The Great Lakes Hydrography Dataset: Consistent, Binational Watersheds for the Laurentian Great Lakes Basin

Ecosystem‐based management of the Laurentian Great Lakes, which spans both the United States and Canada, is hampered by the lack of consistent binational watersheds for the entire Basin. Using comparable data sources and consistent methods, we developed spatially equivalent watershed boundaries for the binational extent of the Basin to create the Great Lakes Hydrography Dataset (GLHD). The GLHD consists of 5,589 watersheds for the entire Basin, covering a total area of approximately 547,967 km2, or about twice the 247,003 km2 surface water area of the Great Lakes. The GLHD improves upon existing watershed efforts by delineating watersheds for the entire Basin using consistent methods; enhancing the precision of watershed delineation using recently developed flow direction grids that have been hydrologically enforced and vetted by provincial and federal water resource agencies; and increasing the accuracy of watershed boundaries by enforcing embayments, delineating watersheds on islands, and delineating watersheds for all tributaries draining to connecting channels. In addition, the GLHD is packaged in a publically available geodatabase that includes synthetic stream networks, reach catchments, watershed boundaries, a broad set of attribute data for each tributary, and metadata documenting methodology. The GLHD provides a common set of watersheds and associated hydrography data for the Basin that will enhance binational efforts to protect and restore the Great Lakes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134077/1/jawr12435_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134077/2/jawr12435.pd

The Great Lakes Hydrography Dataset: Consistent, Binational Watersheds for the Laurentian Great Lakes Basin

Ecosystem‐based management of the Laurentian Great Lakes, which spans both the United States and Canada, is hampered by the lack of consistent binational watersheds for the entire Basin. Using comparable data sources and consistent methods, we developed spatially equivalent watershed boundaries for the binational extent of the Basin to create the Great Lakes Hydrography Dataset (GLHD). The GLHD consists of 5,589 watersheds for the entire Basin, covering a total area of approximately 547,967 km2, or about twice the 247,003 km2 surface water area of the Great Lakes. The GLHD improves upon existing watershed efforts by delineating watersheds for the entire Basin using consistent methods; enhancing the precision of watershed delineation using recently developed flow direction grids that have been hydrologically enforced and vetted by provincial and federal water resource agencies; and increasing the accuracy of watershed boundaries by enforcing embayments, delineating watersheds on islands, and delineating watersheds for all tributaries draining to connecting channels. In addition, the GLHD is packaged in a publically available geodatabase that includes synthetic stream networks, reach catchments, watershed boundaries, a broad set of attribute data for each tributary, and metadata documenting methodology. The GLHD provides a common set of watersheds and associated hydrography data for the Basin that will enhance binational efforts to protect and restore the Great Lakes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134077/1/jawr12435_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134077/2/jawr12435.pd

Biodiversity inventories in high gear:DNA barcoding facilitates a rapid biotic survey of a temperate nature reserve

Abstract Background: Comprehensive biotic surveys, or ‘all taxon biodiversity inventories’ (ATBI), have traditionally been limited in scale or scope due to the complications surrounding specimen sorting and species identification. To circumvent these issues, several ATBI projects have successfully integrated DNA barcoding into their identification procedures and witnessed acceleration in their surveys and subsequent increase in project scope and scale. The Biodiversity Institute of Ontario partnered with the rare Charitable Research Reserve and delegates of the 6th International Barcode of Life Conference to complete its own rapid, barcode-assisted ATBI of an established land trust in Cambridge, Ontario, Canada. New information: The existing species inventory for the rare Charitable Research Reserve was rapidly expanded by integrating a DNA barcoding workflow with two surveying strategies — a comprehensive sampling scheme over four months, followed by a one-day bioblitz involving international taxonomic experts. The two surveys resulted in 25,287 and 3,502 specimens barcoded, respectively, as well as 127 human observations. This barcoded material, all vouchered at the Biodiversity Institute of Ontario collection, covers 14 phyla, 29 classes, 117 orders, and 531 families of animals, plants, fungi, and lichens. Overall, the ATBI documented 1,102 new species records for the nature reserve, expanding the existing long-term inventory by 49%. In addition, 2,793 distinct Barcode Index Numbers (BINs) were assigned to genus or higher level taxonomy, and represent additional species that will be added once their taxonomy is resolved. For the 3,502 specimens, the collection, sequence analysis, taxonomic assignment, data release and manuscript submission by 100+ co-authors all occurred in less than one week. This demonstrates the speed at which barcode-assisted inventories can be completed and the utility that barcoding provides in minimizing and guiding valuable taxonomic specialist time. The final product is more than a comprehensive biotic inventory — it is also a rich dataset of fine-scale occurrence and sequence data, all archived and cross-linked in the major biodiversity data repositories. This model of rapid generation and dissemination of essential biodiversity data could be followed to conduct regional assessments of biodiversity status and change, and potentially be employed for evaluating progress towards the Aichi Targets of the Strategic Plan for Biodiversity 2011–2020

