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Publications | Biochemistry, Food Science and Nutrition

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Head of Institute: Prof. Ido Braslavsky

Administrative manager: Rakefet Kalev

Office Address:
Institute of Biochemistry, Food Science and Nutrition,
Robert H. Smith Faculty of Agriculture, Food and Environment,
The Hebrew University of Jerusalem, 
Herzl 229, Rehovot 7610001, ISRAEL

Tel: +972 - (0)8-9489385
Fax: +972 - (0)8-9363208
Email Address: rakefetk@savion.huji.ac.il

Publications

2018
Braslavsky, I. ; Stavans, J. . Application Of Algebraic Topology To Homologous Recombination Of Dna. iScience 2018, 4, 64 - 67. Publisher's VersionAbstract
SummaryBrouwer's fixed point theorem, a fundamental theorem in algebraic topology proved more than a hundred years ago, states that given any continuous map from a closed, simply connected set into itself, there is a point that is mapped unto itself. Here we point out the connection between a one-dimensional application of Brouwer's fixed point theorem and a mechanism proposed to explain how extension of single-stranded DNA substrates by recombinases of the RecA superfamily facilitates significantly the search for homologous sequences on long chromosomes.
Bahari, L. ; Bein, A. ; Yashunsky, V. ; Braslavsky, I. . Directional Freezing For The Cryopreservation Of Adherent Mammalian Cells On A Substrate. PLOS ONE 2018, 13, e0192265 - . Publisher's VersionAbstract
Successfully cryopreserving cells adhered to a substrate would facilitate the growth of a vital confluent cell culture after thawing while dramatically shortening the post-thaw culturing time. Herein we propose a controlled slow cooling method combining initial directional freezing followed by gradual cooling down to -80°C for robust preservation of cell monolayers adherent to a substrate. Using computer controlled cryostages we examined the effect of cooling rates and dimethylsulfoxide (DMSO) concentration on cell survival and established an optimal cryopreservation protocol. Experimental results show the highest post-thawing viability for directional ice growth at a speed of 30 μm/sec (equivalent to freezing rate of 3.8°C/min), followed by gradual cooling of the sample with decreasing rate of 0.5°C/min. Efficient cryopreservation of three widely used epithelial cell lines: IEC-18, HeLa, and Caco-2, provides proof-of-concept support for this new freezing protocol applied to adherent cells. This method is highly reproducible, significantly increases the post-thaw cell viability and can be readily applied for cryopreservation of cellular cultures in microfluidic devices.
Mangiagalli, M. ; Sarusi, G. ; Kaleda, A. ; Bar Dolev, M. ; Nardone, V. ; Vena, V. F. ; Braslavsky, I. ; Lotti, M. ; Nardini, M. . Structure Of A Bacterial Ice Binding Protein With Two Faces Of Interaction With Ice. The FEBS Journal 2018, 285, 1653 - 1666. Publisher's VersionAbstract
Ice-binding proteins (IBPs) contribute to the survival of many living beings at subzero temperature by controlling the formation and growth of ice crystals. This work investigates the structural basis of the ice-binding properties of EfcIBP, obtained from Antarctic bacteria. EfcIBP is endowed with a unique combination of thermal hysteresis and ice recrystallization inhibition activity. The three-dimensional structure, solved at 0.84 Å resolution, shows that EfcIBP belongs to the IBP-1 fold family, and is organized in a right-handed ?-solenoid with a triangular cross-section that forms three protein surfaces, named A, B, and C faces. However, EfcIBP diverges from other IBP-1 fold proteins in relevant structural features including the lack of a ?capping? region on top of the ?-solenoid, and in the sequence and organization of the regions exposed to ice that, in EfcIBP, reveal the presence of threonine-rich ice-binding motifs. Docking experiments and site-directed mutagenesis pinpoint that EfcIBP binds ice crystals not only via its B face, as common to other IBPs, but also via ice-binding sites on the C face. Database Coordinates and structure factors have been deposited in the Protein Data Bank under accession number 6EIO.
2017
