In vivo and in vitro evaluation of the osteogenic potential of Davallia mariesii T. Moore ex Baker.

ETHNOPHARMACOLOGICAL RELEVANCE: Postmenopausal osteoporosis is a major bone health issue worldwide. There is an unmet medical need for osteoporosis treatments, a disease which disproportionately impacts women. Exploring botanicals to prevent or treat osteoporosis is currently an interest of investigations. Rhizomes of Davallia mariesii T. Moore ex Baker (Davalliacea) are used an indigenous herbal medicine in Asia for injuries due to fractures, contusions, and strains. AIM OF THE STUDY: In the present study, we investigated the osteogenic effect of the water extract of rhizomes of D. mariesii (DMH) on bone loss induced by an ovariectomy (OVX) in mice and also its impact on osteogenesis in primary human osteoblasts (HObs). Additionally, we performed a quantitative analysis of compounds in the DMH extract. MATERIALS AND METHODS: OVX C57BL/6J mice were orally administrated DMH extract for 12 weeks, and microarchitecture parameters were examined by microcomputed tomography. DMH extract was fractionated in a bio-guided manner, and fractions were isolated to obtain active compounds using HObs. Cell viability was evaluated by an MTT assay. Characteristics of early and late osteogenesis were analyzed by alkaline phosphatase activity and a mineralization assay. Molecular mechanisms were explored by a real-time quantitative PCR. Compounds in the DMH extract were identified and quantified using liquid chromatography tandem mass spectroscopy (LC-MS/MS). RESULTS: DMH improved bone mineral densities of vertebrae and the femur. Through microarchitectural observations, DMH significantly decreased the bone surface/volume ratio and trabecular separation, and also increased the connectivity density in the OVX group. Additionally, DMH inhibited osteoclast differentiation in receptor activator of nuclear factor-κB ligand-induced osteoclasts and increased bone formation in HObs. After bio-guided fractionation and isolation, we found that eriodictyol-7-O-ß-d-glucuronide (2) significantly increased alkaline phosphatase activity, and 5-O-ß-d-(6-O-vanilloylglucopyranosyl)gentisic acid (3) substantially enhanced mineral deposition. In HObs, compound 3 was more potent in upregulating expressions of bone morphogenetic protein-2, bone sialoprotein, osteopontin, osterix, and estrogen receptor-α. The amount of bioactive compound 3 in DMH was 5.68 ±â€¯0.64 mg/g of dry weight according to LC-MS/MS. CONCLUSION: For the first time we report that D. mariesii and its isolated compounds demonstrated potent osteogenic activities. Quantitative results of D. mariesii could be a reference for phytochemical analyses.

cytoHubba: identifying hub objects and sub-networks from complex interactome.

BACKGROUND: Network is a useful way for presenting many types of biological data including protein-protein interactions, gene regulations, cellular pathways, and signal transductions. We can measure nodes by their network features to infer their importance in the network, and it can help us identify central elements of biological networks. RESULTS: We introduce a novel Cytoscape plugin cytoHubba for ranking nodes in a network by their network features. CytoHubba provides 11 topological analysis methods including Degree, Edge Percolated Component, Maximum Neighborhood Component, Density of Maximum Neighborhood Component, Maximal Clique Centrality and six centralities (Bottleneck, EcCentricity, Closeness, Radiality, Betweenness, and Stress) based on shortest paths. Among the eleven methods, the new proposed method, MCC, has a better performance on the precision of predicting essential proteins from the yeast PPI network. CONCLUSIONS: CytoHubba provide a user-friendly interface to explore important nodes in biological networks. It computes all eleven methods in one stop shopping way. Besides, researchers are able to combine cytoHubba with and other plugins into a novel analysis scheme. The network and sub-networks caught by this topological analysis strategy will lead to new insights on essential regulatory networks and protein drug targets for experimental biologists. According to cytoscape plugin download statistics, the accumulated number of cytoHubba is around 6,700 times since 2010.

