Finding best algorithmic components for clustering microarray data

The analysis of microarray data is fundamental to microbiology. Although clustering has long been realized as central to the discovery of gene functions and disease diagnostic, researchers have found the construction of good algorithms a surprisingly difficult task. In this paper, we address this problem by using a component-based approach for clustering algorithm design, for class retrieval from microarray data. The idea is to break up existing algorithms into independent building blocks for typical sub-problems, which are in turn reassembled in new ways to generate yet unexplored methods. As a test, 432 algorithms were generated and evaluated on published microarray data sets. We found their top performers to be better than the original, component-providing ancestors and also competitive with a set of new algorithms recently proposed. Finally, we identified components that showed consistently good performance for clustering microarray data and that should be considered in further development of clustering algorithms.     

N‐Lauroylation during the Expression of Recombinant N‐Myristoylated Proteins: Implications and Solutions

Incorporation of myristic acid onto the N terminus of a protein is a crucial modification that promotes membrane binding and correct localization of important components of signaling pathways. Recombinant expression of N‐myristoylated proteins in Escherichia coli can be achieved by co‐expressing yeast N‐myristoyltransferase and supplementing the growth medium with myristic acid. However, undesired incorporation of the 12‐carbon fatty acid lauric acid can also occur (leading to heterogeneous samples), especially when the available carbon sources are scarce, as it is the case in minimal medium for the expression of isotopically enriched samples. By applying this method to the brain acid soluble protein 1 and the 1–185 N‐terminal region of c‐Src, we show the significant, and protein‐specific, differences in the membrane binding properties of lauroylated and myristoylated forms. We also present a robust strategy for obtaining lauryl‐free samples of myristoylated proteins in both rich and minimal media.     

New Cav1.2 Channelopathy with High-Functioning Autism,Affective Disorder,Severe Dental Enamel Defects,a Short QT Interval,and a Novel CACNA1C Loss-of-Function Mutation

Complex neuropsychiatric-cardiac syndromes can be genetically determined. For the first time, the authors present a syndromal form of short QT syndrome in a 34-year-old German male patient with extracardiac features with predominant psychiatric manifestation, namely a severe form of secondary high-functioning autism spectrum disorder (ASD), along with affective and psychotic exacerbations, and severe dental enamel defects (with rapid wearing off his teeth) due to a heterozygous loss-of-function mutation in the CACNA1C gene (NM_000719.6: c.2399A > C; p.Lys800Thr). This mutation was found only once in control databases; the mutated lysine is located in the Cav1.2 calcium channel, is highly conserved during evolution, and is predicted to affect protein function by most pathogenicity prediction algorithms. L-type Cav1.2 calcium channels are widely expressed in the brain and heart. In the case presented, electrophysiological studies revealed a prominent reduction in the current amplitude without changes in the gating behavior of the Cav1.2 channel, most likely due to a trafficking defect. Due to the demonstrated loss of function, the p.Lys800Thr variant was finally classified as pathogenic (ACMG class 4 variant) and is likely to cause a newly described Cav1.2 channelopathy.     

Relation of α2-Antiplasmin Genotype and Genetic Determinants of Fibrinogen Synthesis and Fibrin Clot Formation with Vascular Endothelial Growth Factor Level in Axial Spondyloarthritis

Objective: Coagulation and fibrinolysis are interrelated with the expression of vascular endothelial growth factor (VEGF), which frequently is increased in axial spondyloarthritis (axSpA). We tested whether (i) α₂-antiplasmin (A2AP) Arg6Trp, (ii) fibrinogen, factor XIII A-subunit or B-subunit genotypes are associated with VEGF levels and assessed whether the known association between elevated VEGF and radiographic spinal progression in axSpA depends on genetic background. Methods: One hundred and eighty-six axSpA patients from the German Spondyloarthritis Inception Cohort were genotyped, characterized for VEGF levels, and statistically analyzed. The association between VEGF and radiographic spinal progression was assessed in dependence on genetic background in stratified analyses. Results: A2AP 6Trp carriage was associated with VEGF elevation (OR: 2.37, 95% CI: 1.06–5.29) and VEGF levels (6Trp, 455 ± 334 pg/mL; 6Arg/Arg, 373 ± 293 pg/mL; p < 0.008). Association between elevated VEGF and radiographic spinal progression in axSpA (OR: 3.11, 95% CI: 1.02–8.82) depended remarkably on the fibrinogen (FGA) genotype. When considering axSpA patients with elevated VEGF, in FGA rs6050A>G wild types, 42.1% of patients (8 of 19) progressed, while in G-allele carriers, no radiographic progression happened (0 of 13) (p < 0.04). Conclusions: The A2AP Arg6Trp genotype seems to influence VEGF levels in axSpA. The predictive value of VEGF elevations in respect of radiographic spinal progression in axSpA depends on FGA genotypes.     