Income deprivation and groin wound surgical site infection: cross-sectional analysis from the groin wound infection after vascular exposure multicenter cohort study

Background: Living in deprived areas is associated with poorer outcomes after certain vascular procedures and surgical site infection in other specialties. Our primary objective was to determine whether living in more income-deprived areas was associated with groin wound surgical site infection after arterial intervention. Secondary objectives were to determine whether living in more income-deprived areas was associated with mortality and clinical consequences of surgical site infection. Methods: Postal code data for patients from the United Kingdom who were included in the Groin Wound Infection after Vascular Exposure (GIVE) multicenter cohort study was used to determine income deprivation, based on index of multiple deprivation (IMD) data. Patients were divided into three IMD groups for descriptive analysis. Income deprivation score was integrated into the final multivariable model for predicting surgical site infection. Results: Only patients from England had sufficient postal code data, analysis included 772 groin incisions (624 patients from 22 centers). Surgical site infection occurred in 9.7% incisions (10.3% of patients). Surgical site infection was equivalent between income deprivation tertiles (tertile 1 = 9.5%; tertile 2 = 10.3%; tertile 3 = 8.6%; p = 0.828) as were the clinical consequences of surgical site infection and mortality. Income deprivation was not associated with surgical site infection in multivariable regression analysis (odds ratio [OR], 0.574; 95% confidence interval [CI], 0.038–8.747; p = 0.689). Median age at time of procedure was lower for patients living in more income-deprived areas (tertile 1 = 68 years; tertile 2 = 72 years; tertile 3 = 74 years; p < 0.001). Conclusions: We found no association between living in an income-deprived area and groin wound surgical site infection, clinical consequences of surgical site infection and mortality after arterial intervention. Patients living in more income-deprived areas presented for operative intervention at a younger age, with similar rates of comorbidities to patients living in less income-deprived areas. Groin wound surgical site infection (SSI) after arterial surgery is common [1], and research into reducing SSIs in vascular surgery is recognized as a priority by both clinicians and patient/caregiver representatives [2]. Despite the substantial potential morbidity and mortality of these SSIs [3,4], the available evidence relating to contributory factors is largely historic or reliant on retrospective data [5–7]. Further research on the epidemiology of SSI in this patient group is needed to allow better risk stratification, improve pre-operative discussions of risk with patients, and to guide targeted SSI prevention strategies that often include expensive prophylactic interventions [8]. However, little is currently known about the impact of socioeconomic characteristics on groin wound SSIs in this population. Socioeconomic deprivation is linked to health [9], and lifestyle-influenced cardiovascular diseases are more prevalent in more deprived areas [10]. Higher rates of unhealthy lifestyles (smoking, poor diet, and lack of physical exercise) in deprived areas are postulated to cause higher rates of cardiovascular risk increasing comorbidities, such as obesity and hyperlipidemia [10–12]. Several cardiovascular risk factors (e.g., smoking, body mass index, and diabetes mellitus), and peripheral arterial disease itself, are well recognized risk factors for SSI [13–16]. The association between socioeconomic deprivation and SSIs has previously been demonstrated in orthopedic surgery, cardiac surgery, and general surgery [17–19]. It is currently unknown whether living in an income-deprived area is associated with groin wound SSIs after arterial intervention. It was recently demonstrated in a large registry study in the United Kingdom, that outcomes following endovascular intervention for occlusive peripheral arterial disease were worse for patients living in deprived areas [20]. To the best of our knowledge, this aspect of outcomes after arterial intervention through a groin incision has not been investigated. Furthermore, studies demonstrating higher prevalence of cardiovascular disease risk factors in more deprived areas are now mostly historic and have not specifically investigated those presenting for arterial intervention through a groin incision for demographic differences in relation to deprivation [9–12]. Updated, prospective evidence is required to determine whether health inequalities persist for such patients today. Our primary objective was to determine whether residing in a more income-deprived area was associated with a higher risk of groin wound SSI after arterial intervention, by analyzing a subset of patients enrolled in the Groin wound Infection after Vascular Exposure (GIVE) multicenter cohort study [1,21]. Secondary objectives were to determine whether living in more income-deprived areas was associated with 30-day mortality and the clinical sequelae of SSI, and whether patients living in more income-deprived areas differed in terms of demographics and comorbidities compared with patients from less income-deprived areas

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists