Christian Studies in Contemporary China

Although Christian Studies is a comparatively new discipline in Mainland China, it has a long history in global academia. Thus, while promoting this discipline in China, we are also bringing Chinese scholars to the international arena and exposing international scholars to the Chinese situation. Given that we are all living in a globalized (or glocalized) context, this exchange allows people a better understanding of different religious traditions so as to avoid a clash of civilizations, especially for those living in a multi-religious context like Asia. In this paper I explain how this special phenomenon has emerged in the rapidly changing Chinese situation in the last few decades and to articulate the interesting characteristics of Christian studies and related theology in this context, namely extra ecclesiam (outside of the church)

MannDB – A microbial database of automated protein sequence analyses and evidence integration for protein characterization

BACKGROUND: MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. DESCRIPTION: MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. CONCLUSION: MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high-priority agents on the websites of several governmental organizations concerned with bio-terrorism. MannDB provides the user with a BLAST interface for comparison of native and non-native sequences and a query tool for conveniently selecting proteins of interest. In addition, the user has access to a web-based browser that compiles comprehensive and extensive reports. Access to MannDB is freely available at

Zebrafish Behavioral Profiling Links Drugs to Biological Targets and Rest/Wake Regulation

A major obstacle for the discovery of psychoactive drugs is the inability to predict how small molecules will alter complex behaviors. We report the development and application of a high-throughput, quantitative screen for drugs that alter the behavior of larval zebrafish. We found that the multidimensional nature of observed phenotypes enabled the hierarchical clustering of molecules according to shared behaviors. Behavioral profiling revealed conserved functions of psychotropic molecules and predicted the mechanisms of action of poorly characterized compounds. In addition, behavioral profiling implicated new factors such as ether-a-go-go–related gene (ERG) potassium channels and immunomodulators in the control of rest and locomotor activity. These results demonstrate the power of high-throughput behavioral profiling in zebrafish to discover and characterize psychotropic drugs and to dissect the pharmacology of complex behaviors

Multipotent Embryonic Isl1+ Progenitor Cells Lead to Cardiac, Smooth Muscle, and Endothelial Cell Diversification

SummaryCardiogenesis requires the generation of endothelial, cardiac, and smooth muscle cells, thought to arise from distinct embryonic precursors. We use genetic fate-mapping studies to document that isl1+ precursors from the second heart field can generate each of these diverse cardiovascular cell types in vivo. Utilizing embryonic stem (ES) cells, we clonally amplified a cellular hierarchy of isl1+ cardiovascular progenitors, which resemble the developmental precursors in the embryonic heart. The transcriptional signature of isl1+/Nkx2.5+/flk1+ defines a multipotent cardiovascular progenitor, which can give rise to cells of all three lineages. These studies document a developmental paradigm for cardiogenesis, where muscle and endothelial lineage diversification arises from a single cell-level decision of a multipotent isl1+ cardiovascular progenitor cell (MICP). The discovery of ES cell-derived MICPs suggests a strategy for cardiovascular tissue regeneration via their isolation, renewal, and directed differentiation into specific mature cardiac, pacemaker, smooth muscle, and endothelial cell types

Draft versus finished sequence data for DNA and protein diagnostic signature development

