A Spatial and temporal analysis of microbial communities in Great Boiling Spring, Nevada, U.S.A.

Great Boiling Spring (GBS) is a large, circumneutral, long residence time geothermal spring in the US Great Basin. Twelve samples were taken from four different sediment sites and the planktonic community in the bulk water of GBS on up to four different dates. Microbial community composition and diversity was assessed by using a barcoded, improved universal primer set targeting the V8 portion of the 16S rRNA gene and PCR. Over 200,000 products were sequenced using the Roche 454 GS FLX Titanium System. Sediment and planktonic microbial communities were distinct with very little overlap, regardless of the sampling location or temperature. Planktonic communities were extremely uneven and were dominated by a single phylotype related to Thermocrinis in the Aquificales. Benthic microbial communities grouped according to temperature and sampling location. Two locations, Site A (80-87°C) and Site B (79°C), were predominantly composed of the crenarchaeal class Thermoprotei, the novel archaeal lineage pSL4, and the novel bacterial lineage GAL35. Populations of the ammonia oxidizing archaeon “Candidatus Nitrosocaldus yellowstonii” comprised 5-15% of all samples when Site A was cooler than normal (80°C) and at cooler sites throughout the spring (76-62°C). At cooler temperature sites (76-62°C), the phylum-level diversity and evenness were significantly higher, and bacteria made up a significantly higher percentage of the population. To our knowledge, this is the most detailed study of the spatial and temporal variation in any geothermal spring. The study underscores the distinctness of planktonic and benthic communities and the importance of temperature in driving the spatial variation of microbial phylotypes throughout the mineralogically homogenous source pool. 8

ICON 2019: International Scientific Tendinopathy Symposium Consensus: Clinical Terminology

© Author(s) (or their employer(s)) 2019. No commercial re-use. See rights and permissions. Published by BMJ.Background Persistent tendon pain that impairs function has inconsistent medical terms that can influence choice of treatment.1 When a person is told they have tendinopathy by clinician A or tendinitis by clinician B, they might feel confused or be alarmed at receiving what they might perceive as two different diagnoses. This may lead to loss of confidence in their health professional and likely adds to uncertainty if they were to search for information about their condition. Clear and uniform terminology also assists inter-professional communication. Inconsistency in terminology for painful tendon disorders is a problem at numerous anatomical sites. Historically, the term ‘tendinitis’ was first used to describe tendon pain, thickening and impaired function (online supplementary figure S1). The term ‘tendinosis’ has also been used in a small number of publications, some of which were very influential.2 3 Subsequently, ‘tendinopathy’ emerged as the most common term for persistent tendon pain.4 5 To our knowledge, experts (clinicians and researchers) or patients have never engaged in a formal process to discuss the terminology we use. We believe that health professionals have not yet agreed on the appropriate terminology for painful tendon conditions.Peer reviewedFinal Accepted Versio

ICON 2019—International Scientific Tendinopathy Symposium Consensus: There are nine core health-related domains for tendinopathy (CORE DOMAINS): Delphi study of healthcare professionals and patients

Background: The absence of any agreed-upon tendon health-related domains hampers advances in clinical tendinopathy research. This void means that researchers report a very wide range of outcome measures inconsistently. As a result, substantial synthesis/meta-analysis of tendon research findings is almost futile despite researchers publishing busily. We aimed to determine options for, and then define, core health-related domains for tendinopathy. Methods: We conducted a Delphi study of healthcare professionals (HCP) and patients in a three-stage process. In stage 1, we extracted candidate domains from clinical trial reports and developed an online survey. Survey items took the form: ‘The ‘candidate domain’ is important enough to be included as a core health-related domain of tendinopathy’; response options were: agree, disagree, or unsure. In stage 2, we administered the online survey and reported the findings. Stage 3 consisted of discussions of the findings of the survey at the ICON (International Scientific Tendinopathy Symposium Consensus) meeting. We set 70% participant agreement as the level required for a domain to be considered ‘core’; similarly, 70% agreement was required for a domain to be relegated to ‘not core’ (see Results next). Results: Twenty-eight HCP (92% of whom had >10 years of tendinopathy experience, 71% consulted >10 cases per month) and 32 patients completed the online survey. Fifteen HCP and two patients attended the consensus meeting. Of an original set of 24 candidate domains, the ICON group deemed nine domains to be core. These were: (1) patient rating of condition, (2) participation in life activities (day to day, work, sport), (3) pain on activity/loading, (4) function, (5) psychological factors, (6) physical function capacity, (7) disability, (8) quality of life and (9) pain over a specified time. Two of these (2, 6) were an amalgamation of five candidate domains. We agreed that seven other candidate domains were not core domains: range of motion, pain on clinician applied test, clinical examination, palpation, drop out, sensory modality pain and pain without other specification. We were undecided on the other five candidate domains of physical activity, structure, medication use, adverse effects and economic impact. Conclusion: Nine core domains for tendon research should guide reporting of outcomes in clinical trials. Further research should determine the best outcome measures for each specific tendinopathy (ie, core outcome sets)

