Tamsiniella labiosa gen. et sp. nov., a new freshwater ascomycete from submerged wood

Investigations into the fungi occurring on wood submerged in freshwater ecosystems have revealed a unique, but characteristic group of fungi. In this paper a new pyrenomycete, Tamsiniella labiosa gen. et sp.nov,, is described and illustrated with light, scanning, and transmission electron micrographs. The germs has remarkable short: stipitate cylindrical asei with an internal refractive apical ring that are apically truncate and have an external thickening. Ascospores are ellipsoidal-fusiform and surrounded by a mucilaginous sheath. At the transmission electron microscope level, the annulus iv of the ascus apical apparatus is differentiated from the inner ascus wail layer and is composed of horizontally oriented, eiectron-dense fibrillar material. A narrow plug is present in the centre of the apical ring. An electron-dense amorphous regk oecurs between the outer ascus wall layer and the annulus part of the apical apparatus. The outer ascus wail layer is lacking a the apex. The ultrastructure of the ascus apex differs from those described in the Lasiosphaeriaceae, Sordariaceae, and Xylariaceae.published_or_final_versio

Eutherians experienced elevated evolutionary rates in the immediate aftermath of the Cretaceous-Palaeogene mass extinction.

The effect of the Cretaceous-Palaeogene (K-Pg) mass extinction on the evolution of many groups, including placental mammals, has been hotly debated. The fossil record suggests a sudden adaptive radiation of placentals immediately after the event, but several recent quantitative analyses have reconstructed no significant increase in either clade origination rates or rates of character evolution in the Palaeocene. Here we use stochastic methods to date a recent phylogenetic analysis of Cretaceous and Palaeocene mammals and show that Placentalia likely originated in the Late Cretaceous, but that most intraordinal diversification occurred during the earliest Palaeocene. This analysis reconstructs fewer than 10 placental mammal lineages crossing the K-Pg boundary. Moreover, we show that rates of morphological evolution in the 5 Myr interval immediately after the K-Pg mass extinction are three times higher than background rates during the Cretaceous. These results suggest that the K-Pg mass extinction had a marked impact on placental mammal diversification, supporting the view that an evolutionary radiation occurred as placental lineages invaded new ecological niches during the Early Palaeocene

Chromosomal-level assembly of the Asian Seabass genome using long sequence reads and multi-layered scaffolding

We report here the ~670 Mb genome assembly of the Asian seabass (Lates calcarifer), a tropical marine teleost. We used long-read sequencing augmented by transcriptomics, optical and genetic mapping along with shared synteny from closely related fish species to derive a chromosome-level assembly with a contig N50 size over 1 Mb and scaffold N50 size over 25 Mb that span ~90% of the genome. The population structure of L. calcarifer species complex was analyzed by re-sequencing 61 individuals representing various regions across the species' native range. SNP analyses identified high levels of genetic diversity and confirmed earlier indications of a population stratification comprising three clades with signs of admixture apparent in the South-East Asian population. The quality of the Asian seabass genome assembly far exceeds that of any other fish species, and will serve as a new standard for fish genomics

D-branes at Toric Singularities: Model Building, Yukawa Couplings and Flavour Physics

We discuss general properties of D-brane model building at toric singularities. Using dimer techniques to obtain the gauge theory from the structure of the singularity, we extract results on the matter sector and superpotential of the corresponding gauge theory. We show that the number of families in toric phases is always less than or equal to three, with a unique exception being the zeroth Hirzebruch surface. With the physical input of three generations we find that the lightest family of quarks is massless and the masses of the other two can be hierarchically separated. We compute the CKM matrix for explicit models in this setting and find the singularities possess sufficient structure to allow for realistic mixing between generations and CP violation.Comment: 55 pages, v2: typos corrected, minor comments adde

Phytochemicals as antibiotic alternatives to promote growth and enhance host health

There are heightened concerns globally on emerging drug-resistant superbugs and the lack of new antibiotics for treating human and animal diseases. For the agricultural industry, there is an urgent need to develop strategies to replace antibiotics for food-producing animals, especially poultry and livestock. The 2nd International Symposium on Alternatives to Antibiotics was held at the World Organization for Animal Health in Paris, France, December 12-15, 2016 to discuss recent scientific developments on strategic antibiotic-free management plans, to evaluate regional differences in policies regarding the reduction of antibiotics in animal agriculture and to develop antibiotic alternatives to combat the global increase in antibiotic resistance. More than 270 participants from academia, government research institutions, regulatory agencies, and private animal industries from >25 different countries came together to discuss recent research and promising novel technologies that could provide alternatives to antibiotics for use in animal health and production; assess challenges associated with their commercialization; and devise actionable strategies to facilitate the development of alternatives to antibiotic growth promoters (AGPs) without hampering animal production. The 3-day meeting consisted of four scientific sessions including vaccines, microbial products, phytochemicals, immune-related products, and innovative drugs, chemicals and enzymes, followed by the last session on regulation and funding. Each session was followed by an expert panel discussion that included industry representatives and session speakers. The session on phytochemicals included talks describing recent research achievements, with examples of successful agricultural use of various phytochemicals as antibiotic alternatives and their mode of action in major agricultural animals (poultry, swine and ruminants). Scientists from industry and academia and government research institutes shared their experience in developing and applying potential antibiotic-alternative phytochemicals commercially to reduce AGPs and to develop a sustainable animal production system in the absence of antibiotics.Fil: Lillehoj, Hyun. United States Department of Agriculture. Agricultural Research Service; ArgentinaFil: Liu, Yanhong. University of California; Estados UnidosFil: Calsamiglia, Sergio. Universitat Autònoma de Barcelona; EspañaFil: Fernandez Miyakawa, Mariano Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Patobiología; ArgentinaFil: Chi, Fang. Amlan International; Estados UnidosFil: Cravens, Ron L.. Amlan International; Estados UnidosFil: Oh, Sungtaek. United States Department of Agriculture. Agricultural Research Service; ArgentinaFil: Gay, Cyril G.. United States Department of Agriculture. Agricultural Research Service; Argentin

