Calcium/calmodulin kinase1 and its relation to thermotolerance and HSP90 in Sporothrix schenckii: an RNAi and yeast two-hybrid study

<p>Abstract</p> <p>Background</p> <p><it>Sporothrix schenckii </it>is a pathogenic dimorphic fungus of worldwide distribution. It grows in the saprophytic form with hyaline, regularly septated hyphae and pyriform conidia at 25°C and as the yeast or parasitic form at 35°C. Previously, we characterized a calcium/calmodulin kinase in this fungus. Inhibitors of this kinase were observed to inhibit the yeast cell cycle in <it>S. schenckii</it>.</p> <p>Results</p> <p>The presence of RNA interference (RNAi) mechanism in this fungus was confirmed by the identification of a Dicer-1 homologue in <it>S. schenckii </it>DNA. RNAi technology was used to corroborate the role of calcium/calmodulin kinase I in <it>S. schenckii </it>dimorphism. Yeast cells were transformed with the pSilent-Dual2G (pSD2G) plasmid w/wo inserts of the coding region of the calcium/calmodulin kinase I (<it>sscmk1</it>) gene. Transformants were selected at 35°C using resistance to geneticin. Following transfer to liquid medium at 35°C, RNAi transformants developed as abnormal mycelium clumps and not as yeast cells as would be expected. The level of <it>sscmk1 </it>gene expression in RNAi transformants at 35°C was less than that of cells transformed with the empty pSD2G at this same temperature. Yeast two-hybrid analysis of proteins that interact with SSCMK1 identified a homologue of heat shock protein 90 (HSP90) as interacting with this kinase. Growth of the fungus similar to that of the RNAi transformants was observed in medium with geldanamycin (GdA, 10 μM), an inhibitor of HSP90.</p> <p>Conclusions</p> <p>Using the RNAi technology we silenced the expression of <it>sscmk1 </it>gene in this fungus. RNAi transformants were unable to grow as yeast cells at 35°C showing decreased tolerance to this temperature. The interaction of SSCMK1 with HSP90, observed using the yeast two-hybrid assay suggests that this kinase is involved in thermotolerance through its interaction with HSP90. SSCMK1 interacted with the C terminal domain of HSP90 where effector proteins and co-chaperones interact. These results confirmed SSCMK1 as an important enzyme involved in the dimorphism of <it>S. schenckii</it>, necessary for the development of the yeast phase of this fungus. Also this study constitutes the first report of the transformation of <it>S. schenckii </it>and the use of RNAi to study gene function in this fungus.</p

Clustering Improves the Goemans–Williamson Approximation for the Max-Cut Problem

MAX−CUT is one of the well-studied NP-hard combinatorial optimization problems. It can be formulated as an Integer Quadratic Programming problem and admits a simple relaxation obtained by replacing the integer “spin” variables xi by unitary vectors v⃗ i. The Goemans–Williamson rounding algorithm assigns the solution vectors of the relaxed quadratic program to a corresponding integer spin depending on the sign of the scalar product v⃗ i⋅r⃗ with a random vector r⃗ . Here, we investigate whether better graph cuts can be obtained by instead using a more sophisticated clustering algorithm. We answer this question affirmatively. Different initializations of k-means and k-medoids clustering produce better cuts for the graph instances of the most well known benchmark for MAX−CUT. In particular, we found a strong correlation of cluster quality and cut weights during the evolution of the clustering algorithms. Finally, since in general the maximal cut weight of a graph is not known beforehand, we derived instance-specific lower bounds for the approximation ratio, which give information of how close a solution is to the global optima for a particular instance. For the graphs in our benchmark, the instance specific lower bounds significantly exceed the Goemans–Williamson guarantee

Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in Sporothrix schenckii

<p>Abstract</p> <p>Background</p> <p><it>Sporothrix schenckii </it>is a pathogenic, dimorphic fungus, the etiological agent of sporotrichosis, a subcutaneous lymphatic mycosis. Dimorphism in <it>S. schenckii </it>responds to second messengers such as cAMP and calcium, suggesting the possible involvement of a calcium/calmodulin kinase in its regulation. In this study we describe a novel calcium/calmodulin-dependent protein kinase gene in <it>S. schenckii, sscmk1</it>, and the effects of inhibitors of calmodulin and calcium/calmodulin kinases on the yeast to mycelium transition and the yeast cell cycle.</p> <p>Results</p> <p>Using the PCR homology approach a new member of the calcium/calmodulin kinase family, SSCMK1, was identified in this fungus. The cDNA sequence of <it>sscmk1 </it>revealed an open reading frame of 1,221 nucleotides encoding a 407 amino acid protein with a predicted molecular weight of 45.6 kDa. The genomic sequence of <it>sscmk1 </it>revealed the same ORF interrupted by five introns. Bioinformatic analyses of SSCMK1 showed that this protein had the distinctive features that characterize a calcium/calmodulin protein kinase: a serine/threonine protein kinase domain and a calmodulin-binding domain. When compared to homologues from seven species of filamentous fungi, SSCMK1 showed substantial similarities, except for a large and highly variable region that encompasses positions 330 – 380 of the multiple sequence alignment. Inhibition studies using calmodulin inhibitor W-7, and calcium/calmodulin kinase inhibitors, KN-62 and lavendustin C, were found to inhibit budding by cells induced to re-enter the yeast cell cycle and to favor the yeast to mycelium transition.</p> <p>Conclusion</p> <p>This study constitutes the first evidence of the presence of a calcium/calmodulin kinase-encoding gene in <it>S. schenckii </it>and its possible involvement as an effector of dimorphism in this fungus. These results suggest that a calcium/calmodulin dependent signaling pathway could be involved in the regulation of dimorphism in this fungus. The results suggest that the calcium/calmodulin kinases of yeasts are evolutionarily distinct from those in filamentous fungi.</p

Desafíos de las metrópolis: Efectos ambientales y sociales. Tendencias geográficas II

El libro está conformado de estudios realizados por profesores-investigadores de la Universidad Autónoma del Estado de México, de la Universidad de Varsovia, así como de la Universidad Pedagógica Comisión de Educación Nacional de Cracovia. En esta obra se exponen algunas investigaciones sobre los cambios en los factores sociales, naturales, económicos y ambientales como principales desafios que presentan las zonas de México, Polonia y de contextos de Sudamérica, tales como Sao Paulo, Quito y Bogotá y ciudades medias y pequeñas.Universidad Autónoma del Estado de Méxic

MPI-PHYLIP: Parallelizing Computationally Intensive Phylogenetic Analysis Routines for the Analysis of Large Protein Families

Background: Phylogenetic study of protein sequences provides unique and valuable insights into the molecular and genetic basis of important medical and epidemiological problems as well as insights about the origins and development of physiological features in present day organisms. Consensus phylogenies based on the bootstrap and other resampling methods play a crucial part in analyzing the robustness of the trees produced for these analyses. Methodology: Our focus was to increase the number of bootstrap replications that can be performed on large protein datasets using the maximum parsimony, distance matrix, and maximum likelihood methods. We have modified the PHYLIP package using MPI to enable large-scale phylogenetic study of protein sequences, using a statistically robust number of bootstrapped datasets, to be performed in a moderate amount of time. This paper discusses the methodology used to parallelize the PHYLIP programs and reports the performance of the parallel PHYLIP programs that are relevant to the study of protein evolution on several protein datasets. Conclusions: Calculations that currently take a few days on a state of the art desktop workstation are reduced to calculations that can be performed over lunchtime on a modern parallel computer. Of the three protein methods tested, the maximum likelihood method scales the best, followed by the distance method, and then the maximum parsimony method. However, the maximum likelihood method requires significant memory resources, which limits its application to mor

