SternGinossar N., Achdout H., Ghadially H., Dor Y., Nir T., Doviner V.,
Hershkovitz O., Mendelson M., Naparstek Y. and Mandelboim
O. (2011). The activating receptor NKp46 is essential for the
development of type 1 diabetes. Nat. Immunol. 11:121-128.
Fu W., Ergun A., Lu T., Hill J.A., Haxhinasto S., Fassett M.S., Gazit
R., Adoro S., Glimcher L., Chan .S, Kastner P., Rossi D., Collins
J.J., Mathis D. and Benoist C. (2012). A multiply redundant
genetic switch 'locks in' the transcriptional signature of
regulatory T cells. Nat. Immunol. 13:972-980.
Gazit R, Garrison B.S., Rao T.N., Shay T., Costello J., Ericson
J., Kim F., Collins J.J., Regev A., Wagers A.J. and Rossi D.J.
(2013). Transcriptome analysis identifies novel regulators of
hematopoietic stem and progenitor cells. Stem Cell Report.
8
1. Elucidating the role of Hlf: Hepatic Leukemia Factor (Hlf ) was
recently identified as a potent regulator of multipotency and selfrenewal of mouse cells in-vitro. Although PAR-bZIP transcription
factor is widely recognized in Acute B-cell leukemia with (17:19)
translocation of E2A-HLF fusion oncogene, the endogenous role
of Hlf is still not yet understood. Characterization of molecular
mechanism(s), identification of cooperating factors and
elucidation of how Hlf enhance self-renewal and multipotency,
constitute a significant part of my laboratory’s research efforts.
2. Reprograming human blood cells back to HSC state: Under
normal conditions, mature cells are generated from stem cells
and following differentiation, they cannot form new stem cells.
However, recent methodological advances have provided ways
to reprogram differentiated cells back into stem cells. After
discovering transcription factors that induce HSC-like activity
in mice, we aim to translate such findings into humans. With
the identified and predicted factors, our goal is to validate the
ability to reprogram adult human blood cells into multipotent
and transplantable HSC-like cells. Such cells might eventually be
translated for use into the clinical setting.
3. Modulation of HSCs activity within the immune system: The
generation of blood cells during normal homeostasis perturbed
upon normal and pathological challenges. HSCs are not only the
fundamental source of the hematopoiesis, but also take an active
role in helping to mount immune responses. Identification of
HSC’s receptors that directly respond to immune-mediators is still
in its infancy and functional studies to understand their responses
to infection are urgently needed. Utilizing specific activators of
HSC function will pave the way in guiding our own stem cells
amd direct the source of all blood and immune cells.
4. Generate novel Leukemia models: Leukemia is a severe, lifethreateningdisease affecting hundreds of thousands of children,
adults and elderly populations. While significant advancement
of treatments have been made that offer complete, or at least
partial cure, there are still many types of leukemia that remain
refractory to therapies. The basic understanding of the human
malignancy source and progression is largely dependent upon
animal models, which also provide a platform to develop and
assess novel therapeutics. Using an advanced lentiviral system for
simultaneous overexpression of different transcriptional factors,we
aim to generate a series of leukemias that closely simulate human
Acute Myeloid Leukemia (AML) or Chronic Lymphocytic Leukemia (CLL).
Dr. Dan Levy
Lysine methylation signaling
and epigenetics
Background
Ph.D.: Weizmann Institute of Science, Israel
Post-doctorate: Stanford University, USA
Position: Senior Lecturer
The Shraga Segal Department of Microbiology,
Immunology and Genetics
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Levy D., Adamovich Y., Reuven N. and Shaul Y. (2008). Yap1
phosphorylation by c-Abl is a critical step in selective activation
of pro-apoptotic genes in response to DNA damage. Molecular
Cell 29(3):350-361.
Levy D. and Gozani O. (2010). Decoding chromatin goes high tech.
Cell 142(6):844-846.
Levy D., Kuo A.J., Chang Y., Schaefer U., Kitson U., Cheung P., Espejo
A., Zee B.M., Liu C.L., Tangsombatvisit S., Tennen R.I., Kuo A.Y., Tanjing
S., Cheung C., Chua K.F., Utz P.J., Shi X., Prinjha R.K., Lee K., Garcia B.A.,
Bedford M.T., Tarakhovsky A., Cheng X. and Gozani O. (2011). SETD6
lysine methylation of RelA couples GLP activity at chromatin to tonic
repression of NF-kB signaling. Nature Immunology 12(1):29-36.
Chang Y., Levy D., Horton J.R., Peng J., Zhang X., Gozani O. and
Cheng X. (2011). Structural basis of SETD6-mediated regulation
of the NF-kB network via methyl-lysine signaling. Nucleic Acids
Res.39(15): 6380-6389.
The goal of our research is to understand how
intercellular signaling networks regulate oncogenic
and cell differentiation processes through epigenetic
mechanisms and how dysregulation of these pathways
leads to disease.
Our work centers on the biology of protein lysine
methylation, a post-translational modification that
plays a key role in directing cellular and epigenetic
programs. Lysine methylation catalyzed by protein lysine
methyltransferases (PKMTs) is severely dysregulated in
numerous diseases. Given the reversible nature of this
chemical modification, targeting lysine methylation
holds significant therapeutic promise.
Despite the key role lysine methylation serves in
modulating a wide range of signaling pathways, the
catalytic activity and substrate specificity of the majority
of PKMT enzymes remains unknown. Furthermore,
relatively few protein lysine methylation substrates have
been identified and functionally characterized.
In our laboratory, we are utilizing a multi-disciplinary
biochemical, molecular, cellular, proteomic and genomic
approaches to address fundamental questions at
the intersection between chromatin biology and cell
signaling. We aim to elucidate the molecular mechanisms,
physiological and pathological functions of PKMTs and
lysine methylation biology.
Current research
1. To identify new methylation events of histone and
non-histone proteins and to define the molecular
mechanisms by which these methyl marks are
generated and transduced and to unravel the
biological functions of such methylation events.
2. To define the role of lysine methylation in the
modulation of a variety of biological processes and
disease models, with a focus on oncogenic and cell
differentiation processes.
3. To further develop peptide and protein microarrays
technologies focusing on protein lysine methylation.
4.To develop anti-cancer peptide inhibitors to
target the enzymatic activity of protein-lysine
methyltransferases.
Levy D., Liu C.L., Yang Z., Newman A.M., Alizadeh A.A., Utz P.J.# and
Gozani O.# (2011). A proteomic approach for the identification of
novel lysine methyltransferase substrates. Epigenetics & Chromatin
4(1):19. #Correspondence authors.
Price J.V, Tangsombatvisit S., Xu G., Yu J., Levy D., Baechler E.C.,
Gozani O., Varma M., Utz P.J. and Liu C.L. “(2012). On silico” peptide
microarrays for high resolution mapping of antibody epitopes and
diverse protein-protein interactions. Nature Medicine 18:14349
Dr. Niv Papo
Utilizing combinatorial approach
to target tumor neovasculature for
cancer imaging and therapy
Background
Ph.D.: Weizmann Institute of Science,
Israel
Post-doctorate: Stanford University,
CA, USA
Position: Senior Lecturer
Department of Biotechnology
Engineering
Faculty of Engineering Sciences
E-mail: [email protected]
Selected publications
Papo N. *, Braunstein A. *, Eshhar Z. and Shai Y. (2004).
Suppression of Human Prostate Tumor Growth in Mice by a
Cytolytic D-, L-amino Acid Peptide: Membrane Lysis, Increased
Necrosis, and Inhibition of Prostate-Specific Antigen Secretion.
Cancer Res. 64:5779-5786 (*equal contribution).
Papo N. and Shai Y. (2005). A Molecular Mechanism for
Lipopolysaccharide Protection of Gram-Negative Bacteria
from Antimicrobial Peptides. J. Biol. Chem. 280:10378-10387.
Papo N., Seger D., Makovitzki A., Kalchenko V., Eshhar Z.,
Degani H. and Shai Y. (2006). Inhibition of Tumor Growth and
Elimination of Multiple Metastases in Human Prostate and
Breast Xenografts by Systemic Inoculation of a Host-DefenseLike Lytic Peptide. Cancer Res. 66:5371-5378.
Kipnis Y.*, Papo N.*, Haran G. and Horovitz A. (2007). Concerted
ATP-induced Allosteric Transitions in GroEL Facilitate Release
of Protein Substrate Domains in an All-or-None Manner. Proc.
Natl. Acad. Sci. USA 104:3119-3124 (*equal contribution).
Papo N.*, Kipnis Y.*, Haran G. and Horovitz A. (2008).
Concerted release of substrate domains from GroEL by ATP
is demonstrated with FRET. J. Mol. Biol. 380:717-725 (*equal
contribution).
Papo N., Silverman A.P., Lahti J.L. and Cochran J.R. (2011).
Antagonistic VEGF Variants Engineered to Simultaneously Bind
to and Inhibit VEGFR2 and αvβ3 Integrin. Proc. Natl. Acad. Sci.
USA 108:14067-14072.
10
Evolution has generated the great diversity of proteins with all
different functions required for the processes of life primarily by
using the natural twenty amino acids. Despite all efforts to fully
understand the nature of proteins, we are still far from being able to
create completely new proteins with desired structure and function
simply by rational design. By utilizing state-of-the-art yeast surface
display (YSD) directed evolution technology, it is now possible to
generate protein variants with new functions. Such desired functions
could include improvements in protein physico-chemical properties
(i.e. expression, solubility and stability) or modifications in substrate
affinity and specificity. These optimized properties could be used
for a variety of applications including medical diagnostics where
issues such as high binding affinities, selectivity, and exceptional
thermal, chemical, and protease stability play a major role. In vivo
pharmacokinetic characteristics such as serum stability, tissue
penetration, blood clearance and target retention are critically
important for therapeutic applications. All these parameters can now
be optimized by modern evolution strategies.
Current research
1. Analysing protein interaction interfaces: We are developing a YSD
compatible method for protein scanning to provide a high-throughput
alternative to traditional alanine scanning for mapping of the binding
energy contributions of residues in protein-protein interfaces. To that
end, we are using a binomial mutagenesis approach that utilizes yeastdisplayed protein scaffold libraries in which each site within the protein
scaffold is allowed to vary as only the wild-type or a single substitution
to alanine. Following YSD-based affinity selection to a specific target, a
statistical analysis of the high affinity variant pool is then being used to
assess the binding contributions of individual side chains in the scaffold.
2. Molecular imaging: Cancer treatment is currently shifting towards more
personalized approaches which require knowledge about differences in
expression patterns of cancer markers. We are using the evolved affinity
proteins as in vivo imaging agents to detect and identify these markers.
To evaluate these proteins as molecular imaging agents, we are sitespecifically radiolabeling them and using positron emission tomography
(PET) imaging to measure their tumor uptake and biodistribution in
different cancer models. We are also investigating protein scaffolds as
platforms for integrating cancer imaging and therapy by using a bi- or
trifunctional scaffold coupled to effector compounds (such as smallmolecule toxins and radioactive isotopes) and radiolabeled probes.
3. Cancer therapy: The therapeutic effect of alternative scaffolds is
obtained by blocking and antagonizing cancer-related molecular
targets. In addition, fusions with cytokines or toxins, which are very
difficult to produce with antibodies, provide affinity proteins with
effector functions. Cytokine fusions activate the function of cytotoxic
cells at a tumor site, whereas toxin fusions have a direct killing effect.
Bivalency enhances the affinity of traditional antibodies to surfacebound antigens and their Fc region increases their in vivo half-life. Bi- or
oligovalency is achieved in the alternative scaffolds, either by making
an oligomer genetically as a head-to-tail fusion protein, by Fc-fusions
or by fusing other oligomerization domains to the protein.
Prof. Angel Porgador
Recognition of cancer by
natural killer cells
Background
The successful eradication of an invading pathogen
is dependent upon the coordinated actions of the
innate and adaptive immune systems. Belonging to
the former, natural killer (NK) cells are able to quickly
destroy a wide range of hazardous pathogens such
as viruses, tumors, bacteria and parasites. In recent
years, it has become evident that NK cells rely on a
set of activating receptors, including NKp44, NKp30,
and NKp46 (collectively known as natural cytotoxicity
receptors, NCRs) and NKG2D to kill their targets.
Current research
Ph.D.: Weizmann Institute of Science, Israel
Post-doctorate: Duke University
and National Institutes of Health, USA
Position: Associate Professor
The Shraga Segal Department of
Microbiology, Immunology and Genetics
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Mandelboim O., Lieberman N., Lev M., Paul L., Arnon T., Bushkin Y., Davis D.M.,
Strominger J.L., Yewdell J.W. and Porgador A. (2001). Recognition of hemagglutinins
on virus-infected cells by NKp46 activates lysis by human NK cells. Nature 409:10551060.
Hershkovitz O., Rosental B., Rosenberg L.A., Navarro-Sanchez M.E., Jivov S., Zilka A.,
Gershoni-Yahalom O., Brient-Litzler E., Bedouelle H., Ho J.W., Campbell K.S., RagerZisman B., Despres P. and Porgador A. (2009). NKp44 receptor mediates interaction
of West Nile and dengue envelope E glycoproteins with Natural Killer cells. J. Immunol.
183(4):2610-2621.
**Gur C., Porgador A., Elboim M., Gazit R., Mizrahi S., Stern-Ginossar N., Achdout
H., Ghadially H., Dor Y., Nir T., Doviner V., Hershkovitz O., Mendelson M., Naparstek
Y. and Mandelboim O. (2010). The activating receptor NKp46 is essential
for the development of type 1 diabetes. Nature Immunol. 11(2):121-128.
**AP and OM are equal contributors and co-corresponding authors.
Rosental B., Brusilovsky M., Hadad U., Oz D., Appel M.Y., Afergan F., Yossef R., Rosenberg
L.A., Aharoni A., Cerwenka A., Campbell K.S., Braiman A., and Porgador A. (2011).
Proliferating Cell Nuclear Antigen is a novel inhibitory ligand for the natural cytotoxicity
receptor NKp44. J. Immunol. 187(11):5693-5702.
Jaron-Mendelson M., Yossef R., Appel M.Y., Zilka A., Hadad U., Afergan F., Rosental B.,
Engel S., Nedvetzki S., Braiman A. and Porgador A. (2012). Dimerization of NKp46
Receptor Is Essential for NKp46-Mediated Lysis: Characterization of the Dimerization
Site by Epitope Mapping. J. Immunol. 188(12):6165-6174.
1. Characterization of innate immunity responses
to tumors and viral infections: The ultimate
goal of our research is to understand how NK
cells kill their targets and to identify relevant
pathogen-induced ligands that interact with
NCRs. Accordingly, we are: a) investigating the
in vivo function of NCRs using NKp46 knockout
mice challenged with various pathogens and
determining mortality, NK distribution, activation
and trafficking; b) studying the mechanism by
which hemagglutinin (HA), an identified NCR
ligand, is recognized by NKp46 and NKp44 and
whether the same mechanism applies to other
viral proteins; c) using the data collected in (a)
and (b) to identify novel NCR pathogens and
pathogen-induced ligands. The results of these
studies will serve to develop novel therapeutic
approaches based on NCR recognition of viruses
and tumors. Diseases studied: cancer and
infectious diseases.
2. Characterization of the peptidome in the
blood of disease-bearing hosts: Work in our
group seeks to identify peptide patterns among
disease-associated blood markers (i.e. the
blood peptidome and glyco-peptidome) in the
normal and disease state, to serve as the basis
for diagnostic kits. At a later stage, these results
could lead to the development of peptide-based
immunomodulators, inhibitors and other drugs.
