Identifying essential genes in bacterial metabolic networks with machine learning methods

Background  

Identifying essential genes in bacteria supports to identify potential drug targets and an understanding of minimal requirements for a synthetic cell. However, experimentally assaying the essentiality of their coding genes is resource intensive and not feasible for all bacterial organisms, in particular if they are infective.     

State-of-the art data normalization methods improve NMR-based metabolomic analysis

Extracting biomedical information from large metabolomic datasets by multivariate data analysis is of considerable complexity. Common challenges include among others screening for differentially produced metabolites, estimation of fold changes, and sample classification. Prior to these analysis steps, it is important to minimize contributions from unwanted biases and experimental variance. This is the goal of data preprocessing. In this work, different data normalization methods were compared systematically employing two different datasets generated by means of nuclear magnetic resonance (NMR) spectroscopy. To this end, two different types of normalization methods were used, one aiming to remove unwanted sample-to-sample variation while the other adjusts the variance of the different metabolites by variable scaling and variance stabilization methods. The impact of all methods tested on sample classification was evaluated on urinary NMR fingerprints obtained from healthy volunteers and patients suffering from autosomal polycystic kidney disease (ADPKD). Performance in terms of screening for differentially produced metabolites was investigated on a dataset following a Latin-square design, where varied amounts of 8 different metabolites were spiked into a human urine matrix while keeping the total spike-in amount constant. In addition, specific tests were conducted to systematically investigate the influence of the different preprocessing methods on the structure of the analyzed data. In conclusion, preprocessing methods originally developed for DNA microarray analysis, in particular, Quantile and Cubic-Spline Normalization, performed best in reducing bias, accurately detecting fold changes, and classifying samples.

     

Toll-like receptor 4 deficiency: Smaller infarcts,but nogain in function

Backgound  

It has been reported that Toll-like receptor 4 (TLR4) deficiency reduces infarct size after myocardial ischemia/reperfusion (MI/R). However, measurement of MI/R injury was limited and did not include cardiac function. In a chronic closed-chest model we assessed whether cardiac function is preserved in TLR4-deficient mice (C3H/HeJ) following MI/R, and whether myocardial and systemic cytokine expression differed compared to wild type (WT).     

Biochemical analysis of two cell surface glycoprotein complexes, very common antigen 1 and very common antigen 2. Relationship to very late activation T cell antigens

Two mouse monoclonal antibodies (mAb), AJ2 and J143, define two related human cell surface protein complexes, very common antigen 1 (VCA-1) and very common antigen 2 (VCA-2). In the present report, these complexes have been defined with respect to: (i) subunit arrangement; (ii) monoclonal antibody binding sites; (iii) carbohydrate content; (iv) homology to other cell surface protein complexes; and (v) possible functional roles. Analysis of the antigens from a human melanoma cell line, MeWo, reveals that VCA-1 is a noncovalently linked heterodimer of 170- and 140 (designated 1401)-kDa polypeptides. mAb AJ2 reacts with an epitope on the 1401-kDa polypeptide. VCA-2 is composed of the same 1401-kDa polypeptide as VCA-1 and another 170-kDa species; this 170-kDa species consists of a second distinct 140-kDa (designated 140(2)) and a 30-kDa polypeptide which are disulfide-bonded. Indirect evidence indicates that mAb J143 reacts with an epitope on this 170-kDa complex. Peptide mapping has shown that the complexes are members of a family of cell surface proteins that include antigens present on activated T cells (designated very late activation antigens). Since VCA-2 is found predominantly on the basal membrane of adherent cells and its expression increases 12-fold when HUT-102 lymphoblastoid cells are grown as an adherent cell culture, we suggest that VCA-2 plays a role in cellular adherence.     