Genetic polymorphisms of 12 X-chromosomal STR loci in Taiwanese individuals and likelihood ratio calculations applied to case studies of blood relationships.

Allele frequencies for the 12 short tandem repeat loci of the Investigator Argus X-12 kit were obtained from 514 unrelated Taiwanese individuals (327 males and 187 females). Hardy-Weinberg equilibrium tests with samples demonstrated no significant deviation from expected values for all 12 loci (p > 0.05). The linkage disequilibrium for the 12 loci in the female samples was identical to what was observed in other Han Chinese populations, with only the DXS10103 and DXS10101 loci showing significant linkage disequilibrium after corrected by Bonferroni's correction for multiple testing (p < 0.05/66). No significant differences were observed by population pairwise genetic distance analysis between Taiwanese and other Han Chinese populations. When compared with other Asian, European, and African populations, however, significant differences were observed at more than one locus. The combined mean exclusion chance was 0.99999 in duo cases and 0.99999999 in trio cases. This study used mathematical logic inferred likelihood ratio calculation formulas for full-sister, half-sister from the same father, and paternal grandmother-granddaughter relationships. The results for these three real familial cases suggest that these 12 short tandem repeat loci may appropriate for forensic relationship testing.

Spotlight: assembly of protein complexes by integrating graph clustering methods.

UNLABELLED: As is generally assumed, clusters in protein-protein interaction (PPI) networks perform specific, crucial functions in biological systems. Various network community detection methods have been developed to exploit PPI networks in order to identify protein complexes and functional modules. Due to the potential role of various regulatory modes in biological networks, a single method may just apply a single graph property and neglect communities highlighted by other network properties. This work presents a novel integration method to capture protein modules/protein complexes by multiple network features detected by different algorithms. The integration method is further implemented in a web-based platform with a highly effective interactive network analyzer. Conventionally adopted methods with different perspectives on network community detection (e.g., CPM, FastGreedy, HUNTER, MCL, LE, SpinGlass, and WalkTrap) are also executed simultaneously. Analytical results indicate that the proposed method performs better than the conventional ones. The proposed approach can capture the transcription and RNA splicing machineries from the yeast protein network. Meanwhile, proteins that are highly associated with each other, yet not described in both machineries are also identified. In sum, a protein that is closely connected to components of a known module or a complex in the network view implies the functional association among them. Importantly, our method can detect these unique network features, thus facilitating efforts to discover unknown components of functional modules/protein complexes. AVAILABILITY: Spotlight is freely accessible at http://hub.iis.sinica.edu.tw/spotlight. Video clips for a quick view of usage are available in the website online help page.

Chemical and pharmacological investigation of micropropagated Hygrophila pogonocalyx produced from leaf explants.

BACKGROUND: An optimized method for indirect shoot organogenesis from the leaf explants of Hygrophila pogonocalyx, a rare and endemic species in Taiwan, was developed to supply enough quantity of plant materials for the first chemical and pharmacological investigation. RESULTS: Incubation of the young leaves on Murashige and Skoog (MS) medium supplemented with 6-benzylaminopurine (0.5 mg/l) and indole-3-acetic acid (0.1 mg/l) resulted in the best multiplication rate for organogenesis. The average number of adventitious buds per leaf was 22.8 ± 1.9 after 8-week culture. The adventitious buds rooted and developed into plantlets when cultured simply on MS medium. Using this protocol, up to 37,600 plants were produced from a single leaf explant in one year. From the ethanol extract of the leaves of this micropropagated plant, 13 compounds were isolated and identified, including two flavones (1, 11), four flavonols (9, 10, 12, and 13), three phenylethanoid glycosides (6-8), two alkylated glycosides (2-3), and two steroids (4-5). Of these, acteoside (7) exhibited anti-tyrosinase activity in human epidermal melanocytes and luteolin 7-O-ß-D-glucopyranoside (11) exhibited the greatest neurocytoprotective activity. CONCLUSIONS: The method, indirect shoot organogenesis from leaf explants of H. pogonocalyx, could be developed to supply enough quantity of plant materials for the chemical and pharmacological investigation. In the present study, the isolated active compounds may develop for whitening agents or treating neurodegenerative diseases in the future.

