Sinocurculigo, a new genus of Hypoxidaceae from China based on molecular and morphological evidence

Background

The monocot family Hypoxidaceae consists of nine genera with nearly 200 species. They occur mostly in the Southern Hemisphere with only a few species in the Northern Hemisphere, of which three genera, Hypoxis, Molineria, and Curculigo, with eight species are distributed in China. Recently, we have found a hypoxid-like plant in China that is quite different in floral structure from any of the three genera and even of the known taxa in Hypoxidaceae.

Methodology/Principal Findings

In addition to morphological analysis, we performed maximum parsimony, maximum likelihood, and Bayesian inference analyses based on fragments of the chloroplast matK and rbcL genes of 60 taxa in 12 families representing all major clades of the Hypoxidaceae alliance. Results showed that Hypoxidaceae is monophyletic and and that the new plant belongs to it, forming a distinct clade within the family Hypoxidaceae as a sister of Molineria. Phylogeny of the Hypoxidaceae family was constructed based on a combined matrix of the chloroplast rbcL, trnS-G, and trnL-F regions of 59 taxa in Hypoxidaceae and its alliance. Findings of the molecular investigation is consistent with those of the morphological analysis.

Conclusions/Significance

Based on the results of our molecular and morphological analyses in the present study, we propose a new genus, Sinocurculigo.

Autoimmune hepatitis complicated by Sjogren syndrome and Hashimoto thyroiditis with leukopenia: A report of one case

Autoimmune hepatitis (AIH) is a clinically common type of non-viral hepatitis. Sjogren syndrome (SS) and Hashimoto's thyroiditis (HT) are common autoimmune diseases. However, AIH complicated by SS and HT, which starts with leucopenia, rarely occurs. Here we report such a case and performed a literature review to summarize its clinical manifestations, diagnosis and treatment. Attention should be paid to the possibility of AIH complicated by other autoimmune diseases.

Pharmacokinetic variation of ofloxacin based on gender-related difference in the expression of multidrug resistance-associated protein (Abcc2/Mrp2) in rat kidney

The present study aimed to investigate the pharmacokinetic variation of ofloxacin based on gender-related difference in the expression of multidrug resistance-associated protein (Abcc2/Mrp2) in rat kidney. The concentrations of ofloxacin in rat plasma and urine were determined after tail vein administration (30 mg x kg(-1)) by high-performance liquid chromatography (HPLC) method. Expression of Mrp2 in kidney of male and female rats was qualitatively and quantitatively detected by immunohistochemistry and flow cytometry, separately. The results showed that AUC value of ofloxacin was lower in male rats than that in female rats and the total amount of ofloxacin excreted in the urine was higher in male rats than that in female rats. And the expression of Mrp2 in male rat kidney was higher than that in female rats. All results suggested that gender-related differences in pharmacokinetics of ofloxacin may be attributed to the differences in the expression of Mrp2 in kidney of male and female rats.

Predicted disappearance of Cephalantheropsis obcordata in Luofu Mountain due to changes in rainfall patterns

Background

In the past century, the global average temperature has increased by approximately 0.74°C and extreme weather events have become prevalent. Recent studies have shown that species have shifted from high-elevation areas to low ones because the rise in temperature has increased rainfall. These outcomes challenge the existing hypothesis about the responses of species to climate change.

Methodology/Principal Findings

With the use of data on the biological characteristics and reproductive behavior of Cephalantheropsis obcordata in Luofu Mountain, Guangdong, China, trends in the population size of the species were predicted based on several factors. The response of C. obcordata to climate change was verified by integrating it with analytical findings on meteorological data and an artificially simulated environment of water change. The results showed that C. obcordata can grow only in waterlogged streams. The species can produce fruit with many seeds by insect pollination; however, very few seeds can burgeon to become seedlings, with most of those seedlings not maturing into the sexually reproductive phase, and grass plants will die after reproduction. The current population's age pyramid is kettle-shaped; it has a Deevey type I survival curve; and its net reproductive rate, intrinsic rate of increase, as well as finite rate of increase are all very low. The population used in the artificial simulation perished due to seasonal drought.

Conclusions

The change in rainfall patterns caused by climate warming has altered the water environment of C. obcordata in Luofu Mountain, thereby restricting seed burgeoning as well as seedling growth and shortening the life span of the plant. The growth rate of the C. obcordata population is in descending order, and models of population trend predict that the population in Luofu Mountain will disappear in 23 years.

MiDas: automatic extraction of a common domain of discourse in sleep medicine for multi-center data integration

Clinical studies often use data dictionaries with controlled sets of terms to facilitate data collection, limited interoperability and sharing at a local site. Multi-center retrospective clinical studies require that these data dictionaries, originating from individual participating centers, be harmonized in preparation for the integration of the corresponding clinical research data. Domain ontologies are often used to facilitate multi-center data integration by modeling terms from data dictionaries in a logic-based language, but interoperability among domain ontologies (using automated techniques) is an unresolved issue. Although many upper-level reference ontologies have been proposed to address this challenge, our experience in integrating multi-center sleep medicine data highlights the need for an upper level ontology that models a common set of terms at multiple-levels of abstraction, which is not covered by the existing upper-level ontologies. We introduce a methodology underpinned by a Minimal Domain of Discourse (MiDas) algorithm to automatically extract a minimal common domain of discourse (upper-domain ontology) from an existing domain ontology. Using the Multi-Modality, Multi-Resource Environment for Physiological and Clinical Research (Physio-MIMI) multi-center project in sleep medicine as a use case, we demonstrate the use of MiDas in extracting a minimal domain of discourse for sleep medicine, from Physio-MIMI's Sleep Domain Ontology (SDO). We then extend the resulting domain of discourse with terms from the data dictionary of the Sleep Heart and Health Study (SHHS) to validate MiDas. To illustrate the wider applicability of MiDas, we automatically extract the respective domains of discourse from 6 sample domain ontologies from the National Center for Biomedical Ontologies (NCBO) and the OBO Foundry.

Paraholcoglossum and Tsiorchis, two new orchid genera established by molecular and morphological analyses of the Holcoglossum alliance

BACKGROUND

Holcoglossum is a small orchid genus of 12 species ranging from SW China to Thailand and NE India. Although molecular and morphological analyses have been performed to establish the phylogenetic relationships within this genus, the interspecific relations and its relations with allied genera, such as Rhynchostylis, Aerides and Vanda, remain unclear.

