פרסומים

We propose a model that simulates climate change impacts on crop production and food prices under partial equilibrium. Our model incorporates a system of Laspeyres price and quantity indices that link structurally estimated community-level produce supply functions to market level demand functions. The supply estimation accounts for corner solutions associated with disaggregate land use observations and is constrained to reproduce aggregate supply data. We use the model to assess climate change impacts in Israel, which protects local agriculture by import tariffs and quotas. The simulation results vary greatly when we allow prices to change as a response to supply changes, highlighting the importance of endogenizing prices in climate change simulations. The results imply that climate changes projected for Israel are expected to be beneficial to farmers, particularly due to the positive impact of the forecasted large temperature rise on field crop production. Fruit outputs are projected to decline, and reduce consumer surplus, but to a lower extent than the increase in total agricultural profits. Nearly 20% of the profit rise is attributed to farmers’ adaptation through land reallocation. Adaptation to the projected reduction in precipitation by increasing irrigation is found to be warranted from the farmers’ perspective; however, it is not beneficial to society as a whole. Abolishing import tariffs effectively transfers surpluses from producers to consumers, but the impact of this policy on social welfare is relatively modest.We propose a model that simulates climate change impacts on crop production and food prices under partial equilibrium. Our model incorporates a system of Laspeyres price and quantity indices that link structurally estimated community-level produce supply functions to market level demand functions. The supply estimation accounts for corner solutions associated with disaggregate land use observations and is constrained to reproduce aggregate supply data. We use the model to assess climate change impacts in Israel, which protects local agriculture by import tariffs and quotas. The simulation results vary greatly when we allow prices to change as a response to supply changes, highlighting the importance of endogenizing prices in climate change simulations. The results imply that climate changes projected for Israel are expected to be beneficial to farmers, particularly due to the positive impact of the forecasted large temperature rise on field crop production. Fruit outputs are projected to decline, and reduce consumer surplus, but to a lower extent than the increase in total agricultural profits. Nearly 20% of the profit rise is attributed to farmers’ adaptation through land reallocation. Adaptation to the projected reduction in precipitation by increasing irrigation is found to be warranted from the farmers’ perspective; however, it is not beneficial to society as a whole. Abolishing import tariffs effectively transfers surpluses from producers to consumers, but the impact of this policy on social welfare is relatively modest.

The biosensing of bacterial pathogens is of a high priority. Electrochemical biosensors are an important future tool for rapid bacteria detection. A monolayer of bacterial-binding peptides can serve as a recognition layer in such detection devices. Here, we explore the potential of random peptide mixtures (RPMs) composed of phenylalanine and lysine in random sequences and of controlled length, to form a monolayer that can be utilized for sensing. RPMs were found to assemble in a thin and diluted layer that attracts various bacteria. Faradaic electrochemical impedance spectroscopy was used with modified gold electrodes to measure the charge-transfer resistance (RCT) caused due to the binding of bacteria to RPMs. Pseudomonas aeruginosa was found to cause the most prominent increase in RCT compared to other model bacteria. We show that the combination of highly accessible antimicrobial RPMs and electrochemical analysis can be used to generate a new promising line of bacterial biosensors.

 

The mean ionization state (MIS) is a critical property in dense plasma and warm dense matter research, for example, as an input to hydrodynamics simulations and Monte Carlo simulations. Unfortunately, however, the best way to compute the MIS remains an open question. Average-atom (AA) models are widely used in this context due to their computational efficiency, but as we show here, the canonical approach for calculating the MIS in AA models is typically insufficient. We therefore explore three alternative approaches to compute the MIS. First, we modify the canonical approach to change the way electrons are partitioned into bound and free states; second, we develop a novel approach using the electron localization function; finally, we extend a method, which uses the Kubo-Greenwood conductivity to our average-atom model. Through comparisons with higher-fidelity simulations and experimental data, we find that any of the three new methods usually outperforms the canonical approach, with the electron localization function and Kubo-Greenwood methods showing particular promise.

Publisher's Version                                                              arXiv version

Electron transfer is a fundamental process in chemistry, biology, and physics. One of the most intriguing questions concerns the realization of the transitions between nonadiabatic and adiabatic regimes of electron transfer. Using colloidal quantum dot molecules, we computationally demonstrate how the hybridization energy (electronic coupling) can be tuned by changing the neck dimensions and/or the quantum dot sizes. This provides a handle to tune the electron transfer from the incoherent nonadiabatic regime to the coherent adiabatic regime in a single system. We develop an atomistic model to account for several states and couplings to the lattice vibrations and utilize the mean-field mixed quantum-classical method to describe the charge transfer dynamics. Here, we show that charge transfer rates increase by several orders of magnitude as the system is driven to the coherent, adiabatic limit, even at elevated temperatures, and delineate the inter-dot and torsional acoustic modes that couple most strongly to the charge transfer dynamics.

