Allosteric inhibitors of Bcr-abl-dependent cell proliferation

Chronic myelogenous leukemia (CML) is a myeloproliferative disorder characterized at the molecular level by the expression of Bcr-abl, a 210-kDa fusion protein with deregulated tyrosine kinase activity. Encouraged by the clinical validation of Bcr-abl as the target for the treatment of CML by imatinib, we sought to identify pharmacological agents that could target this kinase by a distinct mechanism. We report the discovery of a new class of Bcr-abl inhibitors using an unbiased differential cytotoxicity screen of a combinatorial kinase-directed heterocycle library. Compounds in this class (exemplified by GNF-2) show exclusive antiproliferative activity toward Bcr-abl-transformed cells, with potencies similar to imatinib, while showing no inhibition of the kinase activity of full-length or catalytic domain of c-abl. We propose that this new class of compounds inhibits Bcr-abl kinase activity through an allosteric non-ATP competitive mechanism.     

Anaerobic Processes as the Core Technology for Sustainable Domestic Wastewater Treatment: Consolidated Applications, New Trends, Perspectives, and Challenges

Anaerobic digesters have been responsible for the removal of large fraction of organic matter (mineralization of waste sludge) in conventional aerobic sewage treatment plants since the early years of domestic sewage treatment (DST). Attention on the anaerobic technology for improving the sustainability of sewage treatment has been paid mainly after the energy crisis in the 1970s. The successful use of anaerobic reactors (especially up-flow anaerobic sludge blanket (UASB) reactors) for the treatment of raw domestic sewage in tropical and sub-tropical regions (where ambient temperatures are not restrictive for anaerobic digestion) opened the opportunity to substitute the aerobic processes for the anaerobic technology in removal of the influent organic matter. Despite the success, effluents from anaerobic reactors treating domestic sewage require post-treatment in order to achieve the emission standards prevailing in most countries. Initially, the composition of this effluent rich in reduced compounds has required the adoption of post-treatment (mainly aerobic) systems able to remove the undesirable constituents. Currently, however, a wealth of information obtained on biological and physical-chemical processes related to the recovery or removal of nitrogen, phosphorus and sulfur compounds creates the opportunity for new treatment systems. The design of DST plant with the anaerobic reactor as core unit coupled to the pre- and post-treatment systems in order to promote the recovery of resources and the polishing of effluent quality can improve the sustainability of treatment systems. This paper presents a broader view on the possible applications of anaerobic treatment systems not only for organic matter removal but also for resources recovery aiming at the improvement of the sustainability of DST.     

Bridging Proteomics and Medical Science - the 5th HUPO Brain Proteome Workshop in Dublin, Ireland

More than 70 interested colleagues attended the 5th Workshop of the HUPO Brain Proteome Project (HUPO BPP) at the UCD Conway Institute, Dublin, Ireland. An overview of the outcome of the pilot study was presented and the new subprojects "Clinical Neuroproteomics of Human Body Fluids" as well as "Cerebellum 2D-mapping" were announced. In addition the election of the HUPO BPP committees and the future directions of this project were discussed and decided. The meeting was enhanced by several talks highlighting the application of proteomics in biomedical research.     

Automated reprocessing pipeline for searching heterogeneous mass spectrometric data of the HUPO Brain Proteome Project pilot phase

The newly available techniques for sensitive proteome analysis and the resulting amount of data require a new bioinformatics focus on automatic methods for spectrum reprocessing and peptide/protein validation. Manual validation of results in such studies is not feasible and objective enough for quality relevant interpretation. The necessity for tools enabling an automatic quality control is, therefore, important to produce reliable and comparable data in such big consortia as the Human Proteome Organization Brain Proteome Project. Standards and well-defined processing pipelines are important for these consortia. We show a way for choosing the right database model, through collecting data, processing these with a decoy database and end up with a quality controlled protein list merged from several search engines, including a known false-positive rate.     

The dissociation of the fluid and particle phase in the forestomach as a physiological characteristic of large grazing ruminants: an evaluation of available, comparable ruminant passage data