Y-chromosomal STRs haplotypes in the Taiwanese Paiwan population.

The distribution of Y-chromosomal short tandem repeat (Y-STR) haplotypes was determined in a population of Taiwanese Paiwan aboriginals. Using 17 Y-STR markers, a total of 135 haplotypes were observed, 102 of which were unique. The overall haplotype diversity for the 17 Y-STR loci tested was 0.9922 and the discrimination capacity was 0.6490. In addition, three novel intermediate alleles at the DYS448 locus were also found.

A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles.

BACKGROUND: Many research results show that the biological systems are composed of functional modules. Members in the same module usually have common functions. This is useful information to understand how biological systems work. Therefore, detecting functional modules is an important research topic in the post-genome era. One of functional module detecting methods is to find dense regions in Protein-Protein Interaction (PPI) networks. Most of current methods neglect confidence-scores of interactions, and pay little attention on using gene expression data to improve their results. RESULTS: In this paper, we propose a novel hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles, and we name it HUNTER. Our method not only can extract functional modules from a weighted PPI network, but also use gene expression data as optional input to increase the quality of outcomes. Using HUNTER on yeast data, we found it can discover more novel components related with RNA polymerase complex than those existed methods from yeast interactome. And these new components show the close relationship with polymerase after functional analysis on Gene Ontology. CONCLUSION: A C++ implementation of our prediction method, dataset and supplementary material are available at http://hub.iis.sinica.edu.tw/Hunter/. Our proposed HUNTER method has been applied on yeast data, and the empirical results show that our method can accurately identify functional modules. Such useful application derived from our algorithm can reconstruct the biological machinery, identify undiscovered components and decipher common sub-modules inside these complexes like RNA polymerases I, II, III.

AtTRP1 encodes a novel TPR protein that interacts with the ethylene receptor ERS1 and modulates development in Arabidopsis.

Arabidopsis AtTRP1 is an orthologue of SlTPR1, a tomato tetratricopeptide repeat protein that interacts with the tomato ethylene receptors LeETR1 and NR in yeast 2-hybrid assays and in vitro, and modulates plant development. AtTRP1 is encoded by a single copy gene in the Arabidopsis genome, and is related to TCC1, a human protein that competes with Raf-1 for Ras binding, and distantly related to the immunophilin-like FK-binding proteins TWD1 and PAS1. The former is involved in auxin transport and the latter is translocated to the nucleus in response to auxin. AtTRP1 interacted preferentially with the Arabidopsis ethylene receptor ERS1 in yeast two-hybrid assays. This association was confirmed by in vivo co-immunoprecipitation. AtTRP1 promoter-GUS was highly expressed in vascular tissue, mature anthers, the abscission zone, and was induced by ACC. Overexpression of AtTRP1 in wild-type Arabidopsis resulted in dwarf plants with reduced fertility, altered leaf/silique morphology, and enhanced expression of the ethylene responsive gene AtChitB. Exogenous GA did not reverse the dwarf habit. Etiolated transgenic seedlings overexpressing AtTRP1 displayed enhanced sensitivity to low ACC and this was correlated with the transgene expression. Seedlings overexpressing AtTRP1 at high levels exhibited shortened and swollen hypocotyls, inhibited root growth, and an altered apical hook. Plants overexpressing AtTRP1 also showed a reduced response to exogenous IAA and altered expression of a subset of auxin early responsive genes. These results indicated that overexpression of AtTRP1 affects cross-talk between ethylene and auxin signalling and enhances some ethylene responses and alters some auxin responses. A model for AtTRP1 action is proposed.