Aplicaciones electroquímicas al tratamiento de aguas residuales

El presente libro tiene como finalidad compilar numerosas investigaciones en el campo de la tecnología electroquímica y sus aplicaciones ambientales, contando con la colaboración de un gran número de investigadores tanto nacionales como extranjeros, proponiendo con ello una visión amplia dentro de la aplicación de la electroquímica. Los temas que integran esta obra se escogieron cuidadosamente considerando desde los principios básicos de la electroquímica aplicada al tratamiento de aguas residuales hasta los parámetros a considerar durante el diseño, operación y evaluación de dichos sistemas, sin dejar de lado las aplicaciones utilizadas en la actualidad en la industria, la docencia y la investigación. Este libro reúne diversas temáticas por lo que puede considerarse como un compendio de aquellos elementos que el lector requiere para poder tener una visión amplia de las aplicaciones de la electroquímica en el campo del tratamiento de agua residual.En el Capítulo 1 se presenta una primera impresión de los Fundamentes de la Electroquímica Ambiental, en donde los autores explican cómo esta disciplina es una nueva área de la ciencia en donde se emplean conocimientos de Electroquímica, Ingeniería Química y Ciencia de Materiales, así como las aplicaciones específicas para la remediación ambiental. En el Capítulo 2 los autores ofrecen una descripción de los principales parámetros fisicoquímicos y biológicos que se emplean para definir a la calidad del agua. Este capítulo describe en función de qué características físicas, químicas y biológicas se puede evaluar a un agua residual así como también la aplicación de estas características como variables de control de un proceso de tratamiento y también como el empleo de ellas para limitar las concentraciones máximas permisibles de descarga de aguas residuales. El Capítulo 3 se refiere a uno de los procesos más empleados en el tratamiento de agua: la coagulación-floculación. Se aborda desde una óptica teórica hasta la descripción de un ejemplo de aplicación en la industria. Resulta importante incluir este capítulo ya que uno de los métodos más prometedores en la electroquímica ambiental es la electrocoagulación, la cual se narra en el Capítulo 6. Las bases de las celdas de laboratorio y reactores industriales electroquímicos se relatan en el Capítulo 4. En particular, se refieren las implicaciones que tienen las principales características físicas y de diseño de celdas de laboratorio y reactores electroquímicos industriales que permiten obtener transformaciones eficientes gracias a un correcto control del potencial de electrodo en estos sistemas. La implementación de procesos electroquímicos para su aplicación a nivel industrial, requiere del diseño eficiente del dispositivo central: el reactor electroquímico. Por lo que, en el Capítulo 5 se presentan los elementos de análisis de reactores electroquímicos para su diseño y caracterización. El Capítulo 7 describe bajo qué circunstancias se puede llevar a cabo el proceso de electroflotación. Los autores muestran cómo este proceso está influenciado por el pH de la solución acuosa, la densidad de corriente y el tipo de electrodos que se emplean. El lector encontrará en el Capítulo 8 las bases teóricas de uno de los procesos que involucra la química de la reacción de Fenton, así como las aplicaciones ambientales para el tratamiento de soluciones sintéticas y reales con diferentes contaminantes refractarios, tales como plaguicidas, colorantes, productos de cuidado personal, fármacos y residuos químicos industriales. En el Capítulo 9 se presentan algunos conceptos fundamentales sobre la Electrooxidación, también conocida como oxidación electroquímica, la cual está enfocada a realizar la oxidación de contaminantes presentes en aguas residuales sobre la superficie de electrodos. La tecnología para la electrogeneración de peróxido de hidrógeno y su empleo en el tratamiento de agua residual se describe en el Capítulo 10. Uno de los metales pesados que tienen un alto grado de toxicidad en el ambiente es el Cr(VI), el cual no puede ser removido por métodos convencionales por lo que una tecnología que puede emplearse en este tratamiento se relata en el Capítulo 11. En el Capítulo 12 se presentan los avances más recientes cuando se emplean los métodos electroquímicos con algún otro tipo de tratamiento, lo que ha resultado en la obtención de sinergias en los procesos, lo que implica una reducción en los costos de operación. Finalmente, en el Capítulo 13, se presenta el tema de usos y aplicaciones de sensores químicos y electroquímicos para la detección de contaminantes en agua y agua residual

