Machine learning study of classifiers trained with biophysiochemical properties of amino acids to predict fibril forming Peptide motifs

It is important to understand the cause of amyloid illnesses by predicting the short protein fragments capable of forming amyloid-like fibril motifs aiding in the discovery of sequence-targeted anti-aggregation drugs. It is extremely desirable to design computational tools to provide affordable in silico predictions owing to the limitations of molecular techniques for their identification. In this research article, we tried to study, from a machine learning perspective, the performance of several machine learning classifiers that use heterogenous features based on biochemical and biophysical properties of amino acids to discriminate between amyloidogenic and non-amyloidogenic regions in peptides. Four conventional machine learning classifiers namely Support Vector Machine, Neural network, Decision tree and Random forest were trained and tested to find the best classifier that fits the problem domain well. Prior to classification, novel implementations of two biologically-inspired feature optimization techniques based on evolutionary algorithms and methodologies that mimic social life and a multivariate method based on projection are utilized in order to remove the unimportant and uninformative features. Among the dimenionality reduction algorithms considered under the study, prediction results show that algorithms based on evolutionary computation is the most effective. SVM best suits the problem domain in its fitment among the classifiers considered. The best classifier is also compared with an online predictor to evidence the equilibrium maintained between true positive rates and false positive rates in the proposed classifier. This exploratory study suggests that these methods are promising in providing amyloidogenity prediction and may be further extended for large-scale proteomic studies.     

The elusive short gene--an ensemble method for recognition for prokaryotic genome

Glucagon-like peptide-1 (GLP-1) and leptin are anorectic hormones produced in the small intestine and white adipose tissue, respectively. Investigating how these hormones act together as an integrated anorectic signal is important to elucidate a mechanism to maintain energy balance. In the present study, coadministration of subthreshold GLP-1 and leptin dramatically reduced feeding in rats. Although coadministration of GLP-1 with leptin did not enhance leptin signal transduction in the hypothalamus, it significantly decreased phosphorylation of AMP-activated protein kinase (AMPK). In addition, coadministration of GLP-1 with leptin significantly increased proopiomelanocortin (POMC) mRNA levels. Considering that α-melanocortin stimulating hormone (α-MSH) is derived from POMC and functions through the melanocortin-4-receptor (MC4-R) as a key molecule involved in feeding reduction, the interaction of GLP-1 and leptin on feeding reduction may be mediated through the α-MSH/MC4-R system. As expected, the interaction of GLP-1 and leptin was abolished by intracerebroventricular preadministration of the MC4-R antagonists agouti-related peptide and SHU9119. Taken together, GLP-1 and leptin cooperatively reduce feeding at least in part via inhibition of AMPK following binding of α-MSH to MC4-R.     

Restriction fragment length polymorphism analysis of polymerase chain reaction products amplified from mapped loci of rice (Oryza sativa L.) genomic DNA

Summary Thirty mapped Indica rice genomic (RG) clones were partially sequenced from each end. From such sequence data, pairs of oligonucleotides were synthesized to act as primers for polymerase chain reaction (PCR) amplification of the corresponding loci in crude total DNA preparations. The PCR products from DNA of Indica varieties were of the sizes expected from the sizes of the corresponding RG clones. However, size polymorphisms were seen between PCR products from Indica and Japonica varieties, and among wildOryza species. Restriction fragment length polymorphism (RFLP) was observed between PCR products of Indica varieties simply by electrophoretic analysis of restricted products, without the need for Southern hybridization or radiolabelling. The RFLPs noted between varieties ARC6650 and Phalguna were inherited in recombinant inbred lines derived from a cross between them. The RFLPs were detectable in PCR products amplified from DNA extracted by a simple procedure from single seedlings or leaves, and revealed genetic heterogeneity in cultivated lines. An approach is described that is relevant to the acceleration of classical plant breeding through molecular techniques.     

Cyclooxygenase-2 enzyme inhibitory triterpenoids from Picrorhiza kurroa seeds

A bioassay guided phytochemical study of the ethyl acetate extract of the seeds of Picrorhiza kurroa afforded a new triterpenoid, 2alpha, 3beta, 19beta, 23-tetrahydroxyolean-12-en-28-O-beta-D-glucoside (1), along with five known triterpenoids, 2alpha, 3beta, 19beta, 23-tetrahydroxyolean-12-en-28-oic acid (2), 2alpha, 3beta, 23-trihydroxyolean-12-en-28-O-beta-d-glucoside (3), 2alpha, 3beta, 23-trihydroxyolean-12-en-28-oic acid (4), 2alpha, 3beta, 19beta, trihydroxyolean-12-en-28-oic acid (5), and 2alpha, 3beta, 6beta, 23-tetrahydroxyolean-12-en-28-oic acid (6). Their structures were established by extensive NMR spectral studies. The acetyl derivatives, compounds 7 and 8, were prepared from compounds 1 and 2, respectively, to aid in their structure elucidation. The inhibition of cyclooxygenase-2 (COX-2) enzyme by compounds 1--6 at 100 microg/mL was 38.3%, 39%, 37%, 49.6%, 25%, and 45.0%, respectively. However, compounds 1--6, at 100 microg/mL, did not inhibit cyclooxygenase-1 (COX-1) enzyme. Compound 1 is a novel triterpenoid and compounds 1--6 are isolated for the first time from the seeds of P. kurroa.     

