Role of Component Traits in Yield Performance of Corn and Sorghum Genotypes Under Different Irrigation Regimes

Grain yield is a trait of economic importance to farmers and agricultural industries. There has been much research at molecular and genetic levels to improve grain yield, but environmental factors can be equally or more important. Drought is a common problem in Texas and other arid and semi-arid regions around the globe, affecting crop production adversely. There is always a need of genotypes that can not only grow and develop but produce high yields in water stress conditions. Corn (Zea mays L.) and sorghum (Sorghum bicolor L.) are two major cereal crops of Texas. To identify physiological characteristics of high yielding and drought tolerant corn and sorghum genotypes, 15 entries of each crop were planted in Uvalde, Texas in 2016 and 2017. Three commercial and 12 experimental hybrids of corn as well as eight hybrids and seven inbred lines of sorghum were tested. Performance was evaluated in full and deficit irrigation regimes through plant height, agronomic canopy and leaf traits, grain composition, and grain yield measurement. A sub-sample of genotypes was also tested for soil-water use and transpiration rates; sorghum was found to absorb water to 100-120 cm of soil depth, while corn was limited to 60-80 cm of soil depth. Corn hybrids REV28HR20 (REV26V21), BH8732VTTP, NP2643GT/Tx777 and GP7169GT/Tx777 and sorghum genotypes ATx631/RTx437, ATx642/RTx437, B.Tx642, and B.Tx623 performed good confirming water efficient behavior. Few other genotypes showed water efficient behavior but contributed more towards vegetative development, thus lowering grain yield. Number of green leaves in corn was negatively correlated with grain yield, while in sorghum positive effect on grain yield was observed. Corn hybrids in 2016 and 2017 and sorghum hybrids in 2017 did not show any significant correlation between grain starch content and grain yield. Corn hybrids showed higher water-use efficiency compared to sorghum in terms of grain yield and aboveground biomass. Linear discriminant analysis showed that leaf thickness, leaf dry matter content, osmotic potential, plant height, and NDVI are the most important predictive traits to focus on in the future for similar research to save resources

Context-Specific Target Definition in Influenza A Virus Hemagglutinin-Glycan Receptor Interactions

Protein-glycan interactions are important regulators of a variety of biological processes, ranging from immune recognition to anticoagulation. An important area of active research is directed toward understanding the role of host cell surface glycans as recognition sites for pathogen protein receptors. Recognition of cell surface glycans is a widely employed strategy for a variety of pathogens, including bacteria, parasites, and viruses. We present here a representative example of such an interaction: the binding of influenza A hemagglutinin (HA) to specific sialylated glycans on the cell surface of human upper airway epithelial cells, which initiates the infection cycle. We detail a generalizable strategy to understand the nature of protein-glycan interactions both structurally and biochemically, using HA as a model system. This strategy combines a top-down approach using available structural information to define important contacts between glycans and HA, with a bottom-up approach using data-mining and informatics approaches to identify the common motifs that distinguish glycan binders from nonbinders. By probing protein-glycan interactions simultaneously through top-down and bottom-up approaches, we can scientifically validate a series of observations. This in turn provides additional confidence and surmounts known challenges in the study of protein-glycan interactions, such as accounting for multivalency, and thus truly defines concepts such as specificity, affinity, and avidity. With the advent of new technologies for glycomics—including glycan arrays, data-mining solutions, and robust algorithms to model protein-glycan interactions—we anticipate that such combination approaches will become tractable for a wide variety of protein-glycan interactions.National Institute of General Medical Sciences (U.S.) (GM 57073)National Institute of General Medical Sciences (U.S.) (U54 GM62116)Singapore-MIT Alliance for Research and Technolog