METHODOLOGY/PRINCIPAL FINDINGS

In addition to morphological analysis, maximum parsimony, maximum likelihood, and Bayesian inference analyses were performed based on fragments of the nuclear ITS and chloroplast trnL-F and matK genes of 31 taxa (15 Holcoglossum, 14 Aeridinae, 2 outgroups) representing all major clades of the Holcoglossum alliance. The results suggest that Holcoglossum is triphyletic, comprising three clades: the Holcoglossum clade, its sister clade, and a distant clade more closely related to Rhynchostylis, Aerides, and Vanda than to the Holcoglossum clade. The Holcoglossum clade is further divided into three subclades; the genetic distances between these three subclades also support this delimitation. The molecular conclusion is consistent with their distinct morphological characters.

CONCLUSIONS

We propose that the latter two clades comprise two new genera, Paraholcoglossum and Tsiorchis, and Holcoglossum clade divides into three sections. In addition, a new section, Holcoglossum sect. Nujiangensia, and a new species, Holcoglossum linearifolium, are proposed. Some new combinations are made, and a new scheme is provided for the classification of all species of Holcoglossum, Paraholcoglossum, and Tsiorchis.

Fast lipid and water levels by extraction with spatial smoothing (FLAWLESS): three-dimensional volume fat/water separation at 7 Tesla

PURPOSE

To quickly and robustly separate fat/water components of 7T MR images in the presence of field inhomogeneity for the study of metabolic disorders in small animals.

MATERIALS AND METHODS

Starting with a Markov random field (MRF) based formulation for the 3-point Dixon separation problem, we incorporated new implementation strategies, including stability tracking, multiresolution image pyramid, and improved initial value generation. We term the new method FLAWLESS (Fast Lipid And Water Levels by Extraction with Spatial Smoothing).

RESULTS

Compared with non-MRF techniques, FLAWLESS decreased the fat-water swapping mistakes in all of the three-dimensional (3D) animal volumes that we tested. FLAWLESS converged in approximately 1/60th of the computation time of other MRF approaches. The initial value generation of FLAWLESS further improved robustness to field inhomogeneity in 3D volume data.

CONCLUSION

We have developed a novel 3-point Dixon technique found to be useful for high field small animal imaging. It is being used to assess lipid depots and metabolic disorders as a function of genes, diet, age, and therapy.

OnWARD: ontology-driven web-based framework for multi-center clinical studies

With a large percentage of clinical trials still using paper forms as the primary data collection tool, there is much potential for increasing efficiency through web-based data collection systems, especially for large-scale multi-center trials. This paper presents OnWARD, an ontology-driven, secure, rapidly-deployed, web-based framework supporting data capture for large-scale multi-center clinical research. Our approach is developed using the agile methodology to provide a flexible, user-centered dynamic form generator, which can be quickly deployed and customized for any clinical study without the need of deep technical expertise. Because of the flexible framework, the data management system can be extended to accommodate a large variety of data types, including genetic, genomic and proteomic data. In this paper, we demonstrate the initial deployment of OnWARD for a Phase II multi-center clinical trial after a development period of merely three months. The study utilizes 23 clinical report forms containing more than 1500 data points. Preliminary evaluation results show that OnWARD exceeded expectations of the clinical investigators in efficiency, flexibility and ease in setting up.

Specific and Sensitive Detection of Enterobacter mori Using Reliable RT-PCR

Enterobacter mori, the causal agent of bacterial wilt in mulberry, is becoming a serious disease in mulberry orchards in China. Because no effective control strategy has been devised for this disease, the reliable screening of mulberry material for latent infection became necessary. Hence, a fast polymerase chain reaction (PCR) assay for the detection of E. mori was developed in this study. The primers were designed within regions of the RNA polymerase β-subunit (rpoB) gene. The method is fast and simple and showed 100% sensitivity (no false negatives) and 100% specificity (no false positives), which was tested with 4 representative E. mori strains, 9 Enterobacter type strains, 2 strains of the other major mulberry bacterial pathogens (Ralstonia solanacearum and Pseudomonas syringae pv. mori) in China, 7 strains of other plant-associated pathogens, and 50 unidentified epiphytic bacterial isolates from mulberry plants. The real-time PCR assays reliably detected the DNA at at least 10 fg/μl and the bacterial cells at 10² CFU/ml from mulberry shoots and roots suspension. The strong positive reaction in testing of all symptomatic plants (with 100% positive) and parts of asymptomatic latent infected plant samples (with 36.4% positive) provided proof that this method is reliable and sensitive and suitable for screening plant material with latent infections of E. mori.

Synthesis, crystal structure and luminescence properties of one inorganic-organic hybrid compound [FTMA]2[Co(NCS)4] (FTMA = ferrocenylmethyltrimethylammonium cation)

A new inorganic-organic hybrid compound [FTMA](2)[Co(NCS)(4)] (FTMA = ferrocenylmethyltrimethylammonium cation) has been synthesized and characterized by IR, UV, elemental analysis and X-ray crystallography. Co(II) atom has a distorted tetrahedral environment with four N atoms of four NCS(-) anions. In the solid state there are C-H⋯π interactions between adjacent ferrocenyl cations, which generate one-dimensional (1-D) supramolecular chain, and C-H⋯S hydrogen bonds between [FTMA](+) cations and cobalt thiocyanate anions. The title compound shows strong purple fluorescence emission in the solid state at room temperature.

A fast iterated conditional modes algorithm for water-fat decomposition in MRI

Decomposition of water and fat in magnetic resonance imaging (MRI) is important for biomedical research and clinical applications. In this paper, we propose a two-phased approach for the three-point water-fat decomposition problem. Our contribution consists of two components: 1) a background-masked Markov random field (MRF) energy model to formulate the local smoothness of field inhomogeneity; 2) a new iterated conditional modes (ICM) algorithm accounting for high-performance optimization of the MRF energy model. The MRF energy model is integrated with background masking to prevent error propagation of background estimates as well as improve efficiency. The central component of our new ICM algorithm is the stability tracking (ST) mechanism intended to dynamically track iterative stability on pixels so that computation per iteration is performed only on instable pixels. The ST mechanism significantly improves the efficiency of ICM. We also develop a median-based initialization algorithm to provide good initial guesses for ICM iterations, and an adaptive gradient-based scheme for parametric configuration of the MRF model. We evaluate the robust of our approach with high-resolution mouse datasets acquired from 7T MRI.

