Archaeal abundance in post-mortem ruminal digesta may help predict methane emissions from beef cattle

The Rowett Institute of Nutrition and Health and SRUC are funded by the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government. The project was supported by DEFRA and DA funded Agricultural Greenhouse Gas Inventory Research Platform. Our thanks are due to the excellent support staff at the SRUC Beef Research Centre, Edinburgh, also to Graham Horgan of BioSS, Aberdeen, for conducting multivariate analysis.Peer reviewedPublisher PD

Synthesis and Evaluation of 11C-Labeled Triazolones as Probes for Imaging Fatty Acid Synthase Expression by Positron Emission Tomography

Cancer cells require lipids to fulfill energetic, proliferative, and signaling requirements. Even though these cells can take up exogenous fatty acids, the majority exhibit a dependency on de novo fatty acid synthesis. Fatty acid synthase (FASN) is the rate-limiting enzyme in this process. Expression and activity of FASN is elevated in multiple cancers, where it correlates with disease progression and poor prognosis. These observations have sparked interest in developing methods of detecting FASN expression in vivo. One promising approach is the imaging of radiolabeled molecular probes targeting FASN by positron emission tomography (PET). However, although [11C]acetate uptake by prostate cancer cells correlates with FASN expression, no FASN-specific PET probes currently exist. Our aim was to synthesize and evaluate a series of small molecule triazolones based on GSK2194069, an FASN inhibitor with IC50 = 7.7 ± 4.1 nM, for PET imaging of FASN expression. These triazolones were labeled with carbon-11 in good yield and excellent radiochemical purity, and binding to FASN-positive LNCaP cells was significantly higher than FASN-negative PC3 cells. Despite these promising characteristics, however, these molecules exhibited poor in vivo pharmacokinetics and were predominantly retained in lymph nodes and the hepatobiliary system. Future studies will seek to identify structural modifications that improve tumor targeting while maintaining the excretion profile of these first-generation 11C-methyltriazolones

Ribose 2′-O-methylation provides a molecular signature for the distinction of self and non-self mRNA dependent on the RNA sensor Mda5

The 5'-cap-structures of higher eukaryote mRNAs are ribose 2'-O-methylated. Likewise, a number of viruses replicating in the cytoplasm of eukayotes have evolved 2'-O-methyltransferases to modify autonomously their mRNAs. However, a defined biological role of mRNA 2'-O-methylation remains elusive. Here we show that viral mRNA 2'-O-methylation is critically involved in subversion of type-I-interferon (IFN-I) induction. We demonstrate that human and murine coronavirus 2'-O-methyltransferase mutants induce increased IFN-I expression, and are highly IFN-I sensitive. Importantly, IFN-I induction by 2'-O-methyltransferase-deficient viruses is dependent on the cytoplasmic RNA sensor melanoma differentiation-associated gene 5 (MDA5). This link between MDA5-mediated sensing of viral RNA and mRNA 2'-O-methylation suggests that RNA modifications, such as 2'-O-methylation, provide a molecular signature for the discrimination of self and non-self mRNA

HIV Infection Linked to Injection Use of Oxymorphone in Indiana, 2014-2015

BACKGROUND: In January 2015, a total of 11 new diagnoses of human immunodeficiency virus (HIV) infection were reported in a small community in Indiana. We investigated the extent and cause of the outbreak and implemented control measures. METHODS: We identified an outbreak-related case as laboratory-confirmed HIV infection newly diagnosed after October 1, 2014, in a person who either resided in Scott County, Indiana, or was named by another case patient as a syringe-sharing or sexual partner. HIV polymerase (pol) sequences from case patients were phylogenetically analyzed, and potential risk factors associated with HIV infection were ascertained. RESULTS: From November 18, 2014, to November 1, 2015, HIV infection was diagnosed in 181 case patients. Most of these patients (87.8%) reported having injected the extended-release formulation of the prescription opioid oxymorphone, and 92.3% were coinfected with hepatitis C virus. Among 159 case patients who had an HIV type 1 pol gene sequence, 157 (98.7%) had sequences that were highly related, as determined by phylogenetic analyses. Contact tracing investigations led to the identification of 536 persons who were named as contacts of case patients; 468 of these contacts (87.3%) were located, assessed for risk, tested for HIV, and, if infected, linked to care. The number of times a contact was named as a syringe-sharing partner by a case patient was significantly associated with the risk of HIV infection (adjusted risk ratio for each time named, 1.9; P<0.001). In response to this outbreak, a public health emergency was declared on March 26, 2015, and a syringe-service program in Indiana was established for the first time. CONCLUSIONS: Injection-drug use of extended-release oxymorphone within a network of persons who inject drugs in Indiana led to the introduction and rapid transmission of HIV. (Funded by the state government of Indiana and others.)

