Pydna: a simulation and documentation tool for DNA assembly strategies using python

Background: Recent advances in synthetic biology have provided tools to efficiently construct complex DNA molecules which are an important part of many molecular biology and biotechnology projects. The planning of such constructs has traditionally been done manually using a DNA sequence editor which becomes error-prone as scale and complexity of the construction increase. A human-readable formal description of cloning and assembly strategies, which also allows for automatic computer simulation and verification, would therefore be a valuable tool.Results: We have developed pydna, an extensible, free and open source Python library for simulating basic molecular biology DNA unit operations such as restriction digestion, ligation, PCR, primer design, Gibson assembly and homologous recombination. A cloning strategy expressed as a pydna script provides a description that is complete, unambiguous and stable. Execution of the script automatically yields the sequence of the final molecule(s) and that of any intermediate constructs. Pydna has been designed to be understandable for biologists with limited programming skills by providing interfaces that are semantically similar to the description of molecular biology unit operations found in literature.Conclusions: Pydna simplifies both the planning and sharing of cloning strategies and is especially useful for complex or combinatorial DNA molecule construction. An important difference compared to existing tools with similar goals is the use of Python instead of a specifically constructed language, providing a simulation environment that is more flexible and extensible by the user.Thanks to Dr. Aric Hagberg Los Alamos National Laboratory, U.S.A and Sergio Simoes, Universidade de Sao Paulo, Brasil for help with NetworkX and graph theory in general. Thanks to Henrik Bengtsson, Dept of Epidemiology & Biostatistics, University of California San Francisco, U.S.A. for critical reading of the manuscript. Thanks to the 2013 Bioinformatics 6605 N4 students A. Coelho, A. Faria, A. Neves D. Yelshyna and E. Costa for testing. This work was supported by the Fundacao para a Ciencia e Tecnologia (FCT) [PTDC/AAC-AMB/120940/2010, EXPL/BBB-BIO/1772/2013]; and the FEDER POFC-COMPETE [PEst-C/BIA/UI4050/2011]. FA and GR were supported by FCT fellowships [SFRH/BD/80934/2011 and SFRH/BD/42565/2007, respectively].info:eu-repo/semantics/publishedVersio

Design and baseline characteristics of the finerenone in reducing cardiovascular mortality and morbidity in diabetic kidney disease trial

Background: Among people with diabetes, those with kidney disease have exceptionally high rates of cardiovascular (CV) morbidity and mortality and progression of their underlying kidney disease. Finerenone is a novel, nonsteroidal, selective mineralocorticoid receptor antagonist that has shown to reduce albuminuria in type 2 diabetes (T2D) patients with chronic kidney disease (CKD) while revealing only a low risk of hyperkalemia. However, the effect of finerenone on CV and renal outcomes has not yet been investigated in long-term trials. Patients and Methods: The Finerenone in Reducing CV Mortality and Morbidity in Diabetic Kidney Disease (FIGARO-DKD) trial aims to assess the efficacy and safety of finerenone compared to placebo at reducing clinically important CV and renal outcomes in T2D patients with CKD. FIGARO-DKD is a randomized, double-blind, placebo-controlled, parallel-group, event-driven trial running in 47 countries with an expected duration of approximately 6 years. FIGARO-DKD randomized 7,437 patients with an estimated glomerular filtration rate >= 25 mL/min/1.73 m(2) and albuminuria (urinary albumin-to-creatinine ratio >= 30 to <= 5,000 mg/g). The study has at least 90% power to detect a 20% reduction in the risk of the primary outcome (overall two-sided significance level alpha = 0.05), the composite of time to first occurrence of CV death, nonfatal myocardial infarction, nonfatal stroke, or hospitalization for heart failure. Conclusions: FIGARO-DKD will determine whether an optimally treated cohort of T2D patients with CKD at high risk of CV and renal events will experience cardiorenal benefits with the addition of finerenone to their treatment regimen. Trial Registration: EudraCT number: 2015-000950-39; ClinicalTrials.gov identifier: NCT02545049

Technological Transformation in the Global Pulp and Paper Industry : Introduction

