BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features

Abstract Background Understanding how biomolecules interact is a major task of systems biology. To model protein-nucleic acid interactions, it is important to identify the DNA or RNA-binding residues in proteins. Protein sequence features, including the biochemical property of amino acids and evolutionary information in terms of position-specific scoring matrix (PSSM), have been used for DNA or RNA-binding site prediction. However, PSSM is rather designed for PSI-BLAST searches, and it may not contain all the evolutionary information for modelling DNA or RNA-binding sites in protein sequences. Results In the present study, several new descriptors of evolutionary information have been developed and evaluated for sequence-based prediction of DNA and RNA-binding residues using support vector machines (SVMs). The new descriptors were shown to improve classifier performance. Interestingly, the best classifiers were obtained by combining the new descriptors and PSSM, suggesting that they captured different aspects of evolutionary information for DNA and RNA-binding site prediction. The SVM classifiers achieved 77.3% sensitivity and 79.3% specificity for prediction of DNA-binding residues, and 71.6% sensitivity and 78.7% specificity for RNA-binding site prediction. Conclusions Predictions at this level of accuracy may provide useful information for modelling protein-nucleic acid interactions in systems biology studies. We have thus developed a web-based tool called BindN+ (http://bioinfo.ggc.org/bindn+/) to make the SVM classifiers accessible to the research community

A geography of residents' worry about the disruptive effects of contaminated sites

© 2018 Institute of Australian Geographers While the links between contaminated sites and adverse effects on human health and well-being are being increasingly recognised, some argue that the magnitude of the health problem is inadequately addressed because it is largely invisible. Health geographies literature has sought to highlight this invisibility by focusing on the link between contaminated sites and health. This study adds to health geographies by presenting unique insights into the geography of residents' worry about the disruptive effect of environmental contamination on health and well-being. It analyses a sample of residents (n = 485) living near 13 contaminated sites across Australia. Ordinal logistic regression analysis of closed-format survey questions was combined with coding of open-ended survey questions to reveal the geography of residents' worry about contamination from nearby sites. First, the study explores some of the main relationships between residents, their environs, and contaminants from nearby source sites, which determines their levels of worry: residents' demographics, residents' proximity to sites, contaminant boundaries and borders, and type of contaminant. Second, the study investigates how worry affects residents' health and well-being, ranging from effects on their personal functioning through to their sense of ontological security, which depends in part upon their perceptions of contaminants' impacts. Despite having identified a range of diverse and negative effects of worry about contamination on residents, we found that worry for contamination can also prompt coping strategies and problem-solving, reinforcing the need for more research on this subject

Thick collagen-based 3D matrices including growth factors to induce neurite outgrowth

Designing synthetic microenvironments for cellular investigations is a very active area of research at the crossroads of cell biology and materials science. The present work describes the design and functionalization of a three-dimensional (3D) culture support dedicated to the study of neurite outgrowth from neural cells. It is based on a dense self-assembled collagen matrix stabilized by 100-nm wide interconnected native fibrils without chemical crosslinking. The matrices were made suitable for cell manipulation and direct observation in confocal microscopy by anchoring them to traditional glass supports with a calibrated thickness of ∼50 μm. The matrix composition can be readily adapted to specific neural cell types, notably by incorporating appropriate neurotrophic growth factors. Both PC-12 and SH-SY5Y lines respond to growth factors (nerve growth factor and brain-derived neurotrophic factor, respectively) impregnated and slowly released from the support. Significant neurite outgrowth is reported for a large proportion of cells, up to 66% for PC12 and 49% for SH-SY5Y. It is also shown that both growth factors can be chemically conjugated (EDC/NHS) throughout the matrix and yield similar proportions of cells with longer neurites (61% and 52%, respectively). Finally, neurite outgrowth was observed over several tens of microns within the 3D matrix, with both diffusing and immobilized growth factors

Synthesis of Well-Defined, Surfactant-Free Co₃O₄ Nanoparticles:The Impact of Size and Manganese Promotion on Co₃O₄ Reduction and Water Oxidation Activity

Abstract: A surfactant-free synthetic route has been developed to produce size-controlled, cube-like cobalt oxide nanoparticles of three different sizes in high yields. It was found that by using sodium nitrite as salt-mediating agent, near-quantitative yields could be obtained. The size of the nanoparticles could be altered from 11 to 22 nm by changing the cobalt concentration and reaction time. These surfactant-free nanoparticles form ideal substrates for facile deposition of further elements such as manganese. The effect of size of the cobalt oxide nanoparticles and the presence of manganese on the reducibility of cobalt oxide to metallic cobalt was investigated. Similarly, the effect of these parameters was investigated with a visible light promoted water oxidation system with cobalt oxide as catalyst, together with [Ru(bpy) 3] 2+ light harvester dye and an electron acceptor. Graphical Abstract: A novel surfactant-free synthetic route has been developed to produce size-controlled, cube shaped cobalt oxide nanoparticles in high yields. [Figure not available: see fulltext.]. </p

