Small irrigation tanks as a source of malaria mosquito vectors: a study in north-central Sri Lanka

Watersheds / Tank irrigation / Rehabilitation / Malaria / Waterborne diseases / Disease vectors / Sri Lanka / Yan Oya

Preferred growth direction of III-V nanowires on differently oriented Si substrates

One of the nanowire (NW) characteristics is its preferred elongation direction. Here, we investigated the impact of Si substrate crystal orientation on the growth direction of GaAs NWs. We first studied the self-catalyzed GaAs NW growth on Si (111) and Si (001) substrates. SEM observations show GaAs NWs on Si (001) are grown along four directions without preference on one or some of them. This non-preferential NW growth on Si (001) is morphologically in contrast to the extensively reported vertical preferred GaAs NW growth on Si (111) substrates. We propose a model based on the initial condition of an ideal Ga droplet formation on Si substrates and the surface free energy calculation which takes into account the dangling bond surface density for different facets. This model provides further understanding of the different preferences in the growth of GaAs NWs along selected directions depending on the Si substrate orientation. To verify the prevalence of the model, NWs were grown on Si (311) substrates. The results are in good agreement with the three-dimensional mapping of surface free energy by our model. This general model can also be applied to predictions of NW preferred growth directions by the vapor-liquid-solid growth mode on other group IV and III–V substrates

Preferred growth direction of III-V nanowires on differently oriented Si substrates

One of the nanowire characteristics is its preferred elongation direction. Here, we investigated the impact of Si substrate crystal orientation on the growth direction of GaAs nanowires. We first studied the self-catalyzed GaAs nanowire growth on Si (111) and Si (001) substrates. SEM observations show GaAs nanowires on Si (001) are grown along four directions without preference on one or some of them. This non-preferential nanowire growth on Si (001) is morphologically in contrast to the extensively reported vertical preferred GaAs nanowire growth on Si (111) substrates. We propose a model based on the initial condition of an ideal Ga droplet formation on Si substrates and the surface free energy calculation which takes into account the dangling bond surface density for different facets. This model provides further understanding of the different preferences in the growth of GaAs nanowires along selected directions depending on the Si substrate orientation. To verify the prevalence of the model, nanowires were grown on Si (311) substrates. The results are in good agreement with the three-dimensional mapping of surface free energy by our model. This general model can also be applied to predictions of nanowire preferred growth directions by the vapor-liquid-solid growth mode on other group IV and III-V substrates

Diversity and relationships of eggplants from three geographically distant secondary centers of diversity

Eggplant (Solanum melongena L.) was domesticated in the Indo-Birmanian region, which is also the primary center of diversity for this crop. From there eggplant spread to other regions, and diversity accumulated in several secondary centers of diversity. We have assessed the diversity and relationships of 52 accessions of eggplant from three geographically distant secondary centers of diversity (China, Spain, and Sri Lanka) using 28 morphological descriptors and 12 highly polymorphic genomic SSRs. A wide variation was found for most morphological traits, and significant differences among the three centers of diversity were detected for 22 of these traits. The PCA analysis showed that eggplants from the three origins were morphologically differentiated, and accessions from each of the three secondary centers of diversity presented a typical combination of morphological characteristics. In this respect, discriminant analysis showed that accessions could be correctly classified to their origin using only six traits. The SSR characterization identified 110 alleles and allowed obtaining a unique genetic fingerprint for each accession. Many alleles were found to be private to each origin, but no universal alleles were found for any of the origins. The PCA analysis showed that the genetic differentiation among origins was less clear than for morphological traits, although the analysis of the population structure shows that accessions mostly group according to the origin, but also provides evidence of migration among the three secondary centers of diversity. The genetic diversity (HT) within each origin was high, ranging between H-T = 0.5400 (Sri Lanka) and H-T = 0.4943 (China), while the standardized genetic differentiation (G'(ST)) among origins was moderate (G'(ST) = 0.2657). The correlation between morphological and SSR distances was non-significant (r = 0.044), indicating that both data are complementary for the conservation of germplasm and breeding of eggplant. These results are relevant for the management of genetic resources, breeding programmes, and evolutionary studies of eggplant.This work was financed by the Ministerio de Ciencia e innovacion (grants AGL2009-07257 and RF-2008-00008-00-00) (http://www.micinn.es). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Hurtado Ricart, M.; Vilanova Navarro, S.; Plazas Ávila, MDLO.; Gramazio, P.; Fonseka, HH.; Fonseka, R.; Prohens Tomás, J. (2012). Diversity and relationships of eggplants from three geographically distant secondary centers of diversity. PLoS ONE. 7:41748-41748. https://doi.org/10.1371/journal.pone.0041748S4174841748

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

Fluorescence in situ hybridization (FISH) is a powerful single-cell technique for studying nuclear structure and organization. Here we report two advances in FISH-based imaging. We first describe the in situ visualization of single-copy regions of the genome using two single-molecule super-resolution methodologies. We then introduce a robust and reliable system that harnesses single-nucleotide polymorphisms (SNPs) to visually distinguish the maternal and paternal homologous chromosomes in mammalian and insect systems. Both of these new technologies are enabled by renewable, bioinformatically designed, oligonucleotide-based Oligopaint probes, which we augment with a strategy that uses secondary oligonucleotides (oligos) to produce and enhance fluorescent signals. These advances should substantially expand the capability to query parent-of-origin-specific chromosome positioning and gene expression on a cell-by-cell basis

Defect-Free Axially Stacked GaAs/GaAsP Nanowire Quantum Dots with Strong Carrier Confinement

