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1.  Phosphorylated Mnk1 and eIF4E Are Associated with Lymph Node Metastasis and Poor Prognosis of Nasopharyngeal Carcinoma 
PLoS ONE  2014;9(2):e89220.
Nasopharyngeal carcinoma (NPC) is a head and neck malignant tumor rare throughout most of the world but common in Southeast Asia, especially in Southern China. The phosphorylation of eukaryotic translation initiation factor 4E (eIF4E) by MAP kinase-interacting kinases (Mnk) on Ser-209 promotes cellular proliferation, survival, malignant transformation and metastasis. However, whether the alterations of the expression of p-eIF4E and p-Mnk1 protein are associated with clinicopathologic/prognostic implication for NPC has not been reported. The purposes of the present study are to examine the expression of p-eIF4E and p-Mnk1 protein in NPC and non-cancerous nasopharyngeal epithelial tissues by immunohistochemistry and evaluate the association between the expression of p-eIF4E and p-Mnk1 protein and clinicopathological characteristics of NPC. The results showed that the positive percentage of p-Mnk1 and p-eIF4E proteins expression in NPC (83.5% and 75.4%, respectively) was significantly higher than that in non-cancerous nasopharyngeal epithelium (40.0% and 32.9%, respectively). The positive expression of p-eIF4E and p-Mnk1 in the NPC with cervical lymph node metastasis was significantly higher than those without lymph node metastasis. Additionally, p-eIF4E expression was more pronouncedly increased in metastatic NPC than the matched primary NPC. Increase of p-eIF4E and p-Mnk1 expression was significantly correlated inversely with overall survival. Spearman’s rank correlation test further showed that expression of p-Mnk1 was strongly positive correlated with expression of p-eIF4E in NPC. The expression of p-Mnk1 and p-eIF4E in NPC was proved to be the independent prognostic factors regardless of lymph node metastasis, clinical stages and combination of radiotherapy and chemotherapy, histological type, age and gender by multivariate analysis. Taken together, high expression of p-Mnk1 and p-eIF4E might be novel valuable biomarkers to predict poor prognosis of NPC and therapeutic targets for developing the valid treatment strategies.
doi:10.1371/journal.pone.0089220
PMCID: PMC3925237  PMID: 24551240
2.  Briarane Diterpenes from the South China Sea Gorgonian Coral, Junceella gemmacea 
Marine Drugs  2014;12(2):589-600.
Four new briarane diterpenoids, junceellolides M–P (1–4), were isolated together with seven known analogs (5–11) from the South China Sea gorgonian, Junceella gemmacea. The structures of these compounds were elucidated by detailed spectroscopic analysis and comparison with the reported data. The absolute configuration of compounds 1–3 were determined based on an ECD experiment, while the absolute configuration of compound 4 was genetically determined. All the compounds were isolated for the first time from J. gemmacea. These compounds showed no growth inhibitory activity against A549, MG63 and SMMC-7721 cell lines in an in vitro bioassay.
doi:10.3390/md12020589
PMCID: PMC3944505  PMID: 24473165
Junceella gemmacea; briarane; diterpenoid; junceellolide
3.  Integrated Analysis of Differential miRNA and mRNA Expression Profiles in Human Radioresistant and Radiosensitive Nasopharyngeal Carcinoma Cells 
PLoS ONE  2014;9(1):e87767.
Background
The purpose of this study was to identify miRNAs and genes involved in nasopharyngeal carcinoma (NPC) radioresistance, and explore the underlying mechanisms in the development of radioresistance.
Methods
We used microarrays to compare the differences of both miRNA and mRNA expression profiles in the radioresistant NPC CNE2-IR and radiosensitive NPC CNE2 cells, applied qRT-PCR to confirm the reliability of microarray data, adopted databases prediction and anticorrelated analysis of miRNA and mRNA expression to identify the miRNA target genes, and employed bioinformatics tools to examine the functions and pathways in which miRNA target genes are involved, and construct a miRNA-target gene regulatory network. We further investigated the roles of miRNA-23a and its target gene IL-8 in the NPC radioresistance.
Results
The main findings were fourfold: (1) fifteen differential miRNAs and 372 differential mRNAs were identified, and the reliability of microarray data was validated for randomly selected eight miRNAs and nine genes; (2) 174 miRNA target were identified, and most of their functions and regulating pathways were related to tumor therapeutic resistance; (3) a posttranscriptional regulatory network including 375 miRNA-target gene pairs was constructed, in which the ten genes were coregulated by the six miRNAs; (4) IL-8 was a direct target of miRNA-23a, the expression levels of IL-8 were elevated in the radioresistant NPC tissues and showed inverse correlation with miRNA-23a expression, and genetic upregulation of miRNA-23a and antibody neutralization of secretory IL-8 could reduce NPC cells radioresistance.