A laccase with antiproliferative activity against tumor cells from an edible mushroom, white common Agrocybe cylindracea

A laccase, with HIV-1 reverse transcriptase inhibitory activity (IC(50)=12.7 μM) and antiproliferative activity against HepG2 cells (IC(50)=5.6 μM) and MCF7 cells (IC(50)=6.5 μM), was purified from fresh fruiting bodies of the edible white common Agrocybe cylindracea mushroom. The laccase, which had a novel N-terminal sequence, displayed a molecular mass of 58 kDa within the range reported for most other mushroom laccases. The purification protocol entailed ion exchange chromatography on DEAE-cellulose, SP-Sepharose, and Q-Sepharose and gel filtration on Superdex 75. The laccase was adsorbed on DEAE-cellulose and Q-Sepharose, but unadsorbed on SP-Sepharose. Its optimum pH was pH 3-4 and its optimum temperature was 50°C. The activity of the isolated laccase differed from one substrate to another. The ranking was ABTS>N,N-dimethyl-1,4-phenylenediamine>hydroquinone>catechol>2-methylcatechol>pyrogallol.

Large-scale, Exhaustive Lattice-based Structural Auditing of SNOMED CT

One criterion for the well-formedness of ontologies is that their hierarchical structure forms a lattice. Formal Concept Analysis (FCA) has been used as a technique for assessing the quality of ontologies, but is not scalable to large ontologies such as SNOMED CT (> 300k concepts). We developed a methodology called Lattice-based Structural Auditing (LaSA), for auditing biomedical ontologies, implemented through automated SPARQL queries, in order to exhaustively identify all non-lattice pairs in SNOMED CT. The percentage of non-lattice pairs ranges from 0 to 1.66 among the 19 SNOMED CT hierarchies. Preliminary manual inspection of a limited portion of the over 544k non-lattice pairs, among over 356 million candidate pairs, revealed inconsistent use of precoordination in SNOMED CT, but also a number of false positives. Our results are consistent with those based on FCA, with the advantage that the LaSA pipeline is scalable and applicable to ontological systems consisting mostly of taxonomic links.

Purification, characterization, and cloning of a novel phytase with low pH optimum and strong proteolysis resistance from Aspergillus ficuum NTG-23

A novel phytase was isolated from Aspergillus ficuum NTG-23 with a procedure involving ion-exchange chromatography on DEAE-cellulose, CM-cellulose and FPLC-gel filtration on Superdex 75. The protein exhibited a molecular mass of 65.5kDa in gel filtration and SDS-PAGE. It possessed an optimal pH of 1.3 and an optimal temperature of 67 degrees C, and manifested a K(m) of 0.295mM and a V(max) of 55.9nmol (phosphate)/min. Phytase activity was not significantly affected by metal ions such as Ca(2+), Mg(2+), Mn(2+), Zn(2+), but was slightly stimulated in the presence of EDTA. The phytase was stable at 60 degrees C with no obvious loss of activity upon its incubation at 70 degrees C for 20min. The enzyme exhibited a broad substrate selectivity and showed strong resistance toward pepsin and trypsin. The unique properties suggest that the phytase has the potential to be useful as an animal feed supplement.

Synergistic penetration of ethosomes and lipophilic prodrug on the transdermal delivery of acyclovir

The aim of this study was to investigate the lipophilic prodrug as a means of promoting acyclovir (ACV) that exhibited biphasic insolubility into the ethosomes for optimum skin delivery. Acyclovir Palmitate (ACV-C(16)) was synthesized as the lipophilic prodrug of ACV. The ethosomal system and the liposomal system bearing ACV or ACV-C(16) were prepared, respectively. The systems were characterized for shape, zeta potential value, particle size, and entrapment efficiency. Franz diffusion cells and confocal laser scanning microscopy were used for the percutaneous absorption studies. The results showed that the entrapment efficiency of ACV-C(16) ethosomes (87.75%) were much higher than that of ACV ethosomes (39.13%). The quantity of drug in the skin from ACV-C(16) ethosomes at the end of the 24 h transdermal experiment (622.89 microg/cm(2)) was 5.30 and 3.43 times higher than that from ACV-C(16) hydroalcoholic solution and ACV ethosomes, respectively. This study indicated that the binary combination of the lipophilic prodrug ACV-C(16) and the ethosomes synergistically enhanced ACV absorption into the skin.

Challenges in the assembly and handling of thin film capped MEMS devices

This paper discusses the assembly challenges considering the design and manufacturability of a Wafer Level Thin Film Package in MEMS applications. The assembly processes are discussed. The loads associated with these processes are illustrated and evaluated. Numerical calculations are combined with experimental observations in order to estimate the assembly risks. Our results emphasize the need for concurrent design for assembly.

Fine mapping of a gene for non-pollen type thermosensitive genic male sterility in rice (Oryza sativa L.)

The thermo-sensitive genic male sterility (TGMS) lines play a crucial role in two-line hybrid rice production. For a practical TGMS line, the stability of male sterility is one of the most important technical indicators. In this study, XianS, a spontaneous mutant with stable male sterility from an indica rice cultivar Xianhuangzhan, was classified as a non-pollen type TGMS line. The critical non-pollen sterility point temperature of XianS was determined as 27 degrees C. Genetic analysis demonstrated that the non-pollen sterility in XianS was controlled by a single recessive gene. Using SSR markers and bulked segregant analysis, the TGMS gene in XianS was fine mapped to a 183 kb interval between RMAN81 and RMX21 on chromosome 2. Two markers, 4039-1 and RMX14 completely cosegregated with this gene. Allelism test indicated that the non-pollen phenotype in seven non-pollen type TGMS lines from different sources, XianS, AnnongS-1, Q523S, Q524S, N28S, G421S, and Q527S is caused by the same TGMS gene. Although the location of TGMS gene in XianS is close to the gene OsNAC6, a previously identified candidate gene of tms5 in AnnongS-1, the sequence of OsNAC6 and its promoter region was identical in TGMS line XianS, AnnongS-1, and wild-type Xianhuangzhan. These results suggest that the non-pollen type TGMS trait probably be controlled by the same TGMS gene in different TGMS rice lines, but its real candidate gene still need to be further studied and identified.

