Search Results (11)

Environmental concerns as well as labor costs associated with the use of polyethylene plastic mulch have turned producers’ focus to alternative mulch treatments. A preliminary study was conducted to evaluate nutsedge control, mulch degradation, and cucumber yields on biodegradable mulches at two locations (Louisiana and Mississippi). Mulch treatments included two paper-based mulch products, two biodegradable plastic mulches, the industry standard non-biodegradable black plastic mulch, and an unmulched control. The heavy weight paper-based mulch and light weight paper mulches in the Louisiana location were reduced to 50% or less coverage at the end of the study. Similarly, the paper-based mulches both degraded below 40% at the conclusion of the study at the Mississippi location. The heavy weight paper mulch was able to hold back nutsedge (p ≤ 0.05) at similar rates as the two biodegradable plastic mulches and industry standard plastic mulch, while the light weight paper mulch and unmulched plots were ineffective at reducing emerged sedges. There were no statistical differences in nutsedge control (averaging < 14 emerged plants per 1.5 m subplots) between all mulch materials at the conclusion of the study in the Mississippi location. Combining both states yield data, the heavyweight mulch (8.7 fruit, 5.3 lb) performed comparably to the industry standard plastic mulch (5.8 fruit, 3.5 lb) in terms of both average fruit number and average weights harvested off 9.1 m rows at each harvest date. Full article

The potential of semiochemicals to lure insect pests to a trap where they can be killed with biopesticides has been demonstrated as an eco-friendly pest management alternative. In this study, we tested two recently characterized male-produced aggregation pheromones of the bean flower thrips Megalurothrips sjostedti (Trybom), namely (R)-lavandulyl 3-methylbutanoate (major) and (R)-lavandulol (minor), for their field efficacy. Moreover, compatibility of these pheromones and two other thrips attractants, Lurem-TR and neryl (S)-2-methylbutanoate, with the entomopathogenic fungus (EPF) Metarhizium anisopliae ICIPE 69 has been determined. Our study revealed that the M. sjostedti aggregation pheromones have dose-dependent antifungal effects on the EPF viability, but showed no fungistatic effect at a field-realistic dose for attraction of thrips. (R)-lavandulyl 3-methylbutanoate had similar antifungal effects as neryl (S)-2-methylbutanoate 8 days after exposure; whereas, Lurem-TR had a stronger antifungal effect than other thrips attractants. In the semi-field experiments, all autoinoculation devices maintained at least 86% viability of M. anisopliae conidia after 12 days of exposure. Field trials demonstrated for the first time that (R)-lavandulyl 3-methylbutanoate increases trap catches. Our findings pave a way for designing a lure-and-kill thrips management strategy to control bean flower thrips using autoinoculation devices or spot spray application. Full article

Drug resistance is an obstacle in the therapy of acute lymphoblastic leukemia (ALL). Whether the physical properties such as the motility of the cells contribute to the survival of ALL cells after drug treatment has recently been of increasing interest, as they could potentially allow the metastasis of solid tumor cells and the migration of leukemia cells. We hypothesized that chemotherapeutic treatment may alter these physical cellular properties. To investigate the motility of chemotherapeutics-treated B-cell ALL (B-ALL) cells, patient-derived B-ALL cells were treated with chemotherapy for 7 days and left for 12 h without chemotherapeutic treatment. Two parameters of motility were studied, velocity and migration distance, using a time-lapse imaging system. The study revealed that compared to non-chemotherapeutically treated B-ALL cells, B-ALL cells that survived chemotherapy treatment after 7 days showed reduced motility. We had previously shown that Tysabri and P5G10, antibodies against the adhesion molecules integrins α4 and α6, respectively, may overcome drug resistance mediated through leukemia cell adhesion to bone marrow stromal cells. Therefore, we tested the effect of integrin α4 or α6 blockade on the motility of chemotherapeutics-treated ALL cells. Only integrin α4 blockade decreased the motility and velocity of two chemotherapeutics-treated ALL cell lines. Interestingly, integrin α6 blockade did not affect the velocity of chemoresistant ALL cells. This study explores the physical properties of the movements of chemoresistant B-ALL cells and highlights a potential link to integrins. Further studies to investigate the underlying mechanism are warranted. Full article

The Steller sea lion is the largest member of the Otariidae family and is found in the coastal waters of the northern Pacific Rim. Here, we present the Steller sea lion genome, determined through DNA sequencing approaches that utilized microfluidic partitioning library construction, as well as nanopore technologies. These methods constructed a highly contiguous assembly with a scaffold N50 length of over 14 megabases, a contig N50 length of over 242 kilobases and a total length of 2.404 gigabases. As a measure of completeness, 95.1% of 4104 highly conserved mammalian genes were found to be complete within the assembly. Further annotation identified 19,668 protein coding genes. The assembled genome sequence and underlying sequence data can be found at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA475770. Full article

