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Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago and are identified by genome-wide polymorphisms or morphological traits. The species are to a high degree reproductively isolated, but hybridization barriers are incomplete. A special type of hybridization barrier is based in the triploid endosperm of the seed, where embryo lethality is caused by endosperm failure to support the developing embryo. The MADS-box type I family of transcription factors are specifically expressed in the endosperm and has been proposed to play a role in endosperm-based hybridization barriers. The gene family is well known for a high evolutionary duplication rate, as well as being regulated by genomic imprinting. Here we address MADS-box type I gene family evolution and the role of type I genes in the context of hybridization. Using two de-novo assembled and annotated chromosome-level genomes of A. arenosa and A. lyrata ssp. petraea we analyzed the MADS-box type I gene family in Arabidopsis to predict orthologs, copy number and structural genomic variation related to the type I loci. Our findings were compared to gene expression profiles sampled before and after the transition to endosperm cellularization in order to investigate the involvement of MADS-box type I loci in endosperm-based hybridization barriers. We observed substantial differences in type-I expression between A. arenosa and A. lyrata ssp. petraea in the endosperm, suggesting a genetic cause for the endosperm-based hybridization barrier in A. arenosa and A. lyrata ssp. petraea hybrid seeds.

Genomic imprinting promotes differential expression of parental alleles in the endosperm of flowering plants and is regulated by epigenetic modification such as DNA methylation and histone tail modifications in chromatin. After fertilization, the endosperm develops through a syncytial stage before it cellularizes and becomes a nutrient source for the growing embryo. Regional compartmentalization has been shown both in early and late endosperm development, and different transcriptional domains suggest divergent spatial and temporal regional functions. The analysis of the role of parent-of-origin allelic expression in the endosperm as a whole and the investigation of domain-specific functions have been hampered by the inaccessibility of the tissue for high-throughput transcriptome analyses and contamination from surrounding tissue. Here, we used fluorescence-activated nuclear sorting (FANS) of nuclear targeted GFP fluorescent genetic markers to capture parental-specific allelic expression from different developmental stages and specific endosperm domains. This approach allowed us to successfully identify differential genomic imprinting with temporal and spatial resolution. We used a systematic approach to report temporal regulation of imprinted genes in the endosperm, as well as region-specific imprinting in endosperm domains. Analysis of our data identified loci that are spatially differentially imprinted in one domain of the endosperm, while biparentally expressed in other domains. These findings suggest that the regulation of genomic imprinting is dynamic and challenge the canonical mechanisms for genomic imprinting.

Genomic imprinting is an epigenetic phenomenon established in the gametes prior to fertilization that causes differential expression of parental alleles, mainly in the endosperm of flowering plants. The overlap between previously identified panels of imprinted genes is limited. To investigate imprinting, we used high-resolution sequencing data acquired with sequence-capture technology. We present a bioinformatics pipeline to assay parent-of-origin allele-specific expression and report more than 300 loci with parental expression bias in Arabidopsis (Arabidopsis thaliana). In most cases, the level of expression from maternal and paternal alleles was not binary, instead supporting a differential dosage hypothesis for the evolution of imprinting in plants. To address imprinting regulation, we systematically employed mutations in regulative epigenetic pathways suggested to be major players in the process. We established the mechanistic mode of imprinting for more than 50 loci regulated by DNA methylation and Polycomb-dependent histone methylation. However, the imprinting patterns of most genes were not affected by these mechanisms. To this end, we also demonstrated that the RNA-directed DNA methylation pathway alone does not substantially influence imprinting patterns, suggesting that more complex epigenetic pathways regulate most of the identified imprinted genes.