VISAGE: A Query Interface for Clinical Research

We present the design and implementation of VISAGE (VISual AGgregator and Explorer), a query interface for clinical research. We follow a user-centered development approach and incorporate visual, ontological, searchable and explorative features in three interrelated components: Query Builder, Query Manager and Query Explorer. The Query Explorer provides novel on-line data mining capabilities for purposes such as hypothesis generation or cohort identification. The VISAGE query interface has been implemented as a significant component of Physio-MIMI, an NCRR-funded, multi-CTSA-site pilot project. Preliminary evaluation results show that VISAGE is more efficient for query construction than the i2b2 web-client.

A storage protein-like Trypsin inhibitor from the Moth Bean (Phaseolus acutifolius) with antiproliferative activity toward lymphoma cells

A 26-kDa trypsin inhibitor with an N-terminal sequence resembling storage proteins was purified from moth beans (Phaseolus acutifolius). It dose-dependently inhibited trypsin with an IC(50) value of about 0.38 microM. It inhibited [methyl-(3)H] thymidine incorporation by lymphoma MBL2 cells with an IC(50) value of 20 microM.

Using SPARQL to Test for Lattices: application to quality assurance in biomedical ontologies

We present a scalable, SPARQL-based computational pipeline for testing the lattice-theoretic properties of partial orders represented as RDF triples. The use case for this work is quality assurance in biomedical ontologies, one desirable property of which is conformance to lattice structures. At the core of our pipeline is the algorithm called NuMi, for detecting the Number of Minimal upper bounds of any pair of elements in a given finite partial order. Our technical contribution is the coding of NuMi completely in SPARQL. To show its scalability, we applied NuMi to the entirety of SNOMED CT, the largest clinical ontology (over 300,000 conepts). Our experimental results have been groundbreaking: for the first time, all non-lattice pairs in SNOMED CT have been identified exhaustively from 34 million candidate pairs using over 2.5 billion queries issued to Virtuoso. The percentage of non-lattice pairs ranges from 0 to 1.66 among the 19 SNOMED CT hierarchies. These non-lattice pairs represent target areas for focused curation by domain experts. RDF, SPARQL and related tooling provide an e cient platform for implementing lattice algorithms on large data structures.

Increased expression of hyaluronic acid binding protein 1 is correlated with poor prognosis in patients with breast cancer

BACKGROUND AND OBJECTIVES

Hyaluronic acid binding protein 1 (HABP1), a family of proteins interacting with hyaluronan (HA), had been associated with cell adhesion and tumor invasion. The aim of this study was to investigate the correlation between clinicopathologic factors and patient survival time with the expression of HABP1 in breast cancer patients.

METHODS

Expression of HABP1 mRNA and protein were detected with real-time quantitative PCR and immunohistochemical staining in 63 breast cancer and non-cancerous matched tissues.

RESULTS

The mRNA expression level of HABP1 was unrelated to the patient's age, tumor size, histological grade, TNM stage. However, it proved to be positively related to axillary nodes metastasis (P = 0.008). Furthermore, it was shown that the survival rate of patients with low HABP1 expression was significantly higher than that of patients with high HABP1 expression (P = 0.025). Multivariate analysis revealed that HABP1 mRNA expression level was a significant factor for predicting prognosis (P = 0.022). The immunohistochemistry results showed that the expression level of HABP1 in breast cancer cells was higher than that in normal breast cells.

CONCLUSION

HABP1 might be an independent predictive factor for breast cancer prognosis and up-regulation of HABP1 might play an important role in the metastasis of breast cancer.

A novel lectin with antiproliferative activity from the medicinal mushroom Pholiota adiposa

Little was known about biological activities of compounds from the medicinal mushroom of the genus Pholiota. A lectin from the Pholiota adiposa has now been isolated and its properties tested. The isolation procedure included ion exchange chromatography on DEAE-cellulose and CM-cellulose, and fast protein liquid chromatography-gel filtration (FPLC) on Superdex 75. The lectin was composed of two identical subunits, each with a molecular mass of 16 kDa. Its N-terminal amino-acid sequence showed little similarity to sequences of other Agaricales lectins. The hemagglutinating activity of the lectin was stable at temperatures up to 50 degrees C, and in NaOH and HCl solutions with concentrations less than 25 mM. It was inhibited by inulin (12.5-200 mM), but enhanced by Cu(2+) (6.25-25 mM), Fe(2+) (12.5-25 mM), and Al(3+) (6.25-25 mM) ions. The lectin showed antiproliferative activity toward hepatoma Hep G2 cells and breast cancer MCF7 cells with an IC(50) of 2.1 microM and approximately 3.2 microM, respectively. It exhibited HIV-1 reverse transcriptase inhibitory activity with an IC(50) of 1.9 microM. When compared with P. aurivella lectin, the only Pholiota lectin published to date, P. adiposa lectin differs in chromatographic behavior, molecular mass, N-terminal sequence, and effect of cations on hemagglutinating activity. In the case of the lectin from P. aurivella, its antifungal, antiproliferative, and HIV-1 reverse transcriptase inhibitory activities have not been determined.

A novel lectin with antiproliferative activity from the medicinal mushroom Pholiota adiposa

Little was known about biological activities of compounds from the medicinal mushroom of the genus Pholiota. A lectin from the Pholiota adiposa has now been isolated and its properties tested. The isolation procedure included ion exchange chromatography on DEAE-cellulose and CM-cellulose, and fast protein liquid chromatography-gel filtration (FPLC) on Superdex 75. The lectin was composed of two identical subunits, each with a molecular mass of 16 kDa. Its N-terminal amino-acid sequence showed little similarity to sequences of other Agaricales lectins. The hemagglutinating activity of the lectin was stable at temperatures up to 50 degrees C, and in NaOH and HCl solutions with concentrations less than 25 mM. It was inhibited by inulin (12.5-200 mM), but enhanced by Cu(2+) (6.25-25 mM), Fe(2+) (12.5-25 mM), and Al(3+) (6.25-25 mM) ions. The lectin showed antiproliferative activity toward hepatoma Hep G2 cells and breast cancer MCF7 cells with an IC(50) of 2.1 microM and approximately 3.2 microM, respectively. It exhibited HIV-1 reverse transcriptase inhibitory activity with an IC(50) of 1.9 microM. When compared with P. aurivella lectin, the only Pholiota lectin published to date, P. adiposa lectin differs in chromatographic behavior, molecular mass, N-terminal sequence, and effect of cations on hemagglutinating activity. In the case of the lectin from P. aurivella, its antifungal, antiproliferative, and HIV-1 reverse transcriptase inhibitory activities have not been determined.

