Protein homology reveals new targets for bioactive small molecules.

MOTIVATION: The functional impact of small molecules is increasingly being assessed in different eukaryotic species through large-scale phenotypic screening initiatives. Identifying the targets of these molecules is crucial to mechanistically understand their function and uncover new therapeutically relevant modes of action. However, despite extensive work carried out in model organisms and human, it is still unclear to what extent one can use information obtained in one species to make predictions in other species. RESULTS: Here, for the first time, we explore and validate at a large scale the use of protein homology relationships to predict the targets of small molecules across different species. Our results show that exploiting target homology can significantly improve the predictions, especially for molecules experimentally tested in other species. Interestingly, when considering separately orthology and paralogy relationships, we observe that mapping small molecule interactions among orthologs improves prediction accuracy, while including paralogs does not improve and even sometimes worsens the prediction accuracy. Overall, our results provide a novel approach to integrate chemical screening results across multiple species and highlight the promises and remaining challenges of using protein homology for small molecule target identification. AVAILABILITY AND IMPLEMENTATION: Homology-based predictions can be tested on our website http://www.swisstargetprediction.ch. CONTACT: david.gfeller@unil.ch or vincent.zoete@isb-sib.ch. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Differential effects of polyphenols and alcohol of red wine on the expression of adhesion molecules and inflammatory cytokines related to atherosclerosis: a randomized clinical trial

Background: Few clinical studies have focused on the alcoholindependent cardiovascular effects of the phenolic compounds of red wine (RW). Objective: We aimed to evaluate the effects of ethanol and phenolic compounds of RW on the expression of inflammatory biomarkers related to atherosclerosis in subjects at high risk of cardiovascular disease. Design: Sixty-seven high-risk, male volunteers were included in a randomized, crossover consumption trial. After a washout period, all subjects received RW (30 g alcohol/d), the equivalent amount of dealcoholized red wine (DRW), or gin (30 g alcohol/d) for 4 wk. Before and after each intervention period, 7 cellular and 18 serum inflammatory biomarkers were evaluated. Results: Alcohol increased IL-10 and decreased macrophage-derived chemokine concentrations, whereas the phenolic compounds of RW decreased serum concentrations of intercellular adhesion molecule- 1, E-selectin, and IL-6 and inhibited the expression of lymphocyte function-associated antigen 1 in T lymphocytes and macrophage-1 receptor, Sialil-Lewis X, and C-C chemokine receptor type 2 expression in monocytes. Both ethanol and phenolic compounds of RW downregulated serum concentrations of CD40 antigen, CD40 ligand, IL-16, monocyte chemotactic protein-1, and vascular cell adhesion molecule-1. Conclusion: The results suggest that the phenolic content of RW may modulate leukocyte adhesion molecules, whereas both ethanol and polyphenols of RW may modulate soluble inflammatory mediators in high-risk patients. The trial was registered in the International Standard Randomized Controlled Trial Number Register at http://www. isrctn.org/ as ISRCTN88720134

Differential effects of polyphenols and alcohol of red wine on the expression of adhesion molecules and inflammatory cytokines related to atherosclerosis: a randomized clinical trial

Background: Few clinical studies have focused on the alcoholindependent cardiovascular effects of the phenolic compounds of red wine (RW). Objective: We aimed to evaluate the effects of ethanol and phenolic compounds of RW on the expression of inflammatory biomarkers related to atherosclerosis in subjects at high risk of cardiovascular disease. Design: Sixty-seven high-risk, male volunteers were included in a randomized, crossover consumption trial. After a washout period, all subjects received RW (30 g alcohol/d), the equivalent amount of dealcoholized red wine (DRW), or gin (30 g alcohol/d) for 4 wk. Before and after each intervention period, 7 cellular and 18 serum inflammatory biomarkers were evaluated. Results: Alcohol increased IL-10 and decreased macrophage-derived chemokine concentrations, whereas the phenolic compounds of RW decreased serum concentrations of intercellular adhesion molecule- 1, E-selectin, and IL-6 and inhibited the expression of lymphocyte function-associated antigen 1 in T lymphocytes and macrophage-1 receptor, Sialil-Lewis X, and C-C chemokine receptor type 2 expression in monocytes. Both ethanol and phenolic compounds of RW downregulated serum concentrations of CD40 antigen, CD40 ligand, IL-16, monocyte chemotactic protein-1, and vascular cell adhesion molecule-1. Conclusion: The results suggest that the phenolic content of RW may modulate leukocyte adhesion molecules, whereas both ethanol and polyphenols of RW may modulate soluble inflammatory mediators in high-risk patients. The trial was registered in the International Standard Randomized Controlled Trial Number Register at http://www. isrctn.org/ as ISRCTN88720134

Thermal Degradation of Small Molecules: A Global Metabolomic Investigation.

