Comparison of two unsupervised learning algorithms

The binary decision element described by the decision rule depending upon weight vector w is a model of neuron examined in this paper. The environment of the element is described by some unknown, stationary distribution p(x). The input signals x[n] of the element appear in each step n independently in accordance with the distribution p(x). During an unsupervised learning process the weight vector w[n] is changed on the base of the input vector x[n]. In the paper there are regarded two self-learning algorithms which are stochastic approximation type. For both algorithms the same rule of past experiences neglecting or the rule of weight decrease has been introduced. The first algorithm differs from the other one by a rule of weight increase. It has been proved that only one of these algorithms always leads to the same decision rule in a given environment p(x).This work was done during stay of Dr. L. Bobrowski at the University of Salerno in the frame of Polish-Italian Agreement on Scientific Cooperation     

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

The expression level of a gene is often used as a proxy for determining whether the protein or RNA product is functional in a cell or tissue. Therefore, it is of fundamental importance to understand the global distribution of gene expression levels, and to be able to interpret it mechanistically and functionally. Here we use RNA sequencing (RNA‐seq) of mouse Th2 cells, coupled with a range of other techniques, to show that all genes can be separated, based on their expression abundance, into two distinct groups: one group comprised of lowly expressed and putatively non‐functional mRNAs, and the other of highly expressed mRNAs with active chromatin marks at their promoters. These observations are confirmed in many other microarray and RNA‐seq data sets of metazoan cell types.     

Discovery libraries targeting the major enzyme classes: The serine hydrolases

Two libraries of modestly reactive ureas containing either electron-deficient acyl anilines or acyl pyrazoles were prepared and are reported as screening libraries for candidate serine hydrolase inhibitors. Within each library is a small but powerful subset of compounds that serve as a chemotype fragment screening library capable of subsequent structural diversification. Elaboration of the pyrazole-based ureas provided remarkably potent irreversible inhibitors of fatty acid amide hydrolase (FAAH, apparent K_i = 100–200 pM) complementary to those previously disclosed enlisting electron-deficient aniline-based ureas.     

Comparison of fatty acid composition in major lipid classes of the dominant benthic invertebrates of the Yenisei river

The composition and content of fatty acids (FAs) in total lipids, triacylglycerols (TAG) and polar lipids (PL) in dominant groups of benthic invertebrates: gammarids (Gammaridae, Amphipoda), chironomid larvae (Chironomidae, Diptera), caddisfly larvae (Trichoptera) and mayfly larvae (Ephemeroptera) were studied in the Yenisei river. For the first time data on the FA composition of species belonging to Trichoptera (Insecta) are presented. The groups of aquatic insect larvae and gammarids weakly differed in total content of essential polyunsaturated fatty acids (PUFAs). Hence, the strong invasion of gammarids which occurred in the last decades in the Yenisei river should not result in a decrease in potential yield of essential PUFA in the ecosystem and corresponding decrease in food resource quality for fish in respect to PUFA content. Significant differences in biomarker FAs in TAG were found which correlated to specific food sources. Different levels of long-chain PUFA in PL of the invertebrates are discussed in relation to the genetic ability of particular taxa to form these FAs.     

Comparison of antigens recognized by xenogeneic and allogeneic anti-Ia antibodies: Evidence for two classes of Ia antigens

Previously published data suggest that both xenogeneic and allogeneic anti-Ia sera can recognize carbohydrate-defined antigenic determinants on the surface of lymphocytes. There is also evidence, based on studies with allogeneic anti-Ia sera, that protein-defined Ia antigens exist. In this paper the relationship between these two types of Ia antigen was examined. It was found that in capping studies, the allogeneic anti-Ia serum could cap off the antigens recognized by the xenogeneic antiserum, whereas the xenogeneic antibodies could, at least partially, clear the surface of lymphocytes of Ia antigens detected by the allogeneic antibodies. On the other hand, when immunoprecipitates of radioiodinated cell-surface antigens were examined by SDS-polyacrylamide-gel electrophoresis, it was found that the xenogeneic anti-Ia serum did not immunoprecipitate any labeled material. In contrast, the allogeneic antiserum immunoprecipitated a labeled molecule which corresponded to the protein-defined Ia antigen described by others. Finally, it was shown that serum Ia antigens could be bound by either mouse or rabbit anti-Ia antibody, and this binding blocked any further reactivity with either serum. These results were interpreted as suggesting that two separate classes of Ia antigen molecule appear on the lymphocyte surface-one class has carbohydrate-defined antigenic specificities and the other has protein-defined determinants. Allogeneic anti-Ia sera contain antibodies against both these antigenic systems, whereas xenogeneic sera recognize only the carbohydratedefined series. The genetic implications of this interpretation are discussed.     

