Publications

Hydrogels are 3-dimensional networks composed of synthetic or natural polymers that absorb and retain water. They are formed when polymeric chains are cross-linked by covalent or non-covalent bonds. Hydrogels formed by peptides and proteins are unique due to their bioactivity and biocompatibility. Particularly interesting peptide- or protein-based hydrogels are metallogels, hydrogels that form by proteins and peptides that interact with metal ions. Metallogels are potential candidates for medical applications because metal ions are essential for living organisms, for example in respiration, proper growth and development of tissues, red blood cell formation, and immune system stimulation. In this review, we describe general principles of hydrogel formation and we demonstrate them using specific metallogels examples. We focus on physically cross-linked hydrogels and briefly review their formation mechanism, characterization, mechanical properties, and applications.

Automatic extraction of narrative elements from text, combining narrative theories with computational models, has been receiving increasing attention over the last few years. Previous works have utilized the oral narrative theory by Labov and Waletzky to identify various narrative elements in personal stories texts. Instead, we direct our focus to informational texts, specifically news stories. We introduce NEAT (Narrative Elements AnnoTation) – a novel NLP task for detecting narrative elements in raw text. For this purpose, we designed a new multi-label narrative annotation scheme, better suited for informational text (e.g. news media), by adapting elements from the narrative theory of Labov and Waletzky (Complication and Resolution) and adding a new narrative element of our own (Success). We then used this scheme to annotate a new dataset of 2,209 sentences, compiled from 46 news articles from various category domains. We trained a number of supervised models in several different setups over the annotated dataset to identify the different narrative elements, achieving an average F1 score of up to 0.77. The results demonstrate the holistic nature of our annotation scheme as well as its robustness to domain category.

In order to maintain the factographic pact with the reader, in non-fiction narratives the authors tend to refrain from relying on the “perfect-memory convention.” In particular, memoirs (prominently including Conrad’s narratives) tend to avoid detailed prolonged dialogues, and direct speech in them usually takes the form of memorable phrases or statements (sound bites) that are supposed to have engraved themselves in the author’s memory. In Conrad’s autobiographical works this tendency is complicated by the fact that some of the sound-bites are translations from other languages (hence with a touch of fictionalization, enhanced by an occasional withholding of names and other verification landmarks). Yet the more extensive use of direct speech in Conrad's A Personal Record may be associated with specific artistic goals or else with the author's keen awareness of touches of fictionalization.

Many scholars stress the role national identities play as an essential element that shapes interests and explains political behaviours. Others, however, contend that national identities are too amorphic and highlight the analytical challenge of employing them as a research variable. We propose the use of metanarratives as a theoretical framework that captures the essence of national identities and allows the comparative study of their similarities and differences. Metanarratives are shared dominant stories that guide values, beliefs and behaviours and help communities understand who they are. We develop a new systematic method for measuring their content and present a three-step process for gauging metanarratives. We demonstrate this method on 159 countries, analysing constitution preambles to assess each nation's metanarrative and create a global identity orientation map. We show how this approach enables the classification and comparison of national identities and discuss its potential contribution to further empiric study of national identities.

Many bacteria in nature exist in multicellular communities termed biofilms, where cells are embedded in an extracellular matrix that provides rigidity to the biofilm and protects cells from chemical and mechanical stresses. In the Gram-positive model bacterium Bacillus subtilis, TasA is the major protein component of the biofilm matrix, where it has been reported to form functional amyloid fibres contributing to biofilm structure and stability. Here, we present electron cryomicroscopy structures of TasA fibres, which show that, rather than forming amyloid fibrils, TasA monomers assemble into fibres through donor-strand exchange, with each subunit donating a β-strand to complete the fold of the next subunit along the fibre. Combining electron cryotomography, atomic force microscopy, and mutational studies, we show how TasA fibres congregate in three dimensions to form abundant fibre bundles that are essential for B. subtilis biofilm formation. Our study explains the previously observed biochemical properties of TasA and shows how a bacterial extracellular globular protein can assemble from monomers into β-sheet-rich fibres, and how such fibres assemble into bundles in biofilms.

