Complex networks: the key to systems biology

Though introduced recently, complex networks research has grown steadily because of its potential to represent, characterize and model a wide range of intricate natural systems and phenomena. Because of the intrinsic complexity and systemic organization of life, complex networks provide a specially promising framework for systems biology investigation. The current article is an up-to-date review of the major developments related to the application of complex networks in biology, with special attention focused on the more recent literature. The main concepts and models of complex networks are presented and illustrated in an accessible fashion. Three main types of networks are covered: transcriptional regulatory networks, protein-protein interaction networks and metabolic networks. The key role of complex networks for systems biology is extensively illustrated by several of the papers reviewed.FAPESPCNP

Efficient Anodically Grown WO3 for Photoelectrochemical Water Splitting

Abstract The potentiostatic anodization of metallic tungsten has been investigated in different solvent/electrolyte compositions with the aim of improving the photoelectrochemical performances of the tungsten oxide layer. Among the explored electrolytes, the anodization in the NMF/H2O/NH4F solvent mixture was found to produce the most efficient WO3 photoanodes, which, combining spectral sensitivity, high electrochemically active surface and improved charge transfer kinetics, outperform, under simulated solar illumination, most of the reported nanocrystalline substrates produced by anodization in aqueous electrolytes and by sol gel methods. While the preparation of the photoelectrodes is a slow process at room temperature (20 °C), it could be greatly accelerated (x 10) by carrying out the anodization at 40-50 °C, thus proving to be a fast and convenient approach to the production of high performing WO3 photoactive substrates directly connected to a metal electron collector

Tumor type M2-pyruvate-kinase levels in pleural fluid versus plasma in cancer patients: a further tool to define the need for invasive procedures

Pleural effusion is a common diagnostic problem and a challenge to the thoracic surgeon. The analysis of serum and body fluids for tumor markers is an established diagnostic procedure. Among various markers, tumors are linked to the overexpression of a glycolytic isoenzyme, M2-pyruvate-kinase (M2-PK). This preliminary study evaluated this enzyme as a tumor marker to differentiate malignant from benign pleural effusion

Investigating the Origin of Mycobacterium chimaera Contamination in Heater-Cooler Units: Integrated Analysis with Fourier Transform Infrared Spectroscopy and Whole-Genome Sequencing

Mycobacterium chimaera is ubiquitously spread in the environment, including factory and hospital water systems. Invasive cases of M. chimaera infection have been associated with aerosols produced by the use of heater-cooler units (HCU) during cardiac surgery. The aim of this study was to evaluate for the first time the performance of IR-Biotyper system on a large number of M. chimaera isolates collected from longitudinal environmental HCUs samples and water sources from hospitals located in three Italian provinces. In addition, IR-Biotyper results were compared with whole-genome sequencing (WGS) analysis, the reference method for molecular epidemiology, to investigate the origin of M. chimaera contamination of HCUs. From November 2018 to May 2021, 417 water samples from 52 HCUs (Stockert 3T, n = 41 and HCU40, n = 11) and 23 hospital taps (used to fill the HCU tanks) were concentrated, decontaminated, and cultured for M. chimaera. Positive cultures (n = 53) were purified by agar plate subcultures and analyzed by IR-Biotyper platform and Ion Torrent sequencing system. IR-Biotyper spectra results were analyzed using a statistical approach of dimensionality reduction by linear discriminant analysis (LDA), generating three separate clusters of M. chimaera, ascribable to each hospital. Furthermore, the only M. chimaera-positive sample from tap water clustered with the isolates from the HCUs of the same hospital, confirming that the plumbing system could represent the source of HCU contamination and, potentially, of patient infection. According to the genome-based phylogenies and following the classification proposed by van Ingen and collaborators in 2017, three distinct M. chimaera groups appear to have contaminated the HCU water systems: subgroups 1.1, 2.1, and branch 2. Most of the strains isolated from HCUs at the same hospital share a highly similar genetic profile. The nonrandom distribution obtained with WGS and IR-Biotyper leads to the hypothesis that M. chimaera subtypes circulating in the local plumbing colonize HCUs through the absolute filter, in addition with the current hypothesis that contamination occurs at the HCU production site. This opens the possibility that other medical equipment, such as endoscope reprocessing device or hemodialysis systems, could be contaminated by M. chimaera. IMPORTANCE Our manuscript focuses on interventions to reduce waterborne disease transmission, improve sanitation, and control infection. Sanitary water can be contaminated by nontuberculous Mycobacteria, including M. chimaera, a causative agent of invasive infections in immunocompromised patients. We found highly similar genetic and phenotypic profiles of M. chimaera isolated from heater-cooler units (HCU) used during surgery to thermo-regulate patients' body temperature, and from the same hospital tap water. These results lead to the hypothesis that M. chimaera subtypes circulating in the local plumbing colonize HCUs through the absolute filter, adding to the current hypothesis that contamination occurs at the HCU production site. In addition, this opens the possibility that other medical equipment using sanitized water, such as endoscope reprocessing devices or hemodialysis systems, could be contaminated by nontuberculous Mycobacteria, suggesting the need for environmental surveillance and associated control measures

