Modeling the Influence of Antifreeze Proteins on Three-Dimensional Ice Crystal Melt Shapes using a Geometric Approach

The melting of pure axisymmetric ice crystals has been described previously by us within the framework of so-called geometric crystal growth. Nonequilibrium ice crystal shapes evolving in the presence of hyperactive antifreeze proteins (hypAFPs) are experimentally observed to assume ellipsoidal geometries ("lemon" or "rice" shapes). To analyze such shapes we harness the underlying symmetry of hexagonal ice Ih and extend two-dimensional geometric models to three-dimensions to reproduce the experimental dissolution process. The geometrical model developed will be useful as a quantitative test of the mechanisms of interaction between hypAFPs and ice.Comment: 15 pages, 5 figures; Proc. R. Soc. A, Published online before print June 27, 201

Changes in aggregation states of light-harvesting complexes as a mechanism for modulating energy transfer in desert crust cyanobacteria.

In this paper we propose an energy dissipation mechanism that is completely reliant on changes in the aggregation state of the phycobilisome light-harvesting antenna components. All photosynthetic organisms regulate the efficiency of excitation energy transfer (EET) to fit light energy supply to biochemical demands. Not many do this to the extent required of desert crust cyanobacteria. Following predawn dew deposition, they harvest light energy with maximum efficiency until desiccating in the early morning hours. In the desiccated state, absorbed energy is completely quenched. Time and spectrally resolved fluorescence emission measurements of the desiccated desert crust Leptolyngbya ohadii strain identified (i) reduced EET between phycobilisome components, (ii) shorter fluorescence lifetimes, and (iii) red shift in the emission spectra, compared with the hydrated state. These changes coincide with a loss of the ordered phycobilisome structure, evident from small-angle neutron and X-ray scattering and cryo-transmission electron microscopy data. Based on these observations we propose a model where in the hydrated state the organized rod structure of the phycobilisome supports directional EET to reaction centers with minimal losses due to thermal dissipation. In the desiccated state this structure is lost, giving way to more random aggregates. The resulting EET path will exhibit increased coupling to the environment and enhanced quenching

Cryo-protective effect of an ice-binding protein derived from Antarctic bacteria

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

Multigrid-Augmented Deep Learning Preconditioners for the Helmholtz Equation using Compact Implicit Layers

We present a deep learning-based iterative approach to solve the discrete heterogeneous Helmholtz equation for high wavenumbers. Combining classical iterative multigrid solvers and convolutional neural networks (CNNs) via preconditioning, we obtain a learned neural solver that is faster and scales better than a standard multigrid solver. Our approach offers three main contributions over previous neural methods of this kind. First, we construct a multilevel U-Net-like encoder-solver CNN with an implicit layer on the coarsest grid of the U-Net, where convolution kernels are inverted. This alleviates the field of view problem in CNNs and allows better scalability. Second, we improve upon the previous CNN preconditioner in terms of the number of parameters, computation time, and convergence rates. Third, we propose a multiscale training approach that enables the network to scale to problems of previously unseen dimensions while still maintaining a reasonable training procedure. Our encoder-solver architecture can be used to generalize over different slowness models of various difficulties and is efficient at solving for many right-hand sides per slowness model. We demonstrate the benefits of our novel architecture with numerical experiments on a variety of heterogeneous two-dimensional problems at high wavenumbers.Comment: Published in SIAM Journal on Scientific Computing Copper Mountain Special Section on Multigrid Methods 202

Interactions of β-Helical Antifreeze Protein Mutants with Ice

The fold of the β-helical antifreeze protein from Tenebrio molitor (TmAFP) proved to be surprisingly tolerant of multiple amino acid substitutions, enabling the construction of a panel of mutants displaying grids of single amino acid types in place of the threonines on the ice-binding face. These mutants, maintaining the regularity of amino acid spacing found in the wild-type protein but with different functional groups on the surface, were tested for antifreeze activity by measuring thermal hysteresis and observing ice grown in their presence. We found that no mutant exhibited the dramatic activity of the wild-type version of this hyperactive antifreeze protein. However, mutants containing four valines or tyrosines in place of the threonines in the center of the TmAFP ice-binding face showed residual thermal hysteresis activity and had marked effects on ice crystal morphology. The results are discussed in the context of a two-stage model for the absorption−inhibition mechanism of antifreeze protein binding to ice surfaces

An Ecological Comparison of Two Abandoned Heritage Orchards in Northern Israel

In this study, we documented two relict traditional Palestinian orchards; one was abandoned following the 1948 war when the farmers were exiled to Lebanon and the second was tended by farmers up until the early 1970s. The orchards examined are located in two different Mediterranean phytogeographic regions, one in the hilly Upper Galilee and the other on the slopes of Mount Carmel in the hinterland of the Mediterranean coast. We found differences in the species composition and spatial layout of trees in each orchard which followed the dictates of the geographic settings, demonstrating the farmer’s knowledge of their environment. We discuss the importance of these orchards as part of the heritage horticultural systems of the region and explore possible measures that can be taken to preserve this unique historical arboricultural landscape and ways to empower local, traditional knowledge in promoting awareness for the conservation and preservation of heritage horticulture

New insights into ice growth and melting modifications by antifreeze proteins

Antifreeze proteins (AFPs) evolved in many organisms, allowing them to survive in cold climates by controlling ice crystal growth. The specific interactions of AFPs with ice determine their potential applications in agriculture, food preservation and medicine. AFPs control the shapes of ice crystals in a manner characteristic of the particular AFP type. Moderately active AFPs cause the formation of elongated bipyramidal crystals, often with seemingly defined facets, while hyperactive AFPs produce more varied crystal shapes. These different morphologies are generally considered to be growth shapes. In a series of bright light and fluorescent microscopy observations of ice crystals in solutions containing different AFPs, we show that crystal shaping also occurs during melting. In particular, the characteristic ice shapes observed in solutions of most hyperactive AFPs are formed during melting. We relate these findings to the affinities of the hyperactive AFPs for the basal plane of ice. Our results demonstrate the relation between basal plane affinity and hyperactivity and show a clear difference in the ice-shaping mechanisms of most moderate and hyperactive AFPs. This study provides key aspects associated with the identification of hyperactive AFPs

CHAMP: Efficient Annotation and Consolidation of Cluster Hierarchies

Various NLP tasks require a complex hierarchical structure over nodes, where each node is a cluster of items. Examples include generating entailment graphs, hierarchical cross-document coreference resolution, annotating event and subevent relations, etc. To enable efficient annotation of such hierarchical structures, we release CHAMP, an open source tool allowing to incrementally construct both clusters and hierarchy simultaneously over any type of texts. This incremental approach significantly reduces annotation time compared to the common pairwise annotation approach and also guarantees maintaining transitivity at the cluster and hierarchy levels. Furthermore, CHAMP includes a consolidation mode, where an adjudicator can easily compare multiple cluster hierarchy annotations and resolve disagreements.Comment: EMNLP 202