Molecular mapping of two reverse photoperiod-sensitive genic male sterility genes (rpms1 and rpms2) in rice (Oryza sativa L.)

The reverse photoperiod-sensitive genic male sterility (PGMS) and thermo-sensitive genic male sterility (TGMS) lines have an opposite phenotype compared with normal PGMS and TGMS lines widely used by the two-line system in current hybrid rice seed production. Thus, the application of reverse PGMS and TGMS lines can compensate PGMS and TGMS lines in hybrid rice production. YiD1S is a reverse PGMS line, in which pollen fertility is mainly regulated by day-length, but also influenced by temperature. Genetic analysis indicated that male sterility of YiD1S was controlled by two recessive major genes. An F(2) population from a cross between YiD1S and 8528 was developed and used for molecular mapping of the two reverse PGMS genes which were first named rpms1 and rpms2. Both simple sequence repeat (SSR) markers and bulked segregant analysis (BSA) were used in this study. As a result, one reverse PGMS gene (rpms1) was mapped to the interval between SSR markers RM22980 (0.9 cM) and RM23017 (1.8 cM) on chromosome 8. Eight SSR markers, YDS818, RM22984, RM22986, RM22997, YDS816, RM23002, RM339 and YDS810 completely co-segregated with the rpms1 gene. Another reverse PGMS gene (rpms2) was mapped to the interval between SSR markers RM23898 (0.9 cM) and YDS926 (0.9 cM) on chromosome 9. The physical mapping information from publicly available resources shows that the rpms1 and rpms2 loci are located in a region of 998 and 68 kb, respectively. The analysis based on marker genotypes showed that the effect of rpms1 was slightly larger than that of rpms2 and that the two genes interacted in controlling male sterility.

Effects of dietary inosinic acid on carcass characteristics, meat quality, and deposition of inosinic acid in broilers

An experiment was conducted to evaluate the effects of dietary inosinic acid (inosine 5'-monophosphate, IMP) on carcass characteristics, meat quality, and deposition of IMP in Arbor Acres broilers. A total of two hundred forty 1-d-old male Arbor Acres broilers were allocated to 4 inosinic acid treatments (0, 0.25, 0.50, and 0.75% dietary IMP supplementation). Birds were slaughtered at 42 d old. Dietary IMP did not significantly affect the carcass characteristics of broilers. No significant difference among treatments was observed in muscle pH within 1 h or at 24 h postmortem (PM), or in the decrease of muscle pH within 24 h PM. Inosinic acid had no marked effect on the color of breast muscle or Hunter L* and a* values of thigh muscle. Hunter b* values in thigh muscle were lower (P < 0.05) in the 0.75% IMP supplementation group than in the control group. Both breast and thigh muscle of birds fed with 0.25% IMP diet resulted in a lower (P < 0.05) shear force value compared with those fed with the other diets. All of the test groups had greater (P < 0.05) deposition of IMP in breast and thigh muscle than that of the control group with the exception of the 0.75% IMP supplementation group for thigh muscle. Greater (P < 0.05) corrected IMP value in breast muscle was detected for the test groups compared with the control group. These results suggest that extraneous IMP addition may contribute to the improvement of growth, meat quality, and deposition of IMP in broilers.

New class of plastic bulk metallic glass

An intrinsic plastic Cu(45)Zr(46)Al(7)Ti(2) bulk metallic glass (BMG) with high strength and superior compressive plastic strain of up to 32.5% was successfully fabricated by copper mold casting. The superior compressive plastic strain was attributed to a large amount of randomly distributed free volume induced by Ti minor alloying, which results in extensive shear band formation, branching, interaction and self-healing of minor cracks. The mechanism of plasticity presented here suggests that the creation of a large amount of free volume in BMGs by minor alloying or other methods might be a promising new way to enhance the plasticity of BMGs.

[Experimental study of prostheses modified by three dimensions porous Ti combined bone morphogenetic proteins]

OBJECTIVE

To observe bone ingrowth of artificial femur which three dimensions (3-D) porous Ti combined bone morphogenetic proteins (BMPs) integrating on the prostheses surface in dogs.

METHODS

The prostheses integrated 3-D porous Ti on the surface, which combined BMPs directly or through FG, were implanted canine. And fluorescent labeling was done at 2, 5 weeks after that, and then the prostheses with femurs were taken out in 3, 6 weeks after operation. These specimens were treated, then observed through microscopy.

RESULTS

At 3 weeks, bone growing 1/2 of full thickness in 3-D porous Ti, but bone growing full thickness in 3-D porous Ti at 6 weeks. Bone formation was obviously higher at 6 weeks than at 3 weeks.

CONCLUSION

The prostheses modified 3-D porous Ti can accelerate osteogenesis and improve bone formation so that mechanical interlock and integration can be come true.

Genomic analysis of two porcine encephalomyocarditis virus strains isolated in China

Two strains of encephalomyocarditis virus (EMCV), designated BJC3 and HB1, were isolated from an aborted fetus and the heart tissue of a dead piglet that had pericardial fluid, respectively. The complete genomic sequences of the two viruses were determined and analyzed. The size of the genomes of BJC3 and HB1 were 7746 and 7735 nucleotides, respectively, including poly(A) tails. Comparative analysis with the genomic sequences of other EMCV strains showed that BJC3 and HB1 shared higher identity (92.5-99.6%) with BEL-2887A/91, EMCV-R and PV21, but lower identity (83.3-84.6%) with EMC-B, EMC-D and D variants, and only 81.0% with Mengo virus. Two amino acid mutations in the leader protein of the two viruses and one amino acid substitution in VP1 of BJC3 were found in comparison to other EMCV strains Phylogenetic analysis based on the amino acid sequences of the entire ORF revealed that the two Chinese isolates BJC3 and HB1 clustered together with the strains BEL-2887/91, EMCV-R and PV21, which belong to the same genetic subgroup as EMCV-30. Our results provide genomic information for EMCV isolated in China.

