Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii.

Wheat (Triticum aestivum) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum timopheevii (2n = 4x = 28) is an allotetraploid wheat wild relative species containing the At and G genomes that has been exploited in many pre-breeding programmes for wheat improvement. In this study, we report the generation of a chromosome-scale reference genome assembly of T. timopheevii accession PI 94760 based on PacBio HiFi reads and chromosome conformation capture (Hi-C). The assembly comprised a total size of 9.35 Gb, featuring a contig N50 of 42.4 Mb and included the mitochondrial and plastid genome sequences. Genome annotation predicted 166,325 gene models including 70,365 genes with high confidence. DNA methylation analysis showed that the G genome had on average more methylated bases than the At genome. In summary, the T. timopheevii genome assembly provides a valuable resource for genome-informed discovery of agronomically important genes for food security.

Assessment of cyanotoxins in water and fish in an African freshwater lagoon (Lagoon Aghien, Ivory Coast) and the application of WHO guidelines.

In comparison with northern countries, limited data are available on the occurrence and potential toxicity of cyanobacterial blooms in lakes and ponds in sub-Saharan countries. With the aim of enhancing our knowledge on cyanobacteria and their toxins in Africa, we performed a 17-month monitoring of a freshwater ecosystem, Lagoon Aghien (Ivory Coast), which is used for multiple practices by riverine populations and for drinking water production in Abidjan city. The richness and diversity of the cyanobacterial community were high and displayed few variations during the entire survey. The monthly average abundances ranged from 4.1 × 104 to 1.8 × 105 cell mL-1, with higher abundances recorded during the dry seasons. Among the five cyanotoxin families analyzed (anatoxin-a, cylindrospermopsin, homoanatoxin, microcystins, saxitoxin), only microcystins (MC) were detected with concentrations ranging from 0 to 0.364 µg L-1 in phytoplankton cells, from 32 to 1092 µg fresh weight (FW) kg-1 in fish intestines, and from 33 to 383 µg FW kg-1 in fish livers. Even if the MC concentrations in water and fish are low, usually below the thresholds defined in WHO guidelines, these data raise the issue of the relevance of these WHO guidelines for sub-Saharan Africa, where local populations are exposed throughout the year to these toxins in multiple ways.

Dataset describing problem factors of partnering relationships in the Malaysian construction industry.

The dataset indicates the problem factors which may influence the development of partnering relationship between two key project parties - the main contractor and the subcontractor. A total of 53 problem factors were identified and were clustered into five categories. An online questionnaire was used to elicit the viewpoints of these key parties with regards to the extent to which the factors have an impact on the partnering relationship in the Malaysian construction industry. The target respondents were managers and engineers of various construction companies in Malaysia with the main contractors or subcontractors who have projects in Kuala Lumpur, Shanghai and New Delhi. Both descriptive and quantitative analysis approaches were used to present the data. Relative Importance Index method was used to determine the top challenges to building favourable partnering relationships; and Partial Least Squares Structural-Equation Modelling (PLS-SEM) analysis was conducted to examine the role played by each cluster of factors in explaining the quality of partnering relationship between the main contractors and subcontractors. This data set would assist practitioners to work on the major problem factors to improve the quality of partnering relationship between the key participants in their present and future construction projects. By eliminating or minimizing these problem factors, practitioners will contribute significantly to effective supply chain management in the construction industry. The data would be of value to academics and industry professionals involved in the construction business domestically and internationally.

Fish gut-associated bacterial communities in a tropical lagoon (Aghien lagoon, Ivory Coast).

Aghien lagoon (Ivory Coast) is a eutrophic freshwater lagoon that harbors high biomasses of phytoplankton. Despite Increasing interest in fish gut microbiomes diversity and functions, little data is currently available regarding wild species from tropical west African lakes. Here, gut-associated bacterial communities are investigated in four fish species that are consumed by locale populations, namely the Cichlidae Hemichromis fasciatus, Tilapia guineensis and Sarotherodon melanotheron, and the Claroteidae Chrysichthys nigrodigitatus. Species-related differences are identified, that can be attributed to host phylogeny and diet. Important variations throughout the year are observed in T. guineensis and C. nigrodigitatus. This result emphasized the importance of time-series sampling and comparison with environmental variables even in tropical regions, that are not often conducted in wild populations. Effects of environmental factors (anthropogenic or not) on the microbiota and potential outcomes for fish health and populations sustainability need to be further explored. Interestingly, fish appear as major reservoirs of bacterial diversity, suggesting that they could contribute to the overall stability and resilience of bacterial communities present in the Aghien lagoon.

