Limiting transpiration rate in high evaporative demand conditions to improve Australian wheat productivity

Limited-transpiration rate at high evaporative demand (‘LTR’ trait) has potential to improve drought adaptation, crop water productivity and food security. The quantification of the implications of LTR for water consumption, biomass accumulation and yield formation requires the use of dynamic crop modelling to simulate physiological and environmental processes and interactions in target environments. Here, a new transpiration module was developed for the Agricultural Production Systems sIMulator (APSIM NextGen) and used to simulate atmospheric and edaphic water stress on wheat crops. This module was parameterised with (i) data from a lysimeter experiment assessing genotypic variability in the LTR trait for four genotypes contrasting in transpiration efficiency, and with (ii) a more pronounced response to high evaporative demand. The potential of the LTR trait for improving crop productivity was investigated across the Australian wheatbelt over 1989-2018. The LTR trait was simulated to allow an increase in national yield by up to 2.6%, mostly due to shift in water use pattern, alleviation of water deficit during grain filling period and a higher harvest index. Greatest productivity gains were found in the northeast (4.9%, on average) where heavy soils allow the conserved water with the LTR trait to be available later at more critical stages. The effect of the LTR trait on yield was enhanced under the future climate scenario, particularly in the northeast. Limiting transpiration at high evaporative demands appears to be a promising trait for selection by breeders, especially in drought-prone environments where crops heavily rely on stored soil moisture

Zidovudine (AZT) Monotherapy Selects for the A360V Mutation in the Connection Domain of HIV-1 Reverse Transcriptase

Background: We previously demonstrated in vitro that zidovudine (AZT) selects for A371V in the connection domain and Q509L in ribonuclease H (RNase H) domain of HIV-1 reverse transcriptase (RT) which, together with the thymidine analog mutations D67N, K70R and T215F, confer greater than 100-fold AZT resistance. The goal of the current study was to determine whether AZT monotherapy in HIV-1 infected patients also selects the A371V, Q509L or other mutations in the C-terminal domains of HIV-1 RT. Methodology/Principal Findings: Full-length RT sequences in plasma obtained pre- and post-therapy were compared in 23 participants who received AZT monotherapy from the AIDS Clinical Trials Group study 175. Five of the 23 participants reached a primary study endpoint. Mutations significantly associated with AZT monotherapy included K70R (p = 0.003) and T215Y (p = 0.013) in the polymerase domain of HIV-1 RT, and A360V (p = 0.041) in the connection domain of HIV-1 RT. HIV-1 drug susceptibility assays demonstrated that A360V, either alone or in combination with thymidine analog mutations, decreased AZT susceptibility in recombinant viruses containing participant-derived full-length RT sequences or site-directed mutant RT. Biochemical studies revealed that A360V enhances the AZT-monophosphate excision activity of purified RT by significantly decreasing the frequency of secondary RNase H cleavage events that reduce the RNA/DNA duplex length and promote template/primer dissociation. Conclusions: The A360V mutation in the connection domain of RT was selected in HIV-infected individuals that received AZT monotherapy and contributed to AZT resistance. © 2012 Brehm et al

Spectrum of antibacterial activity and mode of action of a novel tris-stilbene bacteriostatic compound

The spectrum of activity and mode of action of a novel antibacterial agent, 135C, was investigated using a range of microbiological and genomic approaches. Compound 135C was active against Gram-positive bacteria with MICs for Staphylococcus aureus ranging from 0.12-0.5 μg/ml. It was largely inactive against Gram-negative bacteria. The compound showed bacteriostatic activity in time-kill studies and did not elicit bacterial cell leakage or cell lysis. Checkerboard assays showed no synergy or antagonism when 135C was combined with a range of other antibacterials. Multi-step serial passage of four S. aureus isolates with increasing concentrations of 135C showed that resistance developed rapidly and was stable after drug-free passages. Minor differences in the fitness of 135C-resistant strains and parent wildtypes were evident by growth curves, but 135C-resistant strains did not show cross-resistance to other antibacterial agents. Genomic comparison of resistant and wildtype parent strains showed changes in genes encoding cell wall teichoic acids. 135C shows promising activity against Gram-positive bacteria but is currently limited by the rapid resistance development. Further studies are required to investigate the effects on cell wall teichoic acids and to determine whether the issue of resistance development can be overcome

Resampling methods for parameter-free and robust feature selection with mutual information

Combining the mutual information criterion with a forward feature selection strategy offers a good trade-off between optimality of the selected feature subset and computation time. However, it requires to set the parameter(s) of the mutual information estimator and to determine when to halt the forward procedure. These two choices are difficult to make because, as the dimensionality of the subset increases, the estimation of the mutual information becomes less and less reliable. This paper proposes to use resampling methods, a K-fold cross-validation and the permutation test, to address both issues. The resampling methods bring information about the variance of the estimator, information which can then be used to automatically set the parameter and to calculate a threshold to stop the forward procedure. The procedure is illustrated on a synthetic dataset as well as on real-world examples

Combining Google Earth and GIS mapping technologies in a dengue surveillance system for developing countries

