The Synthetic Biology Laboratory for the Decipherment of Genomic Codes
Asst. Prof. Roee Amit
Our research combines synthetic biology with advanced imaging techniques to study problems associated with information transfer at the molecular level in biology. Our research efforts are aimed at two major fields:
- Synthetic enhancer circuits – Deciphering the regulatory code is one of the great challenges of our time. Our approach is to “hack” this algorithm using the tools of synthetic biology. We do this by designing novel DNA regulatory sequences using characterized components, and testing if our “program” displays the predicted regulatory response. At present, this translates to constructing synthetic enhancer elements from the ground up in bacteria, and coupling them to gene circuits to generate increasingly complex modules. In the future, we intend to expand this work to embryos with a long-term goal of developing therapeutic applications.
- Live tracking of RNA – We approach this problem by utilizing synthetic biology and advanced microscopy methods in order to simultaneously develop a specialized system of genetically encoded fluorescent probes, whose output will be detected by a dedicated imaging system. Our probes will be designed to report interactions of RNA molecules at the single molecule level, and as a result enable quantitative intra-cellular dynamical tracking of RNA and its myriad of biological function and roles.
The Laboratory of Nanostructured Molecular Assemblies
Prof. Dganit Danino
Our team seeks to unfold principles dictating the nanostructure, function and properties of soft molecular assemblies. These are important for understanding mechanisms of biological processes as well as for the development of new functional materials. We use and develop advanced cryogenic electron microscopy techniques (CryoEM) to analyze the often ‘invisible’ morphology and local interactions, and to follow kinetics of soft, self-organizing systems.
Current main research topics include:
(1) Design and development of lipid and protein nanostructured carriers, for potential application in drug delivery and nanomedicine.
(2) Structure-function studies of membrane-remodeling proteins that mediate membrane fission and fusion, or display antiviral activity. These are important for understanding fundamental biological processes and can lead to the development of new therapies.
(3) Mechanistic studies of one-dimensional chiral self-assembly into ribbons and nanotubes, which find applications in medicine and nanotechnology.
(4) Fundamental thermodynamic and structural research of micellar self-assembly of natural and tailored molecules.
The laboratory of Lipids and Soft Matter
Asst. Prof. Maya Davidovich-Pinhas
Over the past few decades, the deleterious effects of trans and saturated fatty acids on human health have been well established. However, it is also well known that trans and saturated fatty acids, which are part of the natural fat components, play a major role in the texture and mouth sensation experienced while consuming fat products due to their unique solid-like properties. Thus, direct replacement of trans and saturated fatty acids with unsaturated fatty acids, rising a considerable technical challenge due to their low melting temperature. The research in our laboratory combines material science and food engineering concepts toward the development of new lipid systems that can mimic natural fat, with improved nutritional profile.
Our goal is studying the structure and properties of fats, and developing fat mimetic systems with an aspiration to understand the structure-function relation of these systems. Oil comprises high levels of unsaturated fatty acids which provide better nutritional profile but is liquid at room temperature. Thus, various oil structuring strategies will be used comprising self-assembly and crystallization processes in order to mimic fat structure. Our research aims to find the correlation between the nanoscale molecular structure, by using imaging and scattering techniques, to the meso-scale characteristics, by using rheological, mechanical, and thermal techniques. Such knowledge can potentially open a path for development of innovative healthier food products.
The Laboratory of Molecular and Applied Biocatalysis
Assoc. Prof. Ayelet Fishman
We engineer enzymes!
Biocatalysis is the use of enzymes to carry out defined chemical reactions under controlled conditions, in order to convert raw materials into commercially more valuable products. The high selectivity of enzymatic transformations, combined with the mild reaction conditions and the use of inexpensive reagents, represent sound advantages for biocatalysis. Our research is aimed at developing novel and efficient processes for synthesizing natural food additives and drug intermediates, as well as to study structure-function correlations of enzymes.
In order to tailor the enzymes for industrial conditions we employ protein engineering techniques. Among methods utilized are random mutation and selection coined Directed Evolution, rational design, data driven mutagenesis, and x-ray structural analysis. Projects in the lab include the synthesis of natural fragrance compounds using Bakers’ yeast, producing enantiopure sulfoxides using oxidizing enzymes, improving lipases for biodiesel production, and studying the structure-function correlations of tyrosinases.
