Identification and characterization of the intracellular poly-3-hydroxybutyrate depolymerase enzyme PhaZ of Sinorhizobium meliloti

<p>Abstract</p> <p>Background</p> <p><it>S. meliloti </it>forms indeterminate nodules on the roots of its host plant alfalfa (<it>Medicago sativa</it>). Bacteroids of indeterminate nodules are terminally differentiated and, unlike their non-terminally differentiated counterparts in determinate nodules, do not accumulate large quantities of Poly-3-hydroxybutyrate (PHB) during symbiosis. PhaZ is in intracellular PHB depolymerase; it represents the first enzyme in the degradative arm of the PHB cycle in <it>S. meliloti </it>and is the only enzyme in this half of the PHB cycle that remains uncharacterized.</p> <p>Results</p> <p>The <it>S. meliloti phaZ </it>gene was identified by <it>in silico </it>analysis, the ORF was cloned, and a <it>S. meliloti phaZ </it>mutant was constructed. This mutant exhibited increased PHB accumulation during free-living growth, even when grown under non-PHB-inducing conditions. The <it>phaZ </it>mutant demonstrated no reduction in symbiotic capacity; interestingly, analysis of the bacteroids showed that this mutant also accumulated PHB during symbiosis. This mutant also exhibited a decreased capacity to tolerate long-term carbon starvation, comparable to that of other PHB cycle mutants. In contrast to other PHB cycle mutants, the <it>S. meliloti phaZ </it>mutant did not exhibit any decrease in rhizosphere competitiveness; however, this mutant did exhibit a significant increase in succinoglycan biosynthesis.</p> <p>Conclusions</p> <p><it>S. meliloti </it>bacteroids retain the capacity to synthesize PHB during symbiosis; interestingly, accumulation does not occur at the expense of symbiotic performance. <it>phaZ </it>mutants are not compromised in their capacity to compete for nodulation in the rhizosphere, perhaps due to increased succinoglycan production resulting from upregulation of the succinoglycan biosynthetic pathway. The reduced survival capacity of free-living cells unable to access their accumulated stores of PHB suggests that PHB is a crucial metabolite under adverse conditions.</p

A Bad Air Day in Houston

© Copyright 2005 American Meteorological Society (AMS). Permission to use figures, tables, and brief excerpts from this work in scientific and educational works is hereby granted provided that the source is acknowledged. Any use of material in this work that is determined to be “fair use” under Section 107 of the U.S. Copyright Act September 2010 Page 2 or that satisfies the conditions specified in Section 108 of the U.S. Copyright Act (17 USC §108, as revised by P.L. 94-553) does not require the AMS’s permission. Republication, systematic reproduction, posting in electronic form, such as on a web site or in a searchable database, or other uses of this material, except as exempted by the above statement, requires written permission or a license from the AMS. Additional details are provided in the AMS Copyright Policy, available on the AMS Web site located at (https://www.ametsoc.org/) or from the AMS at 617-227-2425 or [email protected] case study from the Texas Air Quality Study 2000 field campaign illustrates the complex interaction of meteorological and chemical processes that produced a high-pollution event in the Houston area on 30 August 2000. High 1-h ozone concentrations of nearly 200 ppb were measured near the surface, and vertical profile data from an airborne differential-absorption lidar (DIAL) system showed that these high-ozone concentrations penetrated to heights approaching 2 km into the atmospheric boundary layer. This deep layer of pollution was transported over the surrounding countryside at night, where it then mixed out the next day to become part of the rural background levels. These background levels thus increased during the course of the multiday pollution episode. The case study illustrates many processes that numerical forecast models must faithfully represent to produce accurate quantitative predictions of peak pollutant concentrations in coastal locations such as Houston. Such accurate predictions will be required for useful air-quality forecasts for urban areas.Southern Oxidant Study Texas Commission on Environmental Qualit

Exoplanet Diversity in the Era of Space-based Direct Imaging Missions

This whitepaper discusses the diversity of exoplanets that could be detected by future observations, so that comparative exoplanetology can be performed in the upcoming era of large space-based flagship missions. The primary focus will be on characterizing Earth-like worlds around Sun-like stars. However, we will also be able to characterize companion planets in the system simultaneously. This will not only provide a contextual picture with regards to our Solar system, but also presents a unique opportunity to observe size dependent planetary atmospheres at different orbital distances. We propose a preliminary scheme based on chemical behavior of gases and condensates in a planet's atmosphere that classifies them with respect to planetary radius and incident stellar flux.Comment: A white paper submitted to the National Academy of Sciences Exoplanet Science Strateg

