Gravitomagnetism, clocks and geometry

New techniques to evaluate the clock effect using light are described. These are based on the flatness of the cylindrical surface containing the world lines of the rays constrained to move on circular trajectories about a spinning mass. The effect of the angular momentum of the source is manifested in the fact that inertial observers must be replaced by local non rotating observers. Starting from this an exact formula for circular trajectories is found. Numerical estimates for the Earth environment show that light would be a better probe than actual clocks to evidence the angular momentum influence. The advantages of light in connection with some principle experiments are shortly reviewed.Comment: TCI Latex, 12 pages, 2 figures. To appear in European Journal of Physic

Calibration of a granular matrix sensor for suction measurements in partially saturated pyroclastic soil

Field monitoring of soil moisture and matrix suction is a useful tool for the implementation of a reliable early warning system against rainfall-induced landslide occurrence. Several test fields have been set up in Campania region (southern Italy), frequently affected by flow-like landslides involving pyroclastic soil cover. In particular, at the Mount Faito test site (Lattari Mountains, southeast of Naples), field matric suctions were measured over two years by conventional jet-fill tensiometers and granular matrix sensors (Watermark, Irrometer®) at different depths. Granular matrix sensor is a resistive device that is more and more spread in agriculture applications and that may also be used for geotechnical purposes thanks to a suitable calibration. In order to gain the calibration curve of the Watermark sensor, two small tip tensiometers (STT) and one High Capacity Tensiometer (HCT) were installed at the same depth of the Watermark sensor in the partially saturated pyroclastic soil sampled at the topsoil of the Mount Faito test site. Tests were carried out in the laboratory by performing drying and wetting phases on undisturbed soil sample. By coupling resistance measurements by Watermark and matrix suction provided by the reference tensiometers, it was possible to derive the non-linear relationship between these two quantities. The soil retention curve was also determined thanks to the installation in the soil sample of a decagon probe previously calibrated in the same pyroclastic soil

Prediction of Local Structural Stabilities of Proteins from Their Amino Acid Sequences

Hydrogen exchange experiments provide detailed information about the local stability and the solvent accessibility of different regions of the structures of folded proteins, protein complexes, and amyloid fibrils. We introduce an approach to predict protection factors from hydrogen exchange in proteins based on the knowledge of their amino acid sequences without the inclusion of any additional structural information. These results suggest that the propensity of different regions of the structures of globular proteins to undergo local unfolding events can be predicted from their amino acid sequences with an accuracy of 80% or better. © 2007 Elsevier Ltd. All rights reserved

Geometric treatment of the gravitomagnetic clock effect

We have developed a general geometric treatment of the GCE valid for any stationary axisymmetric metric. The method is based on the remark that the world lines of objects rotating along spacely circular trajectories are in any case, for those kind of metrics, helices drawn on the flat bidimensional surface of a cylinder. Applying the obtained formulas to the special cases of the Kerr and weak field metric for a spinning body, known results for time delays and synchrony defects are recovered.Comment: 14 pages, LATEX, 2 figure

A computational approach for the discovery of protein–RNA networks

Protein–RNA interactions play important roles in a wide variety of cellular processes, ranging from transcriptional and posttranscriptional regulation of genes to host defense against pathogens. In this chapter we present the computational approach catRAPID to predict protein–RNA interactions and discuss how it could be used to find trends in ribonucleoprotein networks. We envisage that the combination of computational and experimental approaches will be crucial to unravel the role of coding and noncoding RNAs in protein networks

BacFITBase: A database to assess the relevance of bacterial genes during host infection

Bacterial infections have been on the rise world-wide in recent years and have a considerable impact on human well-being in terms of attributable deaths and disability-adjusted life years. Yet many mechanisms underlying bacterial pathogenesis are still poorly understood. Here, we introduce the BacFITBase database for the systematic characterization of bacterial proteins relevant for host infection aimed to enable the identification of new antibiotic targets. BacFITBase is manually curated and contains more than 90 000 entries with information on the contribution of individual genes to bacterial fitness under in vivo infection conditions in a range of host species. The data were collected from 15 different studies in which transposon mutagenesis was performed, including top-priority pathogens such as Acinetobacter baumannii and Campylobacter jejuni, for both of which increasing antibiotic resistance has been reported. Overall, BacFITBase includes information on 15 pathogenic bacteria and 5 host vertebrates across 10 different tissues. It is freely available at www.tartaglialab.com/bacfitbase

Physicochemical principles that regulate the competition between functional and dysfunctional association of proteins