The Laboratory of Applied Genomics & Food Microbiology
Prof. Yechezkel Kashi
Our lab is currently focus in three major research fields, which combine methodologies of molecular genetics, SSR genotyping, next generation sequencing, bioinformatics, and classical microbiology in culture and in animal models. These fields have both purely theoretic and applicative aspects:
- Environmental and food microbiology – studding the genetics and evolution of Human pathogens, mainly V. vulnificus and V. cholera in food, clinic and environment, using various genomic technologies including Simple Sequence Repeats (SSRs), a highly dynamic component of the bacterial genome, important to bacterial pathogenicity and evolution
- Gut microbiome – understanding host-microbial interactions and specifically the role of host’s genetics, as well as the host’s immune system on microbial composition and vice versa, contributing to future application of personalized medicine.
- Yeasts genetics – studding the biodiversity of Saccharomyces cerevisiae by isolating, characterizing and mapping natural as well as industrial populations. Development of improved strains via “green” technologies.
The laboratory of chemistry of foods and bioactive compounds
Assoc. Prof. Uri Lesmes
Our lab adopts a holistic approach to food and biotechnology research and seeks to obtain comprehensive understanding and control over foods’ complex compositions, structures, physical and chemical reactions alongside in-depth understanding of the consumer needs. Current research activities involve application of –omics strategies, technologies and advanced analytics in the quest to enable the rational design of foods that deliver health, well-being and pleasure, all tailored to the consumer needs.
Our research activities cluster into three main thrusts: [I] Rational design of functional and value-added products and processes [II] Development of in vitro human digestion models for investigations of food’s digestive fate and [III] Innovations and fundamental research of food colloids and hydrocolloids. Through our studies, we strive to understand how to rationally engineer foods and biotechnological formulations based on the understanding of their digestive fate so as to facilitate the development of tailored and personalized interventions.
The Laboratory of Mammalian Cell Technology
Prof. Ben-Zion Levi
Bone marrow derived hematopoietic stem cells give rise to all blood cell types among which are myeloid cells that constitute an essential arm of innate immunity. This hierarchical cell fate decisions process is orchestrated by key transcription factors. These factors govern and modulate the expression of lineage specific genes. Aberrant expression of these key regulators results in block in the differentiation process and subsequently leads to leukemias. Lineage specific expression is the hallmark of this complex differentiation process, yet the molecular mechanisms that govern this lineage restricted expression are not elucidated. Our research is focused on the molecular mechanisms that govern transcriptional regulation of genes in general and during myeloid cell differentiation in particular. We study a transcription factor termed IRF-8, which is essential for the ability of progenitor cell differentiation toward the monocyte arm of the myeloid cells. We demonstrate that epigenetics modifications are essential for this lineage specific expression. Further, we study gene regulatory network governed by IRF-8 and its role in the differentiation process, the activity of the mature cells and the suppression of leukemias. Our research will allow future drug design to manipulate the immune system and to eliminate cancer cells and invading pathogens.
The Lab of Food Physical Chemistry & Biopolymeric Delivery Systems for Health
Assoc. Prof. Yoav D. Livney
Our lab specializes in physical chemistry of biopolymers in aqueous systems in food and biotechnology. By combining advanced instrumental techniques, modeling and simulations, we study fundamental interactions between low molecular weight compounds, water and biopolymers. We develop new technologies for recovering functional food biopolymers from renewable sources. We create nature-inspired biopolymeric delivery systems for health-promoting bioactives. Some of these systems are aimed for enrichment of food & beverages with nutraceuticals, protecting them from deterioration during processing and shelf life, masking their off-flavors and promoting their bioavailability.
Other systems we develop are multifunctional targeted delivery systems for combined cancer therapy and diagnostics (theranostics) and for overcoming multi-drug resistance.
The Laboratory for Cancer Drug Delivery & Cell Based Technologies
Prof. Marcelle Machluf
The research in our laboratory combines material engineering and life sciences towards the development of nature-inspired synthetic, natural and hybrid platforms for regenerative medicine, and for treating cancer and diabetes.