Mangiagalli, M. ; Bar-Dolev, M. ; Tedesco, P. ; Natalello, A. ; Kaleda, A. ; Brocca, S. ; de Pascale, D. ; Pucciarelli, S. ; Miceli, C. ; Braslavsky, I. ; et al. Cryo-Protective Effect Of An Ice-Binding Protein Derived From Antarctic Bacteria. The FEBS Journal 2017, 284, 163-177. Publisher's VersionAbstract
Cold environments are populated by organisms able to contravene deleterious effects of low temperature by diverse adaptive strategies, including the production of ice binding proteins (IBPs) that inhibit the growth of ice crystals inside and outside cells. We describe the properties of such a protein (EfcIBP) identified in the metagenome of an Antarctic biological consortium composed of the ciliate Euplotes focardii and psychrophilic non-cultured bacteria. Recombinant EfcIBP can resist freezing without any conformational damage and is moderately heat stable, with a midpoint temperature of 66.4 °C. Tested for its effects on ice, EfcIBP shows an unusual combination of properties not reported in other bacterial IBPs. First, it is one of the best-performing IBPs described to date in the inhibition of ice recrystallization, with effective concentrations in the nanomolar range. Moreover, EfcIBP has thermal hysteresis activity (0.53 °C at 50 μm) and it can stop a crystal from growing when held at a constant temperature within the thermal hysteresis gap. EfcIBP protects purified proteins and bacterial cells from freezing damage when exposed to challenging temperatures. EfcIBP also possesses a potential N-terminal signal sequence for protein transport and a DUF3494 domain that is common to secreted IBPs. These features lead us to hypothesize that the protein is either anchored at the outer cell surface or concentrated around cells to provide survival advantage to the whole cell consortium.
Bar Dolev, M. ; Braslavsky, I. . Ice-Binding Proteins—Not Only For Ice Growth Control. Temperature 2017, 4, 112-113. Publisher's Version
Guo, S. ; Stevens, C. A. ; Vance, T. D. R. ; Olijve, L. L. C. ; Graham, L. A. ; Campbell, R. L. ; Yazdi, S. R. ; Escobedo, C. ; Bar-Dolev, M. ; Yashunsky, V. ; et al. Structure Of A 1.5-Mda Adhesin That Binds Its Antarctic Bacterium To Diatoms And Ice. Science Advances 2017, 3. Publisher's VersionAbstract
Bacterial adhesins are modular cell-surface proteins that mediate adherence to other cells, surfaces, and ligands. The Antarctic bacterium Marinomonas primoryensis uses a 1.5-MDa adhesin comprising over 130 domains to position it on ice at the top of the water column for better access to oxygen and nutrients. We have reconstructed this 0.6-μm-long adhesin using a “dissect and build” structural biology approach and have established complementary roles for its five distinct regions. Domains in region I (RI) tether the adhesin to the type I secretion machinery in the periplasm of the bacterium and pass it through the outer membrane. RII comprises  120 identical immunoglobulin-like β-sandwich domains that rigidify on binding Ca2+ to project the adhesion regions RIII and RIV into the medium. RIII contains ligand-binding domains that join diatoms and bacteria together in a mixed-species community on the underside of sea ice where incident light is maximal. RIV is the ice-binding domain, and the terminal RV domain contains several “repeats-in-toxin” motifs and a noncleavable signal sequence that target proteins for export via the type I secretion system. Similar structural architecture is present in the adhesins of many pathogenic bacteria and provides a guide to finding and blocking binding domains to weaken infectivity.
2016
Lewis, J. K. ; Bischof, J. C. ; Braslavsky, I. ; Brockbank, K. G. M. ; Fahy, G. M. ; Fuller, B. J. ; Rabin, Y. ; Tocchio, A. ; Woods, E. J. ; Wowk, B. G. ; et al. The Grand Challenges Of Organ Banking: Proceedings From The First Global Summit On Complex Tissue Cryopreservation. 2016, 72, 169 - 182. Publisher's VersionAbstract