Whether differences in digestive physiology exist between different ruminant feeding types has been an ongoing debate. In this regard, potential differences in ingesta retention have been understood to be of particular importance. We analyzed a data pool in which only mean retention time (MRT) data for the ruminoreticulum (RR) were collated that were obtained using comparable techniques with either chromium or cobalt EDTA as a fluid marker and/or with chromium-mordanted fiber of less than 2 mm in size as a particle marker. Data were compared using one averaged value per species. In general, the paucity of species in such a collection is striking and does not allow—in contrast to earlier statements—any final conclusions regarding the influence of body weight (BW) or feeding type on ruminant MRTs. In particular, there was no significant correlation between MRT_particlesRR or MRT_fluidRR and BW, neither in the interspecific nor in the intraspecific comparisons, and no difference between the feeding types. The trend that indicates longer MRT_particlesRR in grazers is based on too few species to be conclusive. Small browsers seemed to have shorter MRT_fluidRR than similar-sized grazers. In contrast, there was a trend for large grazers to have shorter MRT_fluidRR than large browsers. In direct pair-wise comparisons between cattle and the browsers giraffe, moose, and okapi, the latter difference was significant. Cattle also had the highest relative RR fluid outflow rates among the species investigated. This is in accord with the observation that grazers have larger omasa, a major function of which is water-reabsorption distal to the RR. Grazers seem to have longer MRT_particlesRR per unit MRT_fluidRR, and cattle are particular outliers in this respect. It is hypothesized that potentially shorter MRT_fluidRR in large grazers and higher relative outflow rates are linked to a higher saliva production and a lesser viscosity of both saliva and RR fluids. A constant supply of a fluid phase of low viscosity is proposed to be the prerogative for the physical mechanisms of flotation and sedimentation that result in the stratification of RR contents and its selective particle retention typical for large grazing species.     

HIV-1附属蛋白特异性细胞毒性T细胞应答研究

人类免疫缺陷病毒(Human immunodeficiency virus, HIV)附属蛋白Nef、Vpu、Vpr和Vif 在病毒复制中起着关键作用,并能被细胞毒性T细胞(Cytotoxic T Lymphocyte, CTL)识别.然而,对我国HIV感染者体内附属蛋白特异性的CTL应答研究比较少.本研究应用覆盖HIV-1B、C亚型附属蛋白(Nef、Vpu、Vpr和Vif)的142个肽段作为抗原,通过酶联免疫斑点实验(Enzyme-Linked Immunospot,ELISPOT)检测61例中国HIV/AIDS患者和10例HIV-1血清阴性对照的HIV-1附属蛋白特异性CTL应答.无论对HIV-1B 亚型还是HIV-1C亚型附属蛋白都能产生特异性CTL 应答,特别是Nef区蛋白的反应频率和累积应答强度都较高(P＜0.001),B、C亚型间的应答频率和累积应答强度都无显著差别(P＞0.05),其免疫优势区也大致相同.附属蛋白特异性的累积CTL应答强度将近达到总应答的21%.这些结果表明尽管HIV-1附属蛋白的体积小,但它们在诱导特异性的CTL应答中发挥了重要作用,对评价HIV-1免疫应答的幅度和特异性以及研发针对中国人群的HIV疫苗有重要的意义.     

Effects of high-relief structures on cold temperate fish assemblages: A field experiment

High-relief structures may influence the abundance and diversity of reef-associated fish. We conducted a field experiment to investigate whether the presence of vertical structures (PVC pipes) affects fish communities on artificial reefs. The effect of the height of the structures (1 and 3 m) was also tested. Furthermore, the effects on fish of placing artificial reefs on otherwise featureless bottoms were quantified. Algal and macro-invertebrate colonization of the reefs was also recorded. The experiment was carried out on the west coast of Sweden over a period of 1 year. The vertical structures had a positive effect on fish abundance but not on diversity. The height of the structures did not, however, influence the fish communities. Natural as well as urban vertical structures on the seafloor could have a positive effect on local fish abundance. The positive effects of artificial reefs on total fish abundance and diversity were immediate. Of the 10 species recorded, two, the black goby Gobius niger and the goldsinny wrasse Ctenolabrus rupestris, dominated over the whole survey period. There were significant temporal differences in fish abundance, and diversity increased with time.     

Decreased striatal levels of PEP-19 following MPTP lesion in the mouse

PEP-19 is a neuronal calmodulin-binding protein, and as such, a putative modulator of calcium regulated processes. In the present study, we used proteomics technology approaches such as peptidomics and imaging MALDI mass spectrometry, as well as traditional techniques (immunoblotting and in situ hybridization) to identify PEP-19 and, specifically, to measure PEP-19 mRNA and protein levels in an animal model of Parkinson's disease. 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) administration in mice resulted in a significant decrease in striatal PEP-19 mRNA. Capillary nano-flow liquid chromatography electrospray mass spectrometry analysis of striatal tissue revealed a significant decrease of the PEP-19 protein level. Moreover, imaging MALDI mass spectrometry also showed that PEP-19 protein was predominantly localized to the striatum of the brain tissue cross sections. After MPTP administration, PEP-19 levels were significantly reduced by 30%. We conclude that PEP-19 mRNA and protein expression are decreased in the striatum of a common animal model of Parkinson's disease. Further studies are needed to show the specific involvement of PEP-19 in the neurodegeneration seen in MPTP lesioned animals. Finally, this study has shown that the combination of traditional molecular biology techniques with novel, highly specific and sensitive mass spectrometry methods is advantageous in characterizing molecular events of many diseases, including Parkinson's disease.