Amyloplasts are necessary for full gravitropic sensitivity in roots of Arabidopsis thaliana

The observation that a starchless mutant (TC7) of Arabidopsis thaliana (L.) Heynh. is gravitropic (T. Caspar and B.G. Pickard, 1989, Planta 177, 185–197) raises questions about the hypothesis that starch and amyloplasts play a role in gravity perception. We compared the kinetics of gravitropism in this starchless mutant and the wild-type (WT). Wild-type roots are more responsive to gravity than TC7 roots as judged by several parameters: (1) Vertically grown TC7 roots were not as oriented with respect to the gravity vector as WT roots. (2) In the time course of curvature after gravistimulation, curvature in TC7 roots was delayed and reduced compared to WT roots. (3) TC7 roots curved less than WT roots following a single, short (induction) period of gravistimulation, and WT, but not TC7, roots curved in response to a 1-min period of horizontal exposure. (4) Wild-type roots curved much more than TC7 roots in response to intermittent stimulation (repeated short periods of horizontal exposure); WT roots curved in response to 10 s of stimulation or less, but TC7 roots required 2 min of stimulation to produce a curvature. The growth rates were equal for both genotypes. We conclude that WT roots are more sensitive to gravity than TC7 roots. Starch is not required for gravity perception in TC7 roots, but is necessary for full sensitivity; thus it is likely that amyloplasts function as statoliths in WT Arabidopsis roots. Furthermore, since centrifugation studies using low gravitational forces indicated that starchless plastids are relatively dense and are the most movable component in TC7 columella cells, the starchless plastids may also function as statoliths.Abbreviations S2 story two - S3 story three - WT wild-type     

Appearance of lectin-binding sites during vascularization of the primordium of the central nervous system in 10 to 12-day-old mouse embryos

Summary In the present study lectin-binding sites were investigated for the lectins Ricinus communis agglutinin (RCA I), wheat germ agglutinin (WGA), soya bean agglutinin (SBA), concanavalin A (Con A), Lotus tetragonolobus(LTA) and Limulus polyphemus agglutinin (LPA) during the initial stages of vasculogenesis of the CNS-anlage in 10 to 12-day-old NMRI mouse embryos. Specific binding sites for the lectins RCA I (sugar specificity: -D-galactose, N-acetylgalactosamine), WGA (sugar specificity: N-acetylglucosamine, sialic acid), and SBA (sugar specificity: N-acetylgalactosamine, -D-galactose) were detected in the newly formed capillaries within the neuroepithelial cell layer. In contrast, binding sites for Con A, LTA and LPA could not be observed at the start of the vascularization of the CNS-anlage. From these results, the conclusion can be drawn that glycoconjugates containing D-galactose, N-acetylgalactosamine and N-acetyl-glucosamine moieties are involved in the early vasculogenesis of the embryonic CNS-anlage of the mouse.     

Structure and composition of savanna vegetation in northern Bolivia: A preliminary report

The vegetation of seasonally flooded savannas iin the tropical lowland of the Departamento La Paz, northern Bolivia, was studied. A first collection of vascular plants in this area includes about 600 species, at least three of which are new to the Bolivian flora and four are new to science. The eight major vegetation types distinguished within the savannas are dry bunchgrass savanna (“altura”), seasonally flooded bunch-grass community (“sartenejal”), palm swamp (“palmar”), two types of river floodplains (”bajíos”), a tall shrub community (“chaparral”), the vegetation of termite mounds, and gallery forest. The study area is among the least known in Bolivia. There is a strong need for further studies of these savannas.     

Oxidation of glycerol,lactate, and propionate by Propionibacterium freudenreichii in a poised-potential amperometric culture system

Growth of Propionibacterium freudenreichii was studied with glycerol, lactate, and propionate as energy sources and a three-electrode poised-potential amperometric electrode system with hexacyanoferrate (III) as mediator. In batch culture experiments with glycerol and lactate as substrates, hexacyanoferrate (III) was completely reduced. Growth yields increased and the fermentation patterns were shifted towards higher acetate formation with increasing hexacyanoferrate (III) concentrations (0.25–8.0 mM). In experiments with regulated electrodes, glycerol, lactate, and propionate were oxidized to acetate and CO₂, and the electrons were quantitatively transferred to the working electrode. Growth yields of 29.0, 13.4 and 14.2 g cell material per mol were calculated, respectively. The high cell yield obtained during propionate oxidation cannot be explained solely by substrate level phosphorylation indicating that additional energy was conserved via electron transport phosphorylation. Furthermore, this result indicated complete reversibility of the methyl-malonyl-CoA pathway in propionic acid bacteria.