Advances in implant design, patient familiarity, and surgeon experience have led to a large cohort of patients undergoing total ankle replacement (TAR). Unfortunately, early or late failure can result from soft tissue-related wound problems, deep infection, or technical error in implantation. When a TAR becomes infected, treatment remains controversial with no level 1 evidence to support management. Individual patient characteristics are important when determining the treatment approach to the infected TAR as soft tissue coverage, patient comorbidities, and the ultimate surgical goal of the patient need to be taken into account. Salvage of an infected TAR will consist of eradication of infection, obtaining soft tissue coverage and maintaining function of the limb. Treatment strategies described in the literature consist of irrigation and debridement with or without polyethylene exchange, one-stage revision arthroplasty, and two-stage revision arthroplasty with antibiotic cement spacer. Permanent antibiotic cement spacer has been infrequently reported in the literature; however it does have a significant role in the treatment approach to the failed TAR. There are instances where patient morbidity, significant bone loss, or prolonged recovery severely limit a patient’s appetite to undergo further attempts at implant salvage. In cases where ankle fusion or revision arthroplasty is not within the goals of the patient or surgeon, permanent polymethyl methacrylate (PMMA) antibiotic-impregnated spacer can assist the patient in ultimate limb retention following the devastating complications associated with an infected TAR.

Distinguishing long non-coding RNA from protein-coding RNA is important to molecular and cellular biology. The problem can be addressed with machine learning in general and with artificial neural networks in particular. We explore the effects of various network design choices on the accuracy of human LncRNA identification. Perceptron-based neural network models were found to be almost as accurate as more complex recurrent neural networks, and K-mer representations of the data seemed to assist both. Size selection of training data affected results. These explorations could assist in neural network design for RNA analysis.

The influenza A virus genome contains 8 gene segments encoding 10 commonly recognized proteins. Additional protein products have been identified, including PB1-F2 and PA-X. We report the in-silico identification of novel isoforms of PB1-F2 and PA-X in influenza virus genomes sequenced from avian samples. The isoform observed in PA-X includes a mutated stop codon that should extend the protein product by 8 amino acids. The isoform observed in PB1-F2 includes two nonsense mutations that should truncate the N-terminal region of the protein product and remove the entire mitochondrial targeting domain. Both isoforms were uncovered during automatic annotation of CEIRS sequence data. Nominally termed PA-X8 and PB1-F2-Cterm, both predicted isoforms were subsequently found in other annotated influenza genomes previously deposited in GenBank. Both isoforms were noticed due to discrepant annotations output by two annotation engines, indicating a benefit of incorporating multiple algorithms during gene annotation.

Background: Transition zones between healthy myocardium and scar form a spatially complex substrate that may give rise to reentrant ventricular arrhythmias (VAs). We sought to assess the utility of a novel machine learning approach for quantifying 3-dimensional spatial complexity of grayscale patterns on late gadolinium enhanced cardiac magnetic resonance images to predict VAs in patients with ischemic cardiomyopathy. Methods: One hundred twenty-two consecutive ischemic cardiomyopathy patients with left ventricular ejection fraction ≤35% without prior history of VAs underwent late gadolinium enhanced cardiac magnetic resonance images. From raw grayscale data, we generated graphs encoding the 3-dimensional geometry of the left ventricle. A novel technique, adapted to these graphs, assessed global regularity of signal intensity patterns using Fourier-like analysis and generated a substrate spatial complexity profile for each patient. A machine learning statistical algorithm was employed to discern which substrate spatial complexity profiles correlated with VA events (appropriate implantable cardioverter-defibrillator firings and arrhythmic sudden cardiac death) at 5 years of follow-up. From the statistical machine learning results, a complexity score ranging from 0 to 1 was calculated for each patient and tested using multivariable Cox regression models. Results: At 5 years of follow-up, 40 patients had VA events. The machine learning algorithm classified with 81% overall accuracy and correctly classified 86% of those without VAs. Overall negative predictive value was 91%. Average complexity score was significantly higher in patients with VA events versus those without (0.5±0.5 versus 0.1±0.2; P P =0.002). Conclusions: Substrate spatial complexity analysis of late gadolinium enhanced cardiac magnetic resonance images may be helpful in refining VA risk in patients with ischemic cardiomyopathy, particularly to identify low-risk patients who may not benefit from prophylactic implantable cardioverter-defibrillator therapy. Visual Overview: A visual overview is available for this article.