Genetic polymorphisms of 17 Y-chromosomal short tandem repeat loci in Atayal population of Taiwan.

AIM: To define the Y-chromosomal genetic structure in a sample of Atayal men from Taiwan. METHODS: Buccal swab samples were collected from 170 unrelated healthy male volunteers from Taiwanese aboriginal Atayal population. Genomic DNA was extracted and 17 Y chromosome-specific short tandem repeat loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438, and DYS448) were analyzed using the AmpFlSTR Yfiler Polymerase Chain Reaction Amplification Kit. RESULTS: A total of 99 different haplotypes were identified, 69 (69.7%) of which were unique. Total haplotype diversity was 0.9887. The most common haplotype was shared by 9 individuals in the study sample. Gene diversities ranged from 0.0574 for DYS438 to 0.6749 for DYS456. CONCLUSION: Our results will help provide the molecular genetic evidence for human settlement of the Pacific.

Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology.

One major task in the post-genome era is to reconstruct proteomic and genomic interacting networks using high-throughput experiment data. To identify essential nodes/hubs in these interactomes is a way to decipher the critical keys inside biochemical pathways or complex networks. These essential nodes/hubs may serve as potential drug-targets for developing novel therapy of human diseases, such as cancer or infectious disease caused by emerging pathogens. Hub Objects Analyzer (Hubba) is a web-based service for exploring important nodes in an interactome network generated from specific small- or large-scale experimental methods based on graph theory. Two characteristic analysis algorithms, Maximum Neighborhood Component (MNC) and Density of Maximum Neighborhood Component (DMNC) are developed for exploring and identifying hubs/essential nodes from interactome networks. Users can submit their own interaction data in PSI format (Proteomics Standards Initiative, version 2.5 and 1.0), tab format and tab with weight values. User will get an email notification of the calculation complete in minutes or hours, depending on the size of submitted dataset. Hubba result includes a rank given by a composite index, a manifest graph of network to show the relationship amid these hubs, and links for retrieving output files. This proposed method (DMNC || MNC) can be applied to discover some unrecognized hubs from previous dataset. For example, most of the Hubba high-ranked hubs (80% in top 10 hub list, and >70% in top 40 hub list) from the yeast protein interactome data (Y2H experiment) are reported as essential proteins. Since the analysis methods of Hubba are based on topology, it can also be used on other kinds of networks to explore the essential nodes, like networks in yeast, rat, mouse and human. The website of Hubba is freely available at http://hub.iis.sinica.edu.tw/Hubba.

Discovery of picomolar slow tight-binding inhibitors of alpha-fucosidase.

Glycosidase inhibitors have shown great medicinal and pharmaceutical values as exemplified by the therapeutic treatment of influenza virus and non-insulin-dependent diabetes. We herein report the discovery of picomolar slow tight-binding inhibitors 2-5 against the alpha-fucosidase from Corynebacterium sp. by a rapid screening for an optimal aglycon attached to 1-aminomethyl fuconojirimycin (1). The time-dependent inhibition displays the progressive tightening of enzyme-inhibitor complex from a low nanomolar K(i) to picomolar K(i)* value. Particularly compound 2 with a K(i)* of 0.46 pM represents the most potent glycosidase inhibitor to date. The effect of compound 3 on the intrinsic fluorescence of alpha-fucosidase is both time- and concentration-dependent in a saturation-type manner, which is consistent with the initial formation of a rapid equilibrium complex of enzyme and inhibitor (E.I), followed by the slower formation of a tightly bound enzyme-inhibitor complex (E.I*). The binding affinity increases 3.5 x 10(4)-fold from 1 (K(i) = 16.3 nM) to 2 (K(i)* = 0.46 pM). This work clearly demonstrates the effectiveness of our combinatorial approach leading to the rapid discovery of potent inhibitors.