Pair-Interactions of Self-Propelled SiO2-Pt Janus Colloids

Driven by the necessity to achieve a thorough comprehension of the bottom-up fabrication process of functional materials, this experimental study investigates the pair-wise interactions or collisions between chemically active SiO2-Pt Janus Colloids. These collisions are categorized based on the Janus colloids' orientations before and after they make physical contact. In addition to the hydrodynamic interactions, the Janus colloids are also known to affect each other's chemical field, resulting in chemophoretic interactions, which depend on the reactive nature of the metal site. These interactions lead to a noticeable decrease in particle speed and changes in orientation, which depends on the duration of contact, yielding different collision types. Our findings reveal distinct configurations of contact during collisions, whose mechanisms and likelihood is found to be dependent primarily on the chemical interactions. Such estimates of collision and their characterization in dilute suspensions shall have key impact in determining the arrangement and time scales of dynamical structures and assemblies of denser suspensions, and potentially the functional materials of the future.Comment: 15 pages, 11 figures

Atomic Interaction Networks in the Core of Protein Domains and Their Native Folds

Vastly divergent sequences populate a majority of protein folds. In the quest to identify features that are conserved within protein domains belonging to the same fold, we set out to examine the entire protein universe on a fold-by-fold basis. We report that the atomic interaction network in the solvent-unexposed core of protein domains are fold-conserved, extraordinary sequence divergence notwithstanding. Further, we find that this feature, termed protein core atomic interaction network (or PCAIN) is significantly distinguishable across different folds, thus appearing to be “signature” of a domain's native fold. As part of this study, we computed the PCAINs for 8698 representative protein domains from families across the 1018 known protein folds to construct our seed database and an automated framework was developed for PCAIN-based characterization of the protein fold universe. A test set of randomly selected domains that are not in the seed database was classified with over 97% accuracy, independent of sequence divergence. As an application of this novel fold signature, a PCAIN-based scoring scheme was developed for comparative (homology-based) structure prediction, with 1–2 angstroms (mean 1.61A) Cα RMSD generally observed between computed structures and reference crystal structures. Our results are consistent across the full spectrum of test domains including those from recent CASP experiments and most notably in the ‘twilight’ and ‘midnight’ zones wherein <30% and <10% target-template sequence identity prevails (mean twilight RMSD of 1.69A). We further demonstrate the utility of the PCAIN protocol to derive biological insight into protein structure-function relationships, by modeling the structure of the YopM effector novel E3 ligase (NEL) domain from plague-causative bacterium Yersinia Pestis and discussing its implications for host adaptive and innate immune modulation by the pathogen. Considering the several high-throughput, sequence-identity-independent applications demonstrated in this work, we suggest that the PCAIN is a fundamental fold feature that could be a valuable addition to the arsenal of protein modeling and analysis tools

Glycan receptor specificity as a useful tool for characterization and surveillance of influenza A virus

Influenza A viruses are rapidly evolving pathogens with the potential for novel strains to emerge and result in pandemic outbreaks in humans. Some avian-adapted subtypes have acquired the ability to bind to human glycan receptors and cause severe infections in humans but have yet to adapt to and transmit between humans. The emergence of new avian strains and their ability to infect humans has confounded their distinction from circulating human virus strains through linking receptor specificity to human adaptation. Herein we review the various structural and biochemical analyses of influenza hemagglutinin–glycan receptor interactions. We provide our perspectives on how receptor specificity can be used to monitor evolution of the virus to adapt to human hosts so as to facilitate improved surveillance and pandemic preparedness.National Institutes of Health (U.S.) (Merit Award R37 GM057073-13)Singapore. National Research Foundation (Singapore-MIT Alliance for Research and Technology)Skolkovo Institute of Science and Technolog

Antigenically intact hemagglutinin in circulating avian and swine influenza viruses and potential for H3N2 pandemic