Clinical and pathologic changes in a guinea pig aerosol challenge model of acute Q fever

Acute Q fever is a zoonotic disease caused by the obligate intracellular bacterium Coxiella burnetii and can manifest as a flu-like illness, pneumonia, or hepatitis. A need exists in Q fever research for animal models mimicking both the typical route of infection (inhalation) and the clinical illness seen in human cases of Q fever. A guinea pig aerosol challenge model was developed using C. burnetii Nine Mile phase I (RSA 493), administered using a specialized chamber designed to deliver droplet nuclei directly to the alveolar spaces. Guinea pigs were given 10(1) to 10(6) organisms and evaluated for 28 days postinfection. Clinical signs included fever, weight loss, respiratory difficulty, and death, with the degree and duration of response corresponding to the dose of organism delivered. Histopathologic evaluation of the lungs of animals infected with a high dose showed coalescing panleukocytic bronchointerstitial pneumonia at 7 days postinfection that resolved to multifocal lymphohistiocytic interstitial pneumonia by 28 days. Guinea pigs receiving a killed whole-cell vaccine prior to challenge with the highest dose of C. burnetii were protected against lethal infection and did not develop fever. Clinical signs and pathological changes noted for these guinea pigs were comparable to those seen in human acute Q fever, making this an accurate and valuable animal model of human disease.

Combined use of choledochoscope and duodenoscope in treatment of bile peritonitis after removal of T-tube

BACKGROUND

Biliary leakage after removal of a T-tube has significant morbidity and mortality. Its etiology is multifactorial. The treatment and outcome of this complication vary. In the present study we evaluated the procedures and efficacy of combined use of choledochoscope and duodenoscope in the treatment of bile peritonitis after T-tube removal.

METHODS

The procedures and results of 11 cases of biliary leakage after removal of T-tube who had been treated from January 1998 to June 2004 by combined use of choledochoscope and duodenoscope were analyzed retrospectively.

RESULT

After the treatment, 9 patients were cured, and 2 were reoperated on and cured.

CONCLUSIONS

Biliary leakage after removal of T-tube can be cured successfully by combined use of choledochoscope and duodenoscope. Importantly, the method is simple, effective and safe, and mostly reoperation can be avoided.

ARCS: an aggregated related column scoring scheme for aligned sequences

MOTIVATION

Biologists frequently align multiple biological sequences to determine consensus sequences and/or search for predominant residues and conserved regions. Particularly, determining conserved regions in an alignment is one of the most important activities. Since protein sequences are often several-hundred residues or longer, it is difficult to distinguish biologically important conserved regions (motifs or domains) from others. The widely used tools, Logos, Al2co, Confind, and the entropy-based method, often fail to highlight such regions. Thus a computational tool that can highlight biologically important regions accurately will be highly desired.

RESULTS

This paper presents a new scoring scheme ARCS (Aggregated Related Column Score) for aligned biological sequences. ARCS method considers not only the traditional character similarity measure but also column correlation. In an extensive experimental evaluation using 533 PROSITE patterns, ARCS is able to highlight the motif regions with up to 77.7% accuracy corresponding to the top three peaks.

AVAILABILITY

The source code is available on http://bio.informatics.indiana.edu/projects/arcs and http://goldengate.case.edu/projects/arcs

[The effect of carvedilol on apoptosis gene PDCD5 expression in chronic heart failure patients]

OBJECTIVE

To observe the changes of serum PDCD5 antibody in chronic ischemic heart failure patients and the effect of carvedilol treatment.

METHODS

Twenty chronic ischemic heart failure patients, 11 males and 9 females, aged 58 +/- 13, with the left ventricular ejection fraction (LVEF) < 45% by echocardiography and New York Heart Association (NYHA) cardiac function classification II-III, were treated with carvedilol for 6 months with a target dosage of 50 mg/d. The serum PDCD5 antibody was tested by ELISA before and after carvedilol treatment and compared with those of 20 healthy persons.

RESULTS

The A value of PDCD5 antibody in the heart failure patients was 3.5 +/- 1.4, significantly higher that in than healthy persons (1.9 +/- 1.0, P < 0.01). After treatment of carvedilol, the A value of PDCD5 antibody in the heart failure patients decreased to 2.5 +/- 1.2 (P < 0.05). In 6 months maintenance treatment, 14 (70%) patients reached the dosage 50 mg/d, 4 (20%) reached 25 mg/d, and 2 (10%) reached 12.5 mg/d. Five patients (25%) had side effect such as dizziness, nausea and cough, one patient (5%) was hospitalized for 3 weeks because of heart failure, no patient died. After treatment of carvedilol, the NYHA degree increased by 0.3 (P < 0.05), LVEF increased from 35.5% +/- 7.8% to 42.7% +/- 9.6% (P < 0.05), left ventricular end-diastolic diameter decreased 5.3 mm (P < 0.05), and left ventricular end-systolic diameter decreased by 8.1 mm (P < 0.01).

CONCLUSION

The titer of apoptosis gene PDCD5 antibody in the serum of chronic ischemic heart failure patients are higher, which shows apoptosis and treatment of carvedilol significantly decreases its titer.

Mitochondrial DNA sequence analysis of two mouse hepatocarcinoma cell lines

AIM: To study genetic difference of mitochondrial DNA (mtDNA) between two hepatocarcinoma cell lines (Hca-F and Hca-P) with diverse metastatic characteristics and the relationship between mtDNA changes in cancer cells and their oncogenic phenotype.

METHODS: Mitochondrial DNA D-loop, tRNA^Met+Glu+Ile and ND3 gene fragments from the hepatocarcinoma cell lines with 1100, 1126 and 534 bp in length respectively were analysed by PCR amplification and restriction fragment length polymorphism techniques. The D-loop 3’ end sequence of the hepatocarcinoma cell lines was determined by sequencing.

RESULTS: No amplification fragment length polymorphism and restriction fragment length polymorphism were observed in tRNA^Met+Glu+Ile, ND3 and D-loop of mitochondrial DNA of the hepatocarcinoma cells. Sequence differences between Hca-F and Hca-P were found in mtDNA D-loop.