3. Reactomics approach (with Prof. Raz Jelinek): A
novel disease diagnostic concept based upon the
screening of interactions of body liquids (blood
serum/plasma, urine, saliva, tears, amniotic fluid)
with an array matrix of chromatic biomimetic
vesicle detectors comprising lipid entities and
chromatic reporters.
Brusilovsky M., Cordoba M., Rosental B., Hershkovitz O., Andrake M.D., Pecherskaya A.,
Einarson M.B., Zhou Y., Braiman A., Campbell K.S. and Porgador A. (2013). GenomeWide siRNA Screen Reveals a New Cellular Partner of NK Cell Receptor KIR2DL4:
Heparan Sulfate Directly Modulates KIR2DL4-Mediated Responses. J. Immunol.
191(10):5256-5267.
11
Dr. Barak Rotblat
Functions of long noncoding RNA
and translation inhibitors in cancer
Background
Ph.D.: Tel-Aviv University, Israel
Post-doctorate: University of British
Colombia, Canada and MRC
Toxicology Unit, UK
Position: Senior Lecturer
Department of Life Sciences
The ‘central dogma’ in biology argues that the genetic information
stored in DNA encodes for mRNA, which is translated into proteins
that execute functions leading to the manifestation of a trait.
Current understanding of biology at the cellular and molecular
levels suggests that all stages of the process leading from the
expression of protein-coding genes to the manifestation of a
trait are highly regulated. In particular, there is high selectivity in
terms of which mRNA is translated into a protein in a given cell.
However, the vast majority of the genome is transcribed into RNA
yet does not encode for proteins. One sub-set of these noncoding
RNAs are longer then 200 base pairs and are hence termed long
noncoding RNAs (lncRNAs). Although it was previously held that
lncRNAs correspond to transcriptional noise, recent studies have
demonstrated that they function in all aspects of cell biology.
Specifically, some lncRNAs regulate the interactions of proteins
with DNA, RNA or other proteins. Furthermore, lncRNAs interact
with polysomes, raising the possibility that they may be involved
in regulation of proteins synthesis. Because deregulation of cellular
signalling pathways, in particular those that regulate translation,
is a hallmark of many human diseases, such as cancer, we aim to
elucidate the biological functions of lncRNAs and proteins that
regulate translation in cellular and disease contexts.
Faculty of Natural Sciences
E-mail: [email protected]
Selected publications
Rotblat B., Leprivier G. and Sorensen P.H. (2011). A possible
role for long non-coding RNA in modulating signaling
pathways. Med Hypotheses 77(6):962-965.
Rotblat B., Grunewald T.G., Leprivier G., Melino G. and
Knight R.A. (2013). Anti-oxidative stress response genes:
bioinformatic analysis of their expression and relevance in
multiple cancers. Oncotarget 4(12):2577-2590.
Leprivier G., Remke M., Rotblat B., Dubuc A., Mateo
A.R., Kool M., Agnihotri S., El-Naggar A., Yu B., Prakash
Somasekharan S., Faubert B., Bridon G., Tognon C.E., Mathers
J., Thomas R., Li A., Barokas A., Kwok B., Bowden M., Smith
S., Wu X., Korshunov A., Hielscher T., Northcott P.A., Galpin
J.D., Ahern C.A., Wang Y., McCabe M.G., Collins V.P., Jones
R.G., Pollak M., Delattre O., Gleave M.E., Jan E., Pfister S.M.,
Proud C.G., Derry W.B., Taylor M.D. and Sorensen P.H. (2013).
The eEF2 Kinase Confers Resistance to Nutrient Deprivation
by Blocking Translation Elongation. Cell 153(5):1064-1079.
Rotblat B., Southwell A.L., Ehrnhoefer D.E., Skotte H.N.,
Metzler M., Franciosi S., Leprivier G., Somasekharan
S.P., Barokas A., Deng Y., Tang T., Mathers J., Cetinbas N.,
Daugaard M., Kwok B., Li L., Carnie C.J., Fink D., Nitsch R.,
Galpin D.J., Ahern C.A., Melino G., Penninger J.M., Hayden
M.R. and Sorensen P.H. (2014). HACE1 reduces oxidative
stress and mutant Huntingtin toxicity by promoting the
NRF2 response. Proc. Natl. Acad. Sci. USA 111(8)3032-3037.
12
Current research
1. lncRNA that support cancer stem cells: The cancer stem cell
(CSC) hypothesis argues that in a fraction of the tumor cells
CSCs are endowed with tumor-initiating capacity, promote
tumor growth and are highly resistant to chemotherapy. The
implications of this model are that such cells represent a cell
population that is responsible for the two most deadly traits
of cancer, namely post-treatment relapse and metastasis.
Therefore, it is likely that key molecular components of CSCs
represent attractive drug targets. Accordingly, we study
lncRNAs that are highly expressed in aggressive tumors and
in CSCs so as to identify new molecules that promote cancer,
which, in turn, correspond to attractive new drug targets.
2. Negative regulators of translation that promote cancer: To
support proliferation, cancer cells exhibit increased rates of
protein synthesis and hyper-activation of translation-promoting
signalling pathways. As such, inhibition of translation is an
important aspect of the cellular response to a wide range of
challenges or stresses. Indeed, we have recently demonstrated
that cancer cells depend on a negative regulator of translation
to survive the stressful tumor environment. The goal of our
studies is to identify coding or noncoding sequences that
function as translation inhibitors and which cancer cells exploit
to enable them to survive stress. Based on our results, we will
pursue the development of compounds targeting these
translation inhibitors and test them as potential candidates
for the treatment of cancer.
Prof. Varda
Shoshan-Barmatz
NIBN Director
Novel approaches to cancer therapy
Background
Many cancer cells undergo re-programming of their metabolism
and develop cell survival strategies involving anti-apoptosis defense
mechanisms, a hallmark of the majority of cancer types. Found at
the outer mitochondrial membrane, the voltage-dependent anion
channel (VDAC) assumes a crucial position in the cell serving as a
gatekeeper, controlling the metabolic and energy cross-talk between
mitochondria and the rest of the cell, and is involved in apoptosis.
VDAC is the proposed target for the pro- and anti-apoptotic Bcl2-family
of proteins, as well as functioning in the release of apoptotic proteins
located in the inter-membranal space. Thus VDAC is considered a key
player in cell metabolism and regulation of mitochondria-mediated
apoptosis. As such, VDAC1 represents an excellent target to approach
in order to impair the re-programmed metabolism of cancer cells and
their capability to evade apoptosis.
Current research
Ph.D.: Weizmann Institute of Science, Israel
Post-doctorate: University of WisconsinMadison, USA and University of Toronto,
Canada
Position: Professor, NIBN Director
Department of Life Sciences
Faculty of Natural Sciences
E-mail: [email protected]
Selected publications
Abu-Hamad S., Sivan S. and Shoshan-Barmatz V. (2006).
The Voltage-Dependent Anion Channel Down- and overexpression control Cell's life and death. Proc. Nat. Ac. Sci.
USA 386:73-83.
Shoshan-Barmatz V., de Pinto P., Markus Zweckstetter
M., Raviv, Z., Keinan N. and Arbel N. (2010). VDAC, a multifunctional mitochondrial protein regulating both cell life
and death. Molecular Aspects of Medicine. 31:227-286
Arbel N., Ben-Hail D. and Shoshan-Barmatz V. (2012).
Mediation of the anti-apoptotic activity of BCL-XL upon
interaction with VDAC1. J. Biol. Chem. 287(27):23152-23161.
Shoshan-Barmatz V., Mizrachi D. and Keinan K. (2013).
Oligomerization of the mitochondrial protein VDAC1: From
structure to function and cancer therapy. Prog. Mol. Biol.
Transl. Sci. 117:303-334.
Prezma T., Shteinfer A., Admoni L., Raviv Z., Sela I., Levi I. and
Shoshan-Barmatz V. (2013). VDAC1-based peptides: Novel
pro-apoptotic agents and potential therapeutics for B cell
chronic lymphocytic leukemia. Cell Death and Disease,
e809. doi: 10.1038/cddis.2013.316. PMID:24052077.
Arif, T, Vasilkovsky, L., Refaeli, Y. Konson, A. and
Shoshan-Barmatz, V (2014) Silencing VDAC1 expression
by siRNA inhibits cancer cell proliferation and tumor
growth in vivo, Molecular Therapy–Nucleic Acids 2014
Apr 29;3:e159. doi: 10.1038/mtna.2014.9.
Weisthal, S., Keinan, N., Ben-Hail, D., Arif, T. and
Shoshan-Barmatz, V. (2014) Ca2+-mediated regulation
of VDAC1 expression levels is associated with cell death
induction Biochim. Biophys. Acta, 1843(10):2270-81
Given that mitochondria play a central role in the execution of
apoptosis and that VDAC1 is the gatekeeper of mitochondrial
function and dysfunction, we have generated specific, potent and
highly effective VDAC1-based cancer therapies that facilitate the
death of cancer cells or arrest of cell growth. Four novel strategies
towards developing cancer therapies involving VDAC1 are currently
being pursued in my laboratory:
1. Targeting anti-apoptotic proteins using VDAC1-based peptides
to minimize the self-defense mechanisms of cancer cells, known
to overexpress anti-apoptotic proteins. We have identified
VDAC1 sequences involved in interactions between VDAC1 and
anti-apoptotic proteins and demonstrated that VDAC1-based
peptides prevent the anti-apoptotic proteins’ activity, disturb cell
energy homeostasis and lead to apoptotic cell death specifically.
In-vitro, such peptides were shown to be active in a variety of
cancer cell lines regardless of the carried mutations and inhibited
glioblastoma tumor growth in-vivo.
2.Arresting cell proliferation by down-regulation of VDAC1
expression – Our results have shown that suppression of VDAC1
expression by a single siRNA arrested cell proliferation due to
interrupted energy and metabolite supply to the high energydemanding cancer cells. We have demonstrated proof-of-concept
in animal models with cervical and lung cancers.
3. We have demonstrated that VDAC1 oligomerization is a general
mechanism that is common to many apoptosis inducers, acting
via different pathways. We have developed a high throughput
screening (HTS) assay for modulators of VDAC1 oligomerization
and have identified pro- and anti-apoptotic drugs acting via
modulation of VDAC1 oligomerization. The aim is to develop
molecules that, a) promote VDAC1 oligomerization andthe
subsequent apoptotic cell death, thereby serving as anti-cancer
therapeutics, and b) inhibitVDAC1 oligomerization thereby
preventing cell death and allow the rescue of nerve cells in
neurodegenerative diseases.
4. We have demonstrated an increase in VDAC1 expression levels
following apoptosis induction by various agents, as well as
the correlation between drug efficacy and VDAC1 expression
level. We propose a new concept according to which several
apoptosis-inducing agents and conditions act by up-regulating
VDAC1 expression in a Ca2+-dependent manner, leading to
VDAC1 assembly into high oligomeric structures and thereby to
cell death. Further investigations y of this novel mechanism may
provide a unique platform for developing a new class of anticancer drugs.
13
Autoimmune and Metabolic Diseases
Group
Understanding the mechanisms involved in the maintenance of
homeostatic immune responses as well as those that have gone
awry in disease states, poses a significant challenge. At the NIBN,
a robust platform technology called “direct evolution” is being
used to generate superior, soluble anti-inflammatory proteins to
treat autoimmune diseases such as psoriasis, rheumatoid arthritis
(RA), inflammatory bowel disease (IBD) and asthma. Additionally,
this group’s efforts include understanding how chronic stress is
associated with increased susceptibility to autoimmune disease.
Other activities are focused on understanding metabolic
dysfunctions related to the role of adipose tissue dysfunction
in obesity and associated co-morbidities as well as the causative
link suppression of mitochondrial turnover, β-cell dysfunction,
apoptosis and the development of type 2 diabetes.
•
•
•
•
14
Prof. Amir Aharoni
Prof. Angel Porgador
Prof. Assaf Rudich
Prof. Orian Shirihai
Prof. Amir Aharoni
Protein engineering
using directed evolution
Background
Protein engineering has been used extensively in the past twenty
years for the study of enzyme structure-function and evolution.
Recently, protein engineering using directed evolution has proven
to be highly successful, yielding proteins demonstrating increased
stability under extreme conditions, increased solubility for expression
in heterologous systems, and proteins with novel reaction and
substrate specificities. Directed evolution implements an iterative
Darwinian optimization process, whereby the fittest variants are
selected from a collection of random mutations. Improved variants
are identified and isolated by screening or selection for the property
of interest. This approach is particularly advantageous in cases in
which no prior knowledge of a protein’s mechanism and structure
is available.
Current research
Ph.D.: Weizmann Institute of Science,
Israel
Post-doctorate: Weizmann Institute of
Science, Israel and University of British
Columbia, Canada
Position: Associate Professor
Department of Life Sciences
Faculty of Natural Sciences
E-mail: [email protected]
Selected publications
Fridman Y., Palgi N., Dovrat D., Ben-Aroya S., Hieter P.,
Aharoni A. (2010). Subtle Alterations in PCNA-partner
Interactions Severely Impair DNA Replication and Repair.
PLoS Biology. 8(10):e100.
Sadeh A., Baran D., Volokh M., Aharoni A. (2012).
Conserved Motifs in the Msn2-Activating Domain are
Important for Msn2-mediated Yeast Stress Response. J.
Cell. Sci. 125:3333-3342.
Zamir L., Zaretsky M., Fridman Y., Ner-Gaon H., Rubin E.,
Aharoni A. (2012). Tight co-evolution of PCNA-partner
interaction networks in fungi leads to inter-species
network incompatibility. Proc. Natl. Acad. Sci. USA
109(7):E406-414.
Amar D., Berger I., Amara N., Tafa G., Meijler M., Aharoni A.
(2012). The Transition of Human Estrogen Sulfotransferase
from Generalist to Specialist using Directed Enzyme
Evolution. J. Mol. Biol. 416(1):21-32.
Zaretsky M., Etzyoni R., Kaye K., Sklair-Tavron L., Aharoni A.
(2013). Directed Evolution of a Soluble Human IL-17A
Receptor for the Inhibition of Psoriasis Plaque in Mice
Model. Chemistry and Biology 20:202-211.
1. Cytosolic sulfotransferases (SULTs) are liver enzymes that detoxify a
variety of substrates by transferring sulfate to a variety of acceptor
molecules bearing a hydroxyl or an amine group. Sulfation renders
the product more readily excretable or less pharmacologically
active. The diversity of acceptor compounds for cytosolic SULTs
is remarkable, ranging in size, shape and flexibility, from ethanol
to steroids. These enzymes play important roles in a variety of
biological functions, such as modulating the levels of hormones
and neurotransmitters. Using directed evolution, we aim to
improve the detoxification properties of SULTs by implementing a
new high throughput screening methodology that allows for the
screening of millions of mutant enzymes in parallel for increases
in catalytic efficiency. Improved mutant enzymes may find ex-vivo
biotechnological applications, such as in bioremediation.
2. DNA replication and gene transcription are two ubiquitous
biological processes in all living organisms. We are currently
developing new tools to study these processes using directed
evolution methodology. We are focusing on the proliferating
cellular nuclear antigen (PCNA) which is a hub protein
orchestrating the DNA replication process in eukaryotic cells.
We aim to elucidate the importance of PCNA-protein interaction
for DNA replication, repair and cell viability. Another project is
focused on the study of stress-related transcription factor (TF) in
yeast. We aim to generate TF mutants that increase the ability of
yeast to survive under different stress conditions in order to study
the molecular basis for higher tolerance to different conditions
and the linkage between the yeast responses to different stress
conditions.