Atrasentan and renal events in patients with type 2 diabetes and chronic kidney disease (SONAR): a double-blind, randomised, placebo-controlled trial

Background: Short-term treatment for people with type 2 diabetes using a low dose of the selective endothelin A receptor antagonist atrasentan reduces albuminuria without causing significant sodium retention. We report the long-term effects of treatment with atrasentan on major renal outcomes. Methods: We did this double-blind, randomised, placebo-controlled trial at 689 sites in 41 countries. We enrolled adults aged 18–85 years with type 2 diabetes, estimated glomerular filtration rate (eGFR)25–75 mL/min per 1·73 m 2 of body surface area, and a urine albumin-to-creatinine ratio (UACR)of 300–5000 mg/g who had received maximum labelled or tolerated renin–angiotensin system inhibition for at least 4 weeks. Participants were given atrasentan 0·75 mg orally daily during an enrichment period before random group assignment. Those with a UACR decrease of at least 30% with no substantial fluid retention during the enrichment period (responders)were included in the double-blind treatment period. Responders were randomly assigned to receive either atrasentan 0·75 mg orally daily or placebo. All patients and investigators were masked to treatment assignment. The primary endpoint was a composite of doubling of serum creatinine (sustained for ≥30 days)or end-stage kidney disease (eGFR <15 mL/min per 1·73 m 2 sustained for ≥90 days, chronic dialysis for ≥90 days, kidney transplantation, or death from kidney failure)in the intention-to-treat population of all responders. Safety was assessed in all patients who received at least one dose of their assigned study treatment. The study is registered with ClinicalTrials.gov, number NCT01858532. Findings: Between May 17, 2013, and July 13, 2017, 11 087 patients were screened; 5117 entered the enrichment period, and 4711 completed the enrichment period. Of these, 2648 patients were responders and were randomly assigned to the atrasentan group (n=1325)or placebo group (n=1323). Median follow-up was 2·2 years (IQR 1·4–2·9). 79 (6·0%)of 1325 patients in the atrasentan group and 105 (7·9%)of 1323 in the placebo group had a primary composite renal endpoint event (hazard ratio [HR]0·65 [95% CI 0·49–0·88]; p=0·0047). Fluid retention and anaemia adverse events, which have been previously attributed to endothelin receptor antagonists, were more frequent in the atrasentan group than in the placebo group. Hospital admission for heart failure occurred in 47 (3·5%)of 1325 patients in the atrasentan group and 34 (2·6%)of 1323 patients in the placebo group (HR 1·33 [95% CI 0·85–2·07]; p=0·208). 58 (4·4%)patients in the atrasentan group and 52 (3·9%)in the placebo group died (HR 1·09 [95% CI 0·75–1·59]; p=0·65). Interpretation: Atrasentan reduced the risk of renal events in patients with diabetes and chronic kidney disease who were selected to optimise efficacy and safety. These data support a potential role for selective endothelin receptor antagonists in protecting renal function in patients with type 2 diabetes at high risk of developing end-stage kidney disease. Funding: AbbVie

The Athena X-ray Integral Field Unit: a consolidated design for the system requirement review of the preliminary definition phase