The 2009 swine-origin H1N1 influenza, though antigenically novel to the population at the time, was antigenically similar to the 1918 H1N1 pandemic influenza, and consequently was considered to be “archived” in the swine species before reemerging in humans. Given that the H3N2 is another subtype that currently circulates in the human population and is high on WHO pandemic preparedness list, we assessed the likelihood of reemergence of H3N2 from a non-human host. Using HA sequence features relevant to immune recognition, receptor binding and transmission we have identified several recent H3 strains in avian and swine that present hallmarks of a reemerging virus. IgG polyclonal raised in rabbit with recent seasonal vaccine H3 fail to recognize these swine H3 strains suggesting that existing vaccines may not be effective in protecting against these strains. Vaccine strategies can mitigate risks associated with a potential H3N2 pandemic in humans.National Institutes of Health (U.S.) (R37 GM057073-13

Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants

SummaryAvian H5N1 influenza viruses continue to spread in wild birds and domestic poultry with sporadic infection in humans. Receptor binding specificity changes are a prerequisite for H5N1 viruses and other zoonotic viruses to be transmitted among humans. Previous reported hemagglutinin (HA) mutants from ferret-transmissible H5N1 viruses of A/Vietnam/1203/2004 and A/Indonesia/5/2005 showed slightly increased, but still very weak, binding to human receptors. From mutagenesis and glycan array studies, we previously identified two H5N1 HA mutants that could more effectively switch receptor specificity to human-like α2-6-linked sialosides with avidity comparable to wild-type H5 HA binding to avian-like α2-3-linked sialosides. Here, crystal structures of these two H5 HA mutants free and in complex with human and avian glycan receptor analogs reveal the structural basis for their preferential binding to human receptors. These findings suggest continuous surveillance should be maintained to monitor and assess human-to-human transmission potential of H5N1 viruses

Nonlinear Aerodynamic Damping of Sharp-Edged Beams at Low Keulegan-Carpenter Numbers

Slender sharp-edged flexible beams such as flapping wings of micro air vehicles (MAVs), piezoelectric fans and insect wings typically oscillate at moderate-to-high values of non-dimensional frequency parameter β with amplitudes as large as their widths resulting in Keulegan–Carpenter (KC) numbers of order one. Their oscillations give rise to aerodynamic damping forces which vary nonlinearly with the oscillation amplitude and frequency; in contrast, at infinitesimal KC numbers the fluid damping coefficient is independent of the oscillation amplitude. In this article, we present experimental results to demonstrate the phenomenon of nonlinear aerodynamic damping in slender sharp-edged beams oscillating in surrounding fluid with amplitudes comparable to their widths. Furthermore, we develop a general theory to predict the amplitude and frequency dependence of aerodynamic damping of these beams by coupling the structural motions to an inviscid incompressible fluid. The fluid–structure interaction model developed here accounts for separation of flow and vortex shedding at sharp edges of the beam, and studies vortex-shedding-induced aerodynamic damping in slender sharp-edged beams for different values of the KC number and the frequency parameter β. The predictions of the theoretical model agree well with the experimental results obtained after performing experiments with piezoelectric fans under vacuum and ambient conditions

Harnessing glycomics technologies: Integrating structure with function for glycan characterization

Glycans, or complex carbohydrates, are a ubiquitous class of biological molecule which impinge on a variety of physiological processes ranging from signal transduction to tissue development and microbial pathogenesis. In comparison to DNA and proteins, glycans present unique challenges to the study of their structure and function owing to their complex and heterogeneous structures and the dominant role played by multivalency in their sequence-specific biological interactions. Arising from these challenges, there is a need to integrate information from multiple complementary methods to decode structure–function relationships. Focusing on acidic glycans, we describe here key glycomics technologies for characterizing their structural attributes, including linkage, modifications, and topology, as well as for elucidating their role in biological processes. Two cases studies, one involving sialylated branched glycans and the other sulfated glycosaminoglycans, are used to highlight how integration of orthogonal information from diverse datasets enables rapid convergence of glycan characterization for development of robust structure–function relationships.National Institutes of Health (U.S.) (GM R37 GM057073-13)Singapore-MIT Alliance for Research and Technolog