Axially stacked quantum dots (QDs) in nanowires (NWs) have important applications in nanoscale quantum devices and lasers. However, there is lack of study of defect-free growth and structure optimization using the Au-free growth mode. We report a detailed study of self-catalyzed GaAsP NWs containing defect-free axial GaAs QDs (NWQDs). Sharp interfaces (1.8-3.6 nm) allow closely stack QDs with very similar structural properties. High structural quality is maintained when up to 50 GaAs QDs are placed in a single NW. The QDs maintain an emission line width of <10 meV at 140 K (comparable to the best III-V QDs, including nitrides) after having been stored in an ambient atmosphere for over 6 months and exhibit deep carrier confinement (∼90 meV) and the largest reported exciton-biexciton splitting (∼11 meV) for non-nitride III-V NWQDs. Our study provides a solid foundation to build high-performance axially stacked NWQD devices that are compatible with CMOS technologies

Defining inflammatory cell states in rheumatoid arthritis joint synovial tissues by integrating single-cell transcriptomics and mass cytometry

© 2019, The Author(s), under exclusive licence to Springer Nature America, Inc. To define the cell populations that drive joint inflammation in rheumatoid arthritis (RA), we applied single-cell RNA sequencing (scRNA-seq), mass cytometry, bulk RNA sequencing (RNA-seq) and flow cytometry to T cells, B cells, monocytes, and fibroblasts from 51 samples of synovial tissue from patients with RA or osteoarthritis (OA). Utilizing an integrated strategy based on canonical correlation analysis of 5,265 scRNA-seq profiles, we identified 18 unique cell populations. Combining mass cytometry and transcriptomics revealed cell states expanded in RA synovia: THY1(CD90) + HLA-DRA hi sublining fibroblasts, IL1B + pro-inflammatory monocytes, ITGAX + TBX21 + autoimmune-associated B cells and PDCD1 + peripheral helper T (T PH ) cells and follicular helper T (T FH ) cells. We defined distinct subsets of CD8 + T cells characterized by GZMK + , GZMB + , and GNLY + phenotypes. We mapped inflammatory mediators to their source cell populations; for example, we attributed IL6 expression to THY1 + HLA-DRA hi fibroblasts and IL1B production to pro-inflammatory monocytes. These populations are potentially key mediators of RA pathogenesis

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

Background The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed. Results Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes. Conclusions Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g. in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor

Frequency of natural out-crossing in partially cleistogamous pigeonpea lines in diverse environments

Natural out-crossing is the major cause of loss of varietal purity in pegeonpea [Cajanus cajan (L.) Millsp.]. The frequency of natural out-crossing of partially cleistogamous mutant lines, characterized by a modified keel and filamentous anthers, was studied at two locations in Sri Lanka and three locations in India. Indeterminate growth habit and normal floral morphology were used as dominant markers and the frequency of anural out-crossing was estimated as percentage of the observed hybrid plants. Natural out-crossing in the mutant lines in Sri Lanka ranged from 0.14 to 1.33% in comparison to 6.34 to 19.64% in the controls. In the Indian environments, natural outcrossing ranged from 0.16 to 2.67%. The mutant was higly stable over diverse environments, and may be of considerable economic importance in pigeonpea improvement and seed-production programs

Improving seed germination of the eggplant rootstock Solanum torvum by testing multiple factors using an orthogonal array design

[EN] Solanum torvum is a highly vigorous relative of eggplant that is resistant to a number of harmful soil-borne diseases and is compatible for grafting with eggplant. Being a potential rootstock, this plant frequently presents poor and erratic germination, which makes its practical use difficult. We used an L8 (2(7)) orthogonal array design to evaluate the primary effects of seven factors (soaking of seeds, scarification with sodium hypochlorite (NaClO), application of gibberellic acid (GA(3)), use of potassium mitrate (KNO3) as a moistening agent, cold stratification, application of a heatshock, and light irradiation during germination) at two levels (L0 and L1) using four germination parameters (early and final germination, germination rate and vigour index) in fresh S. torvum seeds. S. torvum seeds had a strong dormancy with no germination in the untreated seeds and high early and final germination (approximately 100%) in certain treatments. An evaluation of the main effects revealed highly positive effects on germination from seed soaking, and the use of GA(3), KNO3, and light irradiation, whereas NaClO scarification had a negative effect. The application of cold stratification and heat shock treatments also had a positive effect on seed germination but to a lesser extent than the other treatments. An improved proposed protocol that consisted of subjecting seeds to soaking, the application of GA(3) and KNO3, cold stratification, heat shock, and light irradiation was validated and demonstrated to be highly effective, with seed germination success greater than 60% being observed at 3 days and final germination reaching a plateau at 6 days. A second validation experiment using a commercial growing substrate also showed a high emergence (approximately 50%) at 7 days and a final germination of approximately 80% was recorded with application of the improved protocol. The seed germination protocol that we have developed will facilitate the use of S. torvum as a rootstock for eggplant and its use in breeding programmes. Our results also reveal that orthogonal array designs are a powerful tool for establishing improved protocols for seed germination. (C) 2015 Elsevier B.V. All rights reserved.This work was completed as part of the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway. The project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and is implemented in partnership with national and international gene banks and plant breeding institutes. For further information see the project website: http://www.cwrdiversity.org/. Isabel Andujar and Pietro Gramazio are grateful to Universitat Politecnica de Valencia for their post-doctoral (PAID-10-14) and pre-doctoral (Programa FPI de la UPV-Subprograma 1) contracts, respectively.Ranil, RH.; Niran, HML.; Plazas Ávila, MDLO.; Fonseka, R.; Hemal Fonseka, H.; Vilanova Navarro, S.; Andújar Pérez, I.... (2015). Improving seed germination of the eggplant rootstock Solanum torvum by testing multiple factors using an orthogonal array design. Scientia Horticulturae. 193:174-181. https://doi.org/10.1016/j.scienta.2015.07.030S17418119