3. Engineering of therapeutic proteins for increased stability and
binding affinity – We are focusing in generating improved soluble
receptors for inhibiting pro-inflammatory cytokines involved in
a variety of different autoimmune diseases. Our initial efforts
were focused on the development of a unique, soluble IL-17
receptor therapeutic with improved properties, that was shown
e to inhibit psoriasis plaque formation in a mouse model. This
protein constitutes an important drug candidate for the treatment
of psoriasis in humans.
15
Prof. Angel Porgador
Innate immunity and diabetes
Background
Natural killer (NK) cells belong to the innate lymphoid cells.
Their cytotoxic activity is regulated through the delicate balance
between activating and inhibitory signals. NKp46 is a member of
the primary activating receptors of NK cells. We previously reported
that islets beta cells express ligand(s) to the human NK activation
receptor NKp46 and that NKp46 is involved in the development
of type 1 diabetes (T1D) autoimmune disease. Subsequently, we
hypothesized that blocking of the NKp46 receptor could prevent
or hinder T1D development.
Current research
Ph.D.: Weizmann Institute of Science, Israel
Post-doctorate: Duke University
and National Institutes of Health, USA
Position: Associate Professor
The Shraga Segal Department of
Microbiology, Immunology and Genetics
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Gur C., Porgador A., Elboim M., Gazit R., Mizrahi S.,
Stern-Ginossar N., Achdout H., Ghadially H., Dor Y., Nir
T., Doviner V., Hershkovitz O., Mendelson M., Naparstek
Y. and Mandelboim O. (2010). The activating receptor
NKp46 is essential for the development of type 1diabetes.
Nature Immunol. 11(2):121-128. ** AP and OM are equal
contributors.
Jaron-Mendelson M., Yossef R., Appel M.Y., Zilka A., Hadad
U., Afergan F., Rosental B., Engel S., Nedvetzki S., Braiman A.
and Porgador A. (2012). Dimerization of NKp46 Receptor
Is Essential for NKp46-Mediated Lysis : Characterization of
the Dimerization Site by Epitope Mapping. J. Immunol.
188(12):6165-6174.
Yossef R., Gur C., Shemesh A., Hadad U., Nedvetzki S.,
Miletić A., Cerwenka A., Jonjic S., Mandelboim O. and
Porgador A. Targeting Natural Killer Cell Reactivity by
Employing Antibody to NKp46: Implications for Type 1
Diabetes. Submitted.
16
Characterization of innate immunity responses to type
1diabetes.
Our research works towards the development of new
tools and the identification of novel mechanisms aimed at
antagonizing the activity of NKp46 during type I diabetes
development. Furthermore, we aim to identify those NKp46
ligand(s) expressed by murine and human islet beta cells.
Specifically, our goals are to develop blocking anti-NKp46
antibodies or NKp46-derived peptides that prevent NKp46
activity, as well as to investigate mechanisms controlling
expression of the NKp46 ligand in islet beta cells followed
by ligand characterization.
To date, we have developed monoclonal antibodies
(mAbs) against murine NKp46. One mAb, termed NCR1.15,
recognizes Ncr1, the mouse homologue of NKp46, and was
able to down-regulate the surface expression of NKp46
on primary murine NK cells following in vivo antibody
injection. Additionally, NCR1.15 treatment led to the
down-regulation of cytotoxic activity mediated by NKp46
but not by other NK receptors. To test the effects of the
antibodies on T1D, we followed development of the
disease in two models, NOD mice and in mice subjected
to low-dose streptozotocin treatment. The results revealed
a significantly lower incidence of diabetes in the NCR1.15treated group, as comparing to control groups. We are
currently developing humanized monoclonal antibodies
to human NKp46 that are cross-reactive to murine NKp46.
Such antibodies will allow us to directly test the humansuggested prototype in mouse models for suppression or
prevention of type 1 diabetes development.
We are also developing a method to insert human NKp46
into hematopoietic stem cells of NCR1-knockout mice
with the expectation that functional human NKp46 will
be expressed in the developing murine NK cells. Such
cells would allow us to test the function of human NKp46derived peptides in the in vivo blocking of human NKp46
function and allow for better characterization of the effects
of this peptide drug-mediated block on the development
of induced T1D.
Prof. Assaf Rudich
The role of adipose tissue
dysfunction in obesity and its
co-morbidities
Background
Over the past 15 years obesity has become the most prevalent
preventable risk factor for morbidity and mortality. Although
the reasons are complex and still incompletely understood, it
is clear that adipose tissue in obesity becomes dysfunctional,
and is a major pathogenic contributor to the morbidity that
accompanies obesity.
Current research
1.
M.D.: Ben-Gurion University, Israel
Ph.D.: Ben-Gurion University, Israel
Post-doctorate: Hospital for Sick
Children, Toronto, Canada
Position: Professor
Department of Clinical Biochemistry
and Pharmacology
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Nov O., Shapiro H., Ovadia H., Tarnovscki T., Dvir I., Shemesh E., Kovsan
J., Shelef I., Carmi Y., Voronov E., Apte R.N., Lewis E., Haim Y., Konrad
D., Bashan N. and Rudich A. (2013). Interleukin-1β regulates fat-liver
crosstalk in obesity by auto-paracrine modulation of adipose tissue
inflammation and expandability. PloSOne 8(1):e53626.
Shapiro H., Pecht T., Shaco-Levy R., Harman-Boehm I., Kirshtein
B., Kuperman Y., Chen A., Blüher M., Shai I. and Rudich A. (2013).
Adipose tissue foam cells are present in human obesity. J. Clin.
Endocrinol. Metab. 98:1173-1181.
Hadad N., Elgazar-Carmon V., Burgazliev O., Solomonov Y., Wueest
S., Item F., Konrad D., Rudich A. and Levy R. (2013). Induction of
cytosolic phospholipase A2α is required for adipose neutrophil
infiltration and hepatic insulin resistance early in the course of high
fat feeding. Diabetes 62:3053-3063.
Beck-Haim Y., Tarnovscki T., Bashari D., Rudich A. (2013). A Chromatin
Immunoprecipitation (ChIP) protocol for use in whole human
adipose tissue. Am. J. Physiol. - Endocrinol. Metab. 305: E1172-E1177.
Mechanisms for human adipose tissue dysfunction
in obesity: Analysis of human adipose tissues is aimed
at unraveling how obesity leads to adipose tissue
dysfunction. Utilizing expression, molecular, imaging,
functional, and ex-vivo studies of human samples, we are
identifying the "human adipose tissue stress response"
and unravel its functional significance. The causal
role of specific pathways and molecular mechanisms
identified (such as the role of autophagy, inflammation,
and a specific MAP kinase signaling cascade) are further
challenged using cellular, ex-vivo and in vivo experimental
models. Functionally we mainly focus on two pathogenic
axes: an adipocyte-macrophage axis that operates within
the adipose tissue, and a fat-liver axis that mediates the
pathogenic role of visceral adiposity.
2. Investigating potential life-style interventions
to alleviate obesity-related morbidities in large
populations: As part of a larger team of investigators
(headed by Prof. Iris Shai), intervention trials are being
conducted to identify life-style approaches to limit the
health burden of the obesity epidemic, and to understand
the mechanisms by which such protective effects occur.
3. Circulating monocytes as mediators of the environmental
impact on adipose tissue in obesity: Circulating
monocytes are the likely precursors of adipose tissue
macrophages that accumulate in obesity. We hypothesize
that monocytes may constitute a marker of adipose
tissue inflammation (and thus, for morbidity-prone
obesity), and are also active players in the pathogenesis
of obesity-associated morbidity. Specifically, we entertain
the possibility that monocytes may communicate a
contributing effect of air-borne environmental particles
(air pollution) to obesity-associated morbidity.
Pecht T., Gutman A., Bashan N. and Rudich A. (2013). Peripheral
blood leucocyte sub-classes as potential biomarkers of adipose
tissue inflammation and obesity sub-phenotypes in humans. Obes.
Rev. (in press).
17
Prof. Orian Shirihai
Mitochondrial dynamics in metabolic
diseases
Background
Mitochondria have a very active social life style involving frequent
fusion and fission events. Mitochondria that lose their ability to
properly respire become excluded from the networking population
and will be consumed by the cellular equivalent of a lion, the
autophagosome. This forms a pathway of quality control. However,
recent studies suggest that arrest of mitochondrial fusion at the
cellular level, also termed "fragmentation", is playing a role in the
adaptation to excess nutrient environment. Recognizing that excess
nutrient environment places mitochondria in a biological conflict of
interest may help understanding the link between metabolic and
aging associated conditions.
We study two disease models in which oxidative damage to
mitochondria play a key role in the development of pathology. In
diabetes, nutrient-induced oxidative damage has been shown to
be a major mediator of endocrine dysfunction and beta cell loss.
In bone marrow, oxidative damage induced by iron and hemeintermediates, leads to the development of sideroblastic anemia and
myelodysplastic syndrome.
Ph.D.: Technion, Israel
Post-doctorate: Harvard University
School of Medicine, USA
Position: Associate Professor
Department of Clinical Biochemistry
and Pharmacology
Current research
Mitochondrial Dynamics in the beta cell: Mitochondria in β-cells
play a key role as integrators of nutrient signals and insulin
secretion. One significant manifestation of diabetes is the
gradual reduction in mitochondrial capacity to produce signals
in response to fuels. The cause of this gradual deterioration is
not yet understood. Our goal is to understand the mechanisms
that underlie deterioration of mitochondrial function during the
development of β-cell dysfunction and diabetes.
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Twig G., Elorza A., Molina A.J., Mohamed H., Wikstrom J.D.,
Walzer G., Stiles L., Haigh S.E., Katz S., Las G., Alroy J., Wu M.,
Py B.F., Yuan J., Deeney J.T., Corkey B.E. and Shirihai O.S.
(2008). Fission and selective fusion govern mitochondrial
segregation and elimination by autophagy. EMBO J. 27:433446.
Molina A.J., Wikstrom J.D., Stiles L., Las G., Mohamed H.,
Elorza A., Walzer G., Twig G., Katz S., Corkey B.E. and Shirihai
O.S. (2009). Mitochondrial networking protects beta-cells
from nutrient-induced apoptosis. Diabetes 58:2303-2315.
Las G., Sereda S., Wikstrom J.D., Twig G., and Shirihai O.S.
(2011). Fatty acids suppress autophagic turnover in β-cells.
J. Biol. Chem. 286:42534-42544.
Liesa M. and Shirihai O.S. (2013). Mitochondrial dynamics
in the regulation of nutrient utilization and energy
expenditure. Cell Metabolism 17:491-506.
Wikstrom J.D., Mahdaviani K., Liesa M., Sereda S.B., Si Y.,
Las G., Twig G., Petrovic N., Zingartti C., Graham A., Cinti
S., Corkey B.E., Cannon B., Nedergaard J. and Shirihai O.S.
(2014). Hormone-induced mitochondrial fission is utilized
by brown adipocytes as an amplification pathway for
energy expenditure. EMBO J. 33(5):418-436.
Ferree A., Trudeau K., Zik E., Benador IY1, Gottlieb R.A. and
Shirihai O.S. (2013). MitoTimer probe reveals the impact of
autophagy, fusion, and motility on subcellular distribution
of young and old mitochondrial protein and on relative
mitochondrial protein age. Autophagy 9(11):1887-1896.
18
We have shown that β-cells respond to the chronic exposure to
high levels of glucose and fatty acids with a drastic reduction
in mitochondrial networking through fusion and fission. This
phenomenon precedes a gradual deterioration of mitochondrial
function that is characterized by the generation of a subpopulation
of mitochondria with reduced membrane potential. Remarkably,
under these conditions, induction of mitochondrial fusion in the
β-cell prevents the appearance of mitochondria with reduced
membrane potential and protects from the detrimental effects of
chronic exposure to a nutrient rich environment (see publications
list: Molina et al. 2009)
Mitochondrial quality control: By tagging and tracking individual
mitochondria in intact β-cells we discovered the existence of a
quality control mechanism that relies on both fusion and fission.
Following mitochondrial fission some daughter units depolarize.
These units display a lower likelihood for subsequent fusion and
are apparent targets of autophagy (see Twig et al. 2008). Moreover,
this model predicts that the inhibition of mitochondrial dynamics
(MtDy) by Gluco-lipo-toxicity (GLT) may have a cumulative effect
and result in an increased portion of dysfunctional units over time.
Such enrichment of dysfunctional mitochondria could explain the
long lasting effect of GLT, a phenomenon that has been shown to
impact animals’ prognosis many months after a high fat diet has
been discontinued (see Liesa and Shirihai, 2013).
Mitochondrial Dynamics in the regulation of Energy efficiency:
Brown fat is a unique tissue that can reduce its energy efficiency
in response to hormonal stimulation. Upon stimulation with
adrenergic agonists brown adipocyte mitochondria switch
from efficient ATP producing metabolism to heat producing
metabolism mediated by uncoupling. We are using this model
to study the role of mitochondrial architecture and dynamics
in energy efficiency. Our findings indicate that fragmented
mitochondrial network enhances energy expenditure and as
such may be a mechanism by which we can increase caloric
consumption by the brown adipose tissue.
Neurodegenerative Diseases Group
With the global phenomenon of aging whereby many countries
worldwide will have at least 20% of their population > 65 years
old by 2030, the progressive loss of structure or function of
neurons, including death of neurons and associated diseases,
represents a major clinical burden. Many neurodegenerative
diseases including Parkinson’s, Alzheimer’s, and Huntington’s
occur as a result of neurodegenerative processes and discovering
cellular mechanisms involved in neuronal loss might offer new
diagnostic and therapeutic advances. At the NIBN, research
groups are focusing on the development of innovative immune
and peptide-based therapeutic strategies for Alzheimer’s disease,
understanding awry protein-protein interactions in ALS (Lou
Gehrig’s disease) as well as utilizing the nematode c. elegans as a
model system to unveil mechanisms of neurodegeneration and
assessment of naturally-occurring plant extracts to halt cell loss.
Furthermore, dissecting the role of the mitochondrial sodium/
calcium exchanger in neuronal diseases such as Parkinson’s, is
also being investigated.
·
·
·
·
Dr. Anat Ben-Zvi
Prof. Alon Monsonego
Prof. Israel Sekler
Prof. Varda Shoshan-Barmatz
19
Dr. Anat Ben-Zvi
Protein folding homeostasis
in a multicellular organism
Background
The long-term health of all metazoan cells is linked to protein quality
control. All cells have highly conserved pathways that detect, prevent
and resolve protein damage. The absence or malfunction of these
pathways can result in developmental arrest, functional decline
of diverse cellular machinery and the onset of protein misfolding
diseases. When protein folding and clearance is balanced with
protein biosynthetic processes, protein homeostasis (proteostasis) is
achieved, thereby preventing the accumulation of mis-folded protein
and aggregates within cells.
Current research
Ph.D.: The Hebrew University of
Jerusalem, Israel
Post-doctorate: Northwestern
University, Evanston, USA
Position: Senior Lecturer
Department of Life Sciences
Faculty of Natural Sciences
E-mail: [email protected]
Selected publications
Gidalevitz T*., Ben-Zvi A*., Ho K.H., Brignull H.R. and
Morimoto R.I (2006). Progressive Disruption of Cellular
Protein Folding in Models of Polyglutamine Diseases.
Science 311(5766):1471-1474.
Ben-Zvi A., Miller E.A and Morimoto R.I (2009). Collapse
of Proteostasis Represents an Early Molecular Event in C.
elegans Aging. Proc. Natl. Acad. Sci. USA 106(35):1491414919.
Bar-Lavan Y., Kosolapov L., Frumkin F. and Ben-Zvi A.
(2011). Regulation of cellular protein quality control
networks in a multi-cellular organism. FEBS J. 279(4):526531.
