Draft Genome Sequence of Rhodococcus sp. Strain ATCC 49988, a Quinoline-Degrading Bacterium.

We report here the 4.9-Mb genome sequence of a quinoline-degrading bacterium, Rhodococcus sp. strain ATCC 49988. The draft genome data will enable the identification of genes and future genetic modification to enhance traits relevant to heteroaromatic compound degradation

Kandyan home gardens: Faunal repositories in Sri Lanka.

Kandyan home gardens are one of the major designs of sustainable land use systems that have evolved over hundreds of years incorporating high biodiversity and providing a diverse and stable supply of socio-economic products and service benefits to householders in Sri Lanka. A study was carried out in three home gardens in the Kandy district from May to December 2009 with the objectives of (a) identifying spatial distribution of terrestrial vertebrates in different vegetation strata, (b) their diurnal and seasonal variations, (c) plant-animal interactions, (d) nesting habits and (e) diet composition. A total of 93 terrestrial vertebrate species including seven amphibians, 23 mammals, 43 birds, and 20 reptiles were recorded. These comprised 14 endemic species, 71 native, four introduced mammals and two migrant birds. Terrestrial vertebrate assemblages were similar in Home garden 1 and 3. According to the fully-nested ANOVA, statistically significant differences were found in the composition of terrestrial vertebrates and the home gardens (P=0.005<0.05), and their vegetation strata (P=0.005<0.05). However, no statistically significant differences were observed between richness of terrestrial vertebrates and the monsoonal periods (P=0.966>0.05), as well as the time of the day (P=0.775>0.05). A positive relationship was obtained between canopy cover and number of bird nests in all home gardens (rs = +1, α = 0.05).Commensalism was the most frequently recorded relationship in all three home gardens. Overall, the diversity of animals and their interactions were different in the three Kandyan Home Gardens studied. Preventing the degradation of home gardens can be considered as a means of conserving biodiversity. There is scope to develop the Kandyan Home Garden system as an important strategy to conserve biodiversity outside the natural and protected area systems

Bird communities and feeding guilds in Monaragala, an isolated hill in the eastern intermediate zone of Sri Lanka

The bird communities and foraging guilds were studied in the entire forest of Monaragala hill, by recording species and their abundances, in 33 plots (each 100x20 m), in four transects laid along its altitudinal gradient. Bird calls and sightings were noted for 30 minutes between 7.00-9.30 am, twice each month from 2004-2008.The communities were determined, by cluster and ordination analyses of data in all plots. For each community, relative abundance (RA) and frequency (RF) were calculated. Species were assigned to bird guilds based on their habitats, main food types and feeding strategies, from published informationWithin and outside the plots sampled, 112 bird species (23% of Sri Lanka‟s avifauna, including eight endemics) in 84 genera, 44 families and 13 orders, were recorded. Three communities were identified: i. a low/mid-elevation disturbed forest community (LDFC), inhabited by 40 species (including seven endemics). The Crimson-Fronted Barbet, Black Crested Bulbul and Tickell‟s Blue Flycatcher co-dominated it. ii. a ridge/upper-elevation undisturbed forest community (RUFC) of 45 species that included eight endemics, nine restricted species, the wet zone Sri Lanka Yellow Fronted Barbet and Sri Lanka Wood Pigeon. The Black Bulbul and Sri Lanka Yellow Fronted Barbet were its dominants. Thirty three species were common to both forest communities. iii. a grassland community, with only 10 non-endemic species, dominated by the Crested Tree Swift and Indian Swiftlet. Three grassland species were also seen in the forest communities.In each forest community ten bird guilds were present. The arboreal frugivore and gleaning insectivore guilds ranked highest in them, followed by the hawking/hovering insectivore guild in the LDFC, and the omnivore gleaning guild in the RUFC. The grassland community had only three guilds. Based on RA the sweeping insectivore guild and on RF the aerial carnivore and the sweeping insectivore guilds were co-dominant. The arboreal granivore guild was restricted to the grasslandThe study revealed that this intermediate zone, 43 km2 isolated hill (1,100 m amsl) harbors a rich avifauna, including some typical wet zone species, and rich populations of the rare Sri Lanka Spur fowl and the Sri Lanka Wood pigeon, justifying its high conservation value