GrainGenes: a data-rich repository for small grains genetics and genomics.

As one of the US Department of Agriculture-Agricultural Research Service flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves the data and community needs of globally distributed small grains researchers for the genetic improvement of the Triticeae family and Avena species that include wheat, barley, rye and oat. GrainGenes accomplishes its mission by continually enriching its cross-linked data content following the findable, accessible, interoperable and reusable principles, enhancing and maintaining an intuitive web interface, creating tools to enable easy data access and establishing data connections within and between GrainGenes and other biological databases to facilitate knowledge discovery. GrainGenes operates within the biological database community, collaborates with curators and genome sequencing groups and contributes to the AgBioData Consortium and the International Wheat Initiative through the Wheat Information System (WheatIS). Interactive and linked content is paramount for successful biological databases and GrainGenes now has 2917 manually curated gene records, including 289 genes and 254 alleles from the Wheat Gene Catalogue (WGC). There are >4.8 million gene models in 51 genome browser assemblies, 6273 quantitative trait loci and >1.4 million genetic loci on 4756 genetic and physical maps contained within 443 mapping sets, complete with standardized metadata. Most notably, 50 new genome browsers that include outputs from the Wheat and Barley PanGenome projects have been created. We provide an example of an expression quantitative trait loci track on the International Wheat Genome Sequencing Consortium Chinese Spring wheat browser to demonstrate how genome browser tracks can be adapted for different data types. To help users benefit more from its data, GrainGenes created four tutorials available on YouTube. GrainGenes is executing its vision of service by continuously responding to the needs of the global small grains community by creating a centralized, long-term, interconnected data repository. Database URL:https://wheat.pw.usda.gov.

GrainGenes: Tools and Content to Assist Breeders Improving Oat Quality.

GrainGenes is the USDA-ARS database and Web resource for wheat, barley, oat, rye, and their relatives. As a community Web hub and database for small grains, GrainGenes strives to provide resources for researchers, students, and plant breeders to improve traits such as quality, yield, and disease resistance. Quantitative trait loci (QTL), genes, and genetic maps for quality attributes in GrainGenes represent the historical approach to mapping genes for groat percentage, test weight, protein, fat, and ß-glucan content in oat (Avena spp.). Genetic maps are viewable in CMap, the comparative mapping tool that enables researchers to take advantage of highly populated consensus maps to increase the marker density around their genes-of-interest. GrainGenes hosts over 50 genome browsers and is launching an effort for community curation, including the manually curated tracks with beta-glucan QTL and significant markers found via GWAS and cloned cellulose synthase-like AsClF6 alleles.

Impacts of nutrient loading and fish grazing on the phytoplankton community and cyanotoxin production in a shallow tropical lake: Results from mesocosm experiments.

Given the increasing eutrophication of water bodies in Africa due to increasing anthropogenic pressures, data are needed to better understand the responses of phytoplankton communities to these changes in tropical lakes. These ecosystems are used by local human populations for multiple purposes, including fish and drinking water production, potentially exposing these populations to health threats if, for example, an increase in toxic cyanobacterial blooms is associated with increasing eutrophication. To test the short-term response of the phytoplankton community to the addition of nutrients (phosphorus and nitrogen, alone or in combination) and Nile tilapia, we developed an in situ mesocosm experiment in a freshwater lagoon located near Abidjan (Ivory Coast). We found that phytoplankton growth (estimated by chlorophyll-a quantification) was highly stimulated when both nitrogen and phosphorus were added, while there was no clear evidence for such colimitation by these two nutrients when considering their concentrations in the lagoon. Phytoplankton growth was accompanied by significant changes in the diversity and composition of this community and did not lead to an increase in the proportions of cyanobacteria. However, the addition of fish to some mesocosms resulted in a drastic decrease in phytoplankton biomass and a dominance of chlorophytes in this community. Finally, these experiments showed that the addition of nitrogen, alone or combined with phosphorus, stimulated microcystin production by cyanobacteria. In addition, no evidence of microcystin accumulation in the fish was found. Taken together, these data allow us to discuss strategies for controlling cyanobacterial blooms in this tropical ecosystem.