Shemesh N., Shai N. and Ben-Zvi A. (2013). Germline stem
cell arrest inhibits the collapse of somatic proteostasis
Early in Caenorhabditis elegans Adulthood. Aging Cell
12(5):814-822.
Karady I., Frumkin A., Dror S., Shemesh N., Shai N. and BenZvi A. (2013). Using Caenorhabditis elegans as a model
system to study protein homeostasis in a multicellular
organism. JoVE (82):e50840
Feldman N., Kosolapov L. and Ben-Zvi A. (2014).
Fluorodeoxyuridine improves Caenorhabditis elegans
proteostasis independent of reproduction onset. PLOS
ONE 9(1):e85964
20
Most protein mis-folding associated diseases exhibit tissue-selective
impairment. However, the mechanism for this selectivity and
vulnerability remains unknown. Cell-type-specific and tissue-specific
regulation of protein expression results in different cellular functions
and morphological characteristics. Thus the requirements for and
regulation of protein folding may also vary between tissues. We aim
to elucidate how cell-specific differences in protein expression affect
cellular quality control networks. Caenorhabditis elegans (C. elegans)
provides an opportunity to study the complex biological networks
that determine proteostasis in an intact organism. We employ the
C. elegans model system to study protein folding in the cell, using
a combination of cellular, biochemical and genetic approaches to:
1. Develop a toolbox of folding sensors to monitor proteostasis
challenges and determine the genetic and physical interactions
with the cellular folding machinery.
2. Identify cell-specific and cell-nonspecific modifiers of proteostasis
in C. elegans and compare the protein folding capacity in
different cell types.
3. Evaluate the impact of the expression of various aggregationprone proteins on the protein folding capacity in different cell
types.
4. Examine the cell non-autonomous regulation of protesostasis
during adulthood and how it modulates the onset and
progression of protein mis-folding diseases.
Prof. Alon Monsonego
Novel approaches for the
treatment of neurodegenerative
and autoimmune diseases
Background
Our laboratory is interested in the characterization of key
regulatory factors that maintain immune homeostasis and
protect against self-originated neurodegenerative and
autoimmune diseases. In contrast to current therapeutics that
mostly offer an anti-inflammatory approach, our goals for cure
and prevention are aimed at immunotherapy, designed to
strengthen endogenous beneficial immune reactions.
Current research
Ph.D.: Weizmann Institute of Science,
Israel
Post-doctorate: Harvard Medical
School, USA
1. Neurodegenerative diseases: Our research is focused on
characterizing the immune mechanisms, which maintain
the neuronal network in health and disease, by studying:
a) the differentiation and functional characteristics of
microglia (the brain macrophages) within the brain tissue;
b) the role of cytokines and chemokines in regulating glianeuron interactions; and c) the migration and function of
lymphocyte subsets within the brain.
Position: Associate Professor
The Shraga Segal Department of
Microbiology, Immunology and Genetics
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Nemirovsky A., Fisher Y., Baron R., Cohen I.R. and Monsonego
A. (2011). Amyloid beta-HSP60 peptide conjugate vaccine
treats a mouse model of Alzheimer's disease. Vaccine
29(23):4043-4050.
Fisher Y., Nemirovsky A., Baron R. and Monsonego A. (2011).
Dendritic cells regulate amyloid-β-specific T-cell entry into
the brain: the role of perivascular amyloid-β. J. Alzheimers Dis.
27(1):99-111.
Abutbul S., Shapiro J., Szaingurten-Solodkin I., Levy N.,
Carmy Y., Baron R., Jung S. and Monsonego A. (2012). TGF-β
signaling through SMAD2/3 induces the quiescent microglial
phenotype within the CNS environment. Glia 60(7):1160-1171.
These aspects of the immune system can mediate neuronal
recovery by affecting the clearance of toxic forms of
amyloid from the brain and by inducing a local milieu
supportive of neuronal repair. We have developed a unique
Alzheimer’s disease (AD) mouse model that lends itself to
the development of safe vaccination approaches aimed at
prevention and therapy of the disease.
2. Autoimmunity: Our research is focused on the following
aspects: a) characterizing the repertoire of brain-specific
T cells and their role in aging and the progression of AD;
b) revealing autoimmune mechanisms associated with
chronic stress; and c) the use of 3D-scaffolds to generate
a transplantable lymphoid-like tissue with immunoregulatory properties.
These approaches offer a platform for the design of
immune-based therapies to a variety of autoimmune
disorders, whether they originate from immune deficiency
(e.g. cancer, neurodegenerative diseases) or hyper-immune
responses (e.g. autoimmune diseases, allergies).
Fisher Y., Strominger I., Biton S., Nemirovsky A., Baron R. and
Monsonego A. (2013). Th1 Polarization of T Cells Injected into
the Cerebrospinal Fluid Induces Brain Immunosurveillance.
J. Immunol. 192(1):92-102.
Monsonego A., Nemirovsky A. and Harpaz I. (2013). CD4 T
cells in immunity and immunotherapy of Alzheimer's disease.
Immunology 139(4):438-446.
Harpaz I., Abutbul S., Nemirovsky A., Gal R., Cohen H. and
Monsonego A. (2013). Chronic exposure to stress predisposes
to higher autoimmune susceptibility in C57BL/6 mice:
glucocorticoids as a double-edged sword. Eur. J. Immunol.
43(3):758-769.
21
Prof. Israel Sekler
Ionic control of Ca2+ signaling and
metabolism
Background
Ionic gradients control signaling and metabolic activity, with their
breakdown being linked to major diseases. The major focus of our lab
is to molecular identify key ion transporters and to determine their
physiological roles, as well as developing novel opto-molecular strategies
for controlling ionic gradients.
Current research
Ph.D.: Weizmann Institute of Science, Israel
Post-doctorate Tenure: Stanford
University, USA
Position: Professor
Department of Physiology and Cell
Biology
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Palty R., Ohana E., Hershfinkel M., Volokita M., Elgazar V., Beharier
O., Silverman W.F., Argaman M. and Sekler I. (2004). Lithiumcalcium exchange is mediated by a distinct potassiumindependent sodium-calcium exchanger. J. Biol. Chem. 279:
25234-25240.
Palty R., Silverman W.F., Hershfinkel M., Caporale T., Sensi S.L.,
Parnis J., Nolte C., Fishman D., Shoshan-Barmatz V., Herrmann
S., Khananshvili D. and Sekler I. (2010). NCLX is an essential
component of mitochondrial Na+/Ca2+ exchange. PNAS
107:436-441.
Nita I.I., Hershfinkel M., Fishman D., Ozeri E., Rutter G.A., Sensi
S.L., Khananshvili D., Lewis E.C. and Sekler I. (2012). The
mitochondrial Na(+)/Ca(2+) exchanger upregulates glucose
dependent Ca(2+) signaling linked to insulin secretion. PLoS
One 7(10):e46649.
Hoch E., Lin W., Chai J., Hershfinkel M., Fu D. and Sekler I. (2012).
Histidine pairing at the metal transport site of mammalian ZnT
transporters controls Zn2+ over Cd2+ selectivity. Proc. Natl.
Acad. Sci. U.S.A. 109(19):7202-7207.
Parnis J., Montana V., Delgado-Martinez I., Matyash V., Parpura
V., Kettenmann H., Sekler I. and Nolte C. (2013). Mitochondrial
exchanger NCLX plays a major role in the intracellular Ca2+
signaling, gliotransmission, and proliferation of astrocytes. J.
Neurosci. 33(17):7206-7219.
22
Mitochondrial Ca2+ signaling
The mitochondrial Na+/Ca2+ exchanger (NCLX) is a key player in
mitochondrial and cellular calcium homeostasis. Although its
existence was documented some 40 years ago, its molecular
identity has remained elusive. By combining molecular silencing,
ectopic expression and dominant negative analysis with imaging
of mitochondrial and cellular calcium levels, we have identified
NCLX as the long-sought exchanger. This finding opens the
door to molecular analysis of the mitochondrial Ca2+ transport
machinery and physiological studies ranging from cardiac
activity to insulin secretion and neuronal activity. Based on an
examination of human mutations of NCLX, we are now linking
mitochondrial signaling to major human maladies ranging from
diabetes to Parkinson’s disease, Alzheimer’s disease and stroke.
Furthermore, by combing molecular modeling with appropriate
screens for potential NCLX agonists and antagonists, we plan
to identify novel drugs that might interrupt these major health
syndromes and presently unmet clinical needs.
Opto-metabolic control
Metabolic activity not only controls the life and death of cells but
is also linked to major diseases when impaired. Although we can
readily monitor metabolic activity, we cannot selectivity control
such processes because currently available reagents are devoid
of selectivity and often act as irreversible metabolic poisons.
In our laboratory, we are focusing on a novel strategy termed
opto-metabolic control. Our aim is to target light-dependent
molecular switches into mitochondria, thereby controlling
metabolic activity in cells both selectively and in a temporally
controlled manner. This strategy will provide global molecular
control of metabolic activities in sub-cellular fractions, cells,
tissues and organs.
Heavy metals in health and disease
Zinc is an essential micronutrient required for growth and
development yet is strikingly similar to cadmium, a highly
toxic environmental pollutant. Indeed, due to their similarity,
zinc transporters can be hijacked by cadmium, thus gaining
access into the body. Indeed, the similarity of the two metals is
so remarkable that there are no chelators that can distinguish
between the two. By combing molecular modeling with
functional assays, we have identified the first mammalian
transporter and ion binding site that can transport zinc yet
reject cadmium. Our current efforts are focused on identifying
the functional mechanism(s) of this and other zinc transporters,
as well as the molecular basis for heavy metal selectivity.
Prof. Varda
Shoshan-Barmatz
VDAC1 as a potential target for
Alzheimer's disease therapy
NIBN Director
Background
Ph.D.: Weizmann Institute of Science, Israel
Post-doctorate: University of
Wisconsin-Madison, USA and
University of Toronto, Canada
Position: Professor, NIBN Director
Department of Life Sciences
Faculty of Natural Sciences
E-mail: [email protected]
Selected publications
Shoshan-Barmatz V., Israelson A., Bridiczka D. and
Sheu S.S. (2006). The Voltage Dependent Anion Channel
(VDAC): Function in Intracellular Signalling, Cell Life and
Cell Death. Current Pharmaceutical design 12(18):22492270.
Shoshan-Barmatz V., de Pinto V., Zweckstetter M., Raviv
Z., Keinan N. and Arbel N. (2010). VDAC, a multi-functional
mitochondrial protein regulating both cell life and death.
Molecular Aspects of Medicine 31:227-286.
Varda Shoshan-Barmatz (2014). Amyloid-Beta binding
peptides and use thereof for treating neurodegenerative
diseases. U.S. Provisional Patent Application No.
61/935,363
Alzheimer’s disease (AD) is the most common form of dementia in the
elderly. AD is characterized by cognitive decline and the occurrence of
brain senile plaques and neurofibrillary tangles, as well as associated
with the loss of brain synapses and synaptic dysfunction. In consort
with these pathologies, increasing evidence also points to structural
and functional abnormalities of mitochondria. Clinical findings
strongly suggest that early aggregation of the amyloid beta peptide
(Aβ) plays a key role in AD pathogenesis. Moreover, Aβ deposits were
found both in extracellular and intra-neuronal in the brains of AD
patients early in the disease process. Moreover, it has been shown that
synaptic damage and mitochondrial dysfunction are early events in
AD pathogenesis, with Aβ-induced cytotoxicity having been shown
to be preceded by mitochondrial dysfunction and signaling events
characteristic of apoptosis in cultured cells. While mitochondrial
dysfunction occurs early in AD and is a prominent feature of the
disease, the underlying mechanisms remain poorly understood.
However, it has been recently shown that the voltage-dependent
anion channel (VDAC), located in the outer mitochondrial membrane
participates in Aβ-induced toxicity. This finding underscores a
definitive causative link between awry mitochondrial function and
the development of AD.
Current research
VDAC1 functions in both cell metabolism and apoptosis can be
modified by Aβ interaction with VDAC1, leading to mitochondrial
dysfunction and apoptosis. Using biophysical and biochemical
methods, we have demonstrated that Aβ directly interacts with
VDAC1 and with a peptide corresponding to VDAC1’s N-terminal
domain. This peptide completely prevents Aβ entry into PC-12
and SHSY-5Y cells and resultant cytotoxicity. In addition, silencing
VDAC1 expression by a specific siRNA prevented Aβ association
with the cell membrane and intracellular accumulation.
Therefore, we hypothesize that Aβ toxicity involves mitochondrial
impairment mediated via Aβ interaction with both mitochondrial
and plasmalemmal (pl)VDAC1. As a VDAC1 N-terminal-based
peptide protects against Aβ-related cytotoxicity and its cell
penetration, we hypothesize that Aβ cytotoxicity is mediated via
its interaction with the VDAC1-N-terminal domain and that Aβ
penetrates the cell via pl-VDAC1 that we predict is over-expressed
in AD brains. However, the exact mechanism by which VDAC1
mediates Aβ cytotoxicity and the sequence of events leading to
such toxicity have yet to be explored.
Our overall goal is to scrutinize the relationship between Aβ
interaction with VDAC1 and apoptosis induction and translate
these findings into the development of VDAC1-based peptide
therapeutics as effective anti-Aβ treatment for AD.
Elucidating the role of the VDAC1-Aβ interaction and the
involvement of pl-VDAC1 in Aβ cytotoxicity will provide new
insights into the mechanisms that control Aβ cytotoxicity in AD
pathogenesis and contribute to the development of VDAC1based pharmacological interventions.
23
Infectious Diseases Group
The development of innovative antibiotics is urgently required
to combat the spread of antibiotic-resistant infectious diseases,
especially hospital-acquired infections. In direct response to
this unmet medical need, groups at the NIBN are developing
both synthetic and naturally-occurring molecules to prevent a
phenomenon termed Quorum Sensing (bacterial communication).
In particular, such molecules are assayed for bioactivity in preventing
biofilm formation, a major bacterial resistance mechanism
that envelops bacteria rendering them far less susceptible to
antibiotics. Other anti-bacterial activities efforts are focused on
screening libraries for inhibitory activities targeting bacterialspecific, proteolytic degradation pathways known to be critical
for bacterial virulence. Such a strategy is used to specifically derail
infectivity associated with Myobacterium tuberculosis infections
(via inhibition of a unique pupylation pathway) and E. coli, Klebsiella,
Vibrio Cholera and Pseudomonas aeruginosa (via inhibition of
Lon protease). Additional activities within the infectious disease
group concern host-pathogen co-evolution concerning T and
B-cell immunodominance, HLA binding prediction and how all
this information can be leveraged for rational vaccine design.
Furthermore, research concerning the cell abscission component
of cytokinesis, namely the ESCRT machinery, is being adapted in
understanding the process of viral budding and infection and how
such a process can be arrested with specific inhibitors.
•
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24
Dr. Natalie Elia
Dr. Eyal Gur
Dr. Tomer Hertz
Prof. Michael .M. Meijler
Dr. Natalie Elia
Ph.D.: The Hebrew University of
Jerusalem, Israel
Post-doctorate: National Institutes of
Health, USA
Position: : Senior Lecturer
Department of Life Sciences
Faculty of Natural Sciences
E-mail: [email protected]
Selected publications
Lee H.H., Elia N., Ghirlando R., Lippincott-Schwartz J.
and Hurley J.H. (2008). Midbody targeting of the ESCRT
machinery by a noncanonical coiled coil in CEP55. Science
322(5901):576-580.