CONCLUSION: Deletion mutations of mitochondrial DNA restriction fragment may not play a significant role in carcinogenesis. Genetic difference of mtDNA D-loop between Hca-F and Hca-P, which may reflect the environmental and genetic influences during tumor progression, could be linked to their tumorigenic phenotypes.

[Inducement of FLICE inhibitory protein antisense oligonucleotides on apoptosis of human gastric cancer cell line BGC823]

BACKGROUND & OBJECTIVE

Cellular FLICE inhibitory protein (cFLIP) plays an important role in cell apoptosis, researches of antisense oligonucleotides (ASODN) of cFLIP gene may provide a new method or protocol for treatment of human gastric cancer. This study was to explore effect of cFLIP ASODN on apoptosis of human gastric cancer cell line BGC823.

METHODS

Human cervical cancer cell line HeLa was used as control, cFLIP ASODN was introduced into BGC823 cells and HeLa cells, reverse transcriptase-polymerase chain reaction (RT-PCR) and Western blot were used to detect cFLIP(L/S) (cellular FLIP(Short) and cellular FLIP(long)) mRNA and protein. The 5'FAM-conjugated ASODN was created complementary to a sequence that included the start site of FLIP open reading frame. After introducing, MTT was used to detect cell inhibition rate,TUNEL and flow cytometry (FCM) were used to detect cell apoptosis, and Western blot was used to detect protein level of cFLIP.

RESULTS

The encoding mRNA and protein of cFLIP(L) and cFLIP(S) can be detected in both HeLa and BGC823 cells. MTT revealed that cFLIP ASODN significantly inhibited proliferation of BGC823 cells (P< 0.05) in a concentration-dependent manner. TUNEL staining detected positive FLIP expression, specific apoptotic peak can be detected before G1 peak by FCM, and Western blot revealed that protein level of cFLIP(L) and cFLIP(S) decreased significantly (P< 0.05).

CONCLUSION

The cFLIP(L/S) mRNA and encoded proteins expressed in both HeLa and BGC823 cells. ASODN may down-regulate cFLIP(L/S) protein level, and initiate apoptosis of BGC823 cells.

[Effects of transfected SOCS3 gene on proliferation of human lung adenocarcinoma cell line A549]

BACKGROUND & OBJECTIVE

Previous studies showed that signal transducers and activators of transcription 3(STAT3) could be constantly activated in many kinds of tumor cells; constantly activated STAT3 could make cell malignant transformation, and enhance the malignant proliferation of tumor cells. The suppressors of cytokine signaling (SOCS) proteins, a recently identified family, could suppress the tyrosine-phosphorylated process of STAT protein to negatively regulate STAT-mediated cytokine signaling, which is closely related to cell survival, proliferation, and apoptosis. Among the SOCS protein family, SOCS3 is the most potent inhibitors of cytokine-induced signaling. This experiment was to investigate the effect of SOCS3 on proliferation of human lung adenocarcinoma cell line A549.

METHODS

A549 cells were co-transfected with pEFSOCS3 and pSV2neo by liposome, expression of SOCS3 mRNA and protein was determined by reverse transcriptase-polymerase chain reaction (RT-PCR), and immunocytochemistry. Tyrosine-phosphorylated STAT3 level was measured by Western blot analysis. MTT assay and (3)-TdR incorporation were used to measure the cell proliferation in pEFSOCS3-transfected group, and control group (non-transfected, and pEF-transfected A549).

RESULTS

Compared with control group, tyrosine-phosphorylated STAT3 level suppressed greatly in pEFSOCS3-transfected A549 cells (P< 0.01). The inhibitory rate of cell growth in pEFSOCS3-transfected group was 40.58%, and in control group was 32.23%. (3)-TdR incorporation (48 056+/-1 331) in pEFSOCS3-transfected group was significantly lower than that of control group (81,481+/-2,584, and 75,590+/-2,678, P< 0.01).

CONCLUSION

SOCS3 protein might inhibit proliferation of A549 cells by lowering the tyrosine-phosphorylated level of STAT3 protein.

Prediction of early recurrence of atrial fibrillation after external cardioversion by means of P wave signal-averaged electrocardiogram

BACKGROUND

Therapy of atrial fibrillation by electrical cardioversion (CV) is limited by the high rate of recurrences. Early recurrence of atrial fibrillation (ERAF) occurs in a subgroup of patients whose characteristics are poorly defined. This prospective study was performed to evaluate if the P wave signal-averaged ECG (PSAECG) is able to identify patients with an increased risk of ERAF after CV.

METHODS

Patients with an indication for elective external CV were enrolled. After successful CV, PSAECGs were recorded at 0.5, 1, 24 h and 1 week. The ability of PSAECG parameters (signal-averaged P wave duration, PWD; root-mean-square of the voltage of the terminal 20, 30, and 40 ms of the signal-averaged P wave; RMS20, RMS30, RMS40) to predict ERAF (prospectively defined as AF recurrence within 4 h after CV) was assessed.

RESULTS

Of 111 consecutive patients, 7 experienced ERAF, 30 patients had AF recurrence later during the 1-week follow-up. Patients with ERAF had a significantly prolonged signal-averaged PWD compared to patients who remained in SR (194+/-16 ms vs 139+/-3 ms at 0.5 h, p<0.001). As ROC analysis revealed, a PWD >/=154 ms at 30 min after CV had the highest predictive accuracy for ERAF (sensitivity 100%, specificity 82%, positive predictive value 33%, negative predictive value 100%). Other parameters of the PSAECG did not reveal significant differences between patients with and without ERAF.

CONCLUSIONS

The PSAECG provides a sensitive noninvasive tool for detection of patients at risk of ERAF. Thus identified, tailored pharmacological therapy is conceivable to prevent ERAF.