Complete genome sequence of the filamentous gliding predatory bacterium Herpetosiphon aurantiacus type strain (114-95T)

Herpetosiphon aurantiacus Holt and Lewin 1968 is the type species of the genus Herpetosiphon, which in turn is the type genus of the family Herpetosiphonaceae, type family of the order Herpetosiphonales in the phylum Chloroflexi. H. aurantiacus cells are organized in filaments which can rapidly glide. The species is of interest not only because of its rather isolated position in the tree of life, but also because Herpetosiphon ssp. were identified as predators capable of facultative predation by a wolf pack strategy and of degrading the prey organisms by excreted hydrolytic enzymes. The genome of H. aurantiacus strain 114-95T is the first completely sequenced genome of a member of the family Herpetosiphonaceae. The 6,346,587 bp long chromosome and the two 339,639 bp and 99,204 bp long plasmids with a total of 5,577 protein-coding and 77 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2005

ESMValTool (v1.0) – a community diagnostic and performance metrics tool for routine evaluation of Earth system models in CMIP

A community diagnostics and performance metrics tool for the evaluation of Earth system models (ESMs) has been developed that allows for routine comparison of single or multiple models, either against predecessor versions or against observations. The priority of the effort so far has been to target specific scientific themes focusing on selected essential climate variables (ECVs), a range of known systematic biases common to ESMs, such as coupled tropical climate variability, monsoons, Southern Ocean processes, continental dry biases, and soil hydrology–climate interactions, as well as atmospheric CO2 budgets, tropospheric and stratospheric ozone, and tropospheric aerosols. The tool is being developed in such a way that additional analyses can easily be added. A set of standard namelists for each scientific topic reproduces specific sets of diagnostics or performance metrics that have demonstrated their importance in ESM evaluation in the peer-reviewed literature. The Earth System Model Evaluation Tool (ESMValTool) is a community effort open to both users and developers encouraging open exchange of diagnostic source code and evaluation results from the Coupled Model Intercomparison Project (CMIP) ensemble. This will facilitate and improve ESM evaluation beyond the state-of-the-art and aims at supporting such activities within CMIP and at individual modelling centres. Ultimately, we envisage running the ESMValTool alongside the Earth System Grid Federation (ESGF) as part of a more routine evaluation of CMIP model simulations while utilizing observations available in standard formats (obs4MIPs) or provided by the user

Origin and quantification of circulating DNA in mice with human colorectal cancer xenografts

Although circulating DNA (ctDNA) could be an attractive tool for early cancer detection, diagnosis, prognosis, monitoring or prediction of response to therapies, knowledge on its origin, form and rate of release is poor and often contradictory. Here, we describe an experimental system to systematically examine these aspects. Nude mice were xenografted with human HT29 or SW620 colorectal carcinoma (CRC) cells and ctDNA was analyzed by Q–PCR with highly specific and sensitive primer sets at different times post-graft. We could discriminate ctDNA from normal (murine) cells and from mutated and non-mutated tumor (human) cells by using species-specific KRAS or PSAT1 primers and by assessing the presence of the BRAF V600E mutation. The concentration of human (mutated and non-mutated) ctDNA increased significantly with tumor growth. Conversely, and differently from previous studies, low, constant level of mouse ctDNA was observed, thus facilitating the study of mutated and non-mutated tumor derived ctDNA. Finally, analysis of ctDNA fragmentation confirmed the predominance of low-size fragments among tumor ctDNA from mice with bigger tumors. Higher ctDNA fragmentation was also observed in plasma samples from three metastatic CRC patients in comparison to healthy individuals. Our data confirm the predominance of mononucleosome-derived fragments in plasma from xenografted animals and, as a consequence, of apoptosis as a source of ctDNA, in particular for tumor-derived ctDNA. Altogether, our results suggest that ctDNA features vary during CRC tumor development and our experimental system might be a useful tool to follow such variations

Complete genome sequence of Polynucleobacter necessarius subsp. asymbioticus type strain (QLW-P1DMWA-1T)

Polynucleobacter necessarius subsp. asymbioticus strain QLW-P1DMWA-1T is a planktonic freshwater bacterium affiliated with the family Burkholderiaceae (class Betaproteobacteria). This strain is of interest because it represents a subspecies with cosmopolitan and ubiquitous distribution in standing freshwater systems. The 16S-23S ITS genotype represented by the sequenced strain comprised on average more than 10% of bacterioplankton in its home habitat. While all strains of the subspecies P. necessarius asymbioticus are free-living freshwater bacteria, strains belonging to the only other subspecies, P. necessarius subsp. necessarius are obligate endosymbionts of the ciliate Euplotes aediculatus. The two subspecies of P. necessarius are the instances of two closely related subspecies that differ in their lifestyle (free-living vs. obligate endosymbiont), and they are the only members of the genus Polynucleobacter with completely sequenced genomes. Here we describe the features of P. necessarius subsp. asymbioticus, together with the complete genome sequence and annotation. The 2,159,490 bp long chromosome with a total of 2,088 protein-coding and 48 RNA genes is the first completed genome sequence of the genus Polynucleobacter to be published and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2006