The human GPCR family comprises circa 800 members, activated by hundreds of thousands of compounds. Bitter taste receptors, TAS2Rs, constitute a large and distinct subfamily, expressed orally and extra-orally and involved in physiological and pathological conditions. TAS2R14 is the most promiscuous member, with over 150 agonists and 3 antagonists known prior to this study. Due to the scarcity of inhibitors and to the importance of chemical probes for exploring TAS2R14 functions, we aimed to discover new ligands for this receptor, with emphasis on antagonists. To cope with the lack of experimental structure of the receptor, we used a mixed experimental/computational methodology which iteratively improved the performance of the predicted structure. The increasing number of active compounds, obtained here through experimental screening of FDA-approved drug library, and through chemically synthesized flufenamic acid derivatives, enabled the refinement of the binding pocket, which in turn improved the structure-based virtual screening reliability. This mixed approach led to the identification of 10 new antagonists and 200 new agonists of TAS2R14, illustrating the untapped potential of rigorous medicinal chemistry for TAS2Rs. 9% of the ~ 1800 pharmaceutical drugs here tested activate TAS2R14, nine of them at sub-micromolar concentrations. The iterative framework suggested residues involved in the activation process, is suitable for expanding bitter and bitter-masking chemical space, and is applicable to other promiscuous GPCRs lacking experimental structures.

Individual entities across levels of biological organization interact to reach collective decisions. In centralized neuronal networks, competing neural populations commonly accumulate information over time while increasing their own activity, and cross-inhibiting other populations until one group passes a given threshold. In social insects, there is good evidence for decisions mediated by positive feedbacks, but we found evidence for similar inhibitory signals only in honey bee (Apis mellifera) stop signals, and Pharaoh’s ant (Monomorium pharaonic) repellent pheromones, with only the former occasionally being used as cross-inhibition. We discuss whether these differences stem from insufficient research effort or represent genuine differences across levels of biological organization.

Fibronectin fibrillogenesis and mechanosensing both depend on integrin-mediated force transmission to the extracellular matrix. However, force transmission is in itself dependent on fibrillogenesis, and fibronectin fibrils are found in soft embryos where high forces cannot be applied, suggesting that force cannot be the sole initiator of fibrillogenesis. Here, we identify a nucleation step prior to force transmission, driven by fibronectin oxidation mediated by lysyl oxidase enzyme family members. This oxidation induces fibronectin clustering, which promotes early adhesion, alters cellular response to soft matrices, and enhances force transmission to the matrix. In contrast, absence of fibronectin oxidation abrogates fibrillogenesis, perturbs cell-matrix adhesion, and compromises mechanosensation. Moreover, fibronectin oxidation promotes cancer cell colony formation in soft agar as well as collective and single-cell migration. These results reveal a force-independent enzyme-dependent mechanism that initiates fibronectin fibrillogenesis, establishing a critical step in cell adhesion and mechanosensing.

The most dynamic period throughout the lifespan of broiler chickens is the pre-post-hatching period, entailing profound effects on their energy status, survival rate, body weight, and muscle growth. Given the significance of this pivotal period, we evaluated the effect of in-ovo feeding (IOF) with creatine monohydrate on late-term embryos’ and hatchlings’ energy reserves and post-hatch breast muscle development. The results demonstrate that IOF with creatine elevates the levels of high-energy-value molecules (creatine and glycogen) in the liver, breast muscle and yolk sac tissues 48 h post IOF, on embryonic day 19 (p < 0.03). Despite this evidence, using a novel automated image analysis tool on day 14 post-hatch, we found a significantly higher number of myofibers with lower diameter and area in the IOF creatine group compared to the control and IOF NaCl groups (p < 0.004). Gene expression analysis, at hatch, revealed that IOF creatine group had significantly higher expression levels of myogenin (MYOG) and insulin-like growth factor 1 (IGF1), related to differentiation of myogenic cells (p < 0.01), and lower expression of myogenic differentiation protein 1 (MyoD), related to their proliferation (p < 0.04). These results imply a possible effect of IOF with creatine on breast muscle development through differential expression of genes involved in myogenic proliferation and differentiation. The findings provide valuable insights into the potential of pre-hatch enrichment with creatine in modulating post-hatch muscle growth and development.

Common fragile sites (CFS) are specific genomic regions prone to chromosomal instability under conditions of DNA replication stress. CFSs manifest as breaks, gaps, and constrictions on metaphase chromosomes under mild replication stress. These replication-sensitive CFS regions are preferentially unstable during cancer development, as reflected by their association with copy number variants (CNVs) frequently arise in most tumor types. Over the years, it became clear that a combination of different characteristics underlies the enhanced sensitivity of CFSs to replication stress. As of today, there is a strong evidence that the core fragility regions along CFSs overlap with actively transcribed large genes with delayed replication timing upon replication stress. Recently, the mechanistic basis for CFS instability was further extended to regions which span topologically associated domain (TAD) boundaries, generating a fragility signature composed of replication, transcription and genome organization. The presence of difficult-to-replicate AT-rich repeats was one of the early features suggested to characterize a subgroup of CFSs. These long stretches of AT-dinucleotide have the potential to fold into stable secondary structures which may impede replication fork progression, leaving the region under-replicated. Here, we focus on the molecular mechanisms underlying repeat instability at CFSs and on the proteins involved in the resolution of secondary structure impediments arising along repetitive sequence elements which are essential for the maintenance of genome stability.