Electron Transfer Reactivity of Type Zero Pseudomonas aeruginosa Azurin

Type zero copper is a hard-ligand analogue of the classical type 1 or blue site in copper proteins that function as electron transfer (ET) agents in photosynthesis and other biological processes. The EPR spectroscopic features of type zero Cu^(II) are very similar to those of blue copper, although lacking the deep blue color, due to the absence of thiolate ligation. We have measured the rates of intramolecular ET from the pulse radiolytically generated C3−C26 disulfide radical anion to the Cu^(II) in both type zero C112D/M121L and type 2 C112D Pseudomonas aeruginosa azurins in pH 7.0 aqueous solutions between 8 and 45 °C. We also have obtained rate/temperature (10−30 °C) profiles for ET reactions between these mutants and the wild-type azurin. Analysis of the rates and activation parameters for both intramolecular and intermolecular ET reactions indicates that the type zero copper reorganization energy falls in a range (0.9−1.1 eV) slightly above that for type 1 (0.7−0.8 eV), but substantially smaller than that for type 2 (>2 eV), consistent with XAS and EXAFS data that reveal minimal type zero site reorientation during redox cycling

Unfolding the European Commission's storytelling on ethical trade relations with Vietnam

This paper constructs the narrative behind EU-Vietnam trade relations as told by the European Commission. A policy plot in three 'acts' focuses in particular on the two most recently concluded trade agreements, which share a common narration of 'a force for good.' The EU and Vietnam star as the main characters, who, in their joint attempts to make bilateral trade 'a force for good', live moments of heroism, encounter fleeting moments of victimhood, and defeat the villains on the path to ethical trade. We find that the Commission's narrative essentially reiterates the longstanding 'development' story, in which the EU as a protagonist shapes the world according to its own values. Identified challenges are to be addressed through Vietnam's 'development', using the EU's one-size- fits-all approach. The particularities of these challenges however remain largely obscured, making it impossible to 'name the culprits' and diverting attention away from inconsistencies and conflicts

Folding and Unfolding in the Blue Copper Protein Rusticyanin: Role of the Oxidation State

The unfolding process of the blue copper protein rusticyanin has been studied from the structural and the thermodynamic points of view at two pH values (pH 2.5 and 7.0). When Rc unfolds, copper ion remains bound to the polypeptide chain. Nuclear magnetic resonance data suggest that three of the copper ligands in the folded state are bound to the metal ion in the unfolded form, while the other native ligand is detached. These structural changes are reflected in the redox potentials of the protein in both folded and unfolded forms. The affinities of the copper ion in both redox states have been also determined at the two specified pH values. The results indicate that the presence of two histidine ligands in the folded protein can compensate the change in the net charge that the copper ion receives from their ligands, while, in the unfolded protein, charges of aminoacids are completely transferred to the copper ion, altering decisively the relative stability of its two-redox states

DIANA—algorithmic improvements for analysis of data-independent acquisition MS data

Motivation: Data independent acquisition mass spectrometry has emerged as a reproducible and sensitive alternative in quantitative proteomics, where parsing the highly complex tandem mass spectra requires dedicated algorithms. Recently, targeted data extraction was proposed as a novel analysis strategy for this type of data, but it is important to further develop these concepts to provide quality-controlled, interference-adjusted and sensitive peptide quantification. Results: We here present the algorithm DIANA and the classifier PyProphet, which are based on new probabilistic sub-scores to classify the chromatographic peaks in targeted data-independent acquisition data analysis. The algorithm is capable of providing accurate quantitative values and increased recall at a controlled false discovery rate, in a complex gold standard dataset. Importantly, we further demonstrate increased confidence gained by the use of two complementary data-independent acquisition targeted analysis algorithms, as well as increased numbers of quantified peptide precursors in complex biological samples. Availability and implementation: DIANA is implemented in scala and python and available as open source (Apache 2.0 license) or pre-compiled binaries from http://quantitativeproteomics.org/diana. PyProphet can be installed from PyPi (https://pypi.python.org/pypi/pyprophet). Supplementary information: Supplementary data are available at Bioinformatics onlin