Verrucae (warts) are the most common viral infections of the skin, affecting 7% to 10% of the general population. Typically caused by human papillomavirus type 1, plantar warts manifest as benign proliferation of the epithelial cells on the feet. It has been cited that up to one-third of nongenital warts become recalcitrant, and biopsy is often required to confirm diagnosis and direct appropriate treatment. These treatments can vary from various types of oral medications, acids, ablative modalities, and injections. In this article, we present a case of a recalcitrant plantar wart that appeared to circumferentially spread from the initial site after first-line treatment and presumed resolution with the product cantharidin. The development of ring warts is a known complication associated with cantharidin use, with little described rationale to the presentation.

We report a retrospective study of 171 consecutive patients with a lateral ankle sprain. All the patients with direct or blunt force trauma were excluded. Within 21 days of injury, 115 (67.25%) patients had undergone magnetic resonance imaging to evaluate for more serious or significant injuries. The average patient age was 44.09 years. Of the 115 patients, 75 (65.23%) had findings noted to be "significant." MRI can serve as a valuable and underused tool in the evaluation of acute lateral ankle injuries. The underuse of MRI might explain the high degree of variability in patients recovering from a lateral ankle sprain.

A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an “app” on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research.

Long-read single-molecule sequencing has revolutionizedde novogenome assembly and enabled the automated reconstruction of reference-quality genomes. However, given the relatively high error rates of such technologies, efficient and accurate assembly of large repeats and closely related haplotypes remains challenging. We address these issues with Canu, a successor of Celera Assembler that is specifically designed for noisy single-molecule sequences. Canu introduces support for nanopore sequencing, halves depth-of-coverage requirements, and improves assembly continuity while simultaneously reducing runtime by an order of magnitude on large genomes versus Celera Assembler 8.2. These advances result from new overlapping and assembly algorithms, including an adaptive overlapping strategy based ontf-idfweighted MinHash and a sparse assembly graph construction that avoids collapsing diverged repeats and haplotypes. We demonstrate that Canu can reliably assemble complete microbial genomes and near-complete eukaryotic chromosomes using either PacBio or Oxford Nanopore technologies, and achieves a contig NG50 of greater than 21 Mbp on both human andDrosophila melanogasterPacBio datasets. For assembly structures that cannot be linearly represented, Canu provides graph-based assembly outputs in graphical fragment assembly (GFA) format for analysis or integration with complementary phasing and scaffolding techniques. The combination of such highly resolved assembly graphs with long-range scaffolding information promises the complete and automated assembly of complex genomes.

Background Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome. Results Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable – estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation. Conclusions Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3654-1) contains supplementary material, which is available to authorized users.

Structural design and optimization of slotted waveguide antenna stiffened structures (SWASS) are considered. Radio frequency (RF) performance was considered by modeling waveguide slots for an antenna imbedded in an aircraft panel subject to external loading. An equivalent two-dimensional plate model was shown to be adequate for simplifying the waveguide core as an equivalent plate layer; however, smearing the stiffness effect of the slots was shown to be inaccurate. For higher fidelity, plate finite elements were used in a three-dimensional model with slots to evaluate the mechanical failure. This modeling technique proved cost-effective, employing few elements compared with three-dimensional solid modeling found in the literature. Validation with published experiments and verification with other published simulations demonstrated that it was sufficiently accurate for design purposes. Four SWASS configurations were compared. A slotted metallic foil waveguide tube wrapped with glass fiber and a carbon fiber inner mold line face sheet was the most effective concept, followed closely by all carbon fiber construction with slots cut through the outer mold line face sheet. Glass fiber face sheets for both inner and outer mold lines were the least effective concepts, whether or not the waveguide tubes were constructed of metallic foil or carbon fiber.

The human cell lines HepG2, HuH-7, and Jurkat are commonly used for amplification of the RNA viruses present in environmental samples. To assist with assays by RNAseq, we sequenced these cell lines and developed a subtraction database that contains sequences expected in sequence data from uninfected cells. RNAseq data from cell lines infected with Sendai virus were analyzed to test host subtraction. The process of mapping RNAseq reads to our subtraction database vastly reduced the number non-viral reads in the dataset to allow for efficient secondary analyses.