Conclusions
We identified fifteen differential miRNAs and 372 differential mRNAs in the radioresistant NPC cells, constructed a posttranscriptional regulatory network including 375 miRNA-target gene pairs, discovered the ten target genes coregulated by the six miRNAs, and validated that downregulated miRNA-23a was involved in NPC radioresistance through directly targeting IL-8. Our data form a basis for further investigating the mechanisms of NPC radioresistance.
doi:10.1371/journal.pone.0087767
PMCID: PMC3909230  PMID: 24498188
4.  Assessing the Effect of Litter Species on the Dynamic of Bacterial and Fungal Communities during Leaf Decomposition in Microcosm by Molecular Techniques 
PLoS ONE  2013;8(12):e84613.
Although bacteria and fungi are well-known to be decomposers of leaf litter, few studies have examined their compositions and diversities during the decomposition process in tropical stream water. Xishuangbanna is a tropical region preserving one of the highest floristic diversity areas in China. In this study, leaf litter of four dominant plant species in Xishuangbanna was incubated in stream water for 42 days during which samples were taken regularly. Following DNA extraction, PCR-DGGE (denaturing gradient gel electrophoresis) and clone-sequencing analyses were performed using bacterial and fungal specific primers. Leaf species have slightly influences on bacterial community rather than fungal community. The richness and diversity of bacteria was higher than that of fungi, which increased towards the end of the 42-day-incubation. The bacterial community was initially more specific upon the type of leaves and gradually became similar at the later stage of decomposition with alpha-proteobacteria as major component. Sequences affiliated to methanotrophs were obtained that indicates potentially occurrence of methane oxidation and methanogenesis. For the fungal community, sequences affiliated to Aspergillus were predominant at the beginning and then shifted to Pleosporales. Our results suggest that the microorganisms colonizing leaf biofilm in tropical stream water were mostly generalists that could exploit the resources of leaves of various species equally well.
doi:10.1371/journal.pone.0084613
PMCID: PMC3868619  PMID: 24367682
5.  Pathway-based drug repositioning using causal inference 
BMC Bioinformatics  2013;14(Suppl 16):S3.
Background
Recent in vivo studies showed new hopes of drug repositioning through causality inference from drugs to disease. Inspired by their success, here we present an in silico method for building a causal network (CauseNet) between drugs and diseases, in an attempt to systematically identify new therapeutic uses of existing drugs.
Methods
Unlike the traditional 'one drug-one target-one disease' causal model, we simultaneously consider all possible causal chains connecting drugs to diseases via target- and gene-involved pathways based on rich information in several expert-curated knowledge-bases. With statistical learning, our method estimates transition likelihood of each causal chain in the network based on known drug-disease treatment associations (e.g. bexarotene treats skin cancer).
Results
To demonstrate its validity, our method showed high performance (AUC = 0.859) in cross validation. Moreover, our top scored prediction results are highly enriched in literature and clinical trials. As a showcase of its utility, we show several drugs for potential re-use in Crohn's Disease.
Conclusions
We successfully developed a computational method for discovering new uses of existing drugs based on casual inference in a layered drug-target-pathway-gene- disease network. The results showed that our proposed method enables hypothesis generation from public accessible biological data for drug repositioning.
doi:10.1186/1471-2105-14-S16-S3
PMCID: PMC3853312  PMID: 24564553
6.  Developing Topic-Specific Search Filters for PubMed with Click-Through Data 
Summary
Objectives
Search filters have been developed and demonstrated for better information access to the immense and ever-growing body of publications in the biomedical domain. However, to date the number of filters remains quite limited because the current filter development methods require significant human efforts in manual document review and filter term selection. In this regard, we aim to investigate automatic methods for generating search filters.
Methods
We present an automated method to develop topic-specific filters on the basis of users’ search logs in PubMed. Specifically, for a given topic, we first detect its relevant user queries and then include their corresponding clicked articles to serve as the topic-relevant document set accordingly. Next, we statistically identify informative terms that best represent the topic-relevant document set using a background set composed of topic irrelevant articles. Lastly, the selected representative terms are combined with Boolean operators and evaluated on benchmark datasets to derive the final filter with the best performance.
Results
We applied our method to develop filters for four clinical topics: nephrology, diabetes, pregnancy, and depression. For the nephrology filter, our method obtained performance comparable to the state of the art (sensitivity of 91.3%, specificity of 98.7%, precision of 94.6%, and accuracy of 97.2%). Similarly, high-performing results (over 90% in all measures) were obtained for the other three search filters.