Assessment of some key indicators of the ecological status of an African freshwater lagoon (Lagoon Aghien, Ivory Coast).

The supply of drinking water is a vital challenge for the people who live on the African continent, as this continent is experiencing strong demographic growth and therefore increasing water demands. To meet these needs, surface water resources are becoming increasingly mobilized because underground resources are not always available or have already been overexploited. This situation is the case in the region of Abidjan in the Ivory Coast, where the drinking water deficit is a growing problem and it is therefore necessary to mobilize new water resources to ensure the supply of drinking water. Among the potential resources, local managers have identified a freshwater lagoon, Lagoon Aghien, That is in close proximity to the city of Abidjan. With the aim of enhancing knowledge on the ecological functioning of the lagoon and contributing to the assessment of its ability to provide drinking water, several physical and chemical parameters of the water and the phytoplankton community of the lagoon were monitored for 17 months (December 2016-April 2018) at six sampling stations. Our findings show that the lagoon is eutrophic, as evidenced by the high concentrations of total phosphorus (>140 µg L-1), nitrogen (1.36 mg L-1) and average chlorophyll-a (26 to 167 µg L-1) concentrations. The phytoplankton community in the lagoon is dominated by genera typical of eutrophic environments including mixotrophic genera such as Peridinium and by cyanobacteria such as Cylindrospermopsis/Raphidiopsis, Microcystis and Dolichospermum that can potentially produce cyanotoxins. The two rainfall peaks that occur in June and October appeared to be major events in terms of nutrient flows entering the lagoon, and the dynamics of these flows are complex. Significant differences were also found in the nutrient concentrations and to a lesser extent in the phytoplankton communities among the different stations, especially during the rainfall peaks. Overall, these results reveal that the quality of the lagoon's water is already severely degraded, and this degradation could increase in future years due to increasing urbanization in the watershed. These results therefore raise questions about the potential use of the lagoon as a source of drinking water if measures are not taken very quickly to protect this lagoon from increasing eutrophication and other pollution sources.

JBrowse Connect: A server API to connect JBrowse instances and users.

We describe JBrowse Connect, an optional expansion to the JBrowse genome browser, targeted at developers. JBrowse Connect allows live messaging, notifications for new annotation tracks, heavy-duty analyses initiated by the user from within the browser, and other dynamic features. We present example applications of JBrowse Connect that allow users 1) to specify and execute BLAST searches by either running on the same host as the webserver, with a self-contained BLAST module leveraging NCBI Blast+ commands, or via a managed Galaxy instance that can optionally run on a different host, and 2) to run the primer design service Primer3. JBrowse Connect allows users to track job progress and view results in the context of the browser. The software is available under a choice of open source licenses including LGPL and the Artistic License.

GrainGenes: centralized small grain resources and digital platform for geneticists and breeders.

GrainGenes (https://wheat.pw.usda.gov or https://graingenes.org) is an international centralized repository for curated, peer-reviewed datasets useful to researchers working on wheat, barley, rye and oat. GrainGenes manages genomic, genetic, germplasm and phenotypic datasets through a dynamically generated web interface for facilitated data discovery. Since 1992, GrainGenes has served geneticists and breeders in both the public and private sectors on six continents. Recently, several new datasets were curated into the database along with new tools for analysis. The GrainGenes homepage was enhanced by making it more visually intuitive and by adding links to commonly used pages. Several genome assemblies and genomic tracks are displayed through the genome browsers at GrainGenes, including the Triticum aestivum (bread wheat) cv. 'Chinese Spring' IWGSC RefSeq v1.0 genome assembly, the Aegilops tauschii (D genome progenitor) Aet v4.0 genome assembly, the Triticum turgidum ssp. dicoccoides (wild emmer wheat) cv. 'Zavitan' WEWSeq v.1.0 genome assembly, a T. aestivum (bread wheat) pangenome, the Hordeum vulgare (barley) cv. 'Morex' IBSC genome assembly, the Secale cereale (rye) select 'Lo7' assembly, a partial hexaploid Avena sativa (oat) assembly and the Triticum durum cv. 'Svevo' (durum wheat) RefSeq Release 1.0 assembly. New genetic maps and markers were added and can be displayed through CMAP. Quantitative trait loci, genetic maps and genes from the Wheat Gene Catalogue are indexed and linked through the Wheat Information System (WheatIS) portal. Training videos were created to help users query and reach the data they need. GSP (Genome Specific Primers) and PIECE2 (Plant Intron Exon Comparison and Evolution) tools were implemented and are available to use. As more small grains reference sequences become available, GrainGenes will play an increasingly vital role in helping researchers improve crops.