At a high level of abstraction, the evolution of any industry is a function of changes in product market demand, availability and supply of capital, knowledge and technology, the surrounding institutional framework and organisational solutions. New technological innovations emerge because of changes in product market demand or institutional framework that encourage entrepreneurs and firms to take advantage of new business opportunities. This contributed volume provides illustrative, well documented case studies of technological transformation in the global pulp and paper industry from the inception of mechanical papermaking in early nineteenth century Europe until its recent developments in today’s business environment with rapidly changing market dynamics and consumer behaviour. The study focuses on the roles of various factors that affected this process, including the availability and supply of inputs on the one hand, and demand characteristics on the other hand, within regional, national and transnational organisational frameworks. It deals with the relationships between technology transfer, technology leadership, raw material dependence, and product variety on a global scale. The introductory chapter outlines the research setting, and briefly summarises the research questions posed, methods used and the case studies analysed.nonPeerReviewe

Localization of the thiazide sensitive Na-Cl cotransporter, rTSC1, in the rat kidney

Localization of the thiazide sensitive Na-Cl cotransporter, rTSC1, in the rat kidney. A thiazide sensitive Na-C1 cotransporter, rTSC1, has recently been cloned from a rat kidney cortex cDNA library. The molecular regulation and nephron localization of this protein is unknown. The purpose of this study was to examine the nephron distribution and subcellular localization of the rTSC1 protein in the rat kidney. In situ hybridization showed rTSC1 transcripts were localized to short, convoluted tubule segments in the kidney cortex. Polyclonal antibodies raised against a 110 amino acid segment from the amino terminus of rTSC1 recognized three major bands of 135, 140 and 155kDa on Western blotting of membrane protein from cortex but not outer medulla of the rat kidney. Immunofluorescence studies using the antibody alone and in double labeling experiments with antibodies against the H+ ATPase and calbindin D28, showed intense labeling of apical membranes in the distal nephron beginning in the initial distal convoluted tubule and terminating within the connecting tubule. The intensity of labeling diminished from proximal to distal sites along the distal tubule. Ultrastructural studies by immunoelectron microscopy showed the cotransporter protein to be localized predominately on apical microvilli of the distal convoluted tubule cells. These results are consistent with rTSC1 encoding the apical thiazide sensitive Na-Cl cotransporter in the distal tubule

Water @ UMN Roundup

As the editors put this issue on "Water @ UMN" together, we realized that the breadth, complexity, and variety of water-related work at the University of Minnesota could never be encompassed in a few articles.  Accordingly, we sent a prompt out as widely as we could, asking water scholars to tell us, in a few paragraphs, what it was about their work that they were most excited about.  The short pieces that follow contain some of their responses..

Surgical Aspects of Primary Hyperparathyroidism

Parathyroidectomy (PTX) is the treatment of choice for symptomatic primary hyperparathyroidism (PHPT). It is also the treatment of choice in asymptomatic PHPT with evidence for target organ involvement. This review updates surgical aspects of PHPT and proposes the following definitions based on international expert consensus: selective PTX (and reasons for conversion to an extended procedure), bilateral neck exploration for non-localized or multigland disease, subtotal PTX, total PTX with immediate or delayed autotransplantation, and transcervical thymectomy and extended en bloc PTX for parathyroid carcinoma. The systematic literature reviews discussed covered (i) the use of intraoperative PTH (ioPTH) for localized single-gland disease and (ii) the management of low BMD after PTX. Updates based on prospective observational studies are presented concerning PTX for multigland disease and hereditary PHPT syndromes, histopathology, intraoperative adjuncts, localization techniques, perioperative management, “reoperative” surgery and volume/outcome data. Postoperative complications are few and uncommon (<3%) in centers performing over 40 PTXs per year. This review is the first global consensus about surgery in PHPT and reflects the current practice in leading endocrine surgery units worldwide

Hydrogen peroxide at the poles of Ganymede

Ganymede is the only satellite in the solar system known to have an intrinsic magnetic field. Interactions between this field and the Jovian magnetosphere are expected to funnel most of the associated impinging charged particles, which radiolytically alter surface chemistry across the Jupiter system, to Ganymede's polar regions. Using observations obtained with JWST as part of the Early Release Science program exploring the Jupiter system, we report the discovery of hydrogen peroxide, a radiolysis product of water ice, specifically constrained to the high latitudes. This detection directly implies radiolytic modification of the polar caps by precipitation of Jovian charged particles along partially open field lines within Ganymede's magnetosphere. Stark contrasts between the spatial distribution of this polar hydrogen peroxide, those of Ganymede's other radiolytic oxidants, and that of hydrogen peroxide on neighboring Europa have important implications for understanding water-ice radiolysis throughout the solar system