Gene Therapy: Developing physical, chemical and natural non-viral vectors for cancer gene delivery such as ultrasound, polymeric nano-particles, and nano-vesicles derived from the cell membranes of naturally targeted stem cells.
Drug Delivery Systems: Developing nano and micro sized particles for controlled release and targeted delivery of small drugs and therapeutic proteins for cancer therapy.
Cell Bioencapsulation: Developing encapsulation systems for cell based therapy combining natural components that improve the cells’ functionality. These systems are used to protect genetically modified cells, primary cells and stem cells from the immune system thus preventing their immune rejection while allowing these cells to exert their therapeutic effect.
Regenerative medicine: Tissue engineering of heart and blood vessels using natural animal-derived 3D acellular scaffolds cultivated with a variety of primary and stem cells. Developing bioreactors that provide electrical and mechanical stimuli for heart tissue maturation and long term culturing of tissue engineered organs.
The laboratory of Molecular Nutrition
Asst. Prof. Esther Meyron Holtz
Iron is an essential nutrient that participates in many central life processes. We are interested in the mechanisms and regulation of iron distribution within tissues and subcellular compartments and the role of iron homeostasis in health and disease. This led us to study the physiology of subcellular iron distribution with special emphasis on trafficking of the iron storage protein ferritin and the specific activity of the two iron regulatory proteins (IRPs) in different cell types of a tissue.
Studying tissue iron distribution we found that ferritin secretion is part of an iron recycling circuit in the protected compartment of the testis where sperm development takes place and that the cell-specific expression of IRPs plays a central role in the regulation of iron homeostasis. The iron cycle that we identified in the testis is an example for dynamic iron distribution between cell-types of a tissue. How tissue iron distribution is regulated, how this regulation is impaired in disease, and how this impaired iron homeostasis affects the course of inflammation or infection, are questions that take us to many different tissues in the body and to the understanding how the balance of a nutrient level can participate in the control of health and disease.
The laboratory of Antimicrobial Peptides Investigations (LAPI)
Prof. Amram Mor
Understanding the peptide function in biological systems through Isolation of peptides of interest from natural sources, their characterization, mechanistic investigation and design of structural analogs with improved properties.
Recent efforts focus on host defense peptides having potential for mono- and/or combination therapy. By exploiting rational design and peptidomimetic strategies for correlating in-vitro target site interactions with in-vivo effects on pathogens and host cells, we aim to peruse pharmaceutically competent peptide analogs for developing a drug delivery system susceptible to challenge multidrug-resistance.
The Laboratory for Biomaterials
Asst. Prof. Boaz Mizrahi
Biomaterials science is the next frontier in biotechnology and in medical therapeutics. Innovations in material design have created interventions and composite devices previously unimaginable with materials whose structure and function evolve with time. Our lab develops a research program in the area of dynamic, functional bio-inspired materials. Research involves the synthesis and characterization of functional polymers with medical applications. This is naturally proceeding to an effort to the development of novel biotechnological innovations based on these materials.
We also attempt to gain a critical level of understanding of structure-activity relationship and tissue-biomaterial interactions in the general context of materials science. Current research includes the synthesis of injectable and of stimuli responsive materials, delivery of nutritious for treating gastro and mucosal disorders, self-assembly of polymeric systems and nano-scale particulate systems.
The Laboratory of Functional Nanomaterials, Biosensors, and Sensors
Assoc. Prof. Ester Segal
The research in our group lies at the broad interface between nanomaterials science and biotechnology. This rapidly advancing research area is commonly termed as nano-biotechnology. Our research includes the basic study of structure-property relationships of nanomaterials and application of this knowledge in development of innovative materials and functional materials systems. We are interested in nanostructured materials such as porous Silicon and their interface with soft matter e.g. hydrogels, biomolecules, and living cells. Understanding these interfaces allows us to rationally design novel materials for the following applications:
- Biosensors for detection of biological and chemical toxins.
- Biosensors and bioassays for medical diagnostics.
- Drug delivery platforms.