Apollo: Democratizing genome annotation.

Genome annotation is the process of identifying the location and function of a genome's encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number of scientists to incorporate sequencing as a routine laboratory technique, there is widespread demand for tools that can assist in the deliberative analytical review of genomic information. To this end, we present Apollo, an open source software package that enables researchers to efficiently inspect and refine the precise structure and role of genomic features in a graphical browser-based platform. Some of Apollo's newer user interface features include support for real-time collaboration, allowing distributed users to simultaneously edit the same encoded features while also instantly seeing the updates made by other researchers on the same region in a manner similar to Google Docs. Its technical architecture enables Apollo to be integrated into multiple existing genomic analysis pipelines and heterogeneous laboratory workflow platforms. Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible.

Transmission scanning electron microscopy: Defect observations and image simulations.

The new capabilities of a FEG scanning electron microscope (SEM) equipped with a scanning transmission electron microscopy (STEM) detector for defect characterization have been studied in parallel with transmission electron microscopy (TEM) imaging. Stacking faults and dislocations have been characterized in strontium titanate, a polycrystalline nickel-base superalloy and a single crystal cobalt-base material. Imaging modes that are similar to conventional TEM (CTEM) bright field (BF) and dark field (DF) and STEM are explored, and some of the differences due to the different accelerating voltages highlighted. Defect images have been simulated for the transmission scanning electron microscopy (TSEM) configuration using a scattering matrix formulation, and diffraction contrast in the SEM is discussed in comparison to TEM. Interference effects associated with conventional TEM, such as thickness fringes and bending contours are significantly reduced in TSEM by using a convergent probe, similar to a STEM imaging modality, enabling individual defects to be imaged clearly even in high dislocation density regions. Beyond this, TSEM provides significant advantages for high throughput and dynamic in-situ characterization.

JBrowse: a dynamic web platform for genome visualization and analysis.

BACKGROUND: JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. RESULTS: Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. CONCLUSIONS: JBrowse is a mature web application suitable for genome visualization and analysis.

STAT3: a central mediator of pulmonary fibrosis?

Pulmonary fibrosis is a devastating, relentlessly progressive, and lethal disease. There is a significant unmet need for effective treatment since currently no FDA-approved therapies exist. Current thinking suggests that idiopathic pulmonary fibrosis (IPF) is initiated by pathways similar to normal wound healing, but relentless fibrosis occurs secondary to absent or defective inhibitory mechanisms that normally terminate wound healing. The heterogeneous pathological presentation of fibrosis suggests that the anatomic location and origin of fibroblasts and other cells might be critical for their phenotype and function and will impact on strategies to prevent or treat fibrotic lung diseases. This review summarizes our current understanding of the pathobiology of IPF, with a specific focus on the role of STAT3 in regulating cellular responses that may contribute to or inhibit pro-fibrotic processes. An improved understanding of the complex cell-type specific roles that this transcription factor plays in normal lung and in fibrosis is required to determine its suitability as an effective therapeutic target.

Fourier relationship between angular position and optical orbital angular momentum.

We demonstrate the Fourier relationship between angular position and angular momentum for a light mode. In particular we measure the distribution of orbital angular momentum states of light that has passed through an aperture and verify that the orbital angular momentum distribution is given by the complex Fourier-transform of the aperture function. We use spatial light modulators, configured as diffractive optical components, to define the initial orbital angular momentum state of the beam, set the defining aperture, and measure the angular momentum spread of the resulting beam. These measurements clearly confirm the Fourier relationship between angular momentum and angular position, even at light intensities corresponding to the single photon level.

Observation of quantum entanglement using spatial light modulators.