The threespine stickleback is a geographically widespread and ecologically highly diverse fish that has emerged as a powerful model system for evolutionary genomics and developmental biology. Investigations in this species currently rely on a single high-quality reference genome, but would benefit from the availability of additional, independently sequenced and assembled genomes. We present here the assembly of four new stickleback genomes, based on the sequencing of microfluidic partitioned DNA libraries. The base pair lengths of the four genomes reach 92–101% of the standard reference genome length. Together with their de novo gene annotation, these assemblies offer a resource enhancing genomic investigations in stickleback. The genomes and their annotations are available from the Dryad Digital Repository (https://doi.org/10.5061/dryad.113j3h7). Full article

The grizzly bear (Ursus arctos ssp. horribilis) represents the largest population of brown bears in North America. Its genome was sequenced using a microfluidic partitioning library construction technique, and these data were supplemented with sequencing from a nanopore-based long read platform. The final assembly was 2.33 Gb with a scaffold N50 of 36.7 Mb, and the genome is of comparable size to that of its close relative the polar bear (2.30 Gb). An analysis using 4104 highly conserved mammalian genes indicated that 96.1% were found to be complete within the assembly. An automated annotation of the genome identified 19,848 protein coding genes. Our study shows that the combination of the two sequencing modalities that we used is sufficient for the construction of highly contiguous reference quality mammalian genomes. The assembled genome sequence and the supporting raw sequence reads are available from the NCBI (National Center for Biotechnology Information) under the bioproject identifier PRJNA493656, and the assembly described in this paper is version QXTK01000000. Full article

We mapped native, endemic, and introduced (i.e., exotic) tree species counts, relative basal areas of functional groups, species basal areas, and forest biomass from forest inventory data, satellite imagery, and environmental data for Puerto Rico and the Virgin Islands. Imagery included time series of Landsat composites and Moderate Resolution Imaging Spectroradiometer (MODIS)-based phenology. Environmental data included climate, land-cover, geology, topography, and road distances. Large-scale deforestation and subsequent forest regrowth are clear in the resulting maps decades after large-scale transition back to forest. Stand age, climate, geology, topography, road/urban locations, and protection are clearly influential. Unprotected forests on more accessible or arable lands are younger and have more introduced species and deciduous and nitrogen-fixing basal areas, fewer endemic species, and less biomass. Exotic species are widespread—except in the oldest, most remote forests on the least arable lands, where shade-tolerant exotics may persist. Although the maps have large uncertainty, their patterns of biomass, tree species diversity, and functional traits suggest that for a given geoclimate, forest age is a core proxy for forest biomass, species counts, nitrogen-fixing status, and leaf longevity. Geoclimate indicates hard-leaved species commonness. Until global wall-to-wall remote sensing data from specialized sensors are available, maps from multispectral image time series and other predictor data should help with running ecosystem models and as sustainable development indicators. Forest attribute models trained with a tree species ordination and mapped with nearest neighbor substitution (Phenological Gradient Nearest Neighbor method, PGNN) yielded larger correlation coefficients for observed vs. mapped tree species basal areas than Cubist regression tree models trained separately on each species. In contrast, Cubist regression tree models of forest structural and functional attributes yielded larger such correlation coefficients than the ordination-trained PGNN models. Full article

Discrepancies exist between theoretical and experimental opacity data for iron, at temperatures 180–195 eV and electron densities near 3 × 10²²/cm³, relevant to the solar radiative-convective boundary. Another discrepancy, between theory and helioseismic measurements of the boundary’s location, would be ameliorated if the experimental opacity is correct. To address these issues, this paper details the first results from new experiments under development at the National Ignition Facility (NIF), using a different method to replicate the prior experimental conditions. In the NIF experiments, 64 laser beams indirectly heat a plastic-tamped rectangular iron-magnesium sample inside a gold cavity. Another 64 beams implode a spherical plastic shell to produce a continuum X-ray flash which backlights the hot sample. An X-ray spectrometer records the transmitted X-rays, the unattenuated X-rays passing around the sample, and the sample’s self-emission. From these data, X-ray transmission spectra are inferred, showing Mg K-shell and Fe L-shell X-ray transitions from plasma at a temperature of ~150 eV and electron density of ~8 × 10²¹/cm³. These conditions are similar to prior Z measurements which agree better with theory. The NIF transmission data show statistical uncertainties of 2–10%, but various systematic uncertainties must be addressed before pursuing quantitative comparisons. The paths to reduction of the largest uncertainties are discussed. Once the uncertainty is reduced, future NIF experiments will probe higher temperatures (170–200 eV) to address the ongoing disagreement between theory and Z data. Full article

The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A. Full article

The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of highly contiguous assembled genomic sequences with a scaffold N50 length of over 38 Mbp. We generated transcriptome data derived from a lymphoma to aid in the determination of functional elements. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA388419. Full article

The field of molecular ecology has expanded enormously in the past two decades, largely because of the growing ease with which neutral molecular genetic data can be obtained from virtually any taxonomic group. However, there is also a growing awareness that neutral molecular data can provide only partial insight into parameters such as genetic diversity, local adaptation, evolutionary potential, effective population size, and taxonomic designations. Here we review some of the applications of neutral versus adaptive markers in molecular ecology, discuss some of the advantages that can be obtained by supplementing studies of molecular ecology with data from non-neutral molecular markers, and summarize new methods that are enabling researchers to generate data from genes that are under selection. Full article