The ability to create mixed morphologies using easily controlled parameters is crucial for the integration of block copolymers in advanced technologies. We have previously shown that casting an ultrathin block copolymer film on a topographically patterned substrate results in different deposited thicknesses on the plateaus and in the trenches, which leads to the co-existence of two patterns. In this work, we highlight the dependence of the dual patterns on the film profile. We suggest that the steepness of the film profile formed across the plateau edge affects the nucleation of microphase-separated domains near the plateau edges, which influences the morphology that develops on the plateau regions. An analysis of the local film thicknesses in multiple samples exhibiting various combinations of plateau and trench widths for different trench depths enabled the construction of phase diagrams, which unraveled the intricate dependence of the formed patterns not only on the curvature of the film profile but also on the fraction of the film that resides in the trenches. Our analysis facilitates the prediction of the patterns that would develop in the trenches and on the plateaus for a given block copolymer film of known thickness from the dimensions of the topographic features.

During recent decades, bumble bees (Bombus terrestris) have continuously expanded their range in the Mediterranean climate regions of Israel. To assess their potential effects on local bee communities, we monitored their diurnal and seasonal activity patterns, as well as those of native bee species in the Judean Hills. We found that all bee species tend to visit pollen-providing flowers at earlier times compared to nectar-providing flowers. Bumble bees and honey bees start foraging at earlier times and colder temperatures compared to other species of bees. This means that the two species of commercially managed social bees are potentially depleting much of the pollen, which is typically non-replenished, before most local species arrive to gather it. Taking into consideration the long activity season of bumble bees in the Judean hills, their ability to forage at the low temperatures of the early morning, and their capacity to collect pollen at early hours in the dry Mediterranean climate, feral and range-expanding bumble bees potentially pose a significant competitive pressure on native bee fauna. Their effects on local bees can further modify pollination networks, and lead to changes in the local flora.

Sensing enzymatic sialylation provides new tools for the evaluation of pathological events and pathogen invasion. Enzymatic sialylation is usually monitored via fluorescence or metabolic labeling, which requires relatively large amounts of the glycan substrate with limited availability. Using a label-free biosensor requires smaller quantities of substrates because the interactions induce measurable changes to an interface, which can be translated into a signal. The downside of label-free biosensors is that they are very sensitive to changes at the interface, and the properties of the surface layer can play a major role. Electrochemical impedance spectroscopy was used here to follow the enzymatic sialylation of a biantennary N-glycan acceptor in mixed monolayers. The surfaces contained either neutral, positively or negatively charged, or zwitterionic functional groups. The systems were characterized by contact potential difference, ellipsometry, and contact angle analyses. We found that the characteristics of the mixed monolayer have a profound effect on the biosensing of the enzymatic sialylation. Positively charged layers were found to adsorb the enzyme under the reaction conditions. Negatively charged and zwitterionic surfaces were nonresponsive to enzymatic sialylation. Only the neutral mixed monolayers provided signals that were related directly to enzymatic sialylation. This work demonstrates the importance of appropriate interface properties for monitoring enzymatic sialylation processes.

{Virus-like particles (VLPs) are noninfectious nanocapsules that can be used for drug delivery or vaccine applications. VLPs can be assembled from virus capsid proteins around a condensing agent like RNA, DNA, or a charged polymer. Electrostatic interactions play an important role in the assembly reaction. VLPs assemble from many copies of capsid protein, with combinatorial intermediates, and therefore the mechanism of the reaction is poorly understood. In this paper, we determined the effect of ionic strength on the assembly of Simian Vacuolating Virus 40 (SV40)-like particles. We mixed poly(styrene sulfonate) with SV40 capsid protein pentamers at different ionic strengths. We then characterized the assembly product by solution small-angle X-ray scattering (SAXS) and cryo-TEM. To analyze the data, we performed Brownian dynamics simulations using a coarse-grained model that revealed incomplete, asymmetric VLP structures that were consistent with the experimental data. We found that close to physiological ionic strength