Comparison between two classes of selective EP(3) antagonists and their biological activities

Two different series of very potent and selective EP(3) antagonists have been reported: a novel series of ortho-substituted cinnamic acids [Belley, M., Gallant, M., Roy, B., Houde, K., Lachance, N., Labelle, M., Trimble, L., Chauret, N., Li, C., Sawyer, N., Tremblay, N., Lamontagne, S., Carrière, M.-C., Denis, D., Greig, G. M., Slipetz, D., Metters, K. M., Gordon, R., Chan, C. C., Zamboni, R. J. Bioorg. Med. Chem. Lett.2005, 15, 527] and the acylsulfonamides of ortho-(arylmethyl)cinnamates. [(a) Juteau, H., Gareau, Y., Labelle, M., Sturino, C. F., Sawyer, N., Tremblay, N., Lamontagne, S., Carrière, M.-C., Denis, D., Metters, K. M. Bioorg. Med. Chem. 2001, 9, 1977; (b) Juteau, H., Gareau, Y., Labelle, M., Lamontagne, S., Tremblay, N., Carrière, M.-C., Denis, D., Sawyer, N., Metters, K. M. Bioorg. Med. Chem. Lett.2001, 11, 747] The structural differences between the two series, along with their biological activity in vivo, in vitro, and metabolism, are analyzed. Some of those compounds, including hybrids containing the best structural features of both series, possess K(i) as low as 0.6 nM on the EP(3) receptor.     

Evolutionary relationships of the classes of major histocompatibility complex genes

A number of hypotheses have been proposed to account for the evolutionary origin of the classes of major histocompatibility complex (MHC) genes of vertebrates. According to one hypothesis the class II MHC evolved first, whereas another hypothesis holds that the class I MHC originated first as a result of a recombination between an immunoglobulin-like C-domain and the peptide-binding domain of an HSP70 heat-shock protein. A phylogenetic tree of C-domains from MHC and related molecules supports a relationship between the class II MHC chain and ₂-microglobulin and between the class II MHC -chain and the class I chain. If this phylogeny is correct, the hypothesis that class I MHC evolved by recombination with HSP70 is less parsimonious than the hypothesis that class II evolved first. Furthermore, when MHC peptide-binding domains are simultaneously aligned with HSP70 domains and with V-domains from members of the immunoglobulin superfamily, they are slightly more similar to the latter than to the former; and the class II ₁ and ₁ domains show much greater similarity to each other than would be expected if they evolved from separate HSP70 domains. Thus, most evidence supports the hypothesis that the ancestral MHC molecule had a class II-like structure.     

Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies

Gene and SNP annotation are among the first and most important steps in analyzing a genome. As the number of sequenced genomes continues to grow, a key question is: how does the quality of the assembled sequence affect the annotations? We compared the gene and SNP annotations for two different Bos taurus genome assemblies built from the same data but with significant improvements in the later assembly. The same annotation software was used for annotating both sequences. While some annotation differences are expected even between high-quality assemblies such as these, we found that a staggering 40% of the genes (>9,500) varied significantly between assemblies, due in part to the availability of new gene evidence but primarily to genome mis-assembly events and local sequence variations. For instance, although the later assembly is generally superior, 660 protein coding genes in the earlier assembly are entirely missing from the later genome''s annotation, and approximately 3,600 (15%) of the genes have complex structural differences between the two assemblies. In addition, 12–20% of the predicted proteins in both assemblies have relatively large sequence differences when compared to their RefSeq models, and 6–15% of bovine dbSNP records are unrecoverable in the two assemblies. Our findings highlight the consequences of genome assembly quality on gene and SNP annotation and argue for continued improvements in any draft genome sequence. We also found that tracking a gene between different assemblies of the same genome is surprisingly difficult, due to the numerous changes, both small and large, that occur in some genes. As a side benefit, our analyses helped us identify many specific loci for improvement in the Bos taurus genome assembly.     

Herpesvirus assembly: a tale of two membranes

Herpes virions are amongst the most complex virus particles: they comprise in excess of thirty virally encoded proteins, and also contain cellular components. Capsid formation and the cleavage and encapsidation of replicated viral DNA occur in the nucleus and resemble similar processes in tailed dsDNA (double-stranded DNA) bacteriophages, which indicates they might have common ancestry. In contrast, final virion maturation takes place in the cytoplasm. Nucleocapsids gain access to this compartment by envelopment at the inner nuclear membrane, which involves the interaction between viral and cellular proteins in order to locally alter nuclear architecture. Fusion of the primary viral envelope with the outer nuclear membrane results in translocation of the nucleocapsid to the cytoplasm. Here, the majority of the tegument - a structure, composed of a multitude of different proteins, that links the capsid and the envelope - is added to nucleocapsids, which obtain their final envelope by budding into glycoprotein-containing Golgi-derived vesicles. Thus, herpesvirus morphogenesis proceeds in two different cellular compartments, involving different viral and cellular proteins.     

Barrier-to-autointegration factor: major roles in chromatin decondensation and nuclear assembly

Barrier-to-autointegration factor (BAF) is a DNA-bridging protein, highly conserved in metazoans. BAF binds directly to LEM (LAP2, emerin, MAN1) domain nuclear membrane proteins, including LAP2 and emerin. We used site-directed mutagenesis and biochemical analysis to map functionally important residues in human BAF, including those required for direct binding to DNA or emerin. We also tested wild-type BAF and 25 point mutants for their effects on nuclear assembly in Xenopus egg extracts, which contain approximately 12 microM endogenous BAF dimers. Exogenous BAF caused two distinct effects: at low added concentrations, wild-type BAF enhanced chromatin decondensation and nuclear growth; at higher added concentrations, wild-type BAF completely blocked chromatin decondensation and nuclear growth. Mutants fell into four classes, including one that defines a novel functional surface on the BAF dimer. Our results suggest that BAF, unregulated, potently compresses chromatin structure, and that BAF interactions with both DNA and LEM proteins are critical for membrane recruitment and chromatin decondensation during nuclear assembly.     

Comparison of odorant specificity of two human olfactory receptors from different phylogenetic classes and evidence for antagonism

Humans are able to detect and discriminate myriads of odorants using only several hundred olfactory receptors (ORs) classified in two major phylogenetic classes representing ORs from aquatic (class I) and terrestrial animals (class II). Olfactory perception results in a combinatorial code, in which one OR recognizes multiple odorants and different odorants are recognized by different combinations of ORs. Moreover, recent data suggest that odorants could also behave as antagonists for other ORs, thus making the combinatorial coding more complex. Here we describe the odorant repertoires of two human ORs belonging to class I and class II, respectively. For this purpose, we set up an assay based on calcium imaging in which 100 odorants were screened using air-phase odorant stimulation at physiological doses. We showed that the human class I OR52D1 is functional, exhibiting a narrow repertoire related to that of its orthologous murine OR, demonstrating than this human class I OR is not an evolutionary relic. The class II OR1G1 was revealed to be broadly tuned towards odorants of 9-10 carbon chain length, with diverse functional groups. The existence of antagonist odorants for the class II OR was also demonstrated. They are structurally related to the agonists, with shorter carbon chain length.     

Structural differences in full-length cDNAs for two classes of sporamin,the major soluble protein of sweet potato tuberous roots

Summary Sporamin, which accounts for 80% of the total soluble proteins in sweet potato tuberous roots, consists of two polypeptide classes, A and B. The sporamin cDNA clones can also be classified into sporamin A and B subfamilies based on their sequence homologies, with intra-subfamily homologies being much higher than inter-subfamily homologies. The sequence of an essentially full-length cDNA for sporamin B was compared with that for sporamin A. The coding sequences of two cDNAs share 83% sequence homology. The sequences in the 5- and 3-noncoding regions show many deletions in addition to base substitutions. The endpoints of deletions longer than 4 bp match precisely to the endpoints of short direct repeats present in the other sequence, which suggests that these deletions are generated by slipped mispairing during DNA replication. In the 5- and 3-noncoding region of sporamin B cDNA, there are 5 bp direct repeats with sequences complementary to each other. Since most of these repeats are absent in sporamin A cDNA, these structural features may cause a difference in the secondary structure between A and B mRNAs and affect the translational efficiencies or stabilities of the mRNAs. Precursors for both classes of sporamin carry N-terminal extra-sequences which can be separated into a putative signal peptide segment and a segment enriched with basic amino acids. A two-step processing mechanism for the maturation of sporamin is suggested.     

Separation and identification of major plant sphingolipid classes from leaves

Sphingolipids are major components of the plasma membrane, tonoplast, and other endomembranes of plant cells. Previous compositional analyses have focused only on individual sphingolipid classes because of the widely differing polarities of plant sphingolipids. Consequently, the total content of sphingolipid classes in plants has yet to be quantified. In addition, the major polar sphingolipid class in the model plant Arabidopsis thaliana has not been previously determined. In this report, we describe the separation and quantification of sphingolipid classes from A. thaliana leaves using hydrolysis of sphingolipids and high performance liquid chromatography (HPLC) analysis of o-phthaldialdehyde derivatives of the released long-chain bases to monitor the separation steps. An extraction solvent that contained substantial proportions of water was used to solubilized >95% of the sphingolipids from leaves. Neutral and charged sphingolipids were then partitioned by anion exchange solid phase extraction. HPLC analysis of the charged lipid fraction from A. thaliana revealed only one major anionic sphingolipid class, which was identified by mass spectrometry as hexose-hexuronic-inositolphosphoceramide. The neutral sphingolipids were predominantly composed of monohexosylceramide with lesser amounts of ceramides. Extraction and separation of sphingolipids from soybean and tomato showed that, like A. thaliana, the neutral sphingolipids consisted of ceramide and monohexosylceramides; however, the major polar sphingolipid was found to be N-acetyl-hexosamine-hexuronic-inositolphosphoceramide. In extracts from A. thaliana leaves, hexosehexuronic-inositolphosphoceramides, monohexosylceramides, and ceramides accounted for approximately 64, 34, and 2% of the total sphingolipids, respectively, suggesting an important role for the anionic sphingolipids in plant membranes.     

Comparison of the amino acid and nucleotide sequences between human and two guinea pig major basic proteins

By means of reverse-phase HPLC, 2 different proteins were obtained from apparently purified pig eosinophil major basic protein (MBP) and these proteins were named GMPB1 and GMBP2. It was revealed that these 2 components of MBP have similar molecular weights and pI values, although the amino acid compositions were slightly different. In the previous study, we cloned and sequenced GMPB1 cDNA. Here we obtained another clone by plaque hybridization using a screening probe synthesized by means of polymerase chain reaction. After sequencing, it became apparent that this clone corresponded to GMBP2. As in the case of GMBP1, the cDNA of GMBP2 encoded pre-proGMBP2 with 3 domains; signal peptide, acidic pro-portion, and mature GMBP2. By comparing the sequences of GMBP1 and GMBP2, it was revealed that the proteins were quite similar to each other. In addition, their sequences also resembled those of human MBP, especially in the basic domain of mature protein; but no such similarity existed in the pro-portion. Although the molecular weights determined by SDS-PAGE of guinea pig and human MBPs were 11,000 and 9,300, respectively, the calculated molecular weights of these 3 MBPs were all 13.8 kDa. The calculated pI values of GMBP1, GMBP2 and human MBP were 11.7, 11.3 and 11.6, respectively. By means of Harr plot analysis, it was revealed that the amino acid sequences, not only in signal peptides but also in the basic domains of mature proteins, were well conserved between guinea pig and human MBPs.     

