Giants among Cnidaria: Large Nuclear Genomes and Rearranged Mitochondrial Genomes in Siphonophores.

Siphonophores (Cnidaria: Hydrozoa) are abundant predators found throughout the ocean and are important constituents of the global zooplankton community. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these roughly 200 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k-mer spectra in six specimens, ranging from 0.7 to 2.3 Gb, with heterozygosity estimates between 0.69% and 2.32%. Incremental k-mer counting indicates k-mer peaks can be absent with nearly 20× read coverage, suggesting minimum genome sizes range from 1.4 to 5.6 Gb in the 25 samples without peaks in the k-mer spectra. This work confirms most siphonophore nuclear genomes are large relative to the genomes of other cnidarians, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled complete mitochondrial genomes for 33 specimens from these new data, indicating a conserved gene order shared among nonsiphonophore hydrozoans, Cystonectae, and some Physonectae, revealing the ancestral mitochondrial gene order of siphonophores. Our results also suggest extensive rearrangement of mitochondrial genomes within other Physonectae and in Calycophorae. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of k-mer-based genome skimming in understanding the genomic diversity of a clade.

Barcoding and mitochondrial phylogenetics of Porites corals.

Coral reefs are the most diverse ecosystem on the planet based on the abundance and diversity of phyla and higher taxa. However, it is still difficult to assess the diversity of lower taxa, especially at the species level. One tool for improving the identification of lower taxa are genetic markers that can distinguish cryptic species and assess species boundaries. Here, we present one such approach for an important and challenging group of reef-building corals. Porites corals are the main reef-builders of many coral reefs in the Indo-Pacific, owing to the massive growth forms of some species. The current number of valid Porites species is controversial, inflated with many synonymies, and often based on gross colony morphology although several morphospecies believed to be widespread and common can only be distinguished based on detailed microstructure analyses by taxonomic experts. Here, we test the suitability of multiple regions of mtDNA as genetic barcodes to identify suitable markers for species differentiation and unambiguous identification. Resulting sequencing data was further used for the first phylogenetic analysis of Guam's Porites species. We tested eight different mitochondrial markers and analyzed four in detail for 135 Porites specimens: mtDNA markers were amplified for 67 Porites specimens from Guam, representing 12 nominal Porites species, and combined with 69 mitochondrial genomes, mostly from Hawaii. The combination of all 4 markers distinguished 10 common and 7 uncommon Central-West Pacific Porites species. Most clades separate species along taxonomic boundaries, which is uncommon for Porites corals and testifies to the suitability of our multi-marker approach, and a combination of the two most promising barcodes distinguished 8/10 common species. These barcodes are thus suitable to distinguish virtually cryptic species in one of the most important and challenging coral genera. They offer a cheap, fast and reliable way to identify Porites species for species-level research, monitoring and conservation.

Changes in coral reef community structure along a sediment gradient in Fouha Bay, Guam.

High sedimentation rates have well-documented, deleterious impacts on coral reefs. However, few previous studies have attempted to quantitatively describe a coral reef community across a large continuous sediment gradient. In this study distinct benthic assemblages in Fouha Bay, Guam, were identified using a Moving Window Analysis conducted along a two-order of magnitude sediment gradient, with transition boundaries that were generally consistent with sediment thresholds identified in the literature. Coral richness dropped exponentially with increasing sedimentation rate. Richness was nearly three times greater in assemblages with sedimentation rates <10 mg cm-2 d-1 compared to assemblages experiencing rates between 10 and 50 mg cm-2 d-1, and nearly 30 times greater than assemblages experiencing rates between 50 and 100 mg cm-2 d-1. No corals were found in assemblages with sedimentation rates >110 mg cm-2 d-1. Reducing sedimentation in this area could result in a shift of more diverse and abundant coral assemblages toward the head of the bay.

Short-Term Effects of Thin-Layer Sand Placement on Salt Marsh Grasses: A Marsh Organ Field Experiment.