Conclusion
Based on PubMed click-through data, we successfully developed a high-performance method for generating topic-specific search filters that is significantly more efficient than existing manual methods. All data sets (topic-relevant and irrelevant document sets) used in this study and a demonstration system are publicly available at http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/downloads/CQ_filter/
doi:10.3414/ME12-01-0054
PMCID: PMC3744813  PMID: 23666447
Information Retrieval; PubMed Search Filter; PubMed Log Analysis; Clinical Topic
7.  Systematic identification of pharmacogenomics information from clinical trials 
Journal of biomedical informatics  2012;45(5):870-878.
Recent progress in high-throughput genomic technologies has shifted pharmacogenomic research from candidate gene pharmacogenetics to clinical pharmacogenomics (PGx). Many clinical related questions may be asked such as ‘what drug should be prescribed for a patient with mutant alleles?’ Typically, answers to such questions can be found in publications mentioning the relationships of the gene–drug–disease of interest. In this work, we hypothesize that ClinicalTrials.gov is a comparable source rich in PGx related information. In this regard, we developed a systematic approach to automatically identify PGx relationships between genes, drugs and diseases from trial records in ClinicalTrials.gov. In our evaluation, we found that our extracted relationships overlap significantly with the curated factual knowledge through the literature in a PGx database and that most relationships appear on average 5 years earlier in clinical trials than in their corresponding publications, suggesting that clinical trials may be valuable for both validating known and capturing new PGx related information in a more timely manner. Furthermore, two human reviewers judged a portion of computer-generated relationships and found an overall accuracy of 74% for our text-mining approach. This work has practical implications in enriching our existing knowledge on PGx gene–drug–disease relationships as well as suggesting crosslinks between ClinicalTrials.gov and other PGx knowledge bases.
doi:10.1016/j.jbi.2012.04.005
PMCID: PMC3760158  PMID: 22546622
Text mining; Clinical outcome; Pharmacogenomics; Clinical trial
8.  Abnormality in face scanning by children with autism spectrum disorder is limited to the eye region: Evidence from multi-method analyses of eye tracking data 
Journal of Vision  2013;13(10):5.
There has been considerable controversy regarding whether children with autism spectrum disorder (ASD) and typically developing children (TD) show different eye movement patterns when processing faces. We investigated ASD and age- and IQ-matched TD children's scanning of faces using a novel multi-method approach. We found that ASD children spent less time looking at the whole face generally. After controlling for this difference, ASD children's fixations of the other face parts, except for the eye region, and their scanning paths between face parts were comparable either to the age-matched or IQ-matched TD groups. In contrast, in the eye region, ASD children's scanning differed significantly from that of both TD groups: (a) ASD children fixated significantly less on the right eye (from the observer's view); (b) ASD children's fixations were more biased towards the left eye region; and (c) ASD children fixated below the left eye, whereas TD children fixated on the pupil region of the eye. Thus, ASD children do not have a general abnormality in face scanning. Rather, their abnormality is limited to the eye region, likely due to their strong tendency to avoid eye contact.
doi:10.1167/13.10.5
PMCID: PMC3739407  PMID: 23929830
autism spectrum disorder; face processing; face recognition; eye movements; eye tracking
9.  The protective effect of geniposide on human neuroblastoma cells in the presence of formaldehyde 
Background
Formaldehyde can induce misfolding and aggregation of Tau protein and β amyloid protein, which are characteristic pathological features of Alzheimer’s disease (AD). An increase in endogenous formaldehyde concentration in the brain is closely related to dementia in aging people. Therefore, the discovery of effective drugs to counteract the adverse impact of formaldehyde on neuronal cells is beneficial for the development of appropriate treatments for age-associated cognitive decline.
Methods
In this study, we assessed the neuroprotective properties of TongLuoJiuNao (TLJN), a traditional Chinese medicine preparation, against formaldehyde stress in human neuroblastoma cells (SH-SY5Y cell line). The effect of TLJN and its main ingredients (geniposide and ginsenoside Rg1) on cell viability, apoptosis, intracellular antioxidant activity and the expression of apoptotic-related genes in the presence of formaldehyde were monitored.
Results
Cell counting studies showed that in the presence of TLJN, the viability of formaldehyde-treated SH-SY5Y cells significantly recovered. Laser scanning confocal microscopy revealed that the morphology of formaldehyde-injured cells was rescued by TLJN and geniposide, an effective ingredient of TLJN. Moreover, the inhibitory effect of geniposide on formaldehyde-induced apoptosis was dose-dependent. The activity of intracellular antioxidants (superoxide dismutase and glutathione peroxidase) increased, as did mRNA and protein levels of the antiapoptotic gene Bcl-2 after the addition of geniposide. In contrast, the expression of the apoptotic-related gene - P53, apoptotic executer - caspase 3 and apoptotic initiator - caspase 9 were downregulated after geniposide treatment.