Thermal processes are widely used in small molecule chemical analysis and metabolomics for derivatization, vaporization, chromatography, and ionization, especially in gas chromatography mass spectrometry (GC/MS). In this study the effect of heating was examined on a set of 64 small molecule standards and, separately, on human plasma metabolite extracts. The samples, either derivatized or underivatized, were heated at three different temperatures (60, 100, and 250 °C) at different exposure times (30 s, 60 s, and 300 s). All the samples were analyzed by liquid chromatography coupled to electrospray ionization mass spectrometry (LC/MS) and the data processed by XCMS Online ( xcmsonline.scripps.edu ). The results showed that heating at an elevated temperature of 100 °C had an appreciable effect on both the underivatized and derivatized molecules, and heating at 250 °C created substantial changes in the profile. For example, over 40% of the molecular peaks were altered in the plasma metabolite analysis after heating (250 °C, 300s) with a significant formation of degradation and transformation products. The analysis of 64 small molecule standards validated the temperature-induced changes observed on the plasma metabolites, where most of the small molecules degraded at elevated temperatures even after minimal exposure times (30 s). For example, tri- and diorganophosphates (e.g., adenosine triphosphate and adenosine diphosphate) were readily degraded into a mono-organophosphate (e.g., adenosine monophosphate) during heating. Nucleosides and nucleotides (e.g., inosine and inosine monophosphate) were also found to be transformed into purine derivatives (e.g., hypoxanthine). A newly formed transformation product, oleoyl ethyl amide, was identified in both the underivatized and derivatized forms of the plasma extracts and small molecule standard mixture, and was likely generated from oleic acid. Overall these analyses show that small molecules and metabolites undergo significant time-sensitive alterations when exposed to elevated temperatures, especially those conditions that mimic sample preparation and analysis in GC/MS experiments.

Quantitative performance of a quadrupole-orbitrap-MS in targeted LC-MS determinations of small molecules.

High-resolution mass spectrometry (HRMS) has been associated with qualitative and research analysis and QQQ-MS with quantitative and routine analysis. This view is now challenged and for this reason, we have evaluated the quantitative LC-MS performance of a new high-resolution mass spectrometer (HRMS), a Q-orbitrap-MS, and compared the results obtained with a recent triple-quadrupole MS (QQQ-MS). High-resolution full-scan (HR-FS) and MS/MS acquisitions have been tested with real plasma extracts or pure standards. Limits of detection, dynamic range, mass accuracy and false positive or false negative detections have been determined or investigated with protease inhibitors, tyrosine kinase inhibitors, steroids and metanephrines. Our quantitative results show that today's available HRMS are reliable and sensitive quantitative instruments and comparable to QQQ-MS quantitative performance. Taking into account their versatility, user-friendliness and robustness, we believe that HRMS should be seen more and more as key instruments in quantitative LC-MS analyses. In this scenario, most targeted LC-HRMS analyses should be performed by HR-FS recording virtually "all" ions. In addition to absolute quantifications, HR-FS will allow the relative quantifications of hundreds of metabolites in plasma revealing individual's metabolome and exposome. This phenotyping of known metabolites should promote HRMS in clinical environment. A few other LC-HRMS analyses should be performed in single-ion-monitoring or MS/MS mode when increased sensitivity and/or detection selectivity will be necessary.

Transforming Maritime Safety Culture. Evaluation of the impacts of the ISM Code on maritime safety culture in Finland

The purpose of the METKU Project (Development of Maritime Safety Culture) is to study how the ISM Code has influenced the safety culture in the maritime industry. This literature review is written as a part of the Work Package 2 which is conducted by the University of Turku, Centre for Maritime Studies. The maritime traffic is rapidly growing in the Baltic Sea which leads to a growing risk of maritime accidents. Particularly in the Gulf of Finland, the high volume of traffic causes a high risk of maritime accidents. The growing risks give us good reasons for implementing the research project concerning maritime safety and the effectiveness of the safety measures, such as the safety management systems. In order to reduce maritime safety risks, the safety management systems should be further developed. The METKU Project has been launched to examine the improvements which can be done to the safety management systems. Human errors are considered as the most important reason for maritime accidents. The international safety management code (the ISM Code) has been established to cut down the occurrence of human errors by creating a safety-oriented organizational culture for the maritime industry. The ISM Code requires that a company should provide safe practices in ship operation and a safe working environment and establish safeguards against all identified risk. The fundamental idea of the ISM Code is that companies should continuously improve safety. The commitment of the top management is essential for implementing a safety-oriented culture in a company. The ISM Code has brought a significant contribution to the progress of maritime safety in recent years. Shipping companies and ships’ crews are more environmentally friendly and more safety-oriented than 12 years ago. This has been showed by several studies which have been analysed for this literature research. Nevertheless, the direct effect and influence of the ISM Code on maritime safety could not be isolated very well. No quantitative measurement (statistics/hard data) could be found in order to present the impacts of the ISM Code on maritime safety. In this study it has been discovered that safety culture has emerged and it is developing in the maritime industry. Even though the roots of the safety culture have been established there are still serious barriers to the breakthrough of the safety management. These barriers could be envisaged as cultural factors preventing the safety process. Even though the ISM Code has been effective over a decade, the old-established behaviour which is based on the old day’s maritime culture still occurs. In the next phase of this research project, these cultural factors shall be analysed in regard to the present safety culture of the maritime industry in Finland.