Salt marshes can build in elevation with sea-level rise through accumulation of inorganic sediment and organic matter, but marshes worldwide are under threat of drowning due to rapid rates of sea-level rise that outpace natural marsh building rates. The application of a thin layer of sediment to the marsh surface (thin-layer placement [TLP]) is a tool to build elevation and decrease flooding stress, but its effects on marsh plants are understudied, especially in New England. In a novel application of a marsh organ experiment (i.e. rows of pots at different elevations), the addition of 10 cm of sand to pots planted with Spartina alterniflora and Spartina patens resulted in fewer stems than controls for S. patens but not S. alterniflora after 2 months. However, total biomass and root mass were not significantly impacted for either species, suggesting plants will fully recover from TLP over longer timescales. Effects of TLP on biomass and stem density did not vary significantly by elevation. Although long-term research is still needed, short-term equivalency in biomass between TLP treatments and controls suggests TLP of 10 cm is a promising strategy to enhance the ability of marshes to build vertically as sea level rises in New England.

Erratum: Publisher Correction: Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare.

[This corrects the article DOI: 10.1038/s41746-020-0235-5.].

Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare.

Storing very large amounts of data and delivering them to researchers in an efficient, verifiable, and compliant manner, is one of the major challenges faced by health care providers and researchers in the life sciences. The electronic health record (EHR) at a hospital or clinic currently functions as a silo, and although EHRs contain rich and abundant information that could be used to understand, improve, and learn from care as part learning health system access to these data is difficult, and the technical, legal, ethical, and social barriers are significant. If we create a microservice ecosystem where data can be accessed through APIs, these challenges become easier to overcome: a service-driven design decouples data from clients. This decoupling provides flexibility: different users can write in their preferred language and use different clients depending on their needs. APIs can be written for iOS apps, web apps, or an R library, and this flexibility highlights the potential ecosystem-building power of APIs. In this article, we use two case studies to illustrate what it means to participate in and contribute to interconnected ecosystems that powers APIs in a healthcare systems.

Applying cumulative effects to strategically advance large-scale ecosystem restoration.

International efforts to restore degraded ecosystems will continue to expand over the coming decades, yet the factors contributing to the effectiveness of long-term restoration across large areas remain largely unexplored. At large scales, outcomes are more complex and synergistic than the additive impacts of individual restoration projects. Here, we propose a cumulative-effects conceptual framework to inform restoration design and implementation and to comprehensively measure ecological outcomes. To evaluate and illustrate this approach, we reviewed long-term restoration in several large coastal and riverine areas across the US: the greater Florida Everglades; Gulf of Mexico coast; lower Columbia River and estuary; Puget Sound; San Francisco Bay and Sacramento-San Joaquin Delta; Missouri River; and northeastern coastal states. Evidence supported eight modes of cumulative effects of interacting restoration projects, which improved outcomes for species and ecosystems at landscape and regional scales. We conclude that cumulative effects, usually measured for ecosystem degradation, are also measurable for ecosystem restoration. The consideration of evidence-based cumulative effects will help managers of large-scale restoration capitalize on positive feedback and reduce countervailing effects.

High resolution carbon stock and soil data for three salt marshes along the northeastern coast of North America.

The data presented here includes a table of soils measurements taken at high resolution depth intervals (5 cm) for three salt marshes, two along the New Brunswick coast of Canada and one on the southern coast of Maine, USA. The data includes a table which includes the bulk density, percent organic matter, percent organic carbon, carbon stock, and rhizome dominance (if identifiable) at 5 cm depth intervals for each soil core. Shapefiles are also included which indicates the GPS position of acquired cores and sites where marsh depth was measured but no material was recovered. These shapefiles also include marsh peat depth and estimates of carbon stock for each point. For further information and interpretation of the included data please see the companion research article titled "The Importance of Geomorphic Context for Estimating the Carbon Stock of Salt Marshes" [1].