The first Organ Banking Summit was convened from Feb. 27 - March 1, 2015 in Palo Alto, CA, with events at Stanford University, NASA Research Park, and Lawrence Berkeley National Labs. Experts at the summit outlined the potential public health impact of organ banking, discussed the major remaining scientific challenges that need to be overcome in order to bank organs, and identified key opportunities to accelerate progress toward this goal. Many areas of public health could be revolutionized by the banking of organs and other complex tissues, including transplantation, oncofertility, tissue engineering, trauma medicine and emergency preparedness, basic biomedical research and drug discovery – and even space travel. Key remaining scientific sub-challenges were discussed including ice nucleation and growth, cryoprotectant and osmotic toxicities, chilling injury, thermo-mechanical stress, the need for rapid and uniform rewarming, and ischemia/reperfusion injury. A variety of opportunities to overcome these challenge areas were discussed, i.e. preconditioning for enhanced stress tolerance, nanoparticle rewarming, cyroprotectant screening strategies, and the use of cryoprotectant cocktails including ice binding agents.
Bar Dolev, M. ; Braslavsky, I. ; Davies, P. L. . Ice-Binding Proteins And Their Function. Annual Review of BiochemistryAnnual Review of Biochemistry 2016, 85, 515 - 542. Publisher's VersionAbstract
Ice-binding proteins (IBPs) are a diverse class of proteins that assist organism survival in the presence of ice in cold climates. They have different origins in many organisms, including bacteria, fungi, algae, diatoms, plants, insects, and fish. This review covers the gamut of IBP structures and functions and the common features they use to bind ice. We discuss mechanisms by which IBPs adsorb to ice and interfere with its growth, evidence for their irreversible association with ice, and methods for enhancing the activity of IBPs. The applications of IBPs in the food industry, in cryopreservation, and in other technologies are vast, and we chart out some possibilities.Ice-binding proteins (IBPs) are a diverse class of proteins that assist organism survival in the presence of ice in cold climates. They have different origins in many organisms, including bacteria, fungi, algae, diatoms, plants, insects, and fish. This review covers the gamut of IBP structures and functions and the common features they use to bind ice. We discuss mechanisms by which IBPs adsorb to ice and interfere with its growth, evidence for their irreversible association with ice, and methods for enhancing the activity of IBPs. The applications of IBPs in the food industry, in cryopreservation, and in other technologies are vast, and we chart out some possibilities.
Bar Dolev, M. ; Bernheim, R. ; Guo, S. ; Davies, P. L. ; Braslavsky, I. . Putting Life On Ice: Bacteria That Bind To Frozen Water. Journal of The Royal Society InterfaceJournal of The Royal Society Interface 2016, 13, 20160210. Publisher's Version
Haleva, L. ; Celik, Y. ; Bar-Dolev, M. ; Pertaya-Braun, N. ; Kaner, A. ; Davies, P.  L. ; Braslavsky, I. . Microfluidic Cold-Finger Device For The Investigation Of Ice-Binding Proteins. 2016, 111, 1143 - 1150. Publisher's VersionAbstract
Ice-binding proteins (IBPs) bind to ice crystals and control their structure, enlargement, and melting, thereby helping their host organisms to avoid injuries associated with ice growth. IBPs are useful in applications where ice growth control is necessary, such as cryopreservation, food storage, and anti-icing. The study of an IBP’s mechanism of action is limited by the technological difficulties of in situ observations of molecules at the dynamic interface between ice and water. We describe herein a new, to our knowledge, apparatus designed to generate a controlled temperature gradient in a microfluidic chip, called a microfluidic cold finger (MCF). This device allows growth of a stable ice crystal that can be easily manipulated with or without IBPs in solution. Using the MCF, we show that the fluorescence signal of IBPs conjugated to green fluorescent protein is reduced upon freezing and recovers at melting. This finding strengthens the evidence for irreversible binding of IBPs to their ligand, ice. We also used the MCF to demonstrate the basal-plane affinity of several IBPs, including a recently described IBP from Rhagium inquisitor. Use of the MCF device, along with a temperature-controlled setup, provides a relatively simple and robust technique that can be widely used for further analysis of materials at the ice/water interface.