Rambold A., Kostelecky B., Elia N. and Lippincott-Schwartz
J. (2011). Tubular network formation protects mitochondria
from autophagosomal degradation during nutrient
starvation. Proc. Natl. Acad. Sci. U.S.A 108(25):10190-10195.
Elia N., Sougrat R., Spurlin T.A., Hurley J.H. and LippincottSchwartz J. (2011). Dynamics of endosomal sorting
complex required for transport (ESCRT) machinery during
cytokinesis and its role in abscission. Proc. Natl. Acad. Sci.
U.S.A 108(12):4846-4851. Ranked “must read” in Faculty of
1000.
Elia N., Fabrikant G., Kozlov M. and Lippincott-Schwartz
J. (2012). Computational model of cytokinetic abscission
driven by ESCRT III polymerization and remodeling.
Biophysical J. 102(10):2309-2320. Selected for cover.
Fridman K., Mader A., Zwerger M., Elia N. and Medalia O.
(2012). Advances in tomography: probing the molecular
architecture of cells. Nat. Rev. Mol. Cell. Bio. 13(11):736-742.
Elia N.*, Ott C. and Lippincott-Schwartz J.* (2013). Incisive
imaging and computation for cellular mysteries: lessons
from abscission. Cell 155(6):1220-1231. *Corresponding
authors
Cellular dynamics and macromolecular
architecture in 3D
Background
Cells are composed of many large, multi-molecular complexes executing
distinct cellular functions in a confined space and operating in a
dynamic, highly coordinated fashion. Understanding the kinetics and 3D
organization of such protein complexes is, therefore, key to understanding
cellular mechanisms. Recent advances in fluorescence light microscopy
techniques now permit the dissection of the spatiotemporal behavior
of proteins in their intact cellular environment. Confocal spinning disk
microscopy provides the high imaging speed, high sensitivity and high
dynamic range required to measure protein dynamics in cells, while
structured illumination microscopy (SIM) is a fluorescence-based
super-resolution imaging technique capable of three-dimensional (3D)
multi-color imaging at 100 nm lateral and 350 nm axial resolution in any
biological sample up to 10 microns in thickness. As such, SIM is one of the
most suitable techniques for mapping the spatial organization of protein
complexes in their native environment at nanometer scale resolution.
The temporal information obtained by spinning disk microscopy and
the detailed spatial information obtained by SIM can be integrated to
generate a spatiotemporal map of protein complexes in a given cellular
process. Constituting such spatiotemporal maps will facilitate mechanistic
understanding of different cellular machineries.
Current research
1. Understanding ESCRT mechanism of action: The ESCRT complex
is emerging as one of the major cellular machineries responsible
for driving membrane fission in cells. Additionally, a fundamental
role for the ESCRT machinery was recently defined in driving the
very late events of cell division that lead to the physical separation
of two daughter cells. We aim to elucidate the mechanism of
action of the ESCRT machinery in driving membrane fission
using mammalian cell division as a model system. We hope to
do so using advanced quantitative imaging approaches, as well
as by developing new tools for arresting the ESCRT pathway. As
the ESCRT machinery is involved in numerous cellular functions,
including receptor degradation, viral budding and cell division,
our results will have applicative implications including for the
development of drugs to block uncontrolled cell division, viral
infectivity and other cellular processes.
2. Dissecting the spatiotemporal regulation of cytokinetic
abscission: Cell division is one of the most regulated and
coordinated processes in cell biology. While much is known
about the temporal regulation of early division steps (prophase
to anaphase), little is known about the temporal regulation of
late division steps. Recent studies indicate that the final steps of
cell division termed cytokinetic abscission are highly coordinated
in time and space. However, the regulatory basis of this process,
which terminates cell division giving rise to the formation of
two independent daughter cells, is still unknown. By generating
spatiotemporal maps of different cytokinetic proteins at different
late stages cytokinesis we aim to elucidate the regulation of
cytokinetic abscission and to determine the mechanistic basis
for abscission timing.
25
Dr. Eyal Gur
Targeting the bacterial Lon protease –
a novel approach for the development
of antibiotic compounds
Background
Quality-control systems, consisting of ATP-dependent proteases,
chaperones, heat-shock proteins and additional regulatory molecules
have evolved to protect cells from the harmful effects of protein
unfolding. These networks execute either degradation or refolding
of misfolded proteins and assist in the disassembly of protein
aggregates. The major enzyme responsible for degrading damaged
proteins in bacteria is a hexameric ATP-dependent protease known
as Lon. Its importance for proper cellular function is manifested in the
phenotypes of Lon mutations, which present various physiological
defects. In recent years, it has been established that Lon activity is
essential for the virulence of many pathogenic bacteria. Therefore,
Lon may serve as a potential target for the development of novel
anti-bacterial compounds.
Ph.D.: Tel Aviv University, Israel
Post-doctorate: Massachusetts
Institute of Technology, USA
Position: Senior Lecturer
Department of Life Sciences
Faculty of Natural Sciences
E-mail: [email protected]
Selected publications
Gur E. and Sauer R.T. (2008). Recognition of misfolded
proteins by Lon, a AAA+ protease. Genes Dev. 22:22672277.
Gur E., Biran D. and Ron E.Z. (2011). Regulated proteolysis
in Gram negative bacteria - how and when? Nat. Rev.
Microbiol. 9:839-848.
Ofer N., Vishkautzan M., Meijler M., Wang Y., Speer A.,
Niederweis M. and Gur E. (2012). Ectoine biosynthesis
in Mycobacterium smegmatis. Appl. Environ. Microbiol.
78:7483-7486.
Forer N., Korman M., Elharar Y., Vishkautzan M. and Gur
E. (2013). The bacterial proteasome and PafA, the Pup
ligase, interact to form a modular protein tagging and
degradation machine. Biochemistry 52(50):9029-9035.
Shenkerman Y., Elharar Y., Vishkautzan M. and Gur E.
(2013). Efficient and simple generation of unmarked gene
deletions in Mycobacterium smegmatis. Gene 533:374378.
Ofer N., Forer N., Korman N., Vishkautzan M., Khalaila I.
and Gur E. (2013). Allosteric transitions direct protein
tagging by PafA, the prokaryotic ubiquitin-like protein
(Pup) ligase. J. Biol Chem 288:11287-11293.
26
Current research
1. The mechanism of protein degradation by Lon (and other
ATP-dependent proteases) is complex and involves multiple
coordinated steps, which act to harvest the energy released from
ATP hydrolysis to propel protein degradation in a regulated fashion.
The multi-step, complex degradation mechanism employed by
Lon offers numerous opportunities to inhibit the protease along
the substrate processing pathway. Understanding the molecular
mechanism of protein degradation by Lon will facilitate the
development of inhibitors of the degradation process. Toward
this aim, we use biochemical, genetic and structural approaches
to study Lon-mediated proteolysis.
2. Small molecules are defined as non-polymeric organic
compounds, often isolated from natural sources. Many times
small molecules are secondary metabolites that serve biological
functions. The advantages of using small molecules are severalfold. The vast diversity of these compounds (numbering hundreds
of thousands of different molecules) and the fact that they have
evolved to fulfill biological roles, result in a very high probability
of finding compounds with a desired activity. Moreover, small
molecules can reach most compartments of the human body.
We have designed a high-throughput screening assay to identify
small molecules that can act as selective Lon inhibitors. Identified
compounds will be further tested for their qualification as antibacterial drugs.
3. Lon is the only ATP-dependent protease known to have a natural
protein inhibitor. The T4-bacteriophage protein, PinA, specifically
inhibits the E. coli Lon protease, apparently by inhibiting
the activity of the Lon ATPase domain. Understanding the
inhibition mechanism of Lon by PinA should facilitate the future
development of novel antibiotic compounds designed to act as
specific inhibitors of bacterial Lon proteases.
Dr. Tomer Hertz
Computational and experimental
approaches to studying
immunodominance
Background
Ph.D.: The Hebrew University of
Jerusalem, Israel
Post-doctorate: Microsoft Research, USA
Position: Senior Lecturer
The Shraga Segal Department of
Microbiology, Immunology and Genetics
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Hertz T., Nolan D., James I., John M., Gaudieri S., Phillips E.,
Huang J.C., Riadi G., Mallal S. and Jojic N. (2011). Mapping the
Landscape of Host-Pathogen Coevolution: HLA Class I Binding
and Its Relationship with Evolutionary Conservation in Human
and Viral Proteins. Journal of Virology 85:1310-1321.
Meroz D., Yoon S.W., Ducatez M.F., Fabrizio T.P., Webby R.J., Hertz
T.* and Ben-Tal* N. (2011). Putative amino acid determinants
of the emergence of the 2009 influenza A (H1N1) virus in the
human population. Proceedings of the National Academy of
Sciences of the United States of America 108: 13522–13527.
Hertz T., Ahmed H., Friedrich D., Horton H., Frahm N., McElrath J., Corey L. and Gilbert P. (2013). HIV-1 Vaccine Induced
T-cell Reponses Cluster in Epitope Hotspots that Differ From
Those Induced in Natural Infection with HIV-1. PLoS Pathogens
9(6):e1003404.
Hertz T., Oshansky-Weilnau, C., Roddam P.L., DeVincenzo
J.P., Caniza M.A., Jojic N., Mallal S., Phillips E., James I., Thomas
P., Halloran B. and Corey L. (2013). HLA Targeting Efficiency
Correlates with Human T-Cell Response Magnitude and with
Mortality from Influenza A Infection. PNAS 110(33):13492-13497.
Keating R., Hertz T., Lukens J.R., Harris T.L., Edwards B.A., Wehenkel
M., McClaren J.L., Brown S.A., Surman S., Hurwitz J., Doherty P.C.,
Thomas P.G. and McGargill M.A. (2013). mTOR modulates the antibody response to provide cross-protective immunity to lethal
influenza infections. Nature immunology 14(12): 1266-1276.
In the arms race between pathogen and host, the adaptive
immune system uses a diverse set of pattern detectors to
identify and eliminate pathogens and pathogen infected
cells. These detectors bind to short contiguous (T-cells,
B-cells) and non-contiguous (B-cells) protein fragments
called epitopes. During the course of an infection the
immune system focuses its response to a small fraction of the
thousands of potential targets. This phenomenon, known
as immunodominance, is a fundamental property of the
adaptive immune response. Understanding the mechanisms
that govern immunodominance is crucial for designing
vaccines. Immunodominance is a result of a large number of
factors including immunological history, antigen processing
and presentation, viral load and kinetics of viral expression,
and host genetics.
We are developing computational and experimental tools to
study the underlying mechanisms that govern T-cell and B-cell
immunodominance in both natural infection and vaccination.
The main research objective is to identify both viral and
host features that define and modulate immunodominance
hierarchies. The nature of our work is translational, integrating
the design and application of computational approaches with
clinical and laboratory studies that provide data for validating
and refining our computational tools.
Current research
1. Using HLA binding predictors to study T-cell
immunodominance: Human Leukocyte Antigen alleles
present short peptides on the surface of cells to cytolytic
T-cells. We and others have developed computational tools
to predict which targets are likely to be presented to cytolytic
T-cells. We are using these tools to develop computational
tools for predicting which pathogenic targets are likely to
become immunodominant, with applications to vaccine
design and analysis of T-cell responses following both
vaccination and natural infection.
2. Quantifying the effects of immunological history on
immune responses to natural infection and vaccination:
Previous exposure to pathogens and vaccination is one of
the key factors that bias the response to a novel vaccine
or infection. We are developing a high-throughput assay
for profiling immunological history using the technology of
antigen microarrays.
3. Using adjuvants to shift vaccine-induced
immunodominance patterns: Adjuvants are widely used
in licensed vaccines to boost the vaccine-induced immune
responses. We are investigating the effects of different
adjuvants on antibody immunodominance patterns.
4. Computational identification of host specificity
determinants in influenza infection: Influenza pandemics
occur when a novel strain is introduced into the human
population from different animal hosts such as birds and
swine. The molecular mechanisms that allow an influenza
virus to adapt to the human host are poorly understood.
We are developing an approach for computationally
elucidating Influenza virus mutations that are essential for
the adaptation to the host.
27
Prof. Michael M. Meijler
Chemical biology
of bacterial communication
Background
Cell-to-cell communication is used by single-cell organisms to
coordinate their behavior and function in such a way that they
can adapt to changing environments and possibly compete with
multicellular organisms. This phenomenon has been termed
“quorum sensing” (QS). Examples of QS-controlled behaviors are
biofilm formation, virulence factor expression, antibiotic production
and bioluminescence. These processes are beneficial to a bacterial
population only when they are carried out in a coordinated fashion.
Current research
Ph.D.: Weizmann Institute of Science,
Israel
Post-doctorate: The Scripps Research
Institute, USA
Position: Associate Professor
Department of Chemistry
Faculty of Natural Sciences
E-mail: [email protected]
Selected publications
Amara N., Mashiach R., Amara D., Krief P., Spieser S.A.,
Bottomley M.J., Aharoni A. and Meijler M.M. (2009).
Covalent Inhibition of Bacterial Quorum Sensing. J. Am.
Chem. Soc. 131:10610-10619.
Dubinsky L., Jarosz L.M., Amara N., Krief P., Kravchenko
V., Krom B.P. and Meijler M.M. (2009). Synthesis and
validation of a probe to identify quorum sensing
receptors. Chem. Commun. 47:7378-7380.
Rayo J., Amara N., Krief P. and Meijler M.M. (2011). Live
cell labeling of native intracellular bacterial receptors
using aniline-catalyzed oxime ligation. J. Am. Chem. Soc.
133:7469-7475.
Ganin H., Danin-Poleg Y., Kashi Y. and Meijler M.M.
(2012). Vibrio cholerae Autoinducer CAI-1 Interferes with
Pseudomonas aeruginosa Quorum Sensing and Inhibits
its Growth. ACS Chem. Biol. 7:659-665.
Dubinsky L., Delago A., Amara N., Krief P., Rayo J., Zor
T., Kravchenko V.V. and Meijler M.M. (2013). Species
selective diazirine positioning in tag-free photoactive
quorum sensing probes. Chem. Commun. 49:5826-5828.
Mandabi A., Ganin H., Rayo J. and Meijler M.M. (2013).
Karrikins from Plant Smoke Modulate Bacterial Quorum
Sensing. Chem. Commun. 50(40): 5322-5325.
28
Quorum Sensing
An important focus of my group’s research is the study of bacterial
intra- and interspecies signaling. Cell-to-cell communication is used
by single-cell organisms to coordinate their behavior and function
in such a way that they can adapt to changing environments and
possibly compete with multicellular organisms. This phenomenon
has been termed “quorum sensing” (QS). Examples of QS-controlled
behaviors are biofilm formation, virulence factor expression,
antibiotic production and bioluminescence. These processes are
beneficial to a bacterial population only when they are carried out in
a coordinated fashion. Quorum sensing systems exist in both grampositive and -negative bacteria and a variety of oligopeptides and
N-acyl-homoserine lactones have been identified as QS molecules.
However, many QS systems have not been characterized fully, thus
we will attempt to clarify the role of various QS molecules in bacterial
signaling (in species such as Pseudomonas aeruginosa, Salmonella
typhimurium, Helicobacter pylori). Through the synthesis and
evaluation of QS molecules and potential antagonists we will develop
methodologies to study a wide variety of newly discovered and
undiscovered QS molecules. Currently, as part of two different studies
to design QS antagonists of P. aeruginosa, we have synthesized several
highly active covalent and non-covalent QS inhibitors.
