Using ensemble classifier to identify membrane protein types

Predicting membrane protein type is both an important and challenging topic in current molecular and cellular biology. This is because knowledge of membrane protein type often provides useful clues for determining, or sheds light upon, the function of an uncharacterized membrane protein. With the explosion of newly-found protein sequences in the post-genomic era, it is in a great demand to develop a computational method for fast and reliably identifying the types of membrane proteins according to their primary sequences. In this paper, a novel classifier, the so-called "ensemble classifier", was introduced. It is formed by fusing a set of nearest neighbor (NN) classifiers, each of which is defined in a different pseudo amino acid composition space. The type for a query protein is determined by the outcome of voting among these constituent individual classifiers. It was demonstrated through the self-consistency test, jackknife test, and independent dataset test that the ensemble classifier outperformed other existing classifiers widely used in biological literatures. It is anticipated that the idea of ensemble classifier can also be used to improve the prediction quality in classifying other attributes of proteins according to their sequences.     

Expression of neolactoglycolipids: sialosyl-, disialosyl-,O-acetyldisialosyl- and fucosyl- derivatives of neolactotetraosyl ceramide and neolactohexaosyl ceramide in the developing cerebral cortex and cerebellum

The following neolacto glycolipids were identified and their developmental expression was studied in the rat cerebral cortex and cerebellum: Fuc1-³IIInLcOse₄Cer,Fuc1-³VnLcOse₆Cer and (Fuc)₂1-³III,³VnLcOse₆Cer, as well as acidic glycolipids, NeuAc2-³IVnLcOse₄Cer [nLM1], (NeuAc)₂2-³IVnLcOse₄Cer [nLD1],O-acetyl (NeuAc)₂2-³IVnLcOse₄Cer [OAc-nLD1] and their higher neolactosaminyl homologues NeuAc2-³VInLcOse₆Cer [nHM1] and (NeuAc)₂2-³VInLcOse₆Cer [nHD1]. These glycolipids were expressed in the cerebral cortex only during embryonic stages and disappeared postnatally. This loss was ascribed to the down regulation of the synthesis of the key precursor LcOse₃Cer which is synthesized by the enzyme lactosylceramide:N-acetylglucosaminyl transferase. On the other hand in the cerebellum, these glycolipids increased with postnatal development due to increasing availability of LcOse₃Cer. In the cerebellum, only nLM1 and fucosyl-neolactoglycolipids declined after postnatal day 10–15, perhaps due to regulation by other glycosyltransferases. Also, in the cerebellum, nLD1 and nHD1 were shown to be specifically associated with Purkinje cells and their dendrites in the molecular layer and with their axon terminals in the deep cerebellar nuclei, similar to other neolactoglycolipids shown previously.     

Binary mixtures containing isomers of nitrobenzo[a]pyrene induce greater-than-additive mutational responses in Salmonella typhimurium. I. Analysis by the total concentration-proportional mixture model

The inhibition of cell division induced by bleomycin (BM) and UV irradiation in the set of rec mutants of E. coli K12 was studied. Data presented in this work indicate that BM treatment requires mainly the RecBC pathway for the induction of cell filamentation. In the recB21 mutant cell filamentation is delayed and reduced compared to the wild type. Cell filamentation is BM-induced with similar kinetics in strains with a proficient RecBC recombination pathway (rec+, recF143 and recN262), as well as in the strain with a fully expressed RecF pathway (recB21recC22sbcB15). Induction is completely abolished in the recB21recF143 double mutant. On the other hand cell filamentation was induced similarly by UV irradiation in all strains with a functional recF gene and in the strain with a fully operative RecF pathway, but it was delayed in the recF143 and recB21recF143 mutants.     

Interleukin-11 increases cell motility and up-regulates intercellular adhesion molecule-1 expression in human chondrosarcoma cells

Interleukin‐11 (IL‐11) was originally identified as the cytokine that could induce the proliferation of human cells. Recent studies have shown that IL‐11 plays a critical role in tumor growth, angiogenesis, and metastasis. Chondrosarcoma is a type of highly malignant tumor with a potent capacity to invade locally and cause distant metastasis. However, the effects of IL‐11 on human chondrosarcoma cells are largely unknown. Here, we found that IL‐11 increased the migration and expression of intercellular adhesion molecule‐1 (ICAM)‐1 in human chondrosarcoma cells. We also found that human chondrosarcoma tissues had significant expression of the IL‐11 which was higher than that in primary chondrocytes. The phosphatidylinositol 3‐kinase (PI3K), Akt, and NF‐κB pathways were activated by IL‐11 treatment, and the IL‐11‐induced expression of ICAM‐1 and migration activity were inhibited by the specific inhibitors and mutant forms of PI3K, Akt, and NF‐κB cascades. Taken together, our results indicate that IL‐11 enhanced the migration of the chondrosarcoma cells by increasing ICAM‐1 expression through the IL‐11Rα receptor, PI3K, Akt, and NF‐κB signal transduction pathway. J. Cell. Biochem. 113: 3353–3362, 2012. © 2012 Wiley Periodicals, Inc.     