A Phylogenomic Approach for the Analysis of Colistin Resistance-Associated Genes in Klebsiella Pneumoniae, its Mutational Diversity and Implications for Phenotypic Resistance

The emergence of carbapenemase-producing Klebsiella pneumoniae strains has triggered the use of old antibiotics such as colistin. This is driving the emergence of colistin resistance in multidrug-resistant strains that underlie life-threatening infections. This study analyses the mutational diversity of 22 genes associated with colistin resistance in 140 K. pneumoniae clinical isolates integrated in a high-resolution phylogenetic scenario. Colistin susceptibility was accessed by broth microdilution. A total of 98 isolates were susceptible and 16 were resistant, 10 of which were carbapenemase producers. Across the 22 genes examined, 171 non-synonymous mutations and 9 mutations associated with promoter regions were found. Eighty-five isolates had a truncation and/or deletion in at least one of the 22 genes. However, only seven mutations, the complete deletion of mgrB or insertion sequence (IS)-mediated disruption, were exclusively observed in resistant isolates. Four of these (mgrBIle13fs, pmrBGly207Asp, phoQHis339Asp and ramAIle28Met) comprised novel mutations that are potentially involved in colistin resistance. One strain bore a ISEcp1-blaCTX-M-15::mgrB disruption, underlying co-resistance to third-generation cephalosporins and colistin. Moreover, the high-resolution phylogenetic context shows that most of the mutational diversity spans multiple phylogenetic clades, and most of the mutations previously associated with colistin resistance are clade-associated and present in susceptible isolates, showing no correlation with colistin resistance. In conclusion, the present study provides relevant data on the genetic background of genes involved with colistin resistance deeply rooted across monophyletic groups and provides a better understanding of the genes and mutations involved in colistin resistance.info:eu-repo/semantics/publishedVersio

Artificial photosynthesis: photoanodes based on polyquinoid dyes onto mesoporous tin oxide surface