- Antimicrobial polymer nanocomposites.
The Protein and Enzyme Engineering Laboratory
Prof. Yuval Shoham
The natural degradation of plant cell wall matter in Nature is a key step in the Carbon cycle on Earth. Lignocellulose is considered the most viable option as a renewable energy source that contributes zero net emission of carbon dioxide. The main difficulty in using cellulose as an energy source is its crystalline nature, which is highly resistance to hydrolysis. Our laboratory is trying to reveal and understand how enzymes and microbial systems breakdown the plant cell wall matter and how can these systems be utilized for biotechnological applications. For example, developing an economic process for generating biofuel from cellulose. Our main research systems include the cellulosome complex from C. thermocellum and the hemicellulolytic system of G. stearothermophilus. We utilize an integrated research approach combining biochemistry, X-ray crystallography, genetic engineering, gene-regulation, microbial physiology and fermentation technology. Studies from our laboratory revealed novel regulatory mechanisms, new crystal structures and the catalytic mechanisms of selected glycoside hydrolases.
The laboratory for Novel food and bioprocessing
Asst. Prof. Avi Shpigelman
The research in our laboratory is based on the growing awareness that a healthy diet improves well-being, extends life expectancy and reduces the risk of illnesses like the metabolic syndrome, cancer, and neurodegenerative diseases. Industrial, commercial and domestic processing and storage can alter the concentration, structure, bio-accessibility, and bioavailability of health-promoting food compounds affecting the eventual biological outcome. The goal of our research is to maximize health-promoting attributes of foods by a more rational utilization of novel and traditional food processing and storage techniques. This target is achieved by in-depth studies, combining experimental and modeling approaches. The effects of various processing techniques on food bio-actives, macromolecules (polysaccharides, proteins, and enzymes), micro and nano-structures, and the way interactions between them upon processing affect the bioactive compounds are being explored. The basic nature of our studies allows us, in addition to maximization of health promoting attributes, to seek for opportunities in the development of foods from novel sources and of processing for the forthcoming era of personalized and group based nutrition.
The Laboratory of Molecular Biology of Pathogens
Prof. Sima Yaron
Extensive use of antimicrobials for medical reasons and in farms and households has led to the rapid development of resistance in disease-causing microorganisms. Our research efforts are aimed at two major fields: (i) to investigate mechanisms of resistance to antibacterial agents and (ii) to design and develop new antimicrobials to combat resistant pathogens. We particularly study food borne pathogens associated with highly protected states of existence. The research has made advances in each of the following points, and thus has important implications for both combating infections and for food safety.
Microbial resistance: characterization of emerging multiple antibiotic resistant food borne pathogens, understanding the mechanisms of cross resistance to antibiotics, food preservatives and sanitizing agents, and development of new antimicrobial agents to combat resistant pathogens.
Microbial biofilms: biofilm development on different surfaces, resistance of biofilm cells to antimicrobials, and development of new technologies for removal of bacterial biofilms.
Food safety: molecular study of the behavior of food-borne pathogens in water and fresh ready to eat foods.
The laboratory of Nano-Bio-hybrid Systems for nanotechnological applications
Asst. Prof. Omer Yehezkeli
The research in our group is multidisciplinary, shifting from biochemistry and bioengineering to bioelectrochemistry and nanotechnology. Generally, we use the unique properties of nanomaterials (electrical, optical) with enzymes to gain synergetic effect in catalysis and sensing. Our goal is to construct novel biohybrid systems with unnatural triggers for enzyme activation. To gain that, we use electrodes or nanomaterials which allow directed or mediated electron transfer into the enzymes active sites. As a multi-disciplinary lab, our tools vary from electrochemical setups and glove box to electrophoresis and separation columns. Major research direction aims to form biohybrids which activates nitrogenase by light stimuli. Furthermore, the nitrogenase will be further coupled to electrodes for the construction of biofuel or photobioelectrochemical cells.
The work in the lab is focused on several topics:
- Enzymes extraction, purification and testing
- NPs and NRs synthesis
- Biohybrid assembly for variety of applications
- Electrode modification
- Enzyme based amperometric biosensors
- Bioelectrochemistry applications