Influence of Different Plant Species on Methane Emissions from Soil in a Restored Swiss Wetland

Plants are a major factor influencing methane emissions from wetlands, along with environmental parameters such as water table, temperature, pH, nutrients and soil carbon substrate. We conducted a field experiment to study how different plant species influence methane emissions from a wetland in Switzerland. The top 0.5 m of soil at this site had been removed five years earlier, leaving a substrate with very low methanogenic activity. We found a sixfold difference among plant species in their effect on methane emission rates: Molinia caerulea and Lysimachia vulgaris caused low emission rates, whereas Senecio paludosus, Carex flava, Juncus effusus and Typha latifolia caused relatively high rates. Centaurea jacea, Iris sibirica, and Carex davalliana caused intermediate rates. However, we found no effect of either plant biomass or plant functional groups – based on life form or productivity of the habitat – upon methane emission. Emissions were much lower than those usually reported in temperate wetlands, which we attribute to reduced concentrations of labile carbon following topsoil removal. Thus, unlike most wetland sites, methane production in this site was probably fuelled chiefly by root exudation from living plants and from root decay. We conclude that in most wetlands, where concentrations of labile carbon are much higher, these sources account for only a small proportion of the methane emitted. Our study confirms that plant species composition does influence methane emission from wetlands, and should be considered when developing measures to mitigate the greenhouse gas emissions

Translocation-coupled DNA cleavage by the Type ISP restriction-modification enzymes

Endonucleolytic double-strand DNA break production requires separate strand cleavage events. Although catalytic mechanisms for simple dimeric endonucleases are available, there are many complex nuclease machines which are poorly understood in comparison. Here we studied the single polypeptide Type ISP restriction-modification (RM) enzymes, which cleave random DNA between distant target sites when two enzymes collide following convergent ATP-driven translocation. We report the 2.7 Angstroms resolution X-ray crystal structure of a Type ISP enzyme-DNA complex, revealing that both the helicase-like ATPase and nuclease are unexpectedly located upstream of the direction of translocation, inconsistent with simple nuclease domain-dimerization. Using single-molecule and biochemical techniques, we demonstrate that each ATPase remodels its DNA-protein complex and translocates along DNA without looping it, leading to a collision complex where the nuclease domains are distal. Sequencing of single cleavage events suggests a previously undescribed endonuclease model, where multiple, stochastic strand nicking events combine to produce DNA scission

Write, draw, show, and tell: a child-centred dual methodology to explore perceptions of out-of-school physical activity

Background Research to increase children’s physical activity and inform intervention design has, to date, largely underrepresented children’s voices. Further, research has been limited to singular qualitative methods that overlook children’s varied linguistic ability and interaction preference. The aim of this study was to use a novel combination of qualitative techniques to explore children’s current views, experiences and perceptions of out-of-school physical activity as well as offering formative opinion about future intervention design. Methods Write, draw, show and tell (WDST) groups were conducted with 35 children aged 10–11 years from 7 primary schools. Data were analysed through a deductive and inductive process, firstly using the Youth Physical Activity Promotion Model as a thematic framework, and then inductively to enable emergent themes to be further explored. Pen profiles were constructed representing key emergent themes. Results The WDST combination of qualitative techniques generated complimentary interconnected data which both confirmed and uncovered new insights into factors relevant to children’s out-of-school physical activity. Physical activity was most frequently associated with organised sports. Fun, enjoyment, competence, and physical activity provision were all important predictors of children’s out-of-school physical activity. Paradoxically, parents served as both significant enablers (i.e. encouragement) and barriers (i.e. restricting participation) to physical activity participation. Some of these key findings would have otherwise remained hidden when compared to more traditional singular methods based approaches. Conclusions Parents are in a unique position to promote health promoting behaviours serving as role models, physical activity gatekeepers and choice architects. Given the strong socialising effect parents have on children’s physical activity, family-based physical activity intervention may offer a promising alternative compared to traditional school-based approaches. Parents' qualitative input is important to supplement children’s voices and inform future family-based intervention design. The WDST method developed here is an inclusive, interactive and child-centred methodology which facilitates the exploration of a wide range of topics and enhances data credibility

Gradual phyletic evolution at the generic level in early Eocene omomyid primates

Analysis of dental morphology in over 600 stratigraphically controlled specimens of tarsier-like primates from early Eocene strata in Bighorn Basin, Wyoming, provides important new data for understanding the tempo and mode of evolution in primates