Conclusions
Our results indicate that geniposide can protect SH-SY5Y cells against formaldehyde stress through modulating the expression of Bcl-2, P53, caspase 3 and caspase 9, and by increasing the activity of intracellular superoxide dismutase and glutathione peroxidase.
doi:10.1186/1472-6882-13-152
PMCID: PMC3702466  PMID: 23815892
Formaldehyde impairment; Geniposide; Neuroprotection
10.  Perforated sarcomatoid carcinoma of the jejunum: Case report 
Oncology Letters  2013;6(2):562-564.
Sarcomatoid carcinomas exhibit features that are common to epithelial and mesenchymal tumors. These carcinomas are rare, particularly in the small intestine. In the current case report, we describe a case of an intestinal sarcomatoid carcinoma in a 70-year-old Chinese female. Sarcomatoid carcinoma was confirmed based on light microscopy and immunohistochemical observations. The patient presented with symptoms of acute abdomen, which was due to an intestinal perforation caused by sarcomatoid carcinoma of the small bowel. Patients with sarcomatoid carcinoma are usually associated with a poor prognosis. However, this patient experienced a relatively favorable prognosis, which may be attributed to low positivity for Ki67 in the tumor.
doi:10.3892/ol.2013.1378
PMCID: PMC3789042  PMID: 24137370
sarcomatoid carcinoma; small intestine; perforation
11.  Oxygen promotes biofilm formation of Shewanella putrefaciens CN32 through a diguanylate cyclase and an adhesin 
Scientific Reports  2013;3:1945.
Although oxygen has been reported to regulate biofilm formation by several Shewanella species, the exact regulatory mechanism mostly remains unclear. Here, we identify a direct oxygen-sensing diguanylate cyclase (DosD) and reveal its regulatory role in biofilm formation by Shewanella putrefaciens CN32 under aerobic conditions. In vitro and in vivo analyses revealed that the activity of DosD culminates to synthesis of cyclic diguanylate (c-di-GMP) in the presence of oxygen. DosD regulates the transcription of bpfA operon which encodes seven proteins including a large repetitive adhesin BpfA and its cognate type I secretion system (TISS). Regulation of DosD in aerobic biofilms is heavily dependent on an adhesin BpfA and the TISS. This study offers an insight into the molecular mechanism of oxygen-stimulated biofilm formation by S. putrefaciens CN32.
doi:10.1038/srep01945
PMCID: PMC3672883  PMID: 23736081
12.  ß-Adrenergic Stimulation Increases RyR2 Activity via Intracellular Ca2+ and Mg2+ Regulation 
PLoS ONE  2013;8(3):e58334.
Here we investigate how ß-adrenergic stimulation of the heart alters regulation of ryanodine receptors (RyRs) by intracellular Ca2+ and Mg2+ and the role of these changes in SR Ca2+ release. RyRs were isolated from rat hearts, perfused in a Langendorff apparatus for 5 min and subject to 1 min perfusion with 1 µM isoproterenol or without (control) and snap frozen in liquid N2 to capture their phosphorylation state. Western Blots show that RyR2 phosphorylation was increased by isoproterenol, confirming that RyR2 were subject to normal ß-adrenergic signaling. Under basal conditions, S2808 and S2814 had phosphorylation levels of 69% and 15%, respectively. These levels were increased to 83% and 60%, respectively, after 60 s of ß-adrenergic stimulation consistent with other reports that ß-adrenergic stimulation of the heart can phosphorylate RyRs at specific residues including S2808 and S2814 causing an increase in RyR activity. At cytoplasmic [Ca2+] <1 µM, ß-adrenergic stimulation increased luminal Ca2+ activation of single RyR channels, decreased luminal Mg2+ inhibition and decreased inhibition of RyRs by mM cytoplasmic Mg2+. At cytoplasmic [Ca2+] >1 µM, ß-adrenergic stimulation only decreased cytoplasmic Mg2+ and Ca2+ inhibition of RyRs. The Ka and maximum levels of cytoplasmic Ca2+ activation site were not affected by ß-adrenergic stimulation.
Our RyR2 gating model was fitted to the single channel data. It predicted that in diastole, ß-adrenergic stimulation is mediated by 1) increasing the activating potency of Ca2+ binding to the luminal Ca2+ site and decreasing its affinity for luminal Mg2+ and 2) decreasing affinity of the low-affinity Ca2+/Mg2+ cytoplasmic inhibition site. However in systole, ß-adrenergic stimulation is mediated mainly by the latter.
doi:10.1371/journal.pone.0058334
PMCID: PMC3606165  PMID: 23533585
13.  Combined hemoglobin and fluorescence diffuse optical tomography for breast tumor diagnosis: a pilot study on time-domain methodology 
Biomedical Optics Express  2013;4(2):331-348.
A combined time-domain fluorescence and hemoglobin diffuse optical tomography (DOT) system and the image reconstruction methods are proposed for enhancing the reliability of breast-dedicated optical measurement. The system equipped with two pulsed laser diodes at wavelengths of 780 nm and 830 nm that are specific to the peak excitation and emission of the FDA-approved ICG agent, and works with a 4-channel time-correlated single photon counting device to acquire the time-resolved distributions of the light re-emissions at 32 boundary sites of tissues in a tandem serial-to-parallel mode. The simultaneous reconstruction of the two optical (absorption and scattering) and two fluorescent (yield and lifetime) properties are achieved with the respective featured-data algorithms based on the generalized pulse spectrum technique. The performances of the methodology are experimentally assessed on breast-mimicking phantoms for hemoglobin- and fluorescence-DOT alone, as well as for fluorescence-guided hemoglobin-DOT. The results demonstrate the efficacy of improving the accuracy of hemoglobin-DOT based on a priori fluorescence localization.
doi:10.1364/BOE.4.000331
PMCID: PMC3567719  PMID: 23412647
(170.3880) Medical and biological imaging; (170.6960) Tomography; (170.6920) Time-resolved imaging; (170.3010) Image reconstruction techniques
14.  CD33+/p-STAT1+ double-positive cell as a prognostic factor for stage IIIa gastric cancer 
Tumor-infiltrating immune cells are associated with tumor prognosis, although the type of immune cells responsible for local immune escape is still unknown. This study examined the relationship between gastric cancer survival and the density of immune cells, including CD8+ T cells, CD20+ B cells, and CD33+/p-STAT1+ cells, which represent myeloid-derived suppressor cells, to evaluate the role of immune cells in the progression of gastric cancer. One hundred pathologically confirmed specimens were obtained from stage IIIa gastric cancers between 2003 and 2006 at Sun Yat-sen University Cancer Center, China. The density of tumor-infiltrating immune cells in tumor tissue was examined using immunohistochemical analysis. Clinicopathologic parameters and the survival rate were analyzed in relation to the density of immune cells. A high density of CD8+ T cells and CD20+ B cells was associated with a good clinical outcome, but a high density of CD33+/p-STAT1+ cells was associated with a poor clinical outcome. Most importantly, the density of CD33+/p-STAT1+ cells was an independent prognostic factor and inversely related to the infiltration of CD8+ T cells. Although the infiltration of CD8+ T cells and CD20+ B cells is involved in the progression of gastric cancer, these data suggest that CD33+/p-STAT1+ cells play a central role in the regulation of the local immune response, suggesting that CD33+/p-STAT1+ cells might be therapeutic targets in gastric cancer.
doi:10.1007/s12032-012-0442-2
PMCID: PMC3586391  PMID: 23307253
Gastric cancer; CD33; STAT1; T cell; B cell; Regulation
15.  C2Maps: a network pharmacology database with comprehensive disease-gene-drug connectivity relationships 
BMC Genomics  2012;13(Suppl 6):S17.
Background
Network pharmacology has emerged as a new topic of study in recent years. It aims to study the myriad relationships among proteins, drugs, and disease phenotypes. The concept of molecular connectivity maps has been proposed to establish comprehensive knowledge links between molecules of interest in a given biological context. Molecular connectivity maps between drugs and genes/proteins in specific disease contexts can be particularly valuable, since the functional approach with these maps helps researchers gain global perspectives on both the therapeutic profiles and toxicological profiles of candidate drugs.
Methods
To assess drug pharmacological effect, we assume that "ideal" drugs for a patient can treat or prevent the disease by modulating gene expression profiles of this patient to the similar level with those in healthy people. Starting from this hypothesis, we build comprehensive disease-gene-drug connectivity relationships with drug-protein directionality (inhibit/activate) information based on a computational connectivity maps (C2Maps) platform. An interactive interface for directionality annotation of drug-protein pairs with literature evidences from PubMed has been added to the new version of C2Maps. We also upload the curated directionality information of drug-protein pairs specific for three complex diseases - breast cancer, colorectal cancer and Alzheimer disease.