Bacterial-Eukaryotic Interkingdom Signaling
Recent reports have shown that several QS molecules can also have
a direct effect on eukaryotes. Diverse eukaryotes have been found
to react strongly to the presence of these compounds. My group
currently examines the hypothesis that diverse eukaryotic species
have developed mechanisms to react to the presence of specific
bacterial QS molecules in a receptor-mediated fashion. We perform
focused experiments designed to provide greater insight into the
primary molecular mechanism of QS molecule induced effects on
mammals, fungi and nematodes. Identification of specific QSM
receptors in eukaryotes will allow us to further understand the
complex mechanisms of coexistence and the evolution of coexistence
between prokaryotes and eukaryotes. Ultimately insights obtained
from these experiments could lead to: a) new approaches for the
treatment of P. aeruginosa infections, most notably in the clinical
setting of cystic fibrosis, as well as to potential new drugs for the
treatment of autoimmune diseases; b) an increased understanding
of the general principles that guide the evolution of symbiotic
relationships between competing species; c) the development of
an integrated platform that will enable the discovery of unknown
receptors for small hydrophobic bioactive compounds.
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Human Genetic Disorders Group
The study of the genetic basis of diseases in defined inbred
communities offers a unique opportunity for identifying and
characterizing disease-associated genes which are direct causes of
clinical disease. The Genetics & Bioinformatics groups' research is
focused on integrating diverse data types for personalized diagnosis,
utilizing protein structure data, understanding and predicting the
behavior of complex biological networks and interpretation of
high throughput experiments, including expression profiles and
next-generation sequencing. It conducts functional genomics and
proteomics studies in order to identify new drug targets, to discover
novel molecular pathways of disease, to validate mechanisms of
actions of drugs, and to develop diagnostic tools for diseases, with
a special focus on genetic diseases of the Bedouins population
in the Negev.
•
•
•
Prof. Ohad Birk
Prof. Ruti Parvari
Dr. Esti Yeger-Lotem
29
Prof. Ohad Birk
Identification and characterization
of genes associated with human
diseases: Unraveling of novel drug
targets and developing tools for
diagnosis of genetic diseases
Background
Genetic studies of unique inbred consanguineous populations in
southern Israel enable unraveling of the molecular basis of hereditary
diseases. The laboratory’s research focuses on the identification and
characterization of genes associated with human diseases. The
research is of importance to three areas:
1. Medicine: Allowing for molecular diagnosis of hereditary human
diseases, enabling carrier detection and prenatal diagnosis.
2. Science: Discovery of the molecular basis for human diseases and
of normal molecular developmental pathways.
M.D.: Tel Aviv University, Israel
Ph.D.: Weizmann Institute of Science, Israel
Post-doctorate: National Institutes of
Health, USA
Residency in Pediatrics: Sheba Medical
Center, Israel
Fellowship in Clinical Human Genetics:
Soroka Medical Center and NIH
Position: Head Genetics Institute, Soroka
University Medical Center
The Shraga Segal Department of
Microbiology, Immunology and Genetics
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
3. Biotechnology: Discovery of novel drug targets for hereditary
disorders, as well as developing diagnostic tools for genetic
diseases.
Current research
Studies being performed rely on:
1. Linkage analysis studies of large inbred families, mostly from
Bedouin communities of southern Israel
2. Molecular analysis of chromosomal aberrations associated with
specific human disorders
3. Microarray analysis of disease vs. normal tissues
4. Functional genomics analysis (in vitro and in vivo) of diseaseassociated genes uncovered in 1-3 above
Once disease-associated genes are identified, study of these genes
is performed – this icludes biochemical and structural analysis
of the encoded proteins, cellular studies of mutated cells and the
generation and analysis of animal models for the diseases. We
have thus far identified the molecular basis of 15 human diseases,
including myopia, short stature, a variant of seborrheic dermatitis
and psoriasis and other rare and common diseases, including 6
severe neurodegenrative diseases in the Bedouin and the Jewish
population. The findings are of both scientific and medical interest
and are immediately implemented in massive carrier testing and
prenatal diagnosis.
Birk O.S., Casiano D.E., Wassif C.A., Cogliati T., Zhao L., Zhao Y., Grinberg
A., Huang S., Kreidberg J.A., Parker K.L., Porter F.D. and Westphal H.
(2000). The LIM homeobox gene Lhx9 is essential for mouse gonad
formation. Nature 403(6772):909-913.
Birnbaum R.Y., Zvulunov A., Hallel-Halevy D., Cagnano E., Finer G., Ofir R.,
Geiger D., Silberstein E., Feferman Y. and Birk O.S. (2006). Seborrhea-like
dermatitis with psoriasiform elements caused by a mutation in ZNF750,
encoding a putative C2H2 zinc finger protein. Nature Genetics 38:749751.
Narkis G., Ofir R., Manor E., Landau D., Elbedour K. and Birk O.S. (2007).
Lethal congenital contractural syndrome type 2 (LCCS2) is caused by a
mutation in ERBB3 (Her3), a modulator of the phosphatidylinositol-3kinase/Akt pathway. Am. J. Hum. Genet. 81:589-595.
30
Barel O., Shalev S.A., Ofir R., Cohen A., Zlotogora J., Shorer Z., Galia Mazor,
Finer G., Khateeb S., Zilberberg N. and Birk O.S. (2008). Maternally
inherited Birk Barel mental retardation dysmorphism syndrome caused
by a mutation in the genomically imprinted potassium channel KCNK9.
Am. J. Hum. Genet. 83:1-7.
Gefen A., Cohen R. and Birk O.S. (2010). Syndrome to gene (S2G): insilico identification of candidate genes for human diseases. Hum. Mutat.
31(3):229-236.
Agamy O., Ben Zeev B., Lev D., Marcus B., Fine D., Su D., Narkis G., Ofir R.,
Hoffmann C., Leshinsky-Silver E., Flusser H., Sivan S., Söll D., Lerman-Sagie T.
and Birk O.S. (2010). Mutations disrupting selenocysteine formation cause
progressive cerebello-cerebral atrophy. Am. J. Hum. Genet. 87(4):538-544.
Prof. Ruti Parvari
Identification and elucidation of
the functions of genes associated
with human genetic diseases
Background
The research conducted in my laboratory aims to identify the
mutations causing human diseases using genetic approaches. This
is enabled by the simple pattern of inheritance of diseases caused
by mutations in single genes in the highly consanguineous families
being treated at the Soroka University Medical Center.
Current research
Ph.D.: Weizmann Institute of Science,
Israel
Post-doctorate: Johns Hopkins
University, USA
Position: Associate Professor
The Shraga Segal Department of
Microbiology, Immunology and Genetics
Faculty of Health Sciences
E-mail: [email protected]
We use exome sequencing and microarray genotyping
techniques to identify the mutated genes in various disease
states. The identification of the mutation is followed by
functional studies to understand the mechanism of action
of the normal compared to the mutated gene. These studies
are carried out in cell cultures as well as animal models.
The diseases presently being studied in the laboratory are:
laterality defects (situs inversus and heterotaxia), primary
ciliary dyskinesia, cardiomyopathies, male infertility,
insensitivity to pain and various hormonal and metabolic
disorders.
The identification of the genetic factors, their function and
the pathways in which they act are expected to contribute
to a better understanding of the pathogenesis of the related
diseases, ultimately leading to improved diagnosis, treatment
and prevention. The elucidation of the pathways leading to
the diseases promises the identification of novel drug targets
for the benefit of a large patient population.
Selected publications
Philip M., Arbellle J.E., Segev Y. and Parvari R. (1998). Male
hypogonadism due to a mutation in the gene for the betasubunit of the follicle stimulating hormone. New England
J. Med. 24:1729-1732.
Parvari R., Hershkovitz E., Grossman N., Gorodischer
R., Loeys B., Zecic, A., Mortier G., Gregory S., Sharony
R., Kambouris M., Sakati N., Meyer B.F., Al Aqeel A.I., Al
Humaidan A.K., Al Zanhrani F., Al Swaid A., Al Othman J.,
Diaz G.A., Weiner R., Khan K.T., Gordon R. and Gelb B.D.; HRD/
Autosomal Recessive Kenny-Caffey SyndromeConsortium.
(2002). Mutation of TBCE causes hypoparathyroidismretardation-dysmorphism and autosomal recessive KennyCaffey syndrome. Nature Genetics 32(3):448-452.
Levy-Litan V., Hershkovitz E., Avizov L., Leventhal N.,
Bercovich D., Chalifa-Caspi V., Manor E., Buriakovsky S.,
Hadad Y., Goding J. and Parvari R. (2010). Autosomalrecessive hypophosphatemic rickets is associated with
an inactivation mutation in the ENPP1 gene. Am. J. Hum.
Genet. 86(2):273-278.
Cox J.J., Sheynin J., Shorer Z., Reimann F., Nicholas A.K., Zubovic
L., Baralle M., Wraige E., Manor E., Levy J., Woods C.G. and Parvari
R. (2010). Congenital insensitivity to pain: novel SCN9A missense
and in-frame deletion mutations. Hum Mutat. 31(9):E1670-E1686.
Mazor M., Alkrinawi S., Chalifa-Caspi V., Manor E., Sheffield V.C.,
Aviram M. and Parvari R. (2011). Primary Ciliary Dyskinesia
Caused by Homozygous Mutation in DNAL1, Encoding Dynein
Light Chain 1. Am. J. Hum. Genet. 88(5):599-607.
Muhammad E., Reish O., Ohno Y., Scheetz T., DeLuca A., Searby
C., Regev M., Benyamini L., Fellig Y., Kihara A., Sheffield V.C. and
Parvari R. (2013). Congenital myopathy is caused by mutation
of HACD1. Hum Mol Genet. 22(25):5229-5236.
31
Dr. Esti Yeger-Lotem
Ph.D.: Technion, Israel Institute of Technology
Post-doctorate: Whitehead Institute for
Biomedical Research, UK & Massachusetts
Institute of Technology, USA
Position: Senior Lecturer
Department of Clinical Biochemistry and
Pharmacology
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Yeger-Lotem E. and Margalit H. (2003). Detection of
regulatory circuits by integrating the cellular networks of
protein-protein interactions and transcription regulation.
Nucleic Acids Research 31:6053-6061.
Yeger-Lotem E., Sattath S., Itzkovitz S., Kashtan N., Milo R.,
Pinter R.Y., Alon U. and Margalit H. (2004). Network motifs in
the integrated cellular network of transcription regulation
and protein-protein interaction. Proceedings of the National
Academy of Sciences USA (PNAS) 101:5934-5939.
Yeger-Lotem E., Riva L., Su L.J., Gitler A., Cashikar A., King O.D.,
Auluck P.K., Geddie M.L., Valastyan J.S., Karger D.R., Lindquist
S. and Fraenkel E. (2009). Bridging the gap between highthroughput genetic and transcriptional data reveals cellular
pathways responding to alpha-synuclein toxicity. Nature
Genetics 41:316-323.
Barshir R., Basha O., Eluk A., Smoly I.Y., Lan A. and Yeger-Lotem
E. (2013). The TissueNet database of human tissue proteinprotein interactions. Nucleic Acids Research 41:D841-844.
Basha O., Tirman S., Eluk A. and Yeger-Lotem E. (2013).
ResponseNet2.0: Revealing signaling and regulatory pathways
connecting your proteins and genes-now with human data.
Nucleic Acids Research 41:W198-203.
Lan A., Ziv-Ukelson M. and Yeger-Lotem E. (2013). A contextsensitive framework for the analysis of human signalling
pathways in molecular interaction networks. ISMB 2013 and
Bioinformatics 29:i210-216.
32
Computational systems
biology of human disease
Background
A comprehensive understanding of the molecular basis of
incurable human diseases is essential for opening new avenues
for treatment. In an effort to elucidate their molecular basis,
human diseases are increasingly studied using high-throughput
approaches, offering unprecedented genomic, transcriptomic
and proteomic views into their etiology. However, independent
analyses of the resulting data typically enable only a limited
understanding of disease processes. For instance, mRNA profiling
assays identify transcriptional changes that occur during disease,
but do not reveal the cellular pathways that lead to these changes.
On the other hand, integrative analysis has great potential to reveal
a much broader view of disease processes, which, in turn, could
improve diagnostics and accelerate the search for a cure.
We are developing computational approaches to meaningfully
integrate diverse large-scale molecular data. By applying these
approaches to top-quality disease data we aim to gain a broad
insight into disease mechanisms.
Current research
1. Network biology of human disease: Molecular interaction
networks have proven to be a leading methodology for
elucidating complex cellular processes from diverse, largescale molecular data. We are developing network optimization
techniques to both distill and meaningfully integrate diverse
molecular data in order to reveal the underlying disease
processes.
2. Illuminating the molecular basis of Parkinson’s disease:
The cellular pathways leading to neuronal cell death in this
common neurodegenerative disorder (1% of the population
over the age of 50) are not fully understood. To reveal these
pathways we are applying network approaches to state-ofthe-art molecular data about the disease.
3. The toxic determinants of protein overexpression: Protein
overexpression is associated with various human diseases
including neurodegenerative disorders and cancer. We are
characterizing the set of proteins whose overexpression is toxic
using a wide range of bioinformatic techniques.
Applied Biotechnology Group
Unraveling the structure-function relationships of proteins and
molecular complexes is pivotal for an improved understanding of
cellular processes. NIBN’s applied biotechnology group comprises
of prominent scientists and state-of-the-art infrastructure in the
fields of microscopy, protein crystallography, protein engineering
as well as nano-technology, which has been further strengthened
through NIBN’s establishment of the Aaron Klug Integrated
Centre for Biomolecular Structure and Function. Current efforts
include electron tomography (3D electron microscopy) of cells
and organelles, understanding magnetosome biology with the
intent to generate tailor-made magnetite particles for various
nano- and bio-technological applications, understanding the
structural basis of ligand receptor interactions important in drug
discovery, optimizing yields of recombinant protein expression
with site-specifically incorporated unnatural amino acids and
functional genomics and proteomics related to reproduction and
calcium biomineralization.
•
•
•
•
Prof. Ohad Medalia
Prof. Amir Sagi
Dr. Raz Zarivach
Dr. Stas Engel
33
Applied uses of electron tomography
Prof. Ohad Medalia
Ph.D.: Weizmann Institute of Science,
Israel
Post-doctorate: Max-Planck-Institute
for Biochemistry, Germany
Position: Associate Professor
Department of Life Sciences, BGU
Faculty of Natural Sciences
Department of Biochemistry, Zurich
University
E-mail: [email protected]
Selected publications
Fridmann K., Mader A., Zwerger M., Elia N. and Medalia O.
(2012). Advances in tomography: probing the molecular
architecture of cells. Nat Rev. Mol. Cell Biol. 13:736-742.
Maimon T., Elad N., Dahan I. and Medalia O. (2012).
The human nuclear pore complex as revealed by cryoelectron tomography. Structure 20:998-1006.
Elad N., Volberg T., Patla I., Hirschfeld-Warneken V.,
Grashoff C., Spatz J.P., Fässler R., Geiger B. and Medalia O.
(2013). The role of integrin-linked kinase in the molecular
architecture of focal adhesions. J. Cell Sci. 126:4099-4107.
Harapin J., Eibauer M. and Medalia O. (2013). Structural
analysis of supramolecular assemblies by cryo-electron
tomography. Structure 21:1522-1530.
34
Background
Improvements in electron microscopy, in conjunction with
advances in computer-controlled systems, now enable biological
specimens to be investigated at sub-critical dose exposure, thereby
minimizing beam-induced radiation damage to negligible levels.
The development of cryo-electron microscopy ensures “close-tolife” preparation by vitrification, even for biological samples as large
as intact organelles and cells. Since neither fixation nor staining is
required, vitrification maintains the integrity of a cell and causes
almost no artifacts. Thus, vitrification allows cells to be arrested
in various functional states. Indeed, electron tomography of iceembedded specimens is the only methodology that allows retrieval
of 3-D structural information from large polymorphic structures, such
as intact cells and organelles, at a resolution of 4-6 nm. Although
tomograms of intact cells cannot be enhanced using averaging
procedures, they exhibit a sufficient signal-to-noise ratio to allow
segmentation and comparison of macromolecular complexes in situ.