Gene content evolution in the arthropods

Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity

The genomes of two key bumblebee species with primitive eusocial organization

Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome sequences of Bombus terrestris and Bombus impatiens, two ecologically dominant bumblebees and widely utilized study species. Comparing these new genomes to those of the highly eusocial honeybee Apis mellifera and other Hymenoptera, we identify deeply conserved similarities, as well as novelties key to the biology of these organisms. Some honeybee genome features thought to underpin advanced eusociality are also present in bumblebees, indicating an earlier evolution in the bee lineage. Xenobiotic detoxification and immune genes are similarly depauperate in bumblebees and honeybees, and multiple categories of genes linked to social organization, including development and behavior, show high conservation. Key differences identified include a bias in bumblebee chemoreception towards gustation from olfaction, and striking differences in microRNAs, potentially responsible for gene regulation underlying social and other traits. Conclusions: These two bumblebee genomes provide a foundation for post-genomic research on these key pollinators and insect societies. Overall, gene repertoires suggest that the route to advanced eusociality in bees was mediated by many small changes in many genes and processes, and not by notable expansion or depauperation

A Synoptical Classification of the Bivalvia (Mollusca)

The following classification summarizes the suprageneric taxono-my of the Bivalvia for the upcoming revision of the Bivalvia volumes of the Treatise on Invertebrate Paleontology, Part N. The development of this classification began with Carter (1990a), Campbell, Hoeks-tra, and Carter (1995, 1998), Campbell (2000, 2003), and Carter, Campbell, and Campbell (2000, 2006), who, with assistance from the United States National Science Foundation, conducted large-scale morphological phylogenetic analyses of mostly Paleozoic bivalves, as well as molecular phylogenetic analyses of living bivalves. Dur-ing the past several years, their initial phylogenetic framework has been revised and greatly expanded through collaboration with many students of bivalve biology and paleontology, many of whom are coauthors. During this process, all available sources of phylogenetic information, including molecular, anatomical, shell morphological, shell microstructural, bio- and paleobiogeographic as well as strati-graphic, have been integrated into the classification. The more recent sources of phylogenetic information include, but are not limited to, Carter (1990a), Malchus (1990), J. Schneider (1995, 1998a, 1998b, 2002), T. Waller (1998), Hautmann (1999, 2001a, 2001b), Giribet and Wheeler (2002), Giribet and Distel (2003), Dreyer, Steiner, and Harper (2003), Matsumoto (2003), Harper, Dreyer, and Steiner (2006), Kappner and Bieler (2006), Mikkelsen and others (2006), Neulinger and others (2006), Taylor and Glover (2006), Kříž (2007), B. Morton (2007), Taylor, Williams, and Glover (2007), Taylor and others (2007), Giribet (2008), and Kirkendale (2009). This work has also benefited from the nomenclator of bivalve families by Bouchet and Rocroi (2010) and its accompanying classification by Bieler, Carter, and Coan (2010).This classification strives to indicate the most likely phylogenetic position for each taxon. Uncertainty is indicated by a question mark before the name of the taxon. Many of the higher taxa continue to undergo major taxonomic revision. This is especially true for the superfamilies Sphaerioidea and Veneroidea, and the orders Pectinida and Unionida. Because of this state of flux, some parts of the clas-sification represent a compromise between opposing points of view. Placement of the Trigonioidoidea is especially problematic. This Mesozoic superfamily has traditionally been placed in the order Unionida, as a possible derivative of the superfamily Unionoidea (see Cox, 1952; Sha, 1992, 1993; Gu, 1998; Guo, 1998; Bieler, Carter, & Coan, 2010). However, Chen Jin-hua (2009) summarized evi-dence that Trigonioidoidea was derived instead from the superfamily Trigonioidea. Arguments for these alternatives appear equally strong, so we presently list the Trigonioidoidea, with question, under both the Trigoniida and Unionida, with the contents of the superfamily indicated under the Trigoniida.Fil: Carter, Joseph G.. University of North Carolina; Estados UnidosFil: Altaba, Cristian R.. Universidad de las Islas Baleares; EspañaFil: Anderson, Laurie C.. South Dakota School of Mines and