Results
For relevant drug-protein pairs with directionality information, we use breast cancer as a case study to demonstrate the functionality of disease-specific searching. Based on the results obtained from searching, we perform pharmacological effect evaluation for two important breast cancer drugs on treating patients diagnosed with different breast cancer subtypes. The evaluation is performed on a well-studied breast cancer gene expression microarray dataset to portray how useful the updated C2Maps is in assessing drug efficacy and toxicity information.
Conclusions
The C2Maps platform is an online bioinformatics resource that provides biologists with directional relationships between drugs and genes/proteins in specific disease contexts based on network mining, literature mining, and drug effect annotating. A new insight to assess overall drug efficacy and toxicity can be provided by using the C2Maps platform to identify disease relevant proteins and drugs. The case study on breast cancer correlates very well with the existing pharmacology of the two breast cancer drugs and highlights the significance of C2Maps database.
doi:10.1186/1471-2164-13-S6-S17
PMCID: PMC3481399  PMID: 23134618
17.  4-(4-Nitro­phen­yl)morpholine 
Aromatic π–π stacking inter­actions stabilize the crystal structure of the title compound, C10H12N2O3, the perpendic­ular distance between parallel planes being 3.7721 (8) Å. The morpholine ring adopts a chair comformation.
doi:10.1107/S1600536812012172
PMCID: PMC3344165  PMID: 22606168
18.  Automatic identification and normalization of dosage forms in drug monographs 
Background
Each day, millions of health consumers seek drug-related information on the Web. Despite some efforts in linking related resources, drug information is largely scattered in a wide variety of websites of different quality and credibility.
Methods
As a step toward providing users with integrated access to multiple trustworthy drug resources, we aim to develop a method capable of identifying drug's dosage form information in addition to drug name recognition. We developed rules and patterns for identifying dosage forms from different sections of full-text drug monographs, and subsequently normalized them to standardized RxNorm dosage forms.
Results
Our method represents a significant improvement compared with a baseline lookup approach, achieving overall macro-averaged Precision of 80%, Recall of 98%, and F-Measure of 85%.
Conclusions
We successfully developed an automatic approach for drug dosage form identification, which is critical for building links between different drug-related resources.
doi:10.1186/1472-6947-12-9
PMCID: PMC3305679  PMID: 22336431
19.  Effective pollinators of Asian sacred lotus (Nelumbo nucifera): contemporary pollinators may not reflect the historical pollination syndrome 
Annals of Botany  2009;104(5):845-851.
Background and Aims
If stabilizing selection by pollinators is a prerequisite for pollinator-mediated floral evolution, spatiotemporal variation in the pollinator assemblage may confuse the plant–pollinator interaction in a given species. Here, effective pollinators in a living fossil plant Nelumbo nucifera (Nelumbonaceae) were examined to test whether beetles are major pollinators as predicted by its pollination syndrome.
Methods
Pollinators of N. nucifera were investigated in 11 wild populations and one cultivated population, and pollination experiments were conducted to examine the pollinating role of two major pollinators (bees and beetles) in three populations.
Key Results
Lotus flowers are protogynous, bowl shaped and without nectar. The fragrant flowers can be self-heating during anthesis and produce around 1 million pollen grains per flower. It was found that bees and flies were the most frequent flower visitors in wild populations, contributing on average 87·9 and 49·4 % of seed set in Mishan and Lantian, respectively. Beetles were only found in one wild population and in the cultivated population, but the pollinator exclusion experiments showed that beetles were effective pollinators of Asian sacred lotus.
Conclusions
This study indicated that in their pollinating role, beetles, probable pollinators for this thermoregulating plant, had been replaced by some generalist insects in the wild. This finding implies that contemporary pollinators may not reflect the pollination syndrome.
doi:10.1093/aob/mcp173
PMCID: PMC2749538  PMID: 19617594
Nelumbo nucifera; beetle pollinated; pollination syndrome; effective pollinator; generalized flower; thermoregulation; Nelumbonaceae
20.  Flower thermoregulation facilitates fertilization in Asian sacred lotus 
Annals of Botany  2009;103(7):1159-1163.
Background and Aims
The thermoregulatory flower of the Asian sacred lotus (Nelumbo nucifera) can maintain a relatively stable temperature despite great variations in ambient temperature during anthesis. The thermoregulation has been hypothesized to offer a direct energy reward for pollinators in lotus flowers. This study aims to examine whether the stable temperature maintained in the floral chamber influences the fertilization process and seed development.
Methods
An artificial refrigeration instrument was employed to cool flowers during the fertilization process and post-fertilization period in an experimental population. The effect of temperature on post-pollination events was also examined by removing petals in two field populations.