The Athena X-ray Integral Unit (X-IFU) is the high resolution X-ray spectrometer, studied since 2015 for flying in the mid-30s on the Athena space X-ray Observatory, a versatile observatory designed to address the Hot and Energetic Universe science theme, selected in November 2013 by the Survey Science Committee. Based on a large format array of Transition Edge Sensors (TES), it aims to provide spatially resolved X-ray spectroscopy, with a spectral resolution of 2.5 eV (up to 7 keV) over an hexagonal field of view of 5 arc minutes (equivalent diameter). The X-IFU entered its System Requirement Review (SRR) in June 2022, at about the same time when ESA called for an overall X-IFU redesign (including the X-IFU cryostat and the cooling chain), due to an unanticipated cost overrun of Athena. In this paper, after illustrating the breakthrough capabilities of the X-IFU, we describe the instrument as presented at its SRR, browsing through all the subsystems and associated requirements. We then show the instrument budgets, with a particular emphasis on the anticipated budgets of some of its key performance parameters. Finally we briefly discuss on the ongoing key technology demonstration activities, the calibration and the activities foreseen in the X-IFU Instrument Science Center, and touch on communication and outreach activities, the consortium organisation, and finally on the life cycle assessment of X-IFU aiming at minimising the environmental footprint, associated with the development of the instrument. Thanks to the studies conducted so far on X-IFU, it is expected that along the design-to-cost exercise requested by ESA, the X-IFU will maintain flagship capabilities in spatially resolved high resolution X-ray spectroscopy, enabling most of the original X-IFU related scientific objectives of the Athena mission to be retained. (abridged).Comment: 48 pages, 29 figures, Accepted for publication in Experimental Astronomy with minor editin

The Athena X-ray Integral Field Unit: a consolidated design for the system requirement review of the preliminary definition phase

The Athena X-ray Integral Unit (X-IFU) is the high resolution X-ray spectrometer studied since 2015 for flying in the mid-30s on the Athena space X-ray Observatory. Athena is a versatile observatory designed to address the Hot and Energetic Universe science theme, as selected in November 2013 by the Survey Science Committee. Based on a large format array of Transition Edge Sensors (TES), X-IFU aims to provide spatially resolved X-ray spectroscopy, with a spectral resolution of 2.5 eV (up to 7 keV) over a hexagonal field of view of 5 arc minutes (equivalent diameter). The X-IFU entered its System Requirement Review (SRR) in June 2022, at about the same time when ESA called for an overall X-IFU redesign (including the X-IFU cryostat and the cooling chain), due to an unanticipated cost overrun of Athena. In this paper, after illustrating the breakthrough capabilities of the X-IFU, we describe the instrument as presented at its SRR (i.e. in the course of its preliminary definition phase, so-called B1), browsing through all the subsystems and associated requirements. We then show the instrument budgets, with a particular emphasis on the anticipated budgets of some of its key performance parameters, such as the instrument efficiency, spectral resolution, energy scale knowledge, count rate capability, non X-ray background and target of opportunity efficiency. Finally, we briefly discuss the ongoing key technology demonstration activities, the calibration and the activities foreseen in the X-IFU Instrument Science Center, touch on communication and outreach activities, the consortium organisation and the life cycle assessment of X-IFU aiming at minimising the environmental footprint, associated with the development of the instrument. Thanks to the studies conducted so far on X-IFU, it is expected that along the design-to-cost exercise requested by ESA, the X-IFU will maintain flagship capabilities in spatially resolved high resolution X-ray spectroscopy, enabling most of the original X-IFU related scientific objectives of the Athena mission to be retained. The X-IFU will be provided by an international consortium led by France, The Netherlands and Italy, with ESA member state contributions from Belgium, Czech Republic, Finland, Germany, Poland, Spain, Switzerland, with additional contributions from the United States and Japan.The French contribution to X-IFU is funded by CNES, CNRS and CEA. This work has been also supported by ASI (Italian Space Agency) through the Contract 2019-27-HH.0, and by the ESA (European Space Agency) Core Technology Program (CTP) Contract No. 4000114932/15/NL/BW and the AREMBES - ESA CTP No.4000116655/16/NL/BW. This publication is part of grant RTI2018-096686-B-C21 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”. This publication is part of grant RTI2018-096686-B-C21 and PID2020-115325GB-C31 funded by MCIN/AEI/10.13039/501100011033