Abstract Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop highquality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors, or NNs) to sequence. We use SAP to assess whether draft data is sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high quality draft with error rates of 10 -3 -10 -5 (~8x coverage) of target organisms is suitable for DNA signature prediction. Low quality draft with error rates of ~1% (3x to 6x coverage) of target isolates is inadequate for DNA signature prediction, although low quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high quality draft of target and low quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation of predicted protein signatures. 3 Introduction Draft sequencing requires that the order of base pairs in cloned fragments of a genome be determined usually at least 4 times (4x depth of coverage) at each position for a minimum degree of draft accuracy. This information is assembled into contigs, or fragments of the genome that cannot be joined further due to lack of sequence information across gaps between the contigs. To generate high-quality draft, usually about 8x coverage is optimal (1). Finished sequence, without gaps or ambiguous base calls, usually requires 8x to 10x coverage, along with additional analyses, often manual, to orient the contigs relative to one another and to close the gaps between them in a process called finishing. In fact, it has been stated that "the defining distinction of draft sequencing is the avoidance of significant human intervention" (1), although there are computational tools that may also be capable of automated finishing in some circumstances (2). While some tabulate the cost differential between high quality draft versus finished sequences to be 3-to 4-fold, and the speed differential to be over 10-fold (1), others state that the cost differential is a more modest 1.3-to 1.5-fold (3). In either case, draft sequencing is cheaper and faster. Experts have debated whether finished sequencing is always necessary, considering the higher costs (1,3,4). Thus, here we set out to determine whether draft sequence data is adequate for the computational prediction of DNA and protein diagnostic signatures. By a "signature" we mean a short region of sequence that is sufficient to uniquely identify an organism down to the species level, without false negatives due to strain variation or false positives due to cross reaction with close phylogenetic relatives. In addition, for DNA signatures, we require that the signature be suitable for a TaqMan reaction (e.g. composed of two primers and a probe of the desired T m 's). Limited funds and facilities in which to sequence biothreat pathogens mean that decision makers must choose wisely which and how many organisms to sequence. Money and time saved as a result of draft rather than finished sequencing enables more target organisms, more isolates of the target, and more NN's of the target to be sequenced. However, if draft data does not facilitate the generation of high quality signatures for detection, the tradeoff of quantity over quality will not be worth it. We used the Sequencing Analysis Pipeline (SAP) (5,6) to compare the value of finished sequence, real draft sequence, and simulated draft sequence of different qualities for the computational prediction of DNA and protein signatures for pathogen detection/diagnostics. Marburg and variola viruses were used as model organisms for these analyses, due to the availability of multiple genomes for these organisms. We hope that variola may serve as a guide for making predictions about bacteria, in which the genomes are substantially larger, and thus the cost of sequencing is much higher than for viruses. Variola was selected as the best available surrogate for bacteria at the time we began these analyses because: 1) it is double-stranded DNA 2) it has a relatively low mutation rate, more like bacteria than like the RNA or shorter DNA viruses that have higher mutation rates and thus higher levels of variation 3) it is very long for a virus, albeit shorter than a bacterial genom

A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal

Embryonic stem (ES) cell self-renewal efficiency is determined by the Nanog protein level. However, the protein partners of Nanog that function to direct self-renewal are unclear. Here, we identify a Nanog interactome of over 130 proteins including transcription factors, chromatin modifying complexes, phosphorylation and ubiquitination enzymes, basal transcriptional machinery members, and RNA processing factors. Sox2 was identified as a robust interacting partner of Nanog. The purified Nanog–Sox2 complex identified a DNA recognition sequence present in multiple overlapping Nanog/Sox2 ChIP-Seq data sets. The Nanog tryptophan repeat region is necessary and sufficient for interaction with Sox2, with tryptophan residues required. In Sox2, tyrosine to alanine mutations within a triple-repeat motif (S X T/S Y) abrogates the Nanog–Sox2 interaction, alters expression of genes associated with the Nanog-Sox2 cognate sequence, and reduces the ability of Sox2 to rescue ES cell differentiation induced by endogenous Sox2 deletion. Substitution of the tyrosines with phenylalanine rescues both the Sox2–Nanog interaction and efficient self-renewal. These results suggest that aromatic stacking of Nanog tryptophans and Sox2 tyrosines mediates an interaction central to ES cell self-renewal

Medical Students Educate Teens About Skin Cancer: What Have We Learned?

Skin cancer is a serious societal problem, and public awareness outreach, including to youth, is crucial. Medical students have joined forces to educate adolescents about skin cancer with significant impacts; even one 50-min interactive outreach session led to sustained changes in knowledge and behavior in a cohort of 1,200 adolescents surveyed. Medical students can act as a tremendous asset to health awareness public outreach efforts: enthusiastic volunteerism keeps education cost-effective, results in exponential spread of information, reinforces knowledge and communication skills of future physicians, and can result in tangible, life-saving benefits such as early detection of melanoma

Microsatellite primers for two threatened orchids in Florida: Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae)1

Premise of the study: The Million Orchid Project at Fairchild Tropical Botanic Garden is an initiative to propagate native orchids for reintroduction into Miami?s urban landscapes. The aim of this study was to develop microsatellites for Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae). Methods and Results: Ten microsatellites were developed for each species. For E. tampensis sampled from the natural population, allele numbers ranged from one to four, with an average observed heterozygosity (Ho) of 0.314 and average expected heterozygosity (He) of 0.281. For the individuals from cultivation, allele numbers ranged from one to six, with an average Ho of 0.35 and an average He of 0.224. For C. punctatum, allele numbers ranged from one to three, with an average Ho of 0.257 and an average He of 0.272. Conclusions: These microsatellites will be used to assess the genetic diversity of natural and cultivated populations with the intention of guiding genetic breeding under the Million Orchid Project