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

Oksidacijski stres u lakirera izloženih niskim razinama olova

Lead toxicity is a public health problem particularly to the children and to occupationally exposed adults. Evidence is mounting successively regarding the adverse health effects of lead at low levels. This study was undertaken to assess the antioxidant status of lead-exposed residential and commercial painters of Lucknow city in Uttar Pradesh, India. Thirty-five painters aged 20 to 50 years who had blood lead levels ≤400 µg L-1 were selected for the study from a population of 56 male painters initially screened for blood lead. The control group included an equal number of subjects of the same age group without any occupational exposure to lead. We studied the association between low lead level exposure and antioxidant status and found that blood lead levels in painters were approximately seven times as high as in controls [(219.2 ± 61.9) µg L-1 vs. (30.6±10.1) µg L-1, respectively]. Among the biomarkers of lead toxicity a significant decrease in the level of delta-aminolevulinic acid dehydratase [(9.13±4.62) UL-1 vs. (39.38±5.05) UL-1] and an increase in the level of zinc protoporphyrin [(187.9±49.8) µg L-1 vs. (26.4±5.5) µg L-1] were observed in painters compared to controls. Among antioxidant enzymes, painters showed a significant decrease in catalase [(56.77±11.11) UL-1 vs. (230.30±42.55) UL-1] and superoxide dismutase [(0.64±0.19) UL-1 vs. (2.68±0.62) UL-1] compared to controls. Lipid peroxidation was monitored by measuring thiobarbituric acid reactive substances (TBARS) that were expressed in terms of malondialdehyde (MDA) equivalents. Concentration of MDA in plasma was higher in painters than in controls [(7.48±1.31) nmol mL-1 vs. (3.08±0.56) nmol mL-1]. Significant changes were also observed in reduced and oxidised glutathione levels. The strong association between blood lead levels and oxidative stress markers in this population suggests that oxidative stress should be considered in the pathogenesis of lead-related diseases among people with low level environmental exposure to lead.Toksičnost olova javnozdravstveni je problem, napose u djece i odraslih osoba koje su im izložene profesionalno. Sve je više dokaza o štetnom djelovanju olova pri niskim razinama. Svrha je ovog ispitivanja bila procijeniti antioksidacijski status u lakirera iz grada Lucknowa u indijskoj pokrajini Uttar Pradesh. Iz skupine od 56 muškaraca lakirera u dobi od 20 do 50 godina s pozitivnim početnim nalazima olova u krvi, za ispitivanje su izabrana 35-orica čije su razine iznosile ≤400 µg L-1. Izabran je i jednaki broj kontrolnih ispitanika iz iste dobne skupine, koji nisu bili profesionalno izloženi olovu. Ispitana je povezanost izme|u izloženosti niskim razinama olova i antioksidacijskoga stanja te je utvrđeno da su razine olova u krvi lakirera [(219,2±61,9) µg L-1] bile oko sedam puta više negoli u kontrolnih ispitanika [(30,6±10,1) µg L-1]. Od biopokazatelja toksičnosti olova u lakirera je zamijećen značajan pad razina delta- ALAD [(9,13±4,62) UL-1 prema (39,38±5,05) UL-1] te rast razina cinkova protoporfirina [(187,9±49,8) µg L-1 prema (26,4±5,5) µg L-1] u odnosu na kontrolne ispitanike. Od antioksidacijskih enzima u lakirera je značajno pala aktivnost katalaze [(56,77±11,11) UL-1 prema (230,30±42,55) UL-1] i superoksid dismutaze [(0,64±0.19) UL-1 prema (2,68±0,62) UL-1] u odnosu na kontrolu, dok je produkt lipidne peroksidacije u plazmi (izv. thiobarbituric acid reactive substances, TBARS) izražen kao koncentracija malondialdehida (MDA) porastao [(7,48±1,31) nmol mL-1 prema (3,08±0,56) nmol mL-1]. Značajne su promjene također zamijećene u smanjenim razinama glutationa i njihovoj oksidaciji. Snažna povezanost razina olova u krvi s pokazateljima oksidacijskoga stresa upućuje na to da u osoba s niskom razinom izloženosti olovu iz okoliša kod razmatranja patogeneze bolesti povezane s olovom u obzir valja uzeti oksidacijski stres

Interactions entre sémaphorines de classe III et molécules d'adhérence de la super famille des immunoglobulines dans le guidage axonal

Les axones possèdent un cône de croissance qui intègre les effets répulsifs et attractifs de signaux environnementaux pour se diriger vers leurs tissus cibles. La Semaphorine3A repousse les cônes de croissance par l activation d un complexe récepteur formé de la Neuropiline-1 qui lie le ligand, et d une Plexin-A, qui contrôle le remodelage du cytosquelette d actine. Un troisième partenaire a été identifié, la molécule d adhérence (IgCAM) L1, dont la fonction reste inconnue. Nous avons démontré la participation d une nouvelle IgCAM au complexe récepteur de deux autres Sémaphorines. Puis, nous avons montré que la sous-unité IgCAM contrôle un processus nécessaire à la réponse répulsive aux Sémaphorines, qui est le désassemblage des contacts adhérents entre les cônes de croissance et leur substratAxons elaborate growth cones, which integrate repulsive and attractive effects of environmental guidance cues to reach their target tissue. The Semaphorin3A repels the growth cones by activating a receptor complex composed of Neuropilin-1, the ligand binding sub-unit, and Plexin-A controlling the cytoskeleton remodeling. The cell adhesion molecule (IgCAM) L1 was found as a third partner of this complex, but its function remains unknown. We identified an IgCAM partner in the receptor complex of two other Semaphorins and demonstrated its implication in their guidance function. We investigated the role of L1 in the Sema3A receptor and found that it controls a crucial process of the repulsive behavior, which is the disassembly of adherent contacts between growth cones and their substrateLYON1-BU.Sciences (692662101) / SudocSudocFranceF