Comparison of the spin-lattice relaxation properties of the two classes of [2Fe-2S] clusters in proteins

Two classes of [2Fe-2S] proteins have been defined according to the mean value gav of their g tensor components (Bertrand, P., Guigliarelli, B., Gayda, J.P., Beardwood, P. and Gibson, J.F. (1985) Biochim. Biophys. Acta 831, 261-266). To characterize their magnetic properties better, we have compared the spin-lattice relaxation behavior of typical proteins which belong to these two classes, namely Spirulina maxima and adrenal ferredoxin for the gav approximately 1.96 class, Thermus thermophilus Rieske protein and Pseudomonas putida benzene dioxygenase for the gav approximately 1.91 class. For all these proteins, the data support the existence of an efficient Orbach process in the highest temperature range, which allows the determination of the exchange coupling parameter, J. From the comparison of the J values obtained in each class, it is concluded that the structural factors which determine the value of the g tensor and the strength of the antiferromagnetic exchange interactions are different.     

Exploration of bacterial community classes in major human habitats

Background

Determining bacterial abundance variation is the first step in understanding bacterial similarity between individuals. Categorization of bacterial communities into groups or community classes is the subsequent step in describing microbial distribution based on abundance patterns. Here, we present an analysis of the groupings of bacterial communities in stool, nasal, skin, vaginal and oral habitats in a healthy cohort of 236 subjects from the Human Microbiome Project.

Results

We identify distinct community group patterns in the anterior nares, four skin sites, and vagina at the genus level. We also confirm three enterotypes previously identified in stools. We identify two clusters with low silhouette values in most oral sites, in which bacterial communities are more homogeneous. Subjects sharing a community class in one habitat do not necessarily share a community class in another, except in the three vaginal sites and the symmetric habitats of the left and right retroauricular creases. Demographic factors, including gender, age, and ethnicity, significantly influence community composition in several habitats. Community classes in the vagina, retroauricular crease and stool are stable over approximately 200 days.

Conclusion

The community composition, association of demographic factors with community classes, and demonstration of community stability deepen our understanding of the variability and dynamics of human microbiomes. This also has significant implications for experimental designs that seek microbial correlations with clinical phenotypes.     

Membrane assembly of the bacteriophage Pf3 major coat protein

The Pf3 major coat protein of the Pf3 bacteriophage is stored in the inner membrane of the infected cell during the reproductive cycle. The protein consists of 44 amino acids, and contains an acidic amphipathic N-terminal domain, a hydrophobic domain, and a short basic C-terminal domain. The mainly alpha-helical membrane-bound protein traverses the membrane once, leaving the C-terminus in the cytoplasm and the N-terminus in the periplasm. A cysteine-scanning approach was followed to measure which part of the membrane-bound Pf3 protein is inside or outside the membrane. In this approach, the fluorescence probe N-[(iodoacetyl)amino]ethyl-1-sulfonaphthylamine (IAEDANS) was attached to single-cysteine mutants of the Pf3 coat protein. The labeled mutant coat proteins were reconstituted into the phospholipid DOPC/DOPG (80/20 molar ratio) and DOPE/DOPG (80/20 molar ratio) model membranes. We subsequently studied the fluorescence characteristics at the different positions in the protein. We measured the local polarity of the environment of the probe, as well as the accessibility of the probe to the fluorescence quencher acrylamide. The results of this study show a single membrane-spanning protein with both the C- and N-termini remaining close to the surface of the membrane. A nearly identical result was seen previously for the membrane-bound M13 coat protein. On the basis of a comparison between the results from both studies, we suggest an "L-shaped" membrane-bound model for the Pf3 coat protein. DOPE-containing model membranes revealed a higher polarity, and quenching efficiency at the membrane/water interface. Furthermore, from the outside to the inside of the membrane, a steeper polarity gradient was measured at the PE/PG interface as compared to the PC/PG interface. These results suggest a thinner interface for DOPE/DOPG than for DOPC/DOPG membranes.