Key Results
Treatments with low floral temperature did not reduce stigma receptivity or pollen viability in undehisced anthers. Low temperature during the fertilization period significantly decreased seed set per flower but low temperature during the phase of seed development had no effect, suggesting that temperature regulation by lotus flowers facilitated fertilization success. Hand-pollination treatments in two field populations indicated that seed set of flowers with petals removed was lower than that of intact flowers in north China, where ambient temperatures are low, but not in south China, confirming that reducing the temperature of carpels did influence post-pollination events.
Conclusions
The experiments suggest that floral thermoregulation in lotus could enhance female reproductive success by facilitating fertilization.
doi:10.1093/aob/mcp051
PMCID: PMC2707905  PMID: 19282320
Nelumbo nucifera; Asian sacred lotus; beetle-pollination syndrome; fertilization process; post-pollination events; pollen viability; stigma receptivity; thermoregulation
21.  Building Disease-Specific Drug-Protein Connectivity Maps from Molecular Interaction Networks and PubMed Abstracts 
PLoS Computational Biology  2009;5(7):e1000450.
The recently proposed concept of molecular connectivity maps enables researchers to integrate experimental measurements of genes, proteins, metabolites, and drug compounds under similar biological conditions. The study of these maps provides opportunities for future toxicogenomics and drug discovery applications. We developed a computational framework to build disease-specific drug-protein connectivity maps. We integrated gene/protein and drug connectivity information based on protein interaction networks and literature mining, without requiring gene expression profile information derived from drug perturbation experiments on disease samples. We described the development and application of this computational framework using Alzheimer's Disease (AD) as a primary example in three steps. First, molecular interaction networks were incorporated to reduce bias and improve relevance of AD seed proteins. Second, PubMed abstracts were used to retrieve enriched drug terms that are indirectly associated with AD through molecular mechanistic studies. Third and lastly, a comprehensive AD connectivity map was created by relating enriched drugs and related proteins in literature. We showed that this molecular connectivity map development approach outperformed both curated drug target databases and conventional information retrieval systems. Our initial explorations of the AD connectivity map yielded a new hypothesis that diltiazem and quinidine may be investigated as candidate drugs for AD treatment. Molecular connectivity maps derived computationally can help study molecular signature differences between different classes of drugs in specific disease contexts. To achieve overall good data coverage and quality, a series of statistical methods have been developed to overcome high levels of data noise in biological networks and literature mining results. Further development of computational molecular connectivity maps to cover major disease areas will likely set up a new model for drug development, in which therapeutic/toxicological profiles of candidate drugs can be checked computationally before costly clinical trials begin.
Author Summary
Molecular connectivity maps between drugs and a wide range of bio-molecular entities can help researchers to study and compare the molecular therapeutic/toxicological profiles of many candidate drugs. Recent studies in this area have focused on linking drug molecules and genes in specific disease contexts using drug-perturbed gene expression experiments, which can be costly and time-consuming to derive. In this paper, we developed a computational framework to build disease-specific drug-protein connectivity maps, by mining molecular interaction networks and PubMed abstracts. Using Alzheimer's Disease (AD) as a case study, we described how drug-protein molecular connectivity maps can be constructed to overcome data coverage and noise issues inherent in automatically extracted results. We showed that this new approach outperformed both curated drug target databases and conventional text mining systems in retrieving disease-related drugs, with an overall balanced performance of sensitivity, specificity, and positive predictive values. The AD molecular connectivity map contained novel information on AD-related genes/proteins, AD candidate drugs, and protein therapeutic/toxicological profiles of all the AD candidate drugs. Bi-clustering of the molecular connectivity map revealed interesting patterns of functionally similar proteins and drugs, therefore creating new opportunities for future drug development applications.
doi:10.1371/journal.pcbi.1000450
PMCID: PMC2709445  PMID: 19649302
22.  (S)-5-Hexyl-1-[(S)-2-hydr­oxy-1-phenyl­ethyl]-4-meth­oxy-1H-pyrrol-2(5H)-one 
The title compound, C19H27NO3, was obtained by the reaction of (3S,7aR)-7a-hexyl-7-meth­oxy-3-phenyl-2,3-dihydro­pyrrolo[2,1-b]oxazol-5(7aH)-one and triethyl­silane using titanium(IV) chloride as catalyst. In the mol­ecule, the phenyl and dihydro­pyrrolone rings form a dihedral angle of 83.8 (1)°. O—H⋯O hydrogen-bonding inter­actions lead to the formation of a chain parallel to the a axis.