HER-2/neu x aromatase double transgenic mice model: the effects of aromatase overexpression on mammary tumorigenesis

A majority of breast cancers are hormone-responsive, and require estrogen for growth, and respond to hormonal therapy that blocks estrogen receptor action. Breast tumors with low levels of or completely lacking estrogen receptor fail to respond to antiestrogen therapy yet require estrogen for tumor initiation. To address the importance of local estrogen in oncogene-mediated breast tumorigenesis, we have crossed MMTV-aromatase with MMTV-HER2/neu and examined the incidence of breast cancer in double transgenic mice in comparison with parental strains. Double transgenic mice show normal mammary development and express both transgenes at similar levels to that of parental strains. Tumor incidence in double transgenic mice (<5%) decreased compared to HER2/neu mice (>65%). In addition to a significant decrease in tumorigenesis, these mice expressed ER as well as high levels of ERβ along with decreased levels of cyclin D1 and phosphorylated pRb among other changes. Furthermore, experiments using THC (ER-agonist and ERβ-antagonist) clearly demonstrate the critical role of ERβ in HER2/neu-mediated tumorigenesis. These studies provide the first genetic evidence that estrogen receptor, mainly ERβ than ER and its dependent changes play an important role in regulating mammary tumorigenesis. These findings provide further evidence for development and testing of novel therapeutic approaches based on selective regulation of estrogen receptors (ER and β)-dependent actions for the treatment and prevention of breast cancers.     

Atomic resolution structures of rieske iron-sulfur protein: role of hydrogen bonds in tuning the redox potential of iron-sulfur clusters

The Rieske [2Fe-2S] iron-sulfur protein of cytochrome bc(1) functions as the initial electron acceptor in the rate-limiting step of the catalytic reaction. Prior studies have established roles for a number of conserved residues that hydrogen bond to ligands of the [2Fe-2S] cluster. We have constructed site-specific variants at two of these residues, measured their thermodynamic and functional properties, and determined atomic resolution X-ray crystal structures for the native protein at 1.2 A resolution and for five variants (Ser-154-->Ala, Ser-154-->Thr, Ser-154-->Cys, Tyr-156-->Phe, and Tyr-156-->Trp) to resolutions between 1.5 A and 1.1 A. These structures and complementary biophysical data provide a molecular framework for understanding the role hydrogen bonds to the cluster play in tuning thermodynamic properties, and hence the rate of this bioenergetic reaction. These studies provide a detailed structure-function dissection of the role of hydrogen bonds in tuning the redox potentials of [2Fe-2S] clusters.     

Genetic and mass spectrometry analyses of the unusual type IV-like pili of the archaeon Methanococcus maripaludis

The structure of pili from the archaeon Methanococcus maripaludis is unlike that of any bacterial pili. However, genetic analysis of the genes involved in the formation of these pili has been lacking until this study. Pili were isolated from a nonflagellated (ΔflaK) mutant and shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis to consist primarily of subunits with an apparent molecular mass of 17 kDa. In-frame deletions were created in three genes, MMP0233, MMP0236, and MMP0237, which encode proteins with bacterial type IV pilin-like signal peptides previously identified by in silico methodology as likely candidates for pilus structural proteins. Deletion of MMP0236 or MMP0237 resulted in mutant cells completely devoid of pili on the cell surface, while deletion of the third pilin-like gene, MMP0233, resulted in cells greatly reduced in the number of pili on the surface. Complementation with the deleted gene in each case returned the cells to a piliated state. Surprisingly, mass spectrometry analysis of purified pili identified the major structural pilin as another type IV pilin-like protein, MMP1685, whose gene is located outside the first pilus locus. This protein was found to be glycosylated with an N-linked branched pentasaccharide glycan. Deletion and complementation analysis confirmed that MMP1685 is required for piliation.     

Flow cytometric evaluation of yeast–bacterial cell–cell interactions

Synthetic cell–cell interaction systems can be useful for understanding multicellular communities or for screening binding molecules. We adapt a previously characterized set of synthetic cognate nanobody–antigen pairs to a yeast–bacteria coincubation format and use flow cytometry to evaluate cell–cell interactions mediated by binding between surface-displayed molecules. We further use fluorescence-activated cell sorting to enrich a specific yeast-displayed nanobody within a mixed yeast-display population. Finally, we demonstrate that this system supports the characterization of a therapeutically relevant nanobody–antigen interaction: a previously discovered nanobody that binds to the intimin protein expressed on the surface of enterohemorrhagic Escherichia coli. Overall, our findings indicate that the yeast–bacteria format supports efficient evaluation of ligand–target interactions. With further development, this format may facilitate systematic characterization and high-throughput discovery of bacterial surface-binding molecules.