Ageing, Temporality and Performance: Joan Rivers’ Body of Work

Joan Rivers’ performance in the public sphere revolved around the visibility and cultural inscription of an ageing and older woman. Linking aesthetic, professional and physiological processes, her body, work and performance merged as and in an extended and finite professional practice. A pioneer of stand-up comedy as a genre, and one of its most significant and visible female practitioners, Rivers is known for her aggressive and often outrageous wit, which was directed at both herself and other celebrities, as well as her extensive plastic surgeries. When she died in 2014, at the age of 81, she was still fully engaged in a relentless schedule of live performances and televised appearances. By then, Rivers was well established as an ubiquitously present elder who refused to conform to long-standing stereotypes of asexuality, able to thrive in a rapidly shifting cultural landscape of surgically enhanced bodies, surveillance as entertainment and public confession. At the heart of the discussion in this article is the spatio-temporality of the performing body, borrowing from Maurice Merleau-Ponty’s understanding of the body as a “nexus of living meanings” and Jacques Derrida’s development of Merleau-Ponty’s use of the term “invagination” to embrace generic textual strategy. In stand-up as a genre, both originality and continuity are paradoxically valued by audiences in equal measure. Success – that is, laughter – is largely determined by the extent to which these align coherently with the comedian’s bodily presence and her onstage social, cultural and/or political positioning. Focusing primarily on the expression of Rivers’ persona via a variety of mutually reinforcing cultural texts in the final three years of her life, this article analyses how her performing body in every medium was importantly always made present through its sexual difference and attendant gendered ageing processes

A prospective longitudinal study of Pasireotide in Nelson's syndrome

PURPOSE: Nelson's syndrome is a challenging condition that can develop following bilateral adrenalectomy for Cushing's disease, with high circulating ACTH levels, pigmentation and an invasive pituitary tumor. There is no established medical therapy. The aim of the study was to assess the effects of pasireotide on plasma ACTH and tumor volume in Nelson's syndrome. METHODS: Open labeled multicenter longitudinal trial in three steps: (1) a placebo-controlled acute response test; (2) 1 month pasireotide 300-600 μg s.c. twice-daily; (3) 6 months pasireotide long-acting-release (LAR) 40-60 mg monthly. RESULTS: Seven patients had s.c. treatment and 5 proceeded to LAR treatment. There was a significant reduction in morning plasma ACTH during treatment (mean ± SD; 1823 ± 1286 ng/l vs. 888.0 ± 812.8 ng/l during the s.c. phase vs. 829.0 ± 1171 ng/l during the LAR phase, p < 0.0001). Analysis of ACTH levels using a random intercept linear mixed-random effects longitudinal model showed that ACTH (before the morning dose of glucocorticoids) declined significantly by 26.1 ng/l per week during the 28-week of treatment (95% CI - 45.2 to - 7.1, p < 0.01). An acute response to a test dose predicted outcome in 4/5 patients. Overall, there was no significant change in tumor volumes (1.4 ± 0.9 vs. 1.3 ± 1.0, p = 0.86). Four patients withdrew during the study. Hyperglycemia occurred in 6 patients. CONCLUSIONS: Pasireotide lowers plasma ACTH levels in patients with Nelson's syndrome. A longer period of treatment may be needed to assess the effects of pasireotide on tumor volume. TRIAL REGISTRATION: Clinical Trials.gov ID, NCT01617733

MEDEAS: a new modeling framework integrating global biophysical and socioeconomic constraints

Producción CientíficaA diversity of integrated assessment models (IAMs) coexists due to the different approaches developed to deal with the complex interactions, high uncertainties and knowledge gaps within the environment and human societies. This paper describes the open-source MEDEAS modeling framework, which has been developed with the aim of informing decision-making to achieve the transition to sustainable energy systems with a focus on biophysical, economic, social and technological restrictions and tackling some of the limitations identified in the current IAMs. MEDEAS models include the following relevant characteristics: representation of biophysical constraints to energy availability; modeling of the mineral and energy investments for the energy transition, allowing a dynamic assessment of the potential mineral scarcities and computation of the net energy available to society; consistent representation of climate change damages with climate assessments by natural scientists; integration of detailed sectoral economic structure (input–output analysis) within a system dynamics approach; energy shifts driven by physical scarcity; and a rich set of socioeconomic and environmental impact indicators. The potentialities and novel insights that this framework brings are illustrated by the simulation of four variants of current trends with the MEDEAS-world model: the consideration of alternative plausible assumptions and methods, combined with the feedback-rich structure of the model, reveal dynamics and implications absent in classical models. Our results suggest that the continuation of current trends will drive significant biophysical scarcities and impacts which will most likely derive in regionalization (priority to security concerns and trade barriers), conflict, and ultimately, a severe global crisis which may lead to the collapse of our modern civilization. Despite depicting a much more worrying future than conventional projections of current trends, we however believe it is a more realistic counterfactual scenario that will allow the design of improved alternative sustainable pathways in future work.Ministerio de Economía, Industria y Competitividad (Project CO2017-85110-R)Ministerio de Economía, Industria y Competitividad (Project JCI-2016–28833)MEDEAS project, funded by the European Union’s Horizon2020 research and innovation programme under grant agree-ment no. 691287.LOCOMOTION project, funded by the EuropeanUnion’s Horizon 2020 research and innovation programmeunder grant agreement no. 82110