To maintain protein homeostasis, a variety of quality control mechanisms, such as the unfolded protein response and the heat shock response, enable proteins to fold and to assemble into functional complexes while avoiding the formation of aberrant and potentially harmful aggregates. We show here that a complementary contribution to the regulation of the interactions between proteins is provided by the physicochemical properties of their amino acid sequences. The results of a systematic analysis of the protein-protein complexes in the Protein Data Bank (PDB) show that interface regions are more prone to aggregate than other surface regions, indicating that many of the interactions that promote the formation of functional complexes, including hydrophobic and electrostatic forces, can potentially also cause abnormal intermolecular association. We also show, however, that aggregation-prone interfaces are prevented from triggering uncontrolled assembly by being stabilized into their functional conformations by disulfide bonds and salt bridges. These results indicate that functional and dysfunctional association of proteins are promoted by similar forces but also that they are closely regulated by the presence of specific interactions that stabilize native states

Atrioventricular canal defect and genetic syndromes: the unifying role of sonic hedgehog

The atrioventricular canal defect (AVCD) is a congenital heart defect (CHD) frequently associated with extracardiac anomalies (75%). Previous observations from a personal series of patients with AVCD and "polydactyly syndromes" showed that the distinct morphology and combination of AVCD features in some of these syndromes is reminiscent of the cardiac phenotype found in heterotaxy, a malformation complex previously associated with functional cilia abnormalities and aberrant Hedgehog (Hh) signaling. Hh signaling coordinates multiple aspects of left-right lateralization and cardiovascular growth. Being active at the venous pole the secondary heart field (SHF) is essential for normal development of dorsal mesenchymal protrusion and AVCD formation and septation. Experimental data show that perturbations of different components of the Hh pathway can lead to developmental errors presenting with partially overlapping manifestations and AVCD as a common denominator. We review the potential role of Hh signaling in the pathogenesis of AVCD in different genetic disorders. AVCD can be viewed as part of a "developmental field," according to the concept that malformations can be due to defects in signal transduction cascades or pathways, as morphogenetic units which may be altered by Mendelian mutations, aneuploidies, and environmental causes

The beneficial effect of physiotherapy on the cervical spine mobility of ACDF patients and healthy individuals: An original observational cohort comparison research protocol

Purpose: Population aging and certain behaviors associated with modern life are contributing factors for the increasing incidence of degenerative cervical spine conditions (DCSC), and the number of cervical spine surgeries every year is. Our aim was to determine, with an original research protocol, the impact of ACDF and physiotherapy on the range of motion and EMG parameters of patients suffering from DCSC. Patients and Methods: Two comparable subgroups of 29 patients each were recruited for the present investigation. The first cohort was composed of ACDF patients, whereas the second cohort was composed by healthy subjects. Inclinometry/Range of Motion (RoM) analyses of the neck, and cervical muscles electromyography (EMG) were used to evaluate the neck mobility. We investigated the effects of physiotherapy on ROM and EMG results in order to identify possible significant differences between healthy subjects and ACDF patients. Results: A total of 58 patients were included in the final cohort. Extensive statistical analysis disclosed that higher NDI values were associated with a reduction of the Extension and Rotation movements, NDI scores, were found to be negatively associated to EMG voltages for Rotation, independently of the physiotherapy performed either. Extension, Lateral Bending, and Rotation showed significant improvement after just one session of physiotherapy, whereas Flexion and Extension proved to be those that contributed most to the overall neck mobility. Conclusion: The cervical spine fusion contributes to an overall reduction of cervical mobility. This data is confirmed by inclinometer and EMG parameters. Physiotherapy increases neck mobility thus possibly improving the clinical status of patients

Post-transcriptional regulatory patterns revealed by protein-RNA interactions

The coordination of the synthesis of functionally-related proteins can be achieved at the post-transcriptional level by the action of common regulatory molecules, such as RNA–binding proteins (RBPs). Despite advances in the genome-wide identification of RBPs and their binding transcripts, the protein–RNA interaction space is still largely unexplored, thus hindering a broader understanding of the extent of the post-transcriptional regulation of related coding RNAs. Here, we propose a computational approach that combines protein–mRNA interaction networks and statistical analyses to provide an inferred regulatory landscape for more than 800 human RBPs and identify the cellular processes that can be regulated at the post-transcriptional level. We show that 10% of the tested sets of functionally-related mRNAs can be post-transcriptionally regulated. Moreover, we propose a classification of (i) the RBPs and (ii) the functionally-related mRNAs, based on their distinct behaviors in the functional landscape, hinting towards mechanistic regulatory hypotheses. In addition, we demonstrate the usefulness of the inferred functional landscape to investigate the cellular role of both well-characterized and novel RBPs in the context of human diseases