Phragmites australis management in the United States: 40 years of methods and outcomes.

Studies on invasive plant management are often short in duration and limited in the methods tested, and lack an adequate description of plant communities that replace the invader following removal. Here we present a comprehensive review of management studies on a single species, in an effort to elucidate future directions for research in invasive plant management. We reviewed the literature on Phragmites management in North America in an effort to synthesize our understanding of management efforts, identify gaps in knowledge and improve the efficacy of management. Additionally, we assessed recent ecological findings concerning Phragmites mechanisms of invasion and integrated these findings into our recommendations for more effective management. Our overall goal is to examine whether or not current management approaches can be improved and whether they promote reestablishment of native plant communities. We found: (i) little information on community-level recovery of vegetation following removal of Phragmites; and (ii) most management approaches focus on the removal of Phragmites from individual stands or groups of stands over a relatively small area. With a few exceptions, recovery studies did not monitor vegetation for substantial durations, thus limiting adequate evaluation of the recovery trajectory. We also found that none of the recovery studies were conducted in a landscape context, even though it is now well documented that land-use patterns on adjacent habitats influence the structure and function of wetlands, including the expansion of Phragmites. We suggest that Phragmites management needs to shift to watershed-scale efforts in coastal regions, or larger management units inland. In addition, management efforts should focus on restoring native plant communities, rather than simply eradicating Phragmites stands. Wetlands and watersheds should be prioritized to identify ecosystems that would benefit most from Phragmites management and those where the negative impact of management would be minimal.

clearScience: Infrastructure for Communicating Data-Intensive Science.

Progress in biomedical research requires effective scientific communication to one's peers and to the public. Current research routinely encompasses large datasets and complex analytic processes, and the constraints of traditional journal formats limit useful transmission of these elements. We are constructing a framework through which authors can not only provide the narrative of what was done, but the primary and derivative data, the source code, the compute environment, and web-accessible virtual machines. This infrastructure allows authors to "hand their machine"- prepopulated with libraries, data, and code-to those interested in reviewing or building off of their work. This project, "clearScience," seeks to provide an integrated system that accommodates the ad hoc nature of discovery in the data-intensive sciences and seamless transitions from working to reporting. We demonstrate that rather than merely describing the science being reported, one can deliver the science itself.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

BACKGROUND: High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. RESULTS: Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. CONCLUSION: The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.

Synthesis and structure-activity relationship of substitutions at the C-1 position of Delta9-tetrahydrocannabinol.

A novel series of Delta9-tetrahydrocannabinol (Delta9-THC) analogues were synthesized to determine their potential as cannabinoid receptor modulators. Chemistry focused on conversion of the phenol of Delta9-THC to other functionality through palladium catalyzed reactions with an intermediate triflate 2. Two analogues with sub 100 nM affinity for the CB1 and CB2 receptors were identified.

Adaptable data management for systems biology investigations.

BACKGROUND: Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ranges from in-house protocols through to high-throughput instrumentation. To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage. RESULTS: The adaptable data management system discussed is designed to support the seamless mining and analysis of biological experiment data that is commonly used in systems biology (e.g. ChIP-chip, gene expression, proteomics, imaging, flow cytometry). We use different content graphs to represent different views upon the data. These views are designed for different roles: equipment specific views are used to gather instrumentation information; data processing oriented views are provided to enable the rapid development of analysis applications; and research project specific views are used to organize information for individual research experiments. This management system allows for both the rapid introduction of new types of information and the evolution of the knowledge it represents. CONCLUSION: Data management is an important aspect of any research enterprise. It is the foundation on which most applications are built, and must be easily extended to serve new functionality for new scientific areas. We have found that adopting a three-tier architecture for data management, built around distributed standardized content repositories, allows us to rapidly develop new applications to support a diverse user community.

Detailed transcriptome atlas of the pancreatic beta cell.