Lyme disease is the result of Borrelia burgdorferi bacterial infection after exposure from a tick bite. A pathognomonic finding in early-stage Lyme disease is an expanding, red macular ring known as erythema migrans. Lyme arthritis is a late-stage manifestation of this disease, affecting the large, weightbearing joints with intermittent pain and swelling. The existing data on Lyme disease and subsequent arthritis have reported manifestations in the lower extremity, primarily in the knee and ankle and less commonly the small joints of the foot. We present a retrospective case series of 11 cases of painful arthritis in the foot and ankle with confirmatory Lyme disease testing.

Sesamoid bones and accessory ossicles are common incidental findings on radiographs. These can occasionally become symptomatic, usually after a precipitating event such as an injury or overuse, or they can be incidental findings unrelated to the presenting pathology. The aim of this study was to highlight a rare case of a bipartite fifth metatarsal sesamoid bone and to review previous literature regarding sesamoid bones and accessory ossicles.

Vitamin D is an essential, fat-soluble nutrient that is a key modulator of bone health. Despite the gaining popularity throughout published medical studies, no consensus has been reached regarding a serum vitamin D level that will guarantee adequate skeletal health in a patient with an increased functional demand. The purpose of the present investigation was to examine the serum concentrations of vitamin D in patients with confirmed stress fractures. A total of 124 patients were included in our retrospective cohort study. Of the 124 patients, 53 had vitamin D levels measured within 3 months of diagnosis. An association was seen in patients with a stress fracture and vitamin D level measured, as 44 (83.02%) of the 53 patients had a serum 25-hydroxyvitamin D level

Background The 50-year-old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome. Results The C6/36 genome assembly has the largest contig N50 (3.3 Mbp) of any mosquito assembly, presents the sequences of both haplotypes for most of the diploid genome, reveals independent null mutations in both alleles of the Dicer locus, and indicates a male-specific genome. Gene annotation was computed with publicly available mosquito transcript sequences. Gene expression data from cell line RNA sequence identified enrichment of growth-related pathways and conspicuous deficiency in aquaporins and inward rectifier K+ channels. As a test of utility, RNA sequence data from Zika-infected cells were mapped to the C6/36 genome and transcriptome assemblies. Host subtraction reduced the data set by 89%, enabling faster characterization of nonhost reads. Conclusions The C6/36 genome sequence and annotation should enable additional uses of the cell line to study arbovirus vector interactions and interventions aimed at restricting the spread of human disease.

Background Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. Methods We developed a hybrid assembly pipeline called “Alpaca” that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation. Results Compared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies. Conclusion Our results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3927-8) contains supplementary material, which is available to authorized users.

BackgroundThe 50-year old Aedes albopictus C6/36 cell line is a resource for the detection, amplification, and analysis of mosquito-borne viruses including Zika, dengue, and chikungunya. The cell line is derived from an unknown number of larvae from an unspecified strain of Aedes albopictus mosquitoes. Toward improved utility of the cell line for research in virus transmission, we present an annotated assembly of the C6/36 genome.ResultsThe C6/36 genome assembly has the largest contig N50 (3.3 Mbp) of any mosquito assembly, presents the sequences of both haplotypes for most of the diploid genome, reveals independent null mutations in both alleles of the Dicer locus, and indicates a male-specific genome. Gene annotation was computed with publicly available mosquito transcript sequences. Gene expression data from cell line RNA sequence identified enrichment of growth-related pathways and conspicuous deficiency in aquaporins and inward rectifier K+ channels. As a test of utility, RNA sequence data from Zika-infected cells was mapped to the C6/36 genome and transcriptome assemblies. Host subtraction reduced the data set by 89%, enabling faster characterization of non-host reads.ConclusionsThe C6/36 genome sequence and annotation should enable additional uses of the cell line to study arbovirus vector interactions and interventions aimed at restricting the spread of human disease.