Development and validation of a targeted gene sequencing panel for application to disparate cancers

Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. We aimed to develop a targeted gene sequencing panel for application to disparate cancer types with particular focus on tumours of the head and neck, plus test for utility in liquid biopsy. The final panel designed through Roche/Nimblegen combined 451 cancer-associated genes (2.01 Mb target region). 136 patient DNA samples were collected for performance and application testing. Panel sensitivity and precision were measured using well-characterised DNA controls (n = 47), and specificity by Sanger sequencing of the Aryl Hydrocarbon Receptor Interacting Protein (AIP) gene in 89 patients. Assessment of liquid biopsy application employed a pool of synthetic circulating tumour DNA (ctDNA). Library preparation and sequencing were conducted on Illumina-based platforms prior to analysis with our accredited (ISO15189) bioinformatics pipeline. We achieved a mean coverage of 395x, with sensitivity and specificity of >99% and precision of >97%. Liquid biopsy revealed detection to 1.25% variant allele frequency. Application to head and neck tumours/cancers resulted in detection of mutations aligned to published databases. In conclusion, we have developed an analytically-validated panel for application to cancers of disparate types with utility in liquid biopsy

Homologous recombination DNA repair defects in PALB2- associated breast cancers

Abstract: Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD

How Can We Improve Oncofertility Care for Patients? A Systematic Scoping Review of Current International Practice and Models of Care

© The Author(s) 2018. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. BACKGROUND: Fertility preservation (FP) is an important quality of life issue for cancer survivors of reproductive age. Despite the existence of broad international guidelines, the delivery of oncofertility care, particularly amongst paediatric, adolescent and young adult patients, remains a challenge for healthcare professionals (HCPs). The quality of oncofertility care is variable and the uptake and utilization of FP remains low. Available guidelines fall short in providing adequate detail on how oncofertility models of care (MOC) allow for the real-world application of guidelines by HCPs. OBJECTIVE AND RATIONALE: The aim of this study was to systematically review the literature on the components of oncofertility care as defined by patient and clinician representatives, and identify the barriers, facilitators and challenges, so as to improve the implementation of oncofertility services. SEARCH METHODS: A systematic scoping review was conducted on oncofertility MOC literature published in English between 2007 and 2016, relating to 10 domains of care identified through consumer research: communication, oncofertility decision aids, age-appropriate care, referral pathways, documentation, training, supportive care during treatment, reproductive care after cancer treatment, psychosocial support and ethical practice of oncofertility care. A wide range of electronic databases (CINAHL, Embase, PsycINFO, PubMed, AEIPT, Education Research Complete, ProQuest and VOCED) were searched in order to synthesize the evidence around delivery of oncofertility care. Related citations and reference lists were searched. The review was undertaken following registration (International prospective register of systematic reviews (PROSPERO) registration number CRD42017055837) and guidelines of Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). OUTCOMES: A total of 846 potentially relevant studies were identified after the removal of duplicates. All titles and abstracts were screened by a single reviewer and the final 147 papers were screened by two reviewers. Ten papers on established MOC were identified amongst the included papers. Data were extracted from each paper and quality scores were then summarized in the oncofertility MOC summary matrix. The results identified a number of themes for improving MOC in each domain, which included: the importance of patients receiving communication that is of a higher quality and in different formats on their fertility risk and FP options; improving provision of oncofertility care in a timely manner; improving access to age-appropriate care; defining the role and scope of practice of all HCPs; and improving communication between different HCPs. Different forms of decision aids were found useful for assisting patients to understand FP options and weigh up choices. WIDER IMPLICATIONS: This analysis identifies core components for delivery of oncofertility MOC. The provision of oncofertility services requires planning to ensure services have safe and reliable referral pathways and that they are age-appropriate and include medical and psychological oncofertility care into the survivorship period. In order for this to happen, collaboration needs to occur between clinicians, allied HCPs and executives within paediatric and adult hospitals, as well as fertility clinics across both public and private services. Training of both cancer and non-cancer HCPs is needed to improve the knowledge of HCPs, the quality of care provided and the confidence of HCPs with these consultations