Identification and cloning potentially protective antigens of Coxiella burnetii using sera from mice experimentally infected with Nine Mile phase I

Coxiella burnetii is an obligate intracellular bacterium that causes acute Q fever and occasional chronic infections in humans. To determine the immunodominant antigens during infection with C. burnetii, sera from mice experimentally infected with Nine Mile phase I were tested by immunoblotting. The mouse sera recognized antigens with a variety of molecular weights, including proteins of 14, 22, 28, 34, and 60 kDa as immunodominant antigens. In order to clone potential protective antigens, a genomic DNA library of Nine Mile phase I was constructed in the expression vector Lambda ZAP Express and screened with sera from mice that recovered from C. burnetii infection. A total of 102 immunoreactive clones with various signal intensities were identified from about 8,000 plaques. These clones were purified and expressed in the excised plasmid pBK-CMV. The proteins expressed by these recombinant plasmids were analyzed by SDS-PAGE and immunoblotting. Fifty-four clones expressed immunoreactive proteins of molecular masses ranging from approximately 14 to 60 kDa. Sequence analysis and BLAST search of the recently completed genome sequence identified a variety of novel immunoreactive proteins. These proteins are logical vaccine candidates for testing protective activity against C. burnetii challenge. We established a sublethal challenge model in BALB/c mice with protection from the development of severe splenomegaly as an indicator of vaccinogenic activity. Further characterization of these proteins will provide essential information for developing novel, specific diagnostic reagents and potential subunit vaccine candidates against C. burnetii infection.

Effect of tetramethyl pyrazine on L-type calcium channel in rat ventricular myocytes

To elucidate possible ionic mechanisms of antimyocardial ischemia and antiarrythmia of tetramethyl pyrazine (TP), we studied L-type Ca2+ currents (I(Ca.L)) in adult rat ventricular myocytes using the whole-cell patch-clamp technique. The results showed: (i) under physiological conditions, 0.25 mmol/L TP decreased amplitude of I(Ca.L) to 60.6% and this inhibition was increased with increasing concentration of TP. ID50 was 0.20 mmol/L. (ii) The Ca2+-antagonistic effect of TP was voltage-dependent. A marked negative shift of the steady-state inactivation curve was observed with long (10 s) conditioning prepulses, but not with short (350 ms) ones. (iii) The time course of inhibition during TP treatment was increased with an increase in drug concentration, and recovery from TP-induced inactivation of I(Ca.L) was slower than in control cases. (iv) Tonic block and use-dependent block with TP treatment, which was induced by increasing the frequency of stimulation, occurred. We suggest that TP inhibits the I(Ca.L) mainly by binding to inactivated Ca2+ channels. The high affinity of TP for the inactivated state of I(Ca.L) may play an important role in developing therapies for pathological conditions.

[Application of BRL conditioned medium in ES cells culture]

AIM

To study the method of using BRL conditioned medium in ES cells culture.

METHODS

ES cells were cultured in BRL conditioned medium, MEF feeder layer, and BRL conditioned medium plus MEF feeder layer respectively. Both the numbers of ES cells and embryonic bodies and the differentiated cells around the ES cell colonies at certain stages were studied to find the differences of growing speed of ES cells in three culture mediums.

RESULTS

On promoting the growth and maintaining the undifferentiated state of ES cells at the early stage after recovery, the effects of BRL conditioned medium were less than those of MEF feeder layer and those of BRL conditioned medium plus MEF feeder layer (P < 0.01), and there was no difference between MEF feeder layer and BRL conditioned medium plus MEF feeder layer (P > 0.05).

CONCLUSION

ES cells should be cultivated on MEF feeder layer or in BRL conditioned medium plus MEF feeder layer at the early stage after recovering.

[Separation and determination of pseudoephedrine in bufferin cold tablet by capillary electrophoresis with hydropropyl-beta-cyclodextrin as chiral selective reagent]

A method for the separation and analysis of the chiral pseudoephedrine enantiomers using capillary electrophoresis was established. The buffer solution for separation was 25 mmol/L Tris-phosphate, including 38 mmol/L hydropropyl-beta-cyclodextrin with pH value of 2.65. (1S, 2S)(+) Pseudoephedrine in Bufferin Cold tablet was determined. The method has good precision, recovery and linear relationship.

Groin hernias in adults: value of color Doppler sonography in their classification

PURPOSE

We assessed the abilities of color Doppler and power Doppler sonography to distinguish among types of groin hernias by demonstrating the inferior epigastric artery (IEA) and its relationship with the hernia sac.

METHODS

Nineteen consecutive patients (14 men and 5 women), clinically diagnosed as having groin hernias and scheduled to undergo herniorrhaphy, were prospectively enrolled in this study. Ultrasound examinations were performed preoperatively with a 6-12-MHz linear-array transducer. The IEA was identified, if possible, and its relationship to the hernia sac assessed. The sonographic diagnoses were compared with the operative findings.

RESULTS

There were 15 indirect inguinal hernias, 4 direct inguinal hernias, and 1 femoral hernia; 1 patient had bilateral inguinal hernias (indirect and direct). In 18 (90%) of 20 hernia cases, the trunk segment of the IEA could be visualized. In 11 (55%) of 20 hernia cases, the origin segment of the IEA could be visualized and its relationship with the hernia sac assessed. In 9 (82%) of the 11 hernia cases, hernia types were correctly diagnosed by sonography. The overall accuracy of sonography for diagnosing the type of hernia was 45% (9 of 20 hernias).

CONCLUSIONS

Color Doppler sonography can accurately differentiate types of groin hernias if the origin segment of the IEA and the hernia sac can be visualized simultaneously. However, color Doppler sonography sometimes failed to visualize this segment.

[Bepridil inhibition on the delayed rectifier K+ currents in thyroxine induced hypertrophied guinea pig ventricular myocytes]

AIM

To study the effects of bepridil on the rapidly activating component (IKr), the slowly activating component (IKs) of the delayed rectifier potassium current and the inward rectifier potassium current (IK1) in hypertrophied guinea pig ventricular myocytes.

METHODS

The whole cell patch clamp techniques were used.

RESULTS

In hypertrophied guinea pig ventricular myocytes, bepridil 30 mumol.L-1 markedly inhibited IKr and IKs (by 20.9% and 27.2% at 0 mV and mV, respectively). The effect of bepridil on IKs was larger than on IKr. Bepridil 30 mumol.L-1 also significantly inhibited the inward component of IK1 (by 15.1% at +100 mV), but the reverse potential of IK1 was unaffected. Bepridil (1-100 mumol.L-1) was shown to inhibit IKr and IKs in a concentration-dependent manner. Their IC50 were 46.7 mumol.L-1 and 23.8 mumol.L-1, respectively.

CONCLUSION

Bepridil inhibit IKr, IKs and IK1 in hypertrophied guinea pig ventricular myocytes, which may be important in understanding the antiarrhythmic effects of this drug.