Background Third generation sequencing technologies, with sequencing reads in the tens- of kilo-bases, facilitate genome assembly by spanning ambiguous regions and improving continuity. This has been critical for plant genomes, which are difficult to assemble due to high repeat content, gene family expansions, segmental and tandem duplications, and polyploidy. Recently, high-throughput mapping and scaffolding strategies have further improved continuity. Together, these long-range technologies enable quality draft assemblies of complex genomes in a cost-effective and timely manner. Results Here, we present high quality genome assemblies of the model legume plant, Medicago truncatula (R108) using PacBio, Dovetail Chicago (hereafter, Dovetail) and BioNano technologies. To test these technologies for plant genome assembly, we generated five assemblies using all possible combinations and ordering of these three technologies in the R108 assembly. While the BioNano and Dovetail joins overlapped, they also showed complementary gains in continuity and join numbers. Both technologies spanned repetitive regions that PacBio alone was unable to bridge. Combining technologies, particularly Dovetail followed by BioNano, resulted in notable improvements compared to Dovetail or BioNano alone. A combination of PacBio, Dovetail, and BioNano was used to generate a high quality draft assembly of R108, a M. truncatula accession widely used in studies of functional genomics. As a test for the usefulness of the resulting genome sequence, the new R108 assembly was used to pinpoint breakpoints and characterize flanking sequence of a previously identified translocation between chromosomes 4 and 8, identifying more than 22.7 Mb of novel sequence not present in the earlier A17 reference assembly. Conclusions Adding Dovetail followed by BioNano data yielded complementary improvements in continuity over the original PacBio assembly. This strategy proved efficient and cost-effective for developing a quality draft assembly compared to traditional reference assemblies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3971-4) contains supplementary material, which is available to authorized users.

In this review, the authors offer a critical analysis of published interventions for improving mathematics performance among middle and high school students with EBD in light of the Common Core State Standards. An exhaustive review of literature from 1975 to December 2012 yielded 20 articles that met criteria for inclusion. The authors analyzed the body of research for the nature of participants, settings, interventionists, interventions, and alignment with Common Core State Standards. Despite limitations with the body of research, the results of the review indicate a number of promising practices exist for secondary students with EBD in mathematics, including: (a) peer-mediated approaches, (b) interventions that address academic performance as well as behavior, (d) use of technology, and (e) use of strategy instruction to support conceptual understanding. Implications for research and practice are provided.

Background: The first Atlantic cod (Gadus morhua) genome assembly published in 2011 was one of the early genome assemblies exclusively based on high-throughput 454 pyrosequencing. Since then, rapid advances in sequencing technologies have led to a multitude of assemblies generated for complex genomes, although many of these are of a fragmented nature with a significant fraction of bases in gaps. The development of long-read sequencing and improved software now enable the generation of more contiguous genome assemblies.Results: By combining data from Illumina, 454 and the longer PacBio sequencing technologies, as well as integrating the results of multiple assembly programs, we have created a substantially improved version of the Atlantic cod genome assembly. The sequence contiguity of this assembly is increased fifty-fold and the proportion of gap-bases has been reduced fifteen-fold. Compared to other vertebrates, the assembly contains an unusual high density of tandem repeats (TRs). Indeed, retrospective analyses reveal that gaps in the first genome assembly were largely associated with these TRs. We show that 21 % of the TRs across the assembly, 19 % in the promoter regions and 12 % in the coding sequences are heterozygous in the sequenced individual.Conclusions: The inclusion of PacBio reads combined with the use of multiple assembly programs drastically improved the Atlantic cod genome assembly by successfully resolving long TRs. The high frequency of heterozygous TRs within or in the vicinity of genes in the genome indicate a considerable standing genomic variation in Atlantic cod populations, which is likely of evolutionary importance.