Surface modification and immobilization in poly(acrylic acid) of Ag/ZnO for photocatalytic degradation of endocrine‐disrupting compounds

Silver‐modified ZnO particles (Ag/ZnO) are effective catalysts for the photodegradation of water pollutants such as bisphenol‐A. However, until now, their use in continuous processes was back‐drawn because of difficulties associated with their recovery. To overcome this problem, the present work aimed at immobilizing Ag/ZnO in cross‐linked poly(acrylic acid) ‐PAA‐. Ag/ZnO was first silanized using (3‐glycidyloxypropyl)trimethoxysilane and thoroughly dispersed in a water‐acrylic acid solution. The suspension was then submitted to radical polymerization in presence of a cross‐linker (N,N′‐Methylenebisacrylamide). The resulting composites were characterized in terms of chemical structure, morphology, crystallinity, thermal properties, and photostability. Their analyses showed that the silanized particles were chemically anchored to PAA and homogeneously distributed in the matrix. UV‐assisted photocatalysis of bisphenol‐A aqueous solutions showed that immobilized Ag/ZnO can achieve photodegradation performances comparable to pure Ag/ZnO and allows its use in successive cycles and, consequently, in continuous processes. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 133, 43528.     

Palmitoylated SDF1α shows increased resistance against proteolytic degradation in liver homogenates

The chemokine stromal cell-derived factor-1α (SDF1α) is strongly involved in organogenesis, as well as inflammation and tissue repair, and acts by attracting different kinds of stem and progenitor cells. Therefore, it constitutes an interesting compound for drug development in regenerative medicine. However, it is prone to inactivation by proteolytic cleavage in human serum. Accordingly, it has to be stabilized against enzymatic degradation for any therapeutic application. We synthesized a palmitoylated SDF1α analogue by native chemical ligation. Both the N-terminal thioester and the C-terminal palmitoylated fragment were prepared by solid-phase peptide synthesis. The activity of the refolded and pure compound was determined by an inositol phosphate turnover assay and revealed no loss in receptor activation. Additionally, resistance to proteolytic degradation was investigated in porcine liver homogenates and showed a near sevenfold increased half time. This study is a proof of principle approach for the lipidation of SDF1α and provides a basis for further engineering of the chemokine in order to increase its therapeutic value.     

Detoxification of Polycyclic Aromatic Hydrocarbon Diol Epoxides by Human Glutathione Transferases: Efficiency of Conjugation in Intact Cells Relative to Purified Enzymes

V79MZ cells expressing human glutathione transferases (hGST) have been constructed and used to study glutathione (GSH) conjugation of anti -diol epoxides (DEs) of dibenzo[ a,l ]pyrene ( DBPDE ), and benzo[ a ]pyrene ( BPDE ). Cells expressing hGSTM1-1 were more effective with ( m )- anti - DBPDE than hGSTP1-1. The opposite was observed with (+)- anti - BPDE . Rates of cellular DE uptake and solvolysis in conjunction with oil/water partition coefficients were used to calculate the amount of DEs available for GST-catalyzed conjugation in the cells. Using this information and the known values of k cat /K M for (+)- anti - BPDE and ( m )- anti - DBPDE with purified hGSTs, it was calculated that up to 3% of available (+)- anti - BPDE forms GSH conjugates whereas the corresponding figure with the less reactive and more lipophilic ( m )- anti - DBPDE was about 19%. In part, the lower fraction of (+)- anti -BPDE conjugated in cells is probably due to rapid and competing reactions with cellular constituents.     

A General Method for the Enantioselective Hydrogenation of β‐Keto Esters using Monodentate Binaphthophosphepine Ligands

17 monodentate phosphepine ligands with a 4,5‐dihydro‐3H‐dinaphtho[2,1‐c;1′,2′‐e]phosphepine structural motif have been synthesized and tested in the asymmetric hydrogenation of various β‐keto esters. By variation of the substituents of the aryl group on the phosphorus atom a fine tuning of the selectivity of the catalytic system is possible. Quantitative yield and enantioselectivities up to 95% ee have been achieved for the hydrogenation of methyl acetoacetate ( 7a ), methyl 3‐oxovalerate ( 7b ) and ethyl 4‐phenyl‐3‐oxo‐propionate ( 7d ) using 4‐(4‐methoxyphenyl)‐4,5‐dihydro‐3H‐dinaphtho‐[2,1‐c;1′,2′‐e]phosphepine ( 4g ) as ligand. Best enantioselectivities were obtained at comparably high temperatures (100–120 °C), which had the advantage of increased reaction rates.     

An Unusual Thioesterase Promotes Isochromanone Ring Formation in Ajudazol Biosynthesis

The ajudazols are antifungal secondary metabolites produced by a hybrid polyketide synthase (PKS)‐nonribosomal peptide synthetase (NRPS) multienzyme “assembly line” in the myxobacterium Chondromyces crocatus Cm c5. The most striking structural feature of these compounds is an isochromanone ring system; such an aromatic moiety is only known from two other complex polyketides, the electron transport inhibitor stigmatellin and the polyether lasalocid. The cyclization and aromatization reactions in the stigmatellin pathway are presumed to be catalyzed by a cyclase domain located at the end of the PKS, while the origin of the lasalocid benzenoid ring remains obscure. Notably, the ajudazol biosynthetic machinery does not incorporate a terminal cyclase, but instead a variant thioesterase (TE) domain. Here we present detailed phylogenetic and sequence analysis, coupled with experiments both in vitro and in vivo, that suggest that this TE promotes formation of the isochromanone ring, a novel reaction for this type of domain. As the ajudazol TE has homologues in several other secondary‐metabolite pathways, these results are likely to be generalizable.