Non-thermal emission from microquasar/ISM interaction

Context. The interaction of microquasar jets with their environment can produce non-thermal radiation as in the case of extragalactic outflows impacting on their surroundings. Significant observational evidence of jet/medium interaction in galactic microquasars has been collected in the past few years, although little theoretical work has been done regarding the resulting non-thermal emission. Aims. In this work, we investigate the non-thermal emission produced in the interaction between microquasar jets and their environment, and the physical conditions for its production. Methods. We developed an analytical model based on those successfully applied to extragalactic sources. The jet is taken to be a supersonic and mildly relativistic hydrodynamical outflow. We focus on the jet/shocked medium structure in its adiabatic phase, and assume that it grows in a self-similar way. We calculate the fluxes and spectra of the radiation produced via synchrotron, inverse Compton, and relativistic bremsstrahlung processes by electrons accelerated in strong shocks. A hydrodynamical simulation is also performed to investigate further the jet interaction with the environment and check the physical parameters used in the analytical model. Results. For reasonable values of the magnetic field, and using typical values of the external matter density, the non-thermal particles could produce significant amounts of radiation at different wavelengths, although they do not cool primarily radiatively, but by adiabatic losses. The physical conditions of the analytical jet/medium interaction model are consistent with those found in the hydrodynamical simulation. Conclusions. Microquasar jet termination regions could be detectable at radio wavelengths for current instruments sensitive to ~arcminute scales. At X-ray energies, the expected luminosities are moderate, although the emitter is more compact than the radio one. The source may be detectable by XMM-Newton or Chandra, with 1-10 arcsec of angular resolution. The radiation at gamma-ray energies may be within the detection limits of the next generation of satellite and ground-based instruments.

A brief introduction to molecular orbital theory of simple polyatomic molecules for undergraduate chemistry students

A simple, four-step method for better introducing undergraduate students to the fundamentals of molecular orbital (MO) theory of the polyatomic molecules H2O, NH3, BH3 and SiH4 using group theory is reported. These molecules serve to illustrate the concept of ligand group orbitals (LGOs) and subsequent construction of MO energy diagrams on the basis of molecular symmetry requirements.

Efficiency of the ISM Code in Finnish Shipping Companies

Due to increasing waterborne transportation in the Gulf of Finland, the risk of a hazardous accident increases and therefore manifold preventive actions are needed. As a main legislative authority in the maritime community, The International Maritime Organization (IMO) has set down plenary laws and recommendations which are e.g., utilised in the safe operations in ships and pollution prevention. One of these compulsory requirements, the ISM Code, requires proactive attitude both from the top management and operational workers in the shipping companies. In this study, a crosssectional approach was taken to analyse whether the ISM Code has actively enhanced maritime safety in the Gulf of Finland. The analysis included; 1) performance of the ISM Code in Finnish shipping companies, 2) statistical measurements of maritime safety, 3) influence of corporate top management to the safety culture and 4) comparing safety management practices in shipping companies and port operations of Finnish maritime and port authorities. The main results found were that maritime safety culture has developed in the right direction after the launch of the ISM Code in the 1990´s. However, this study does not exclusively prove that the improvements are the consequence of the ISM Code. Accident prone ships can be recognized due to their behaviour and there is a lesson to learn from the safety culture of some high standard safety disciplines such as, air traffic. In addition, the reporting of accidents and nearmisses should be more widely used in shipping industry. In conclusion, there is still much to be improved in the maritime safety culture of the Finnish Shipping industry, e.g., a “no blame culture” needs to be adopted.

Estimation of standard enthalpy of formation of alkanes in gaseous state by calculating size, structural and electronic parameters in the molecules

A quantitative analysis is made on the correlation ship of thermodynamic property, i.e., standard enthalpy of formation (ΔH fº) with Kier's molecular connectivity index(¹Xv),vander waal's volume (Vw) electrotopological state index (E) and refractotopological state index (R) in gaseous state of alkanes. The regression analysis reveals a significant linear correlation of standard enthalpy of formation (ΔH fº) with ¹Xv, Vw, E and R. The equations obtained by regression analysis may be used to estimate standard enthalpy of formation (ΔH fº) of alkanes in gaseous state.