<p>Abstract</p> <p>Background</p> <p>Dengue fever is a mosquito-borne illness that places significant burden on tropical developing countries with unplanned urbanization. A surveillance system using Google Earth and GIS mapping technologies was developed in Nicaragua as a management tool.</p> <p>Methods and Results</p> <p>Satellite imagery of the town of Bluefields, Nicaragua captured from Google Earth was used to create a base-map in ArcGIS 9. Indices of larval infestation, locations of tire dumps, cemeteries, large areas of standing water, etc. that may act as larval development sites, and locations of the homes of dengue cases collected during routine epidemiologic surveying were overlaid onto this map. Visual imagery of the location of dengue cases, larval infestation, and locations of potential larval development sites were used by dengue control specialists to prioritize specific neighborhoods for targeted control interventions.</p> <p>Conclusion</p> <p>This dengue surveillance program allows public health workers in resource-limited settings to accurately identify areas with high indices of mosquito infestation and interpret the spatial relationship of these areas with potential larval development sites such as garbage piles and large pools of standing water. As a result, it is possible to prioritize control strategies and to target interventions to highest risk areas in order to eliminate the likely origin of the mosquito vector. This program is well-suited for resource-limited settings since it utilizes readily available technologies that do not rely on Internet access for daily use and can easily be implemented in many developing countries for very little cost.</p

Identification of a Novel Staphylococcus aureus Two-Component Leukotoxin Using Cell Surface Proteomics

Staphylococcus aureus is a prominent human pathogen and leading cause of bacterial infection in hospitals and the community. Community-associated methicillin-resistant S. aureus (CA-MRSA) strains such as USA300 are highly virulent and, unlike hospital strains, often cause disease in otherwise healthy individuals. The enhanced virulence of CA-MRSA is based in part on increased ability to produce high levels of secreted molecules that facilitate evasion of the innate immune response. Although progress has been made, the factors that contribute to CA-MRSA virulence are incompletely defined. We analyzed the cell surface proteome (surfome) of USA300 strain LAC to better understand extracellular factors that contribute to the enhanced virulence phenotype. A total of 113 identified proteins were associated with the surface of USA300 during the late-exponential phase of growth in vitro. Protein A was the most abundant surface molecule of USA300, as indicated by combined Mascot score following analysis of peptides by tandem mass spectrometry. Unexpectedly, we identified a previously uncharacterized two-component leukotoxin–herein named LukS-H and LukF-G (LukGH)-as two of the most abundant surface-associated proteins of USA300. Rabbit antibody specific for LukG indicated it was also freely secreted by USA300 into culture media. We used wild-type and isogenic lukGH deletion strains of USA300 in combination with human PMN pore formation and lysis assays to identify this molecule as a leukotoxin. Moreover, LukGH synergized with PVL to enhance lysis of human PMNs in vitro, and contributed to lysis of PMNs after phagocytosis. We conclude LukGH is a novel two-component leukotoxin with cytolytic activity toward neutrophils, and thus potentially contributes to S. aureus virulence

Detecting Sorghum Plant and Head Features from Multispectral UAV Imagery

In plant breeding, unmanned aerial vehicles (UAVs) carrying multispectral cameras have demonstrated increasing utility for high-throughput phenotyping (HTP) to aid the interpretation of genotype and environment effects on morphological, biochemical, and physiological traits. A key constraint remains the reduced resolution and quality extracted from “stitched” mosaics generated from UAV missions across large areas. This can be addressed by generating high-quality reflectance data from a single nadir image per plot. In this study, a pipeline was developed to derive reflectance data from raw multispectral UAV images that preserve the original high spatial and spectral resolutions and to use these for phenotyping applications. Sequential steps involved (i) imagery calibration, (ii) spectral band alignment, (iii) backward calculation, (iv) plot segmentation, and (v) application. Each step was designed and optimised to estimate the number of plants and count sorghum heads within each breeding plot. Using a derived nadir image of each plot, the coefficients of determination were 0.90 and 0.86 for estimates of the number of sorghum plants and heads, respectively. Furthermore, the reflectance information acquired from the different spectral bands showed appreciably high discriminative ability for sorghum head colours (i.e., red and white). Deployment of this pipeline allowed accurate segmentation of crop organs at the canopy level across many diverse field plots with minimal training needed from machine learning approaches

Interlaced spectrally encoded confocal scanning laser ophthalmoscopy and spectral domain optical coherence tomography

Scanning laser ophthalmoscopy (SLO) and spectral domain optical coherence tomography (SDOCT) have become essential clinical diagnostic tools in ophthalmology by allowing for video-rate noninvasive en face and depth-resolved visualization of retinal structure. Current generation multimodal imaging systems that combine both SLO and OCT as a means of image tracking remain complex in their hardware implementations. Here, we combine a spectrally encoded confocal scanning laser ophthalmoscope (SECSLO) with an ophthalmic SDOCT system. This novel implementation of an interlaced SECSLO-SDOCT system allows for video-rate SLO fundus images to be acquired alternately with high-resolution SDOCT B-scans as a means of image aiming, guidance, and registration as well as motion tracking. The system shares the illumination source, detection system, and scanning optics between both SLO and OCT as a method of providing a simple multimodal ophthalmic imaging system that can readily be implemented as a table-top or hand-held device