Hidden Markov models incorporating fuzzy measures and integrals for protein sequence identification and alignment

Profile hidden Markov models （HMMs） based on classical HMMs have been widely applied for protein sequence identification. The formulation of the forward and backward variables in profile HMMs is made under statistical independence assumption of the probability theory. We propose a fuzzy profile HMM to overcome the limitations of that assumption and to achieve an improved alignment for protein sequences belonging to a given family. The proposed model fuzzifies the forward and backward variables by incorporating Sugeno fuzzy measures and Choquet integrals, thus further extends the generalized HMM. Based on the fuzzified forward and backward variables, we propose a fuzzy Baum-Welch parameter estimation algorithm for profiles. The strong correlations and the sequence preference involved in the protein structures make this fuzzy architecture based model as a suitable candidate for building profiles of a given family, since the fuzzy set can handle uncertainties better than classical methods.     

Genome-Wide Analysis of Repetitive Elements in Papaya

Papaya (Carica papaya L.) is an important fruit crop cultivated in tropical and subtropical regions worldwide. A first draft of its genome sequence has been recently released. Together with Arabidopsis, rice, poplar, grapevine and other genomes in the pipeline, it represents a good opportunity to gain insight into the organization of plant genomes. Here we report a detailed analysis of repetitive elements in the papaya genome, including transposable elements (TEs), tandemly-arrayed sequences, and high copy number genes. These repetitive sequences account for ～56% of the papaya genome with TEs being the most abundant at 52%, tandem repeats at 1.3% and high copy number genes at 3%. Most common types of TEs are represented in the papaya genome with retrotransposons being the dominant class, accounting for 40% of the genome. The most prevalent retrotransposons are Ty3-gypsy (27.8%) and Ty1-copia (5.5%). Among the tandem repeats, microsatellites are the most abundant in number, but represent only 0.19% of the genome. Minisatellites and satellites are less abundant, but represent 0.68% and 0.43% of the genome, respectively, due to greater repeat length. Despite an overall smaller gene repertoire in papaya than many other angiosperms, a significant fraction of genes (>2%) are present in large gene families with copy number greater than 20. This repeat database clarified a major part of the papaya genome organization and partly explained the lower gene repertoire in papaya than in Arabidopsis.     

An immunosuppressive tryptophan-derived alkaloid from Lepidagathis cristata.

An immunosuppressive, tryptophan-derived alkaloid cristatin A (1), and two known compounds, cycloartenol and stigmasta-5,11(12)-diene-3 beta-ol, were isolated from the whole plant Lepidagathis cristata Willd. The structures of the isolates were established by interpretation of their spectral data.     

The plant cytoskeleton takes center stage in abiotic stress responses and resilience

Stress resilience behaviours in plants are defensive mechanisms that develop under adverse environmental conditions to promote growth, development and yield. Over the past decades, improving stress resilience, especially in crop species, has been a focus of intense research for global food security and economic growth. Plants have evolved specific mechanisms to sense external stress and transmit information to the cell interior and generate appropriate responses. Plant cytoskeleton, comprising microtubules and actin filaments, takes a center stage in stress-induced signalling pathways, either as a direct target or as a signal transducer. In the past few years, it has become apparent that the function of the plant cytoskeleton and other associated proteins are not merely limited to elementary processes of cell growth and proliferation, but they also function in stress response and resilience. This review summarizes recent advances in the role of plant cytoskeleton and associated proteins in abiotic stress management. We provide a thorough overview of the mechanisms that plant cells employ to withstand different abiotic stimuli such as hypersalinity, dehydration, high temperature and cold, among others. We also discuss the crucial role of the plant cytoskeleton in organellar positioning under the influence of high light intensity.     

Analysis of a framework using material balances in metabolic pathways to elucidate cellular metabolism

A framework using material balances in metabolic pathways to study cellular metabolism is examined and the results are discussed. Rate measurements on extracellular compounds alone were found to be not always sufficient to validate proposed unique intracellular mechanisms. The conditions to delineate among candidate mechanisms based solely on extracellular measurements are established. The number of half reactions comprising the reaction network is found to be an important parameter.     

Triterpenoids of Scoparia dulcis

The triterpenoids of Scoparia dulcis were identified as friedelin, glutinol, α-amyrin, betulinic acid, ifflaionic acid and dulcioic acid.     

In VivoEffects of Hepatocyte Growth Factor/Scatter Factor on Mouse Mammary Gland Development

We have recently demonstrated the regulated expression ofHGF/SFand its receptor (c-met) during mouse mammary gland development together with the mitogenic, motogenic and morphogenic effects of exogenous HGF/SF on primary mammary epithelial cells in culture. This study was undertaken to analyze the influence of HGF/SF on reconstituted mouse mammary gland developmentin vivo.Here we report that overexpression of HGF/SF induces a range of alterations in the architecture of virgin mouse mammary gland. These include an enhancement of ductal end bud (mammary gland morphoregulatory control point) size and numbers and hyperplastic branching morphogenesis. These data are the first demonstration of the effects of HGF/SF on mammary epitheliumin vivo.