Mass Spectrometric Characterization of Oligomers in Pseudomonas aeruginosa Azurin Solutions

We have employed laser-induced liquid bead ion desorption mass spectroscopy (LILBID MS) to study the solution behavior of Pseudomonas aeruginosa azurin as well as two mutants and corresponding Re-labeled derivatives containing a Re(CO)_(3)(4,7-dimethyl-1,10-phenanthroline)^+ chromophore appended to a surface histidine. LILBID spectra show broad oligomer distributions whose particular patterns depend on the solution composition (pure H_(2)O, 20−30 mM NaCl, 20 and 50 mM NaP_i or NH_(4)P_i at pH = 7). The distribution maximum shifts to smaller oligomers upon decreasing the azurin concentration and increasing the buffer concentration. Oligomerization is less extensive for native azurin than its mutants. The oligomerization propensities of unlabeled and Re-labeled proteins are generally comparable, and only Re126 shows some preference for the dimer that persists even in highly diluted solutions. Peak shifts to higher masses and broadening in 20−50 mM NaP_i confirm strong azurin association with buffer ions and solvation. We have found that LILBID MS reveals the solution behavior of weakly bound nonspecific protein oligomers, clearly distinguishing individual components of the oligomer distribution. Independently, average data on oligomerization and the dependence on solution composition were obtained by time-resolved anisotropy of the Re-label photoluminescence that confirmed relatively long rotation correlation times, 6−30 ns, depending on Re−azurin and solution composition. Labeling proteins with Re-chromophores that have long-lived phosphorescence extends the time scale of anisotropy measurements to hundreds of nanoseconds, thereby opening the way for investigations of large oligomers with long rotation times

Progress towards a Nordic standard for the investigation of hematuria: 2019

Objective: To describe the management of patients with hematuria in the Nordic countries in relation to bladder cancer epidemiology, especially in the context of introducing fast track pathways with the aim of proposing a common guideline.Materials and methods: Epidemiological data on bladder cancer from each country, and the combined cancer registry, Nordcan, were analyzed. The evolution of the different national recommendations and the introduction of fast track pathways were assessed. Patients' demographics, type of hematuria and cancer detection rates were analysed if available.Results: The crude incidence of bladder cancer has increased substantially since the 1960s, while the age standardized incidence has been stable during recent decades. The relative survival has increased in all countries, while the mortality has been stable. For those with microscopic hematuria there has been a clear trend towards less rigorous investigations. In the fast track pathways, introduced in three of five countries, about one in five patients with macroscopic hematuria had a cancer diagnosis. Data show that time to diagnosis has been reduced.Conclusions: The number of patients with bladder cancer is increasing in the Nordic region. The introduction of fast track pathways has been important in improving the management of patients with suspicion of the disease. Our recommendation is to focus on macroscopic hematuria in the fast track pathways. Microhematuria without any symptoms should not be an indication for cystoscopy. However, urinary tract symptoms accompanied by microhematuria can still be investigated according to respective guidelines but not necessarily within fast track pathways.</p

Estimation of permafrost thawing rates in a sub-arctic catchment using recession flow analysis

Permafrost thawing is likely to change the flow pathways taken by water as it moves through arctic and sub-arctic landscapes. The location and distribution of these pathways directly influence the carbon and other biogeochemical cycling in northern latitude catchments. While permafrost thawing due to climate change has been observed in the arctic and sub-arctic, direct observations of permafrost depth are difficult to perform at scales larger than a local scale. Using recession flow analysis, it may be possible to detect and estimate the rate of permafrost thawing based on a long-term streamflow record. We demonstrate the application of this approach to the sub-arctic Abiskojokken catchment in northern Sweden. Based on recession flow analysis, we estimate that permafrost in this catchment may be thawing at an average rate of about 0.9 cm/yr during the past 90 years. This estimated thawing rate is consistent with direct observations of permafrost thawing rates, ranging from 0.7 to 1.3 cm/yr over the past 30 years in the region

