Structural Biology by NMR: Structure, Dynamics, and Interactions

The function of bio-macromolecules is determined by both their 3D structure and conformational dynamics. These molecules are inherently flexible systems displaying a broad range of dynamics on time-scales from picoseconds to seconds. Nuclear Magnetic Resonance (NMR) spectroscopy has emerged as the method of choice for studying both protein structure and dynamics in solution. Typically, NMR experiments are sensitive both to structural features and to dynamics, and hence the measured data contain information on both. Despite major progress in both experimental approaches and computational methods, obtaining a consistent view of structure and dynamics from experimental NMR data remains a challenge. Molecular dynamics simulations have emerged as an indispensable tool in the analysis of NMR data

Focus on collagen: in vitro systems to study fibrogenesis and antifibrosis _ state of the art

Fibrosis represents a major global disease burden, yet a potent antifibrotic compound is still not in sight. Part of the explanation for this situation is the difficulties that both academic laboratories and research and development departments in the pharmaceutical industry have been facing in re-enacting the fibrotic process in vitro for screening procedures prior to animal testing. Effective in vitro characterization of antifibrotic compounds has been hampered by cell culture settings that are lacking crucial cofactors or are not holistic representations of the biosynthetic and depositional pathway leading to the formation of an insoluble pericellular collagen matrix. In order to appreciate the task which in vitro screening of antifibrotics is up against, we will first review the fibrotic process by categorizing it into events that are upstream of collagen biosynthesis and the actual biosynthetic and depositional cascade of collagen I. We point out oversights such as the omission of vitamin C, a vital cofactor for the production of stable procollagen molecules, as well as the little known in vitro tardy procollagen processing by collagen C-proteinase/BMP-1, another reason for minimal collagen deposition in cell culture. We review current methods of cell culture and collagen quantitation vis-à-vis the high content options and requirements for normalization against cell number for meaningful data retrieval. Only when collagen has formed a fibrillar matrix that becomes cross-linked, invested with ligands, and can be remodelled and resorbed, the complete picture of fibrogenesis can be reflected in vitro. We show here how this can be achieved. A well thought-out in vitro fibrogenesis system represents the missing link between brute force chemical library screens and rational animal experimentation, thus providing both cost-effectiveness and streamlined procedures towards the development of better antifibrotic drugs

Spotlight on Differentially Expressed Genes in Urinary Bladder Cancer

INTRODUCTION: We previously identified common differentially expressed (DE) genes in bladder cancer (BC). In the present study we analyzed in depth, the expression of several groups of these DE genes. MATERIALS AND METHODS: Samples from 30 human BCs and their adjacent normal tissues were analyzed by whole genome cDNA microarrays, qRT-PCR and Western blotting. Our attention was focused on cell-cycle control and DNA damage repair genes, genes related to apoptosis, signal transduction, angiogenesis, as well as cellular proliferation, invasion and metastasis. Four publicly available GEO Datasets were further analyzed, and the expression data of the genes of interest (GOIs) were compared to those of the present study. The relationship among the GOI was also investigated. GO and KEGG molecular pathway analysis was performed to identify possible enrichment of genes with specific biological themes. RESULTS: Unsupervised cluster analysis of DNA microarray data revealed a clear distinction in BC vs. control samples and low vs. high grade tumors. Genes with at least 2-fold differential expression in BC vs. controls, as well as in non-muscle invasive vs. muscle invasive tumors and in low vs. high grade tumors, were identified and ranked. Specific attention was paid to the changes in osteopontin (OPN, SPP1) expression, due to its multiple biological functions. Similarly, genes exhibiting equal or low expression in BC vs. the controls were scored. Significant pair-wise correlations in gene expression were scored. GO analysis revealed the multi-facet character of the GOIs, since they participate in a variety of mechanisms, including cell proliferation, cell death, metabolism, cell shape, and cytoskeletal re-organization. KEGG analysis revealed that the most significant pathway was that of Bladder Cancer (p = 1.5×10(-31)). CONCLUSIONS: The present work adds to the current knowledge on molecular signature identification of BC. Such works should progress in order to gain more insight into disease molecular mechanisms

Capturing geographically-varying uncertainty in earthquake ground motion models or what we think we know may change

Our knowledge of earthquake ground motions of engineering significance varies geographically. The prediction of earthquake shaking in parts of the globe with high seismicity and a long history of observations from dense strong-motion networks, such as coastal California, much of Japan and central Italy, should be associated with lower uncertainty than ground-motion models for use in much of the rest of the world, where moderate and large earthquakes occur infrequently and monitoring networks are sparse or only recently installed. This variation in uncertainty, however, is not often captured in the models currently used for seismic hazard assessments, particularly for national or continental-scale studies. In this theme lecture, firstly I review recent proposals for developing ground-motion logic trees and then I develop and test a new approach for application in Europe. The proposed procedure is based on the backbone approach with scale factors that are derived to account for potential differences between regions. Weights are proposed for each of the logic-tree branches to model large epistemic uncertainty in the absence of local data. When local data are available these weights are updated so that the epistemic uncertainty captured by the logic tree reduces. I argue that this approach is more defensible than a logic tree populated by previously published ground-motion models. It should lead to more stable and robust seismic hazard assessments that capture our doubt over future earthquake shaking

Measurements of atmospheric electricity aloft

Measurements of the electrical characteristics of the atmosphere above the surface have been made for over 200 years, from a variety of different platforms, including kites, balloons, rockets and aircraft. From these measurements, a great deal of information about the electrical characteristics of the atmosphere has been gained, assisting our understanding of the global atmospheric electric circuit, thunderstorm electrification and lightning generation mechanisms, discovery of transient luminous events above thunderstorms, and many other electrical phenomena. This paper surveys the history of atmospheric electrical measurements aloft, from the earliest manned balloon ascents to current day observations with free balloons and aircraft. Measurements of atmospheric electrical parameters in a range of meteorological conditions are described, including clear air conditions, polluted conditions, non-thunderstorm clouds, and thunderstorm clouds, spanning a range of atmospheric conditions, from fair weather, to the most electrically active