Solid-phase synthesis of naphthylamidines as factor VIIa/tissue factor inhibitors

Reductive amination followed by acylation of polymer-linked formyl aryl amidines generate combinatorial libraries of aryl amidines 8-13. Potent small molecule naphthylamidine inhibitors 12 (Ki<100 nM) of FVIIa/TF have been discovered and their activity against other serine proteases in the coagulation cascade is reported.     

Protein profiling of sickle cell versus control RBC core membrane skeletons by ICAT technology and tandem mass spectrometry

A proteomic approach using a cleavable ICAT reagent and nano-LC ESI tandem mass spectrometry was used to perform protein profiling of core RBC membrane skeleton proteins between sickle cell patients (SS) and controls (AA), and determine the efficacy of this technology. The data was validated through Peptide/Protein Prophet and protein ratios were calculated through ASAPratio. Through an ANOVA test, it was determined that there is no significant difference in the mean ratios from control populations (AA1/AA2) and sickle cell versus control populations (AA/SS). The mean ratios were not significantly different from 1.0 in either comparison for the core skeleton proteins (α spectrin, β spectrin, band 4.1 and actin). On the natural-log scale, the variation (standard deviation) of the method was determined to be 14.1% and the variation contributed by the samples was 13.8% which together give a total variation of 19.7% in the ratios. Invited paper     

Optimization of microencapsulation parameters: Semipermeable microcapsules as a bioartificial pancreas

An improved membrane has been developed for the microencapsulation of islets of Langerhans which protects these cells from the immune system. These requirements were accomplished through the optimization of important microencapsulation parameters and through the improved biocompatibility of a new alginate-poly-l-lysine (PLL)-alginate capsule membrane. Spherical and smooth microcapsules could be formed by utilizing a purer sodium alginate and by keeping the viscosity of the sodium alginate solution above 30 cps. The strength of the capsule membrane was enhanced by increasing the alginate-PLL reaction time as well as the PLL concentration. The permeability of the membrane [4 mum thick, 93% (w/w) water] was a function of the viscosity average molecular weight (Mv) of the PLL (Mv = 4000-4 x 10(5)) used in the encapsulation procedure. Microcapsules prepared with PLL with Mv = 1.7 x 10(4) were the least permeable, being impermeable to normal serum immunoglobulin, albumin, and haemoglobin. The microencapsulation procedure, by protecting transplanted tissue from the components of the immune system, has great clinical potential as a new form of treatment for diseases such as diabetes and liver disease.     

Photodegradation of Dialkyl 1,3-Dithiolan-2-ylidenemalonates and Some Other Pesticides on Solid Particles

On irradiation with UV light the fungicide isoprothiolane (diisopropyl 1,3-dithiolan-2-ylidenemalonate) decomposed rapidly on the silica gel surface. The degradation pathways involved dithiolane ring cleavage, ester hydrolysis, decarboxylation, heterocycles formation such as dithietane and trithiolane, and sulfur liberation. The photoproducts confirmed were oxalic acid, dithiolanylidenemalonic acid, dithiolanylideneacetic acid, 2,4-bis[bis(isopropoxycar-bonyl)methylene]-1, 3-dithietane, 3, 5-bis[bis(isopropoxy-carbonyl)methylene]-1,2,4-trithiolane and sulfur. The methyl and ethyl homologs of isoprothiolane similarly gave the corresponding photoproducts. The surface area where isoprothiolane was placed appeared to be related closely with the photolysis rate. Isoprothiolane decomposed much more rapidly on sand than on a glass plate. This surface effect was greatly depressed under nitrogen atmosphere. Similar phenomena were observed with some other pesticides, with particularly those containing sulfur atoms in the molecule.     

Survey of Ixodes pacificus Ticks in California Reveals a Diversity of Microorganisms and a Novel and Widespread Anaplasmataceae Species

Ixodes pacificus ticks can harbor a wide range of human and animal pathogens. To survey the prevalence of tick-borne known and putative pathogens, we tested 982 individual adult and nymphal I. pacificus ticks collected throughout California between 2007 and 2009 using a broad-range PCR and electrospray ionization mass spectrometry (PCR/ESI-MS) assay designed to detect a wide range of tick-borne microorganisms. Overall, 1.4% of the ticks were found to be infected with Borrelia burgdorferi, 2.0% were infected with Borrelia miyamotoi and 0.3% were infected with Anaplasma phagocytophilum. In addition, 3.0% were infected with Babesia odocoilei. About 1.2% of the ticks were co-infected with more than one pathogen or putative pathogen. In addition, we identified a novel Anaplasmataceae species that we characterized by sequencing of its 16S rRNA, groEL, gltA, and rpoB genes. Sequence analysis indicated that this organism is phylogenetically distinct from known Anaplasma species with its closest genetic near neighbors coming from Asia. The prevalence of this novel Anaplasmataceae species was as high as 21% at one site, and it was detected in 4.9% of ticks tested statewide. Based upon this genetic characterization we propose that this organism be called ‘Candidatus Cryptoplasma californiense’. Knowledge of this novel microbe will provide awareness for the community about the breadth of the I. pacificus microbiome, the concept that this bacterium could be more widely spread; and an opportunity to explore whether this bacterium also contributes to human or animal disease burden.