Technology; Estados UnidosFil: Araujo, Rafael. Consejo Superior de Investigaciones Cientificas. Museo Nacional de Ciencias Naturales; EspañaFil: Biakov, Alexander S.. Russian Academy of Sciences; RusiaFil: Bogan, Arthur E.. North Carolina State Museum of Natural Sciences; Estados UnidosFil: Campbell, David. Paleontological Research Institution; Estados UnidosFil: Campbell, Matthew. Charleston Southern University; Estados UnidosFil: Chen, Jin Hua. Chinese Academy of Sciences. Nanjing Institute of Geology and Palaeontology; República de ChinaFil: Cope, John C. W.. National Museum of Wales. Department of Geology; Reino UnidoFil: Delvene, Graciela. Instituto Geológico y Minero de España; EspañaFil: Dijkstra, Henk H.. Netherlands Centre for Biodiversity; Países BajosFil: Fang, Zong Jie. Chinese Academy of Sciences; República de ChinaFil: Gardner, Ronald N.. No especifica;Fil: Gavrilova, Vera A.. Russian Geological Research Institute; RusiaFil: Goncharova, Irina A.. Russian Academy of Sciences; RusiaFil: Harries, Peter J.. University of South Florida; Estados UnidosFil: Hartman, Joseph H.. University of North Dakota; Estados UnidosFil: Hautmann, Michael. Paläontologisches Institut und Museum; SuizaFil: Hoeh, Walter R.. Kent State University; Estados UnidosFil: Hylleberg, Jorgen. Institute of Biology; DinamarcaFil: Jiang, Bao Yu. Nanjing University; República de ChinaFil: Johnston, Paul. Mount Royal University; CanadáFil: Kirkendale, Lisa. University Of Wollongong; AustraliaFil: Kleemann, Karl. Universidad de Viena; AustriaFil: Koppka, Jens. Office de la Culture. Section d’Archéologie et Paléontologie; SuizaFil: Kříž, Jiří. Czech Geological Survey. Department of Sedimentary Formations. Lower Palaeozoic Section; República ChecaFil: Machado, Deusana. Universidade Federal do Rio de Janeiro; BrasilFil: Malchus, Nikolaus. Institut Català de Paleontologia; EspañaFil: Márquez Aliaga, Ana. Universidad de Valencia; EspañaFil: Masse, Jean Pierre. Universite de Provence; FranciaFil: McRoberts, Christopher A.. State University of New York at Cortland. Department of Geology; Estados UnidosFil: Middelfart, Peter U.. Australian Museum; AustraliaFil: Mitchell, Simon. The University of the West Indies at Mona; JamaicaFil: Nevesskaja, Lidiya A.. Russian Academy of Sciences; RusiaFil: Özer, Sacit. Dokuz Eylül University; TurquíaFil: Pojeta, John Jr.. National Museum of Natural History; Estados UnidosFil: Polubotko, Inga V.. Russian Geological Research Institute; RusiaFil: Pons, Jose Maria. Universitat Autònoma de Barcelona; EspañaFil: Popov, Sergey. Russian Academy of Sciences; RusiaFil: Sanchez, Teresa Maria. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de Córdoba; ArgentinaFil: Sartori, André F.. Field Museum of National History; Estados UnidosFil: Scott, Robert W.. Precision Stratigraphy Associates; Estados UnidosFil: Sey, Irina I.. Russian Geological Research Institute; RusiaFil: Signorelli, Javier Hernan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico; ArgentinaFil: Silantiev, Vladimir V.. Kazan Federal University; RusiaFil: Skelton, Peter W.. Open University. Department of Earth and Environmental Sciences; Reino UnidoFil: Steuber, Thomas. The Petroleum Institute; Emiratos Arabes UnidosFil: Waterhouse, J. Bruce. No especifica;Fil: Wingard, G. Lynn. United States Geological Survey; Estados UnidosFil: Yancey, Thomas. Texas A&M University; Estados Unido

Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest

Background Halyomorpha halys (Stål), the brown marmorated stink bug, is a highly invasive insect species due in part to its exceptionally high levels of polyphagy. This species is also a nuisance due to overwintering in human-made structures. It has caused significant agricultural losses in recent years along the Atlantic seaboard of North America and in continental Europe. Genomic resources will assist with determining the molecular basis for this species’ feeding and habitat traits, defining potential targets for pest management strategies. Results Analysis of the 1.15-Gb draft genome assembly has identified a wide variety of genetic elements underpinning the biological characteristics of this formidable pest species, encompassing the roles of sensory functions, digestion, immunity, detoxification and development, all of which likely support H. halys’ capacity for invasiveness. Many of the genes identified herein have potential for biomolecular pesticide applications. Conclusions Availability of the H. halys genome sequence will be useful for the development of environmentally friendly biomolecular pesticides to be applied in concert with more traditional, synthetic chemical-based controls