Babesia bovis: expression of adhesion molecules in bovine umbilical endothelial cells stimulated with plasma from infected cattle

Ten male, 12-month-old Jersey with intact spleens, serologically and parasitologically free from Babesia were housed individually in an arthropod-free isolation system from birth and throughout entire experiment. The animals were randomly divided into two groups. Five animals (group A) were intravenously inoculated with 6.6 X10(7) red blood cells parasitized with pathogenic sample of Babesia bovis (passage 7 BboUFV-1), for the subsequent "ex vivo" determination of the expression of adhesion molecules. Five non-inoculated animals (group B) were used as the negative control. The expression of the adhesion molecules ICAM-1, VCAM, PECAM-1 E-selectin and thrombospondin (TSP) was measured in bovine umbilical vein endothelial cells (BUVECs). The endothelial cells stimulated with a pool of plasma from animals infected with the BboUFV-1 7th passage sample had a much more intense immunostaining of ICAM-1, VCAM, PECAM-1 E-selectin and TSP, compared to the cells which did not received the stimulus. The results suggest that proinflammatory cytokines released in the acute phase of babesiosis may be involved in the expression of adhesion molecules thereby implicating them in the pathophysiology of babesiosis caused by B. bovis.

Modulation of Signaling Molecules by Human Leucocyte Antigen B27; Special Reference to STAT1

Reactive arthritis (ReA) is an inflammatory joint disease, which belongs to the group of Spondyloarthritis (SpA). It may occur after infections with certain gram-negative bacteria such as Salmonella and Yersinia. SpAs are strongly associated with the human leucocyte antigen (HLA)-B27. Despite active research, the mechanism by which HLA-B27 causes disease susceptibility is still unknown. However, HLA-B27 has a tendency to misfold during assembly. It is possible that the misfolding of HLA-B27 could alter signaling pathways and/or molecules involved in inflammatory response in cells. We have earlier discovered that in HLA-B27-positive cells the interaction between the host and causative bacteria is disturbed. Our recent studies indicate that the expression of HLA-B27 may alter certain signaling molecules by disturbing their activation. The aim of this study was to investigate whether the expression of HLA-B27 disturbs the signaling molecules, especially the phosphorylation of transcription factor STAT1. STAT1 is an important mediator of inflammatory responses. Our results show that the phosphorylation of the STAT1 is significantly altered in HLA-B27-expressing U937 monocytic cells compared with control cells. STAT1 tyrosine 701 is more strongly phosphorylated in HLAB27- expressing cells; whereas the phosphorylation of STAT1 serine 727 is prolonged. Phosphorylation of STAT1 was discovered to be dependent on protein kinase PKR. Furthermore, we found out that the expression of posttranscriptional gene regulator HuR was altered in HLA-B27-expressing cells. We also detected that HLA-B27-positive cells secrete more interleukin 6, which is an important mediator of inflammation. These results help to understand how HLA-B27 may confer susceptibility to SpAs.

Regulation of T cell response to leishmania antigens by determinants of histocompatibility leukocyte class I and II molecules

It has been shown that HLA class I molecules play a significant role in the regulation of the proliferation of T cells activated by mitogens and antigens. We evaluated the ability of mAb to a framework determinant of HLA class I molecules to regulate T cell proliferation and interferon gamma (IFN-g) production against leishmania, PPD, C. albicans and tetanus toxoid antigens in patients with tegumentary leishmaniasis and healthy subjects. The anti-major histocompatibility complex (MHC) mAb (W6/32) suppressed lymphocyte proliferation by 90% in cultures stimulated with aCD3, but the suppression was variable in cultures stimulated with leishmania antigen. This suppression ranged from 30-67% and was observed only in 5 of 11 patients. IFN-g production against leishmania antigen was also suppressed by anti-HLA class I mAb. In 3 patients IFN-g levels were suppressed by more than 60%, while in the other 2 cultures IFN-g levels were 36 and 10% lower than controls. The suppression by HLA class I mAb to the proliferative response in leishmaniasis patients and in healthy controls varied with the antigens and the patients or donors tested. To determine whether the suppression is directed at antigen presenting cells (APCs) or at the responding T cells, experiments with antigen-primed non-adherent cells, separately incubated with W6/32, were performed. Suppression of proliferation was only observed when the W6/32 mAb was added in the presence of T cells. These data provide evidence that a mAb directed at HLA class I framework determinants can suppress proliferation and cytokine secretion in response to several antigens.