As such, cryo-electron tomography can be a useful tool in medical
research and drug discovery processes.
Current research
1. Structural analysis of the nuclear lamina: Forming a boundary
between the nucleus and the cytoplasm, the nuclear envelope
consists of two concentric membranes (outer and inner)
connected at nuclear pores and an underlying lamina, which
is a network-like scaffold structure providing mechanical
stability for the nucleus, cell and tissue. As the main structural
constituents of the nuclear lamina, lamins are also present in the
nucleoplasm. These proteins are members of the intermediate
filament (IF) protein superfamily and are probably the ancestors
of all IF proteins. Point mutations in lamin proteins cause a set of
diseases recently detected in the elderly. As such, we are presently
addressing the structure of the nuclear lamina.
2. Structural analysis of integrin-mediated cell adhesion: Cell
adhesions play an important role in the organization, growth,
maturation and function of living cells. The interaction of cells
with the extracellular matrix also plays an essential role in a variety
of disease states, including tumor formation and metastasis
inflammation and repair of wounded tissues. However, the
structure of the machinery involved remains unknown. By
understanding the structure of these macromolecular assemblies
we will be able to suggest new approaches for inhibiting cell
adhesion.
3. Electron tomography and drug discovery: Individual proteins
and macromolecular complexes can be detected in 3-D by
electron tomography. By using labeled drug candidates (lead
compounds), the specificity as well as the affinities of a drug
inside a cell can be resolved in situ. For example, drug-antigen
interactions can be detected and visualized in living cells at early
stages in the drug development process and at relatively low cost.
We are developing strategies for labeling drugs in order to resolve
their network of interactions within cells.
Prof. Amir Sagi
Genes and gene products
in comparative and applied
endocrinology: Regulation of sexual
differentiation, reproduction,
calcium mobilization and growth in
marine and freshwater invertebrates
Background
Ph.D.: The Hebrew University of
Jerusalem, Israel
Post-doctorate: Woods Hole Marine
Biological Laboratory and University
of Connecticut, USA
Position: Professor
Department of Life Sciences
Faculty of Natural Sciences
Crustacean models are employed in our laboratory for the study
of genes and gene products related to processes of sexual
differentiation and skeletal biomineralization. In particular, we study
the endocrine regulation of sexual differentiation, gonad maturation,
growth, molt and the related processes of calcium mobilization
and biomineralization. Control of the above events will enable the
development of biotechnological tools for; crop improvement via
monosex culturing, soft shell-based products and human food
additives and drugs.
Current research
1. Gonad maturation, vitellogenesis and lipoprotein synthesis.
The vitellogenin gene, its expression pattern and bioinformatic
entities.
2. Regulation of growth, molt and calcium mobilization. The role
of ecdysteroids and eyestalk neuropeptides in the regulation of
events related to the molt cycle, exoskeleton, gastrolith formation
and gene expression in the above target organs.
E-mail: [email protected]
3. Functional genomics of growth regulators and skeletal proteins
related to gender and biomineralization.
Selected publications
4. Sex-determination, a search for sex-specific genomic,
transcriptomic and proteomic markers to asses the role of the
androgenic gland and its secretion.
Shechter A., Glazer L., Cheled S., Mor E., Weil S., Berman A.,
Bentov S., Aflalo E.D., Khalaila I. and Sagi A. (2008). A gastrolith
protein serving a dual role in the formation of an amorphous
mineral containing extracellular matrix. Proc. Nat. Acad. Sci. USA.
106(20):7129-7134.
Ventura T., Rosen O. and Sagi A. (2011). From the discovery of
the crustacean androgenic gland to the insulin-like hormone in
six decades. Gen. Comp. Endocrinol. 173(3):381-388. Including
cover art.
5. Sexual plasticity, including the regulatory role of the androgenic
gland in sex-differentiation and intersexuality of crustaceans.
Development of biotechnologies for the production of monosex
crustacean populations.
6. Food additives and drugs based on natural products derived from
edible crustaceans. Both cellular and extracellular components
are being tested.
Ventura T. and Sagi A. (2012). The insulin-like androgenic
gland hormone in crustaceans: from a single gene silencing
to a wide array of sexual manipulation-based biotechnologies.
Biotechnology Advances 30:1543-1550.
Sagi A., Manor R. and Ventura T. (2013). Gene Silencing in
Crustaceans: From Basic Research to Biotechnologies. Genes
4:620-645.
Ventura T., Manor R., Aflalo E.D., Chalifa-Caspi V., Weil S., Sharabi O.
and Sagi A. (2013). Post-embryonic transcriptomes of the prawn
Macrobrachium rosenbergii: multigenic succession through
metamorphosis. PLoS ONE 8(1):e55322.
Rosen O., Weil S., Manor R., Roth Z., Khalaila I. and Sagi A.
(2013). A crayfish insulin-like binding protein: Another piece in
the androgenic gland insulin-like hormone puzzle is revealed.
Journal of Biological Chemistry 288:22289-22298.
35
Dr. Raz Zarivach
Crystallographic studies
of biological macromolecules
Background
Structural biology aims to understand the chemistry, interactions
and basic biological functions governed by the three-dimensional
structure of macromolecules. Knowledge of the 3-D structure of
a protein can provide enormous insight into the function of that
protein, facilitating elucidation of its biochemical function and its
interactions with other proteins, RNA, DNA, or membranes in the cell.
Similarly, protein-ligand interactions are crucial in many biological
processes with implications for drug targeting and gene expression.
Ph.D.: Weizmann Institute of Science,
Israel
Post-doctorate: University of British
Columbia, Canada
Position: Senior Lecturer
Department of Life Sciences
Faculty of Natural Sciences
E-mail: [email protected]
Selected publications
Zeytuni N., Ozyamak E., Ben-Harush K., Davidov G., Levin
M., Gat Y., Moyal T., Brik A., Komeili A. and Zarivach
R. (2011). Self-recognition mechanism of MamA, a
magnetosome-associated TPR-containing protein,
promotes complex assembly. Proc. Natl. Acad. Sci. USA.
108(33):E480-E487.
Zeytuni N., Baran D., Davidov G. and Zarivach R.
(2012). Inter-phylum structural conservation of the
magnetosome-associated TPR-containing protein,
MamA. J. Struct. Biol. 180(3):479-487.
Zeytuni N. and Zarivach R. (2012). Structural and
functional discussion of the tetra-trico-peptide repeat,
a protein interaction module. Structure 20(3):397-405.
Guttman C., Davidov G., Shaked H., Kolusheva S., Bitton
R., Ganguly A., Miller J.F., Chill J.H. and Zarivach R. (2013).
Characterization of the N-terminal domain of BteA: A
Bordetella Type III secreted cytotoxic effector. PLoS ONE
8(1):e55650.
Guttman C., Davidov G., Yahalom A., Shaked H., Kolusheva
S., Bitton R., Barber-Zucker S., Chill J.H. and Zarivach R.
(2013). BtcA, a Class IA Type III Chaperone, Interacts with
the BteA N-Terminal Domain through a Globular/NonGlobular Mechanism. PLoS ONE 8(12):e81557.
36
X-ray crystallography is the most prolific technique for the structural
analysis of proteins and protein complexes and remains the 'gold
standard' in terms of accuracy. Using X-ray crystallography, we can
now determine high-resolution structures, up to atomic or even
electronic details, enabling a full understanding of macromolecules
and their interactions. Crystallography is the key methodology
for macromolecule-ligand interaction research in structure-based
drug design, either shedding light on the molecular details of such
interactions or for use in ligand-screening of large ligand libraries.
Current research
1. Magnetotactic bacteria are a phylogenetically and
morphologically diverse group of microorganisms that share an
ability to create magnetosomes. Magnetosomes are biomineral
organelles that sense geomagnetic fields and aid the bacteria in
aligning themselves accordingly. The magnetosome organelle
is comprised of 30-50 nm aligned iron oxide magnetite crystals,
surrounded by a lipid bilayer membrane vesicle. There are several
types of magnetosome-forming proteins, all encoded by genes
within a genomic island common to magnetotactic bacteria.
These proteins include a set of incorporated membrane proteins
that facilitate vesicle formation, vesicle localization and iron
transport and a set of proteins that control magnetite formation
and size. A large number of the proteins involved in magnetosome
formation are of unknown function. Magnetite crystals formed by
magnetotactic bacteria have a high potential for applications in
nanotechnology and biotechnology, which require specifically
designed particle surfaces of distinct shape and size. Abiomimetic
approach, utilizing purified proteins, possibly mutated forms,
enables design and control of the magnetite crystals, for uses such
as protein tags and fluorophores. For commercial use, magnetite
crystals with a permanent stable magnetic dipole moment at
room temperature and with a specific size can be designed.
2. As a member of the Faculty of Natural Sciences at BGU, the
laboratory serves as a core facility and is involved in protein
structure determination and structural studies of other proteins.
Collaborative research is performed with the laboratories of
Dr. Amir Aharoni, which addresses directed evolution, Prof.
Varda Shoshan-Barmatz, which studies membrane proteins
and ion channels and Prof. Amir Sagi, which investigatess
biomineralization.
Dr. Stas Engel
Interactions between bio-molecules
as a target for pharmacological
intervention
Background
Protein-protein interactions (PPI) play an essential role in virtually
all cellular processes. In biological systems, information is conveyed
by the action of small-molecule messengers (Ca2+, cAMP,
neurotransmitters, etc.) and via PPI. While mimetics of the former are
widely used to intervene in the functions of biological systems, we
have only a rudimentary capacity to manipulate PPI. Increasingly, PPI
are considered to be potential targets for the development of selective
tools to modulate the functions of biological systems. Targeting PPI
using drugs may represent a new strategy to combat diseases that
have remained intractable through conventional therapies.
Current research
Ph.D.: Ben-Gurion University, Israel
Post-doctorate: The National Institutes
of Health, USA
Position: Senior Lecturer
Department of Clinical Biochemistry
and Pharmacology
Faculty of Health Sciences
E-mail: [email protected]
Selected publications
Tikhonova I.G., Sum C.S., Neumann S., Engel S., Raaka B.M.,
Costanzi S. and Gershengorn M.C. (2008). Discovery of novel
agonists and antagonists of the free fatty acid receptor
(FFAR1) using virtual screening. Journal of Medicinal
Chemistry 51(3): 625–633.
Engel S., Skoumbourdis A., Childress J., Neumann S.,
Deschamps J.R., Thomas C.J., Colson A.O., Stefano C. and
Gershengorn M.C. (2008). A Virtual Screen for Diverse
Ligands: Discovery of Selective G Protein-Coupled Receptor
Antagonists. Journal of the American Chemical Society
130(15):5115-5123.
Tikhonova I.G., Best R.B., Engel S., Hummer G., Gershengorn
M.C. and Costanzi S. (2008). Atomistic insights into rhodopsin
activation from a dynamic model. Journal of the American
Chemical Society 130(31):10141-10149.
Mendelson M., Yossef R., Appel M.Y., Zilka A., Hadad U.,
Afergan F., Rosental B., Engel S., Braiman A., and Porgador A.
(2012). Dimerization of NKp46 receptor is essential for NKp46mediated lysis: characterization of the dimerization site by
epitope mapping. Journal of Immunology 188(12):61656174.
Kuttner Y.Y. and Engel S. (2012). Protein hot spots - the islands
of stability. Journal of Molecular Biology 415(2):419-428.
Kuttner Y.Y., Nagar T. and Engel S. (2013). Surface dynamics
in allosteric regulation of protein-protein interactions:
Modulation of calmodulin functions by Ca2+. PLOS
Computational Biology 9(4): e1003028.
1. Functional mimetics of the intracellular domain (ICD) of
G protein coupled receptors (GPCR) as a tool for studying
the structural basis of GPCR interactions with intracellular
molecular targets and for drug discovery: We are developing
soluble mimetics of the ICD to solve the problem of receptor
availability for structural studies and thus enable the direct study
of GPCR interactions with intracellular effector molecules such as
G proteins, arrestins, etc. In particular, soluble mimetics will allow
NMR spectroscopy and crystallography, which have only had
limited use to date, to be performed. Furthermore, ICD mimetics
could provide a novel and suitable platform for developing
compounds that interfere with the formation of GPCR complexes
with intracellular effector molecules. Such compounds will aid
GPCR signal transduction research and may provide substantial
therapeutic benefit.
2. Combinatorial in vitro selection methods to identify active
compounds targeting protein-protein interactions, in
particular the formation of GPCR/G protein complexes:
Despite recent progress in the discovery of small-molecules
that bind to protein-protein contact surfaces, the logistics of
targeting small-molecule compounds to large protein-protein
interfaces remains a challenge. When definitive structural data
are unavailable, statistical approaches of bulk selection, such as
in vitro display methods, are instrumental in the discovery of new
active compounds. We will use combinatorial in vitro selection
methods to identify active peptides that target the formation of
specific GPCR/G protein complexes. Active peptides targeting
the ICD/G protein interfaces may represent a starting point for
the development of a new class of signaling, pathway-specific
therapeutics to treat GPCR-related disorders.
3. Molecular modeling in structure-based drug discovery: It
is a known fact that the binding pockets (cavities) observed
in the structure of protein/ligand complexes are frequently
undetectable in the absence of the ligand. We are developing
novel computational approaches to predict the location of “hotspots” on the surface of proteins, which have a propensity to form
interactions with small molecules. This approach will potentially
facilitate the rational design of ligands that bind at proteinprotein interfaces.
37
Infra-Structure Supporting Group
The Core Facilities group is focused on providing expertise in
consort with state-of-the-art equipment to advance all research
projects in an optimal manner. NIBN’s core services include:
the Genetics Unit, the Proteomics Unit, the Bioinformatics Unit,
the Crystallography Unit and the Microscopy Unit. These units
provide advanced services including: identifying novel proteins
and their interactions with macromolecules (proteins, RNA and
DNA), DNA microarrays analysis, DNA sequencing, cells sorting,
high resolution microscopy, Cell-sorting Unit, Center for Protein
Crystallization, robotic high-throughput screening and bioinformatics units.
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38
Dr. Vered Caspi
Dr. Anat Shahar
Dr. Micha Volokita
Dr. Alon Zilka
Core Facilities
Bioinformatics Core Facility
Headed by
Dr. Vered Caspi
Ph.D.: Weizmann Institute of Science, Israel
Post-Doctorate: Weizmann Institute of Science, Israel
Position: Research Associate
Bioinformatics Core Facility, Head
E-mail: [email protected]
Mission and services
The NIBN Bioinformatics Core Facility was established in September 2003 with the aim of providing scientists with
opportunities to significantly advance their research with cutting edge bioinformatics resources and methodologies.
To date, the Core Facility provides data analysis services, consultation and training to scientists all over Israel from both
academia and industry. Our main areas of expertise include the analysis and re-analysis of data obtained from genomic
technologies (e.g. Next Generation Sequencing, Mass spec proteomics profiling and DNA microarrays), as well as in
mining biological databases, bioinformatics programming and biostatistics. In addition, assistance is provided in designing
appropriate experiments using genomic technologies and in writing relevant sections in grant proposals.
Our team includes bioinformaticians and programmers with strong backgrounds in biology, bioinformatics and statistics,
with much prior expertise in analyzing high-throughput genomic datasets. Our efforts are supported by the necessary
hardware infrastructure, including cutting-edge commercial and publicly available software.