BACKGROUND: Gene expression patterns provide a detailed view of cellular functions. Comparison of profiles in disease vs normal conditions provides insights into the processes underlying disease progression. However, availability and integration of public gene expression datasets remains a major challenge. The aim of the present study was to explore the transcriptome of pancreatic islets and, based on this information, to prepare a comprehensive and open access inventory of insulin-producing beta cell gene expression, the Beta Cell Gene Atlas (BCGA). METHODS: We performed Massively Parallel Signature Sequencing (MPSS) analysis of human pancreatic islet samples and microarray analyses of purified rat beta cells, alpha cells and INS-1 cells, and compared the information with available array data in the literature. RESULTS: MPSS analysis detected around 7600 mRNA transcripts, of which around a third were of low abundance. We identified 2000 and 1400 transcripts that are enriched/depleted in beta cells compared to alpha cells and INS-1 cells, respectively. Microarray analysis identified around 200 transcription factors that are differentially expressed in either beta or alpha cells. We reanalyzed publicly available gene expression data and integrated these results with the new data from this study to build the BCGA. The BCGA contains basal (untreated conditions) gene expression level estimates in beta cells as well as in different cell types in human, rat and mouse pancreas. Hierarchical clustering of expression profile estimates classify cell types based on species while beta cells were clustered together. CONCLUSION: Our gene atlas is a valuable source for detailed information on the gene expression distribution in beta cells and pancreatic islets along with insulin producing cell lines. The BCGA tool, as well as the data and code used to generate the Atlas are available at the T1Dbase website (T1DBase.org).

T1DBase: integration and presentation of complex data for type 1 diabetes research.

T1DBase (http://T1DBase.org) [Smink et al. (2005) Nucleic Acids Res., 33, D544-D549; Burren et al. (2004) Hum. Genomics, 1, 98-109] is a public website and database that supports the type 1 diabetes (T1D) research community. T1DBase provides a consolidated T1D-oriented view of the complex data world that now confronts medical researchers and enables scientists to navigate from information they know to information that is new to them. Overview pages for genes and markers summarize information for these elements. The Gene Dossier summarizes information for a list of genes. GBrowse [Stein et al. (2002) Genome Res., 10, 1599-1610] displays genes and other features in their genomic context, and Cytoscape [Shannon et al. (2003) Genome Res., 13, 2498-2504] shows genes in the context of interacting proteins and genes. The Beta Cell Gene Atlas shows gene expression in beta cells, islets, and related cell types and lines, and the Tissue Expression Viewer shows expression across other tissues. The Microarray Viewer shows expression from more than 20 array experiments. The Beta Cell Gene Expression Bank contains manually curated gene and pathway annotations for genes expressed in beta cells. T1DMart is a query tool for markers and genotypes. PosterPages are 'home pages' about specific topics or datasets. The key challenge, now and in the future, is to provide powerful informatics capabilities to T1D scientists in a form they can use to enhance their research.

T1DBase, a community web-based resource for type 1 diabetes research.

T1DBase (http://T1DBase.org) is a public website and database that supports the type 1 diabetes (T1D) research community. The site is currently focused on the molecular genetics and biology of T1D susceptibility and pathogenesis. It includes the following datasets: annotated genome sequence for human, rat and mouse; information on genetically identified T1D susceptibility regions in human, rat and mouse, and genetic linkage and association studies pertaining to T1D; descriptions of NOD mouse congenic strains; the Beta Cell Gene Expression Bank, which reports expression levels of genes in beta cells under various conditions, and annotations of gene function in beta cells; data on gene expression in a variety of tissues and organs; and biological pathways from KEGG and BioCarta. Tools on the site include the GBrowse genome browser, site-wide context dependent search, Connect-the-Dots for connecting gene and other identifiers from multiple data sources, Cytoscape for visualizing and analyzing biological networks, and the GESTALT workbench for genome annotation. All data are open access and all software is open source.