doi:10.1107/S1600536809014160
PMCID: PMC2977772  PMID: 21583908
23.  (3S,7aR)-7-Meth­oxy-7a-methyl-3-phenyl-2,3-dihydro­pyrrolo[2,1-b]oxazol-5(7aH)-one 
In the title chiral butterfly-like bicyclic lactam, C14H15NO3, the phenyl and methyl groups are syn with respect to each other. The dihydro­pyrrrole ring adopts a boat conformation, whereas the oxazole ring has a slightly distorted boat conformation. The packing of mol­ecules in the crystal structure is stabilized by inter­molecular C—H⋯O hydrogen bonds.
doi:10.1107/S1600536808040105
PMCID: PMC2967946  PMID: 21581670
24.  Selected polymorphisms of DNA repair genes and risk of pancreatic cancer 
Cancer detection and prevention  2006;30(3):284-291.
Background
Genetic variants of DNA repair genes may contribute to pancreatic carcinogenesis. O6-methylguanine-DNA methyltransferase (MGMT) is the major protein that removes alkylating DNA adducts, and apurinic/apyrimidinic endonuclease 1 (APE1) and X-ray repair cross-complementing group 1 (XRCC1) play important roles in the base excision repair pathway.
Methods
We investigated the association between polymorphisms of MGMT (Leu84Phe and Ile143Val), APE1 (Asp148Glu), and XRCC1 (Arg194Trp and Arg399Gln) and risk of pancreatic cancer in a case-control study. Exposure information from 384 patients with primary pancreatic ductal adenocarcinoma and 357 cancer-free healthy controls were collected and genomic DNAs were genotyped for five markers. Controls were frequency matched to patients by age at enrollment (±5 years), gender, and race. We estimated odds ratios (ORs) and 95% confidence intervals (CIs) by using unconditional logistic regression models.
Results
There was no significant main effect or interaction with smoking of these genetic variants on the risk of pancreatic cancer. However, the XRCC1194 polymorphism had a significant interaction with the APE1148 (p = 0.005) or MGMT84 polymorphism (p = 0.02) in modifying the risk of pancreatic cancer.
Conclusions
This study suggests that polymorphisms of genes involved in the repair of alkylating DNA adduct and DNA base damage may play a role in modulating the risk of pancreatic cancer. Larger studies are required to validate these preliminary findings. The mechanism of the combined genotype effects remains to be elucidated.
doi:10.1016/j.cdp.2006.05.002
PMCID: PMC1857309  PMID: 16844323
Pancreatic cancer risk; Hardy-Weinberg equilibrium; Smoking status; Risk factors; Exposure information; MGMT84 polymorphism; MGMT; APE1; XRCC1; Single nucleotide polymorphism; Alkylating DNA adduct; Single-strand break; Base excision repair; Gene-environment interaction; Gene-gene interaction
25.  K-ras Mutation and p16 and Preproenkephalin Promoter Hypermethylation in Plasma DNA of Pancreatic Cancer Patients 
Pancreas  2007;34(1):55-62.
Objectives
To examine the profiles of K-ras mutations and p16 and preproenkephalin (ppENK) promoter hypermethylation and their associations with cigarette smoking in pancreatic cancer patients.
Methods
In plasma DNA of 83 patients with untreated primary pancreatic ductal adenocarcinoma, DNA hypermethylation was determined by methylation-specific polymerase chain reaction and K-ras codon 12 mutations by enriched-nested polymerase chain reaction followed by direct sequencing. Information on smoking exposure was collected by in-person interview. Pearson χ2 test and Fisher exact test were used in statistical analysis.
Results
K-ras mutations, ppENK, and p16 promoter hypermethylation were detected in 32.5%, 29.3%, and 24.6% of the patients, respectively. Sixty-three percent (52/83) of patients exhibited at least one of the alterations. Smoking was associated with the presence of K-ras mutations (P = 0.003). A codon 12 G-to-A mutation was predominantly observed in regular smokers and in heavy smokers (pack-year of smoking ≥36). Smoking was not associated with p16 or ppENK hypermethylation.
Conclusions
These preliminary observations suggest that plasma DNA might be a useful surrogate in detecting genetic and epigenetic alterations of pancreatic cancer. The findings on the association between K-ras mutation and smoking were in consistency with previous studies. Further studies on environmental modulators of epigenetic changes in pancreatic cancer are warranted.
doi:10.1097/01.mpa.0000246665.68869.d4
PMCID: PMC1905887  PMID: 17198183
plasma DNA; K-ras mutation; DNA methylation; p16; preproenkephalin; cigarette smoking; pancreatic cancer

Results 1-25 (27)