DESIGN, PERFORMANCE ANALYSIS AND EFFICIENCY OPTIMIZATION OF COPPER INDIUM GALLIUM SELENIDE (CIGS) SOLAR CELL

A comparative investigation of the cell performance of Copper Indium Gallium Selenide (CIGS) thin-film solar cell, fabricated using ZnO:Al/i-ZnO/CdS/CIGS layers, has been reported. ADEPT 2.0, a 1D simulation software, were used throughout the whole research for the simulation of light J-V characteristics for different designs. Energy conversion efficiency for each design was calculated from its corresponding light J-V characteristics curve. The efficiency variation were investigated under 1 sun, AM1.5G illumination and optimized layer parameters (thickness) for each layer of the device. The device has designed with an ntype ZnO window layer, an n-type CdS as buffer layer and a p-type CIGS as absorber layer. Molybdenum (Mo) substrate is used for the structure. A totalarea efficiency of 19·75% for ZnO:Al/i-ZnO/CdS/CIGS based thin-film solar cells had been found. Performance is improved due to higher fill factor. The device parameters are optimized separately for each layer. Based on these optimizations, the ultra-thin film solar cell design is proposed after careful consideration of lattice mismatch between two adjacent layers of the device

Non-muscle-invasive bladder cancer: a vision for the future

The management of non-muscle-invasive bladder cancer (NMIBC) has evolved from the first reports on bladder endoscopy and transurethral resection to the introduction of adjuvant intravesical treatment. However, disease recurrence and progression remain an ongoing risk, placing a heavy burden on healthcare resources and on patients' quality of life. Deeper understanding of the molecular basis of the disease and developments in optics, lasers and computer science are already offering opportunities to revolutionize care and improve long-term prognosis. This article discusses developments likely to cause a paradigm shift towards the delivery of personalized care and reduced burden of disease in NMIBC

Catalog of prognostic tissue-based biomarkers in patients treated with neoadjuvant systemic therapy for urothelial carcinoma of the bladder: a systematic review

PURPOSE The present systematic review aimed to identify prognostic values of tissue-based biomarkers in patients treated with neoadjuvant systemic therapy (NAST), including chemotherapy (NAC) and checkpoint inhibitors (NAI) for urothelial carcinoma of the bladder (UCB). MATERIAL AND METHODS The PubMed, Web of Science, and Scopus databases were searched in August 2020 according to the PRISMA statement. Studies were deemed eligible if they compared oncologic or pathologic outcomes in patients treated with NAST for UCB with and without detected pretreatment tissue-based biomarkers. RESULTS Overall, 44 studies met our eligibility criteria. Twenty-three studies used immunohistochemistry (IHC), 19 – gene expression analysis, three - quantitative polymerase chain reaction (QT PCR), and two – next-generation sequencing (NGS). According to the currently available literature, predictive IHC-assessed biomarkers, such as receptor tyrosine kinases and DNA repair pathway alterations, do not seem to convincingly improve our prediction of pathologic response and oncologic outcomes after NAC. Luminal and basal tumor subtypes based on gene expression analysis showed better NAC response, while claudin-low and luminal-infiltrated tumor subtypes did not. In terms of NAI, PD-L1 seems to maintain value as a predictive biomarker, while the utility of both tumor mutational burden and molecular subtypes remains controversial. Specific genomic alterations in DNA repair genes have been shown to provide significant predictive value in patient treated with NAC. QT PCR quantification of specific genes selected through microarray analysis seems to classify cases regarding their NAC response. CONCLUSION We believe that the present systematic review may offer a robust framework that will enable the testing and validation of predictive biomarkers in future prospective clinical trials. NGS has expanded the discovery of molecular markers that are reflective of the mechanisms of the NAST response