We use spatial light modulators to observe the quantum entanglement of down-converted photon pairs. Acting as diffractive optical elements within one of the beams, they can be reconfigured in real time to set the spatial profile of the measured mode. Such configurations are highly applicable to the measurement of orbital angular momentum states or other spatial modes, such as those associated with quantum imaging.

Gene expression profiles associated with response to chemotherapy in epithelial ovarian cancers.

PURPOSE: The goal of this study was to determine whether distinct gene expression profiles are associated with intrinsic and/or acquired chemoresistance in epithelial ovarian carcinoma. EXPERIMENTAL DESIGN: Gene expression profiles were generated from 21 primary chemosensitive tumors and 24 primary chemo-resistant tumors using cDNA-based microarrays. Gene expression profiles of both groups of primary tumors were then compared with those of 15 ovarian carcinomas obtained following platinum-based chemotherapy ("post-chemotherapy" tumors). A theme discovery tool was used to identify functional categories of genes involved in drug resistance. RESULTS: Comparison of primary chemosensitive and chemo-resistant tumors revealed differential expression of 85 genes (P < 0.001). Comparison of gene expression profiles of primary chemosensitive tumors and post-chemotherapy tumors revealed more robust differences with 760 genes differentiating the two groups (P < 0.001). In contrast, only 230 genes were differentially expressed between primary chemo-resistant and post-chemotherapy groups (P < 0.001). Common to both gene lists were 178 genes representing transcripts differentially expressed between post-chemotherapy tumors and all primary tumors irrespective of intrinsic chemosensitivity. The gene expression profile of post-chemotherapy tumors compared with that of primary tumors revealed statistically significant overrepresentation of genes encoding extracellular matrix-related proteins. CONCLUSIONS: These data show that gene expression profiling can discriminate primary chemo-resistant from primary chemosensitive ovarian cancers. Gene expression profiles were also identified that correlate with states of intrinsic and acquired chemoresistance and that represent targets for future investigation and potential therapeutic interventions.

Necrolytic migratory erythema: clinicopathologic study of 13 cases.

BACKGROUND: The clinical mucocutaneous manifestations of glucagonoma syndrome are recognized easily when they occur in the classic pattern of acral or periorificial lesions evolving in recurrent crops, with an annular and migratory distribution, in a patient with diabetes mellitus who has had recent weight loss and anemia. Not infrequently, noncharacteristic clinical and histopathologic features are observed and, in these cases, the diagnosis of pancreatic neoplasm may be delayed. AIM: To review the clinical and histopathologic features of cutaneous manifestations of glucagonoma syndrome. METHODS: The clinicopathologic features of 13 patients (eight women) with widespread or localized cutaneous eruption as a manifestation of islet cell pancreatic carcinoma with marked glucagon secretion (glucagonoma) were reviewed. RESULTS: The definitive diagnosis of the cutaneous eruption was established at the time of diagnosis of the pancreatic neoplasm (three patients) or afterwards (10 patients). In nine patients, the mucocutaneous manifestations preceded the diagnosis of the pancreatic neoplasm by 1 month to 3 years (mean, 12 months). In only eight biopsy specimens were the histopathologic features considered to be suggestive or characteristic of necrolytic migratory erythema. Diffuse parakeratosis, that occasionally arose abruptly from normal epidermis, was observed in 12 biopsy specimens. By the time necrolytic migratory erythema was diagnosed, the pancreatic carcinoma had metastasized to the liver, regional lymph nodes, or bone in 12 patients. CONCLUSION: Increased awareness of the polymorphic mucocutaneous and nonspecific histopathologic features of glucagonoma syndrome is needed to avoid unnecessary delay in the diagnosis of this syndrome.

Interactive application in holographic optical tweezers of a multi-plane Gerchberg-Saxton algorithm for three-dimensional light shaping.

Phase-hologram patterns that can shape the intensity distribution of a light beam in several planes simultaneously can be calculated with an iterative Gerchberg-Saxton algorithm [T. Haist et al., Opt. Commun. 140, 299 (1997)]. We apply this algorithm in holographic optical tweezers. This allows us to simultaneously trap several objects in individually controllable arbitrary 3-dimensional positions. We demonstrate the interactive use of our approach by trapping microscopic spheres and moving them into an arbitrary 3-dimensional configuration.