Dye-sensitized photoelectrochemical cells represent an appealing solution for artificial photosynthesis, aimed at the conversion of solar light into fuels or commodity chemicals. Extensive efforts have been directed towards the development of photoelectrodes combining semiconductor materials and organic dyes; the use of molecular components allows to tune the absorption and redox properties of the material. Recently, we have reported the use of a class of pentacyclic quinoid organic dyes (KuQuinone) chemisorbed onto semiconducting tin oxide as photoanodes for water oxidation. In this work, we investigate the effect of the SnO2 semiconductor thickness and morphology and of the dye-anchoring group on the photoelectrochemical performance of the electrodes. The optimized materials are mesoporous SnO2 layers with 2.5 mu m film thickness combined with a KuQuinone dye with a 3-carboxylpropyl-anchoring chain: these electrodes achieve light-harvesting efficiency of 93% at the maximum absorption wavelength of 533 nm, and photocurrent density J up to 350 mu A/cm(2) in the photoelectrochemical oxidation of ascorbate, although with a limited incident photon-to-current efficiency of 0.075%. Calculations based on the density functional theory (DFT) support the role of the reduced species of the KuQuinone dye via a proton-coupled electron transfer as the competent species involved in the electron transfer to the tin oxide semiconductor. Finally, a preliminary investigation of the photoelectrodes towards benzyl alcohol oxidation is presented, achieving photocurrent density up to 90 mu A/cm(2) in acetonitrile in the presence of N-hydroxysuccinimide and pyridine as redox mediator and base, respectively. These results support the possibility of using molecular-based materials in synthetic photoelectrochemistry.[GRAPHICS]

Development and validation of low-intensity pulsed ultrasound systems for highly controlled in vitro cell stimulation

This work aims to describe the development and validation of two low-intensity pulsed ultrasound stimulation systems able to control the dose delivered to the biological target. Transducer characterization was performed in terms of pressure field shape and intensity, for a high-frequency range (500 kHz to 5 MHz) and for a low- frequency value (38 kHz). This allowed defining the distance, on the beam axis, at which biological samples should be placed during stimulation and to exactly know the intensity at the target. Carefully designed retaining systems were developed, for hosting biological samples. Sealing tests proved their impermeability to external contaminants. The assembly/de-assembly time of the systems resulted ~3 min. Time-domain acoustic simula- tions allowed to precisely estimate the ultrasound beam within the biological sample chamber, thus enabling the possibility to precisely control the pressure to be transmitted to the biological target, by modulating the trans- ducer’s input voltage. Biological in vitro tests were also carried out, demonstrating the sterility of the system and the absence of toxic and inflammatory effects on growing cells after multiple immersions in water, over seven day

Inspiratory fraction and exercise impairment in COPD patients GOLD stages II-III

The inspiratory-to-total lung capacity ratio or inspiratory fraction (inspiratory capacity (IC)/total lung capacity (TLC)) may be functionally more representative than traditional indices of resting airflow limitation and lung hyperinflation in patients with chronic obstructive pulmonary disease (COPD).In the present retrospective study, a comparison was made of the individual performance of post-bronchodilator IC, IC/TLC and forced expiratory volume in one second (FEV1) in predicting a severely reduced peak oxygen uptake (V'o(2); < 60% predicted) in 44 COPD patients Global Initiative for Chronic Obstructive Lung Disease stages II-III (post-bronchodilator FEV1 ranging from 31-79% pred).Patients with lower IC/TLC values (<= 0.28) showed increased lung volumes and reduced exercise capacity as compared with other subjects. Following a multiple linear regression analysis, only IC/TLC and FEV1 remained as independent predictors of V'o(2) (r(2)=0.33). A receiver operating characteristic (ROC) curve analysis revealed that an IC/TLC <= 0.28 had the highest specificity (89.6%), positive predictive value (80%) and overall accuracy (86.3%) in identifying patients with V'o(2)< 60% pred. in addition, the area under the ROC curve tended to be higher for IC/TLC than IC.In conclusion, post-bronchodilator total lung capacity-corrected inspiratory fraction provides useful information in addition to forced expiratory volume in one second and inspiratory capacity, to estimate the likelihood of chronic obstructive pulmonary disease patients to present with severely reduced maximal exercise capacity.Universidade Federal de São Paulo, Paulista Sch Med, Pulm Funct & Clin Exercise Physiol Unit, Resp Div,Dept Med,EPM, BR-04020050 São Paulo, BrazilUniversidade Federal de São Paulo, Paulista Sch Med, Pulm Funct & Clin Exercise Physiol Unit, Resp Div,Dept Med,EPM, BR-04020050 São Paulo, BrazilWeb of Scienc