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase

Microbial genome annotation is the process of identifying structural and functional elements in DNA sequences and subsequently attaching biological information to those elements. DRAM is a tool developed to annotate bacterial, archaeal, and viral genomes derived from pure cultures or metagenomes. DRAM goes beyond traditional annotation tools by distilling multiple gene annotations to genome level summaries of functional potential. Despite these benefits, a downside of DRAM is the requirement of large computational resources, which limits its accessibility. Further, it did not integrate with downstream metabolic modeling tools that require genome annotation. To alleviate these constraints, DRAM and the viral counterpart, DRAM-v, are now available and integrated with the freely accessible KBase cyberinfrastructure. With kb_DRAM users can generate DRAM annotations and functional summaries from microbial or viral genomes in a point-and-click interface, as well as generate genome-scale metabolic models from DRAM annotations.Availability and implementationFor kb_DRAM users, the kb_DRAM apps on KBase can be found in the catalog at https://narrative.kbase.us/#catalog/modules/kb_DRAM. For kb_DRAM users, a tutorial workflow with all documentation is available at https://narrative.kbase.us/narrative/129480. For kb_DRAM developers, software is available at https://github.com/shafferm/kb_DRAM

Dry Markets and Superreplication Bounds of American Derivatives

This paper studies the impact of dry markets for underlying assets on the pricing of American derivatives, using a discrete time framework. Dry markets are characterized by the possibility of non-existence of trading at certain dates. Such non-existence may be deterministic or probabilistic. Using superreplicating strategies, we derive expectation representations for the range of arbitrage-free values of the dervatives. In the probabilistic case, if we consider an enlarged filtration induced by the price process and the market existence process, ordinary stopping times are required. If not, randomized stopping times are required. Several comparisons of the ranges obtained with the two market restrictions are performed. Finally, we conclude that arbitrage arguments are not enough to define the optimal exercise policy.N/

Imaging Mass Spectrometry: Hype or Hope?

Imaging mass spectrometry is currently receiving a significant amount of attention in the mass spectrometric community. It offers the potential of direct examination of biomolecular patterns from cells and tissue. This makes it a seemingly ideal tool for biomedical diagnostics and molecular histology. It is able to generate beautiful molecular images from a large variety of surfaces, ranging from cancer tissue sections to polished cross sections from old-master paintings. What are the parameters that define and control the implications, challenges, opportunities, and (im)possibilities associated with the application of imaging MS to biomedical tissue studies. Is this just another technological hype or does it really offer the hope to gain new insights in molecular processes in living tissue? In this critical insight this question is addressed through the discussion of a number of aspects of MS imaging technology and sample preparation that strongly determine the outcome of imaging MS experiments

Lymphangiogenesis Is Required for Pancreatic Islet Inflammation and Diabetes

Lymphangiogenesis is a common phenomenon observed during inflammation and engraftment of transplants, but its precise role in the immune response and underlying mechanisms of regulation remain poorly defined. Here we showed that in response to injury and autoimmunity, lymphangiogenesis occurred around islets and played a key role in the islet inflammation in mice. Vascular endothelial growth factors receptor 3 (VEGFR3) is specifically involved in lymphangiogenesis, and blockade of VEGFR3 potently inhibited lymphangiogenesis in both islets and the draining LN during multiple low-dose streptozotocin (MLDS) induced autoimmune insulitis, which resulted in less T cell infiltration, preservation of islets and prevention of the onset of diabetes. In addition to their well-known conduit function, lymphatic endothelial cells (LEC) also produced chemokines in response to inflammation. These LEC attracted two distinct CX3CR1hi and LYVE-1+ macrophage subsets to the inflamed islets and CX3CR1hi cells were influenced by LEC to differentiate into LYVE-1+ cells closely associated with lymphatic vessels. These observations indicate a linkage among lymphangiogenesis and myeloid cell inflammation during insulitis. Thus, inhibition of lymphangiogenesis holds potential for treating insulitis and autoimmune diabetes

A genomic catalog of Earth’s microbiomes

The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology and evolution of environmental and host-associated microbiomes. Here we applied this approach to >10,000 metagenomes collected from diverse habitats covering all of Earth’s continents and oceans, including metagenomes from human and animal hosts, engineered environments, and natural and agricultural soils, to capture extant microbial, metabolic and functional potential. This comprehensive catalog includes 52,515 metagenome-assembled genomes representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. The catalog expands the known phylogenetic diversity of bacteria and archaea by 44% and is broadly available for streamlined comparative analyses, interactive exploration, metabolic modeling and bulk download. We demonstrate the utility of this collection for understanding secondary-metabolite biosynthetic potential and for resolving thousands of new host linkages to uncultivated viruses. This resource underscores the value of genome-centric approaches for revealing genomic properties of uncultivated microorganisms that affect ecosystem processes

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits