Discovery of MicroRNAs in Cardamom (Elettaria cardamomum Maton) under Drought Stress

MicroRNAs (miRNAs) are endogenous, 19–24-nucleotide-long, noncoding RNAs found in animals, plants, and some viruses. Drought is one of the major limiting factors that negatively affect productivity of plants. To date, nothing is known about the regulatory roles of miRNAs in response to drought stress in cardamom. Cardamom collected from the natural forest area in Therakkudi in the Idamalayar forest range was selected for the study. Total RNA was isolated from leaves and stems of control and drought treated cardamom plant, which was used for library construction. Ion torrent sequencing of the two small RNA libraries prepared from plants raised under well irrigated and drought stressed treatments, respectively, created 3,938,342 and 4,083,181 primary reads. A total of 150 conserved and 20 novel microRNAs were identified from both the control and the treated libraries. Discovery of 17 differentially expressed miRNAs under drought stress suggests that these might have been involved in various biological processes to improve plant tolerance to water stress. This study is the first report of drought responsive miRNAs and their targets in cardamom. The outcome of this research could provide insights into the miRNA based regulatory mechanisms in response to drought stress in monocot plants.

Anopheles gambiae: Metabolomic Profiles in Sugar-Fed, Blood-Fed, and Plasmodium falciparum-Infected Midgut

The mosquito midgut is a physiological organ essential for nutrient acquisition as well as an interface that encounters various mosquito-borne pathogens. Metabolomic characterization would reveal biochemical fingerprints that are generated by various cellular processes. The metabolite profiles of the mosquito midgut will provide an overview of the biochemical events in both physiological states and the dynamic responses to pathogen infections. In this study, the midgut metabolic profiles of Anopheles gambiae mosquitoes following feeding with sugar, human blood, mouse blood, and Plasmodium falciparum-infected human blood were examined. A mass spectrometry system coupled to liquid and gas chromatography produced a time series of metabolites in the midgut at discrete conditions (sugar feeding, 24 h and 48 h post-normal blood and P. falciparum-infected blood feeding). Triplicates were included to ensure system validity. A total of 512 individual compounds were identified; 511 were assigned to 8 superpathways and 75 subpathways. The dataset can be used for further inquiry into the metabolic dynamics of sugar and blood digestion and of malaria parasite infection. The dataset is accessible at the repository Dryad.

Use of the CatWalk Gait Device to Assess Differences in Locomotion between Genders in Rats Inherently and following Spinal Cord Injury

A possible cause of differences in recovery after spinal cord injury (SCI) is gender. The effect of gender on locomotor recovery following SCI, however, remains controversial and has produced conflicting results regarding gender’s impact on outcome. A significant shortcoming of previous studies was small sample size. The current work tested what, if any, significant differences existed between genders after SCI with CatWalk Gait Analysis that uses an automated device to measure the foot placement and gait of animals as they voluntarily cross an illuminated glass runway. We hypothesized that, by employing larger sample sizes in a reproducible and clinically relevant contusive SCI paradigm, subtle distinctions in locomotor recovery between sexes, if they exist, would be elucidated. During 13 weeks of functional assessment after SCI, a number of CatWalk parameters, including swing, single stance, and stride length, were significantly affected by gender only as identified by use of ANCOVA analysis, considering age, weight, and baseline performance as covariates. We report here our findings for 197 parameters that were assessed before and after SCI. Evaluating differences in locomotor recovery between sexes after SCI could point to a gender-related advantage and provide novel directions for the development of future therapeutics.

Spatial and Temporal Abundance of Interacting Populations of White Clover and Grass Species as Assessed by Image Analyses

The dataset comprises detailed mappings of two communities of interacting populations of white clover (Trifolium repens L.) and grass species under differing experimental treatments over 4-5 years. Information from digital photographs acquired two times per season has been processed into gridded data and documents the temporal and spatial dynamics of the species that followed from a wide range of spatial configurations that arose during the study period. The data contribute a unique basis for validation and further development of previously published models for the dynamics and population oscillations in grass-white clover swards. They will be well suited for estimating parameters in spatially explicit versions of these models, like neighborhood based models that incorporate both the dispersal and the local nature of plant-plant interactions.

An Observatory Plot System for Grain Production in the Neotropical Savannas

The neotropical savanna is the second largest biome in South America, with significant potential for agricultural development. In Colombia, this biome is experiencing rapid land-use change leading to the conversion of seminatural landscapes into to intensive agricultural systems. Our Dataset Paper documents the emerging intensive grain production systems. Between 2011 and 2013, we established 336 observatory plots within farmer’s maize, rice, and soybean fields along a 200 Km transect from Puerto Lopez (Meta) to Viento (Vichada). From each of these plots, we submit 184 descriptors or variables capturing their location, rotation history, management, and environment. Our specific objective in collecting the data was to identify key factors explaining yield variation, with emphasis on interactions between management and environmental factors potentially informing the development of site-specific management protocols. Beyond this objective, the dataset submitted here is intended to support additional inquiries contributing to the sustainable development of agriculture in the neotropical savannas.

Mapping Biophysical Parameters for Land Surface Modeling over the Continental US Using MODIS and Landsat

In terms of the space cities occupy, urbanization appears as a minor land transformation. However, it permanently modifies land’s ecological functions, altering its carbon, energy, and water fluxes. It is therefore necessary to develop a land cover characterization at fine spatial and temporal scales to capture urbanization’s effects on surface fluxes. We develop a series of biophysical vegetation parameters such as the fraction of photosynthetically active radiation, leaf area index, vegetation greenness fraction, and roughness length over the continental US using MODIS and Landsat products for 2001. A 13-class land cover map was developed at a climate modeling grid (CMG) merging the 500 m MODIS land cover and the 30 m impervious surface area from the National Land Cover Database. The landscape subgrid heterogeneity was preserved using fractions of each class from the 500 m and 30 m into the CMG. Biophysical parameters were computed using the 8-day composite Normalized Difference Vegetation Index produced by the North American Carbon Program. In addition to urban impact assessments, this dataset is useful for the computation of surface fluxes in land, vegetation, and urban models and is expected to be widely used in different land cover and land use change applications.

Comprehensive Analysis of MicroRNA and mRNA Expression in Normal and Tumorous Human Esophageal Squamous Cell Lines Using Microarray Datasets

Despite the undisputed importance of altered microRNA (miRNA) expression in various cancers, there is limited information on the clinicopathologic significance of cancer-related miRNAs in esophageal squamous cell carcinoma (ESCC). Previously, it was reported that the expression of several miRNAs was dysregulated in ESCC. However, the target genes of these miRNAs have not been identified. Furthermore, additional miRNAs in humans have been discovered recently, indicating that revised miRNA and gene expression profiling for ESCC are necessary. Here, we provide datasets from microarray analyses to identify miRNA and mRNA expression comprehensively in Het-1A, a normal human esophageal squamous cell line, and three human ESCC cell lines.

DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology

We have developed DockScreen, a database of in silico biomolecular interactions designed to enable rational molecular toxicological insight within a computational toxicology framework. This database is composed of chemical/target (receptor and enzyme) binding scores calculated by molecular docking of more than 1000 chemicals into 150 protein targets and contains nearly 135 thousand unique ligand/target binding scores. Obtaining this dataset was achieved using eHiTS (Simbiosys Inc.), a fragment-based molecular docking approach with an exhaustive search algorithm, on a heterogeneous distributed high-performance computing framework. The chemical landscape covered in DockScreen comprises selected environmental and therapeutic chemicals. The target landscape covered in DockScreen was selected based on the availability of high-quality crystal structures that covered the assay space of phase I ToxCast in vitro assays. This in silico data provides continuous information that establishes a means for quantitatively comparing, on a structural biophysical basis, a chemical’s profile of biomolecular interactions. The combined minimum-score chemical/target matrix is provided.

The Equine CD4+ Lymphocyte Proteome

CD4+ T cells are key players in immunology and disease pathology, including relapsing autoimmune uveitis. Equine recurrent uveitis is the only spontaneous animal model for this disease in man. Knowledge about the CD4+ cell proteome is crucial for studies on possible changes in proteome expression of CD4+ effector cells in disease. For this purpose, we generated a reference dataset of the equine CD4+ cell proteome by sorting equine CD4+ lymphocytes followed by analysis of whole cell lysate as well as membrane protein fraction using mass spectrometry.

ECLAT Cluster Spacecraft Magnetotail Plasma Region Identifications (2001–2009)

The European Space Agency’s four-spacecraft Cluster mission has been observing the Earth’s dynamical magnetotail region since early 2001. The magnetotail, and in particular the hot trapped plasma sheet, is a critical region in the coupled Sun-Earth system. Changes in the solar wind have direct influence on the properties and dynamical processes occurring in this region, which in turn directly influence operational near-Earth space, the upper atmosphere, and even induce large-scale currents in the ground. As part of the European Cluster Assimilation Technology (ECLAT) project, a magnetotail plasma region dataset has been produced to facilitate magnetospheric research and further our understanding of the important processes linking the solar wind-magnetospheric-ionospheric system. The dataset consists of a comprehensive list of plasma regions encountered in the nightside magnetosphere of the Earth by each of the four Cluster spacecraft in the years 2001–2009. The regions identified are those where major energy transport/conversion processes take place and are important regions for system level science. Characteristic averaged parameters describing the behavior of each region are provided for further understanding. The dataset facilitates the use of the large repository of Cluster data by the wider scientific community.