Like a bolt from the blue : phthalocyanines in biomedical optics

The purpose of this review is to compile preclinical and clinical results on phthalocyanines (Pcs) as photosensitizers (PS) for Photodynamic Therapy (PDT) and contrast agents for fluorescence imaging. Indeed, Pcs are excellent candidates in these fields due to their strong absorbance in the NIR region and high chemical and photo-stability. In particular, this is mostly relevant for their in vivo activation in deeper tissular regions. However, most Pcs present two major limitations, i.e., a strong tendency to aggregate and a low water-solubility. In order to overcome these issues, both chemical tuning and pharmaceutical formulation combined with tumor targeting strategies were applied. These aspects will be developed in this review for the most extensively studied Pcs during the last 25 years, i.e., aluminium-, zinc- and silicon-based Pcs

A whole earth approach to nature-positive food: biodiversity and agriculture

Agriculture is the largest single source of environmental degradation, responsible for over 30% of global greenhouse gas (GHG) emissions, 70% of freshwater use and 80% of land conversion: it is the single largest driver of biodiversity loss (Foley JA, Science 309:570–574, 2005, Nature 478:337–342, 2011; IPBES. Global assessment report on biodiversity and ecosystem services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. IPBES Secretariat, Bonn, 2019; Willett W et al. The Lancet 393:447–492, 2019). Agriculture also underpins poor human health, contributing to 11 million premature deaths annually. While too many still struggle from acute hunger, a growing number of individuals, including in low to middle-income countries (LMICs), struggle to access healthy foods. Greater consideration for, and integration of, biodiversity in agriculture is a key solution space for improving health, eliminating hunger and achieving nature-positive development objectives. This rapid evidence review documents the best available evidence of agriculture’s relationships with biodiversity, drawing on the contributions of leading biodiversity experts, and recommends actions that can be taken to move towards more biodiversity/nature-positive production through the delivery of integrated agricultural solutions for climate, biodiversity, nutrition and livelihoods. The analysis, which takes a whole-of-food-system approach, brings together a large body of evidence. It accounts for aspects not typically captured in a stand-alone primary piece of research and indicates where there are critical gaps.Fil: Declerck, Fabrice A.J.. The Alliance of Bioversity International and the International Center for Tropical Agriculture ; FranciaFil: Koziell, Izabella T.. The International Centre for Integrated Mountain Development; NepalFil: Benton, Tim. Chatham House; Reino UnidoFil: Garibaldi, Lucas Alejandro. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Patagonia Norte. Instituto de Investigaciones En Recursos Naturales, Agroecologia y Desarrollo Rural. - Universidad Nacional de Rio Negro. Instituto de Investigaciones En Recursos Naturales, Agroecologia y Desarrollo Rural.; ArgentinaFil: Kremen, Claire. University of British Columbia; CanadáFil: Maron, Martine. University of Queensland; AustraliaFil: Rumbaitis Del Rio, Cristina. World Resources Institute; Estados UnidosFil: Sidhu, Aman. The Alliance of Bioversity International and the International Center for Tropical Agricultura; FranciaFil: Wirths, Jonathan. The Consortium of International Agricultural Research Centers ; Sri LankaFil: Clark, Michael. University of Oxford; Reino UnidoFil: Dickens, Chris. International Water Management Institute; Sri LankaFil: Estrada Carmona, Natalia. The Alliance of Bioversity International and the International Center for Tropical Agriculture ; FranciaFil: Fremier, Alexander K.. Washington State University; Estados UnidosFil: Jones, Sarah K.. The Alliance of Bioversity International and the International Center for Tropical Agriculture ; FranciaFil: Khoury, Colin K.. The Alliance of Bioversity International and the International Center for Tropical Agriculture ; FranciaFil: Lal, Rattan. Ohio State University; Estados UnidosFil: Obersteiner, Michael. University of Oxford; Reino UnidoFil: Remans, Roseline. The Alliance of Bioversity International and the International Center for Tropical Agriculture ; FranciaFil: Rusch, Adrien. Institut National de la Recherche Agronomique; FranciaFil: Schulte, Lisa A.. Natural Resource Ecology and Management; Estados UnidosFil: Simmonds, Jeremy. University of Queensland; AustraliaFil: Stringer, Lindsay C.. University of York; Reino UnidoFil: Weber, Christopher. World Wide Fund For Nature; Estados UnidosFil: Winowiecki, Leigh. World Agroforestry Center; Keni

10 Recommended core outcome domains for tendinopathy derived from a delphi of patients and health care professionals: the groningen ISTS2018 consensus

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