Details of our main areas of expertise and the services we provide are shown below.
Next Generation Sequencing (NGS) data analysis
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de novo sequence assembly and annotation of novel genomes and transcriptomes
Gene expression profiling (RNA-Seq)
Protein-DNA and protein-RNA interaction analysis (Chip-Seq)
Micro-RNA discovery and profiling
Comparative bacterial genome analyses and metagenomics
Mass Spectrometry Proteomics Profiling
• Construction of a reference proteome
• Differential protein expression analysis
• Pathway and gene ontology enrichment analyses
DNA microarray data Analysis and meta-analysis
• Differential gene expression analysis
• Genetic studies using SNP and CNV arrays
Selected publications
Amir E.D., Bartal O., Morad E., Nagar T., Sheynin J., Parvari R. and Chalifa-Caspi V. (2010). KinSNP software for homozygosity
mapping of disease genes using SNP microarrays. Hum Genomics 4(6):394-401.
Grafi G., Chalifa-Caspi V., Nagar T., Plaschkes I., Barak S. and Ransbotyn V. (2011). Plant response to stress meets
dedifferentiation. Planta, 233(3):433-438.
Mazor M., Alkrinawi S., Chalifa-Caspi V., Manor E., Sheffield V.C., Aviram M. and Parvari R. (2011). Primary ciliary dyskinesia
caused by homozygous mutation in DNAL1, encoding dynein light chain 1. Am. J. Hum. Genet. 88(5):599-607.
Ventura T., Manor R., Aflalo E.D., Chalifa-Caspi V., Weil S., Sharabi O. and Sagi A. (2013). Post-embryonic transcriptomes
of the prawn Macrobrachium rosenbergii: multigenic succession through metamorphosis. PLoS One 8(1):e55322.
Bakshi S., Chalifa-Caspi V., Plaschkes I., Perevozkin I., Gurevich M. and Schwartz R. (2013). Gene expression analysis reveals
functional pathways of glatiramer acetate activation. Expert Opin. Ther. Targets 17(4):351-362.
Toker L., Bersudsky Y., Plaschkes I., Chalifa-Caspi V., Berry G.T., Buccafusca R., Moechars D., Belmaker R.H. and Agam G.
(2014). Inositol-Related Gene Knockouts Mimic Lithium's Effect on Mitochondrial Function. Neuropsychopharmacology
39(2):319-328.
39
Core Facilities
Crystallography Unit
Headed by
Dr. Anat Shahar
Ph.D.: Technion, Israel Institute of Technology
Position: Research Associate
Macromolecular Crystallography Research Center (MCRC), Head
E-mail: [email protected]
Background
Macromolecular Crystallography uses X-ray radiation to determine the three dimensional structure of proteins
and nucleic acids. X-ray crystallography remains the gold standard technique achieving results in the highresolution range, up to atomic details. The knowledge of molecular structures at atomic level resolution.
facilitates research into protein-ligand and protein-protein interactions, is a pre-requisite for structure-based
functional studies and rational drug design as well as for understanding various biochemical processes and
biological systems. The Macromolecular Crystallography Research Center (MCRC) was established in order to
address a variety of such biological questions.
Structure determination of biological macromolecules by X-ray crystallography is a
linear process, which involves several steps including cloning, expression, purification
and crystallization of the target molecules as well as data collection and model
building. However, producing high-quality and well diffracting crystals remains the
major bottleneck in this process. In order to overcome this challenge, the MCRC is fully
equipped with the appropriate reagents and robotics for providing the services below:
Services
• Crystallization setup experiments using various commercial kits to screen for
appropriate crystallization conditions
• Optimization of crystal growth conditions
• Diffraction analysis using either a home source diffractometer or the European Synchrotron Radiation Facility
(ESRF) in Grenoble, France
• 3D structure determination
Equipment
1. Rigaku RU-H3RHB X-Ray diffractometer composed of:
– Rotating-anode X-ray generator (Rigaku)
– Confocal Max-FluxTM (CMF) beam conditioning optics (Osmic Inc.)
– MAR345 image plate detector (Marresearch)
2. Marresearch MarμX X-ray system composed of:
– GeniX-3D Cu Microbeam X-ray generator (Xenocs)
– MAR345 image plate detector (Marresearch)
– Low temperature system (Oxford cryosystems)
Crystallization system including:
• Rock maker (Formulatrix) software for designing, automatic set-up and tracking of crystallization experiments
• Formultor (Formulatrix) liquid handler
• NT8 Drop Setter (Formulatrix) automated dispenser
• Rock Imager (Formulatrix) automated imaging system
• Rock Maker Web (Formulatrix) for following after images of the
crystallization plates. The website can be reached from both inside and outside Ben-Gurion University.
40
Core Facilities
Genetics Unit
Headed by
Dr. Micha Volokita
Ph.D.: The Hebrew University of Jerusalem, Israel
Post-Doctorate: Michigan State University, USA
Position: Research Associate
DNA microarray and sequencing laboratory, Head
E-mail: [email protected]
Background
The NIBN core laboratory for DNA microarrays and DNA sequencing provides a number of services that
rely on high-priced instruments not usually at the daily disposal of a standard level research laboratory.
Services:
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DNA Sequencing
Genotyping by analysis of DNA fragments
Whole genome expression analyses
Whole genome methylation mapping
Whole genome mapping of cis-regulatory elements
Single nucleotide polymorphisms (SNPs) genotyping
Detection of unknown genetic mutations and SNPs
Resequencing
Tiling arrays
Equipment
• ABI Prism 3100 genetic analyzer
• Affymetrix DNA microarray platform, which includes a GeneChip Scanner 3000 7G, a Fluidics Station
450, a Hybridization Oven 640, and a powerful computer workstation with dual Xeon processors
loaded with GeneChip Operating Software (GCOS)
• Transgenomics WAVE system instruments: A denaturing high pressure liquid chromatography
(dHPLC) machine
• 2100 Electrophoresis Bioanalyzer
Selected publications
Narkis G., Ofir R., Landau D., Manor E., Volokita M., Hershkowitz R., Elbedour K. and Birk O.S. (2007). Lethal Contractural
Syndrome Type 3 (LCCS3) Is Caused by a Mutation in PIP5K1C,
Which Encodes PIPKI gamma of the Phophatidylinsitol Pathway.
Am J Hum Genet. 81:530-539.
Najami N., Janda T., Barriah W., Kayam G., Tal M., Guy M. and
Volokita M. (2008). Ascorbate Peroxidase Gene Family in Tomato:
Its Identification and Characterization. Molec Genet Genomics.
279:171-82.
Volokita M, Rosilio-Brami T and Rivkin N, Zik M. (2011) Combining
comparative sequence and genomic data to ascertain phylogenetic
relationships and explore the evolution of the large GDSL-lipase
family in land plants. Mol Biol Evol. 28(1):551-65.
41
Core Facilities
Cytometry, Proteomic and Microscopy Unit
Headed by
Dr. Alon Zilka
Ph.D.: Ben-Gurion University of the Negev, Israel
Post-Doctorate: Ben-Gurion University of the Negev, Israel
Position: Research Associate
Cytometry, Proteomic and Microscopy Unit, Head
E-mail: [email protected]
Background
The service unit is equipped with high end instruments to help identify inter-molecular interactions between
proteins, peptides, nucleic acids and other small molecules. The unit contains a confocal microscope and a
high throughput Fluorescent/confocal microscope for quality/large scale image acquisition and analysis.
Flow cell analyzers and a high speed sorter enable the analysis and sorting of cell sub populations. A Robot
and a high speed plate reader provide a high throughput workbench connected to a powerful fluorescence/
luminescence/absorbance analyzer.
The unit contains the following instruments:
• A laser scanning confocal microscope FV1000 equipped with 405, 488 and 543nm lasers (Olympus).
• Proteon - A protein interaction array system (Surface Plasmon Resonance) for measuring inter-molecular affinity
in a high throughput mode (Biorad).
• Monolith - A Micro Scale Thermophoresis instrument for measuring inter-molecular affinity using capillaries
to minimize the amounts of materials needed (Nanotemper).
• Operetta - A high throughput fluorescent/confocal microscope for large scale image acquisition and
statistical image analysis (Perkin Elmer)
• Synergy - A high speed cell sorter containing 2 independent sorting modules with 375, 488 and 561/594nm
lasers on module 1 and 405, 488 and 640nm lasers on module 2. Each module has 6 fluorescent channels and
can sort up to 4 sub populations (iCyt)
• Two Flow cytometers analyzers, one with 488 and 633nm lasers and 4 fluorescent channels (Calibur) and
another with 405 and 640nm lasers and 5 fluorescent channels an EV channel and a sample auto loader (Eclipse)
(BD and iCyt, respectively).
• A high throughput freedom Evo Robot system connected to a high speed sophisticated plate reader (M1000)
(Tecan)
Selected publications
Zilka A., Garlapati S., Dahan E., Yalosky V. and Shapira M. (2001). Developmental regulation of Heat Shock Protein 83 in
Leishmania; 3’ processing and mRNA stability control transcript abundance and translation is directed by a determinant
in the 3’- untranslated region. Journal of Biological Chemistry. 276:47922-47929.
Zilka A., Landau G., Hershkovitz O., Bloushtain N., Bar-Ilan A., Benchetrit F., Fima E., van Kuppevelt T.H., Gallagher J.T., Elgavish
S. and Porgador A. (2005). Characterization of the Heparin/Heparan Sulfate Binding Site of the Natural Cytotoxicity Receptor
NKp46. Biochemistry. 44:14477-14485.
Hershkovitz O., Jivov S., Bloushtain N., Zilka A., Landau G., Bar-Ilan A., Glicklis R., van Kuppevelt T. H. and Porgador A. (2007).
Characterization of the recognition of tumor cells bythe natural cytotoxicity receptor, NKp44. Biochemistry. 46:7426-7436.
Cagnanol E., Hershkovitz O., Zilka A., Bar-Ilan A., Sion-Vardy1 N., Mandelboim O., Benharroch D. and Porgador A. (2008).
Expression of ligands to NKp46 in benign and malignant melanocyte. Journal of Investigative Dermatology. 128:972-979.
Zilka A, Mendelson M, Rosental B, Hershkovitz O and Porgador A. (2010). Generating NK cell receptor-Fc chimera proteins
from 293T cells and considerations of appropriate glycosylation. Methods Mol Biol. 612:275-283.
42
Dr. Roee Atlas
Deputy Director
Transforming basic biological
research into therapy for Patients
Professional background:
Prior to his appointment at NIBN, Dr. Roee Atlas held various positions in the biotech
industry. As such, he gained considerable expertise in managing the development
of pharmaceuticals/biologicals from the initial phases to the preclinical and clinical
stages. Specifically, he led tissue regeneration product development in an earlystage company developing an autologous cell therapy technology. Prior to that,
Dr. Atlas led a seed company centered on the development of small molecules
for use as anesthesia/pain indications. While at Omrix Bio-pharmaceuticals in
Rehovot, he headed the tissue regeneration unit of the R&D department. Leading a
multidisciplinary team consisting of scientists, engineers, and regulatory personnel,
Dr. Atlas focused on the development of therapeutic products based on cells, proteins
and polymer combinations to treat bone, blood vessel and muscle pathologies.
Ph.D.:Weizmann Institute of Science,
Israel
Post-doctorate: Columbia Medical
School, New York City
E-mail: [email protected]
Selected publications
Caspi M., Atlas R., Kantor A., Sapir T. and Reiner O. (2000).
Interaction between LIS1 and doublecortin, two lissencephaly
gene products. Hum. Mol. Genet. 9:2205-2213.
Atlas R., Behar L., Elliott E. and Ginzburg I. (2004). The insulinlike growth factor mRNA binding-protein IMP-1 and the Rasregulatory protein G3BP associate with tau mRNA and HuD
protein in differentiated P19 neuronal cells. J. Neurochemistry
89:613-626.
Elliott E*., Atlas R*., Lange A. and Ginzburg I. (2005). BDNF induces
a rapid dephosphorylation of tau protein in differentiated P19
neurons. European Journal of Neuroscience 22:1081-1089.
(*authors contributed equally to the study).
Atlas R., Behar L., Sapoznik S. and Ginzburg I. (2007). A dynamic
association with Polysomes during P19 neuronal differentiation
and a UTR-dependent translation regulation of the tau mRNA
by the tau mRNA-associated proteins IMP1, HuD, and G3BP1.
Journal of Neuroscience Research 85:173-183.
Lesman A., Koffler J., Atlas R., Blinder Y.J., Kam Z. and Levenberg
S. (2011). Engineering vessel-like networks within multicellular
fibrin-based constructs. Biomaterials 32(31):7856-7869.
Patent Applications:
Functions of the NIBN Deputy Director:
The NIBN is a unique institute that provides scientists with both the environment
and tools to explore the applied potential of their basic research. To realize this
potential, it is essential that projects be developed in an industry-oriented
manner. Accordingly, a major role of the Deputy Director is to facilitate efforts
by leading NIBN scientists to transfer basic academic research onto an applied
path, culminating in a commercially viable technology or therapeutic product.
Implementation of those strategies leading to an industry-oriented research
program with the concomitant scientific leverage necessary for commercial
interest is of the utmost importance for the NIBN. To generate this traction, NIBN
supports many outsourcing activities often beyond the scope of an academic
setting that serve to complement and propel basic R&D efforts into commercialvalued candidate technologies or therapeutic products.
NIBN places significant emphasis on early dialogue with regulatory and clinical
experts to understand unmet medical needs, the fastest route to clinical testing,
and the most reliable path for the development of clinically safe and reliable
products. Under the guidance of the Deputy Director, NIBN’s multi-pronged
scientific approach relies on an experienced management team to fuel external
interest in NIBN’s projects in the form of collaborations, out-licensing and spin-off
opportunities.
Major Activities of the Deputy Director:
• Implementation of appropriate strategies to translate basic
research into projects bearing significant leverage, ultimately
creating therapeutic product candidates of commercial value to
the NIBN.
• Strengthening NIBN-funded projects through in-depth
understanding of the underlying science and commercial
competition.
“A Fibrin based therapeutic preparation and use thereof”,
Application # 207586 Roee Atlas, Israel Nur, Lily Bar, Roberto
Meidler, Dharanajh Sridevi, Charito Buenusceco, Anthony Kim.
12/2010
• Engaging appropriate VC’s, investment bodies, SMEs and big
Pharma for potential collaborations, business opportunities, and
commercialization of NIBN applied technologies.
“Device for Administrating fluids and uses thereof”, Application #
207715 Moti Meron, Israel Nur, Roee Atlas. 12/2010
• Maintenance, expansion, and strengthening of the NIBN patent
portfolio.
“Device for spraying fluids in proximity to a surface”, Application
# 213375 Roee Atlas, Moti Meron, Assaf Gershonovitch, Amatzia
Gantz. 6/2011
• Creating spin-off companies, licensing of technologies and
providing services based on NIBN state-of-the-art facilities.
“Anesthetic Neutralization methods”, Application # 61748453
Sagi Polani, Asher Polani, Roee Atlas 03/2013
• Promoting collaborations with research institutes, governmental
bodies and non-profit organizations to accelerate development
of NIBN technologies.
“Cytotoxic methods using Peroxynitrite”, Application # 61738410
Sagi Polani, Asher Polani, Roee Atlas 12/2012
• Pursue relevant grant opportunities to support on-going projects.
43
National Institute for
Biotechnology in the Negev Ltd.
The
Ben-Gurion University of the Negev, Beer-Sheva, 84105, Israel
Tel: 972-8-6477193 | Fax: 972-8-6472983
Website: www.bgu.ac.il/nibn | E-mail: [email protected]