International audience; Background: Helicoverpa armigera and Helicoverpa zea are major caterpillar pests of Old and New World agriculture, respectively. Both, particularly H. armigera, are extremely polyphagous, and H. armigera has developed resistance to many insecticides. Here we use comparative genomics, transcriptomics and resequencing to elucidate the genetic basis for their properties as pests. Results: We find that, prior to their divergence about 1.5 Mya, the H. armigera/H. zea lineage had accumulated up to more than 100 more members of specific detoxification and digestion gene families and more than 100 extra gustatory receptor genes, compared to other lepidopterans with narrower host ranges. The two genomes remain very similar in gene content and order, but H. armigera is more polymorphic overall, and H. zea has lost several detoxification genes, as well as about 50 gustatory receptor genes. It also lacks certain genes and alleles conferring insecticide resistance found in H. armigera. Non-synonymous sites in the expanded gene families above are rapidly diverging, both between paralogues and between orthologues in the two species. Whole genome transcriptomic analyses of H. armigera larvae show widely divergent responses to different host plants, including responses among many of the duplicated detoxification and digestion genes. Conclusions: The extreme polyphagy of the two heliothines is associated with extensive amplification and neofunctionalisation of genes involved in host finding and use, coupled with versatile transcriptional responses on different hosts. H. armigera's invasion of the Americas in recent years means that hybridisation could generate populations that are both locally adapted and insecticide resistant.

ThaleMine (https://apps.araport.org/thalemine/) is a comprehensive data warehouse that integrates a wide array of genomic information of the model plant Arabidopsis thaliana. The data collection currently includes the latest structural and functional annotation from the Araport11 update, the Col-0 genome sequence, RNA-seq and array expression, co-expression, protein interactions, homologs, pathways, publications, alleles, germplasm and phenotypes. The data are collected from a wide variety of public resources. Users can browse gene-specific data through Gene Report pages, identify and create gene lists based on experiments or indexed keywords, and run GO enrichment analysis to investigate the biological significance of selected gene sets. Developed by the Arabidopsis Information Portal project (Araport, https://www.araport.org/), ThaleMine uses the InterMine software framework, which builds well-structured data, and provides powerful data query and analysis functionality. The warehoused data can be accessed by users via graphical interfaces, as well as programmatically via web-services. Here we describe recent developments in ThaleMine including new features and extensions, and discuss future improvements. InterMine has been broadly adopted by the model organism research community including nematode, rat, mouse, zebrafish, budding yeast, the modENCODE project, as well as being used for human data. ThaleMine is the first InterMine developed for a plant model. As additional new plant InterMines are developed by the legume and other plant research communities, the potential of cross-organism integrative data analysis will be further enabled.

We present a draft sequence of the genome of Aedes aegypti , the primary vector for yellow fever and dengue fever, which at ∼1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae . Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of ∼4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster . Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of ∼2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.

The lack of a common data interchange format for CEM is hampering progress, causing duplicate workloads and opening the door for error. We propose a standard format based on JSON for flexible data interchange. The format is designed to be self-describing, extensible, open, and freely available.

Traditionally, an infinite ground plane is used to represent the water surface for analysis of antennas installed on ships or otherwise situated over water. While this is sufficient for some scenarios, we have found the need for more accuracy in representing short-range propagation close to a water surface. In this paper, we generate randomized, realistic water surfaces and use these in CEM simulations.

A variety of microbial communities and their genes (the microbiome) exist throughout the human body, with fundamental roles in human health and disease. The National Institutes of Health (NIH)-funded Human Microbiome Project Consortium has established a population-scale framework to develop metagenomic protocols, resulting in a broad range of quality-controlled resources and data including standardized methods for creating, processing and interpreting distinct types of high-throughput metagenomic data available to the scientific community. Here we present resources from a population of 242 healthy adults sampled at 15 or 18 body sites up to three times, which have generated 5,177 microbial taxonomic profiles from 16S ribosomal RNA genes and over 3.5 terabases of metagenomic sequence so far. In parallel, approximately 800 reference strains isolated from the human body have been sequenced. Collectively, these data represent the largest resource describing the abundance and variety of the human microbiome, while providing a framework for current and future studies.

Using carefully selected thematic books, teachers can use literature to reach students experiencing difficult situations.