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1.  Hessian fly larval feeding triggers enhanced polyamine levels in susceptible but not resistant wheat 
BMC Plant Biology  2015;15:3.
Hessian fly (Mayetiola destructor), a member of the gall midge family, is one of the most destructive pests of wheat (Triticum aestivum) worldwide. Probing of wheat plants by the larvae results in either an incompatible (avirulent larvae, resistant plant) or a compatible (virulent larvae, susceptible plant) interaction. Virulent larvae induce the formation of a nutritive tissue, resembling the inside surface of a gall, in susceptible wheat. These nutritive cells are a rich source of proteins and sugars that sustain the developing virulent Hessian fly larvae. In addition, on susceptible wheat, larvae trigger a significant increase in levels of amino acids including proline and glutamic acid, which are precursors for the biosynthesis of ornithine and arginine that in turn enter the pathway for polyamine biosynthesis.
Following Hessian fly larval attack, transcript abundance in susceptible wheat increased for several genes involved in polyamine biosynthesis, leading to higher levels of the free polyamines, putrescine, spermidine and spermine. A concurrent increase in polyamine levels occurred in the virulent larvae despite a decrease in abundance of Mdes-odc (ornithine decarboxylase) transcript encoding a key enzyme in insect putrescine biosynthesis. In contrast, resistant wheat and avirulent Hessian fly larvae did not exhibit significant changes in transcript abundance of genes involved in polyamine biosynthesis or in free polyamine levels.
The major findings from this study are: (i) although polyamines contribute to defense in some plant-pathogen interactions, their production is induced in susceptible wheat during interactions with Hessian fly larvae without contributing to defense, and (ii) due to low abundance of transcripts encoding the rate-limiting ornithine decarboxylase enzyme in the larval polyamine pathway the source of polyamines found in virulent larvae is plausibly wheat-derived. The activation of the host polyamine biosynthesis pathway during compatible wheat-Hessian fly interactions is consistent with a model wherein the virulent larvae usurp the polyamine biosynthesis machinery of the susceptible plant to acquire nutrients required for their own growth and development.
Electronic supplementary material
The online version of this article (doi:10.1186/s12870-014-0396-y) contains supplementary material, which is available to authorized users.
PMCID: PMC4308891  PMID: 25592131
Polyamines; Wheat; Hessian fly; Compatible; Incompatible; RT-qPCR; Odc; Samdc; Spds
2.  RCT of Web-based Personalized Normative Feedback for College Drinking Prevention: Are Typical Student Norms Good Enough? 
Personalized normative feedback (PNF) interventions are generally effective at correcting normative misperceptions and reducing risky alcohol consumption among college students. However, research has yet to establish what level of reference group specificity is most efficacious in delivering PNF. This study compared the efficacy of a web-based PNF intervention employing eight increasingly-specific reference groups against a Web-BASICS intervention and a repeated-assessment control in reducing risky drinking and associated consequences.
Participants were 1663 heavy drinking Caucasian and Asian undergraduates at two universities. The referent for web-based PNF was either the typical same-campus student, or a same-campus student at one (either gender, race, or Greek-affiliation), or a combination of two (e.g., gender and race), or all three levels of specificity (i.e., gender, race, and Greek-affiliation). Hypotheses were tested using quasi-Poisson generalized linear models fit by generalized estimating equations.
The PNF intervention participants showed modest reductions in all four outcomes (average total drinks, peak drinking, drinking days, and drinking consequences) compared to control participants. No significant differences in drinking outcomes were found between the PNF group as a whole and the Web-BASICS group. Among the eight PNF conditions, participants receiving typical student PNF demonstrated greater reductions in all four outcomes compared to those receiving PNF for more specific reference groups. Perceived drinking norms and discrepancies between individual behavior and actual norms mediated the efficacy of the intervention.
Findings suggest a web-based PNF intervention using the typical student referent offers a parsimonious approach to reducing problematic alcohol use outcomes among college students.
PMCID: PMC3983963  PMID: 23937346
alcohol; social norms; personalized normative feedback; college students
3.  MicroRNA-7 directly targets insulin-like growth factor 1 receptor to inhibit cellular growth and glucose metabolism in gliomas 
Diagnostic Pathology  2014;9(1):211.
Recent studies observed that altered energy metabolism has become widespread in cancer cells along with other cancer-associated traits that have been accepted as hallmarks of cancer. Akt signaling pathway is involved in the aerobic glycolysis program. However, mechanisms underlying the regulation of aerobic glycolysis and Akt activity in gliomas remain unclear. MicroRNAs are a group of small non-coding RNAs that can function as endogenous RNA interference to regulate expression of targeted genes. This study was conducted to detect the function of miR-7 targeting insulin-like growth factor 1 receptor (IGF-1R), which is an upstream regulator of Akt.
MicroRNA expression data for gliomas and normal controls were downloaded from The Cancer Genome Atlas (TCGA) database. Quantitative real-time PCR was used to measure the microRNA-7 (miR-7) expression level, and Western blot was performed to detect protein expression in U87 and U251 cells. Colony formation assay and glycolysis stress test were also conducted. Luciferase reporter assay was used to identify the mechanism of IGF-1R and miR-7 regulation.
miR-7 was downregulated in human glioma tissues based on TCGA database. Forced expression of miR-7 or IGF-1R knockdown inhibited colony formation and glucose metabolic capabilities of glioma cells in vitro and decreased the p-Akt expression level. Bioinformatics analysis results indicated that IGF-1R could be a target of miR-7. Western blot and luciferase reporter assays showed that miR-7 modulated IGF-1R expression by directly targeting the binding site within the 3′-untranslated region.
This study provides the first evidence that miR-7 inhibits cellular growth and glucose metabolism in gliomas, at least partially, by regulating the IGF-1R/Akt signaling pathway. Therefore, miR-7 is a promising molecular drug for glioma treatment.
Virtual Slides
The virtual slide(s) for this article can be found here:
PMCID: PMC4236426  PMID: 25394492
Glioblastoma multiforme; miR-7; IGF-1R; AKT
4.  Indicated Prevention for College Student Marijuana Use: A Randomized Controlled Trial 
Marijuana is the most frequently reported illicit substance used on college campuses. Despite the prevalence, few published intervention studies have focused specifically on addressing high-risk marijuana use on college campuses. The present study evaluated the efficacy of an in-person brief motivational enhancement intervention for reducing marijuana use and related consequences among frequently using college students.
Participants included 212 college students from two campuses who reported frequent marijuana use (i.e., using marijuana at least 5 times in the past month). Participants completed web-based screening and baseline assessments and upon completion of the baseline survey were randomized to either receive an in-person brief intervention or an assessment control group. Follow-up assessments were completed approximately three and six months post-baseline. Marijuana use was measured by number of days used in the last 30 days, typical number of joints used in a typical week in the last 60 days, and marijuana-related consequences.
Results indicated significant intervention effects on number of joints smoked in a typical week and a trend toward fewer marijuana-related consequences compared to the control group at three-month follow-up.
This study provides preliminary data on short-term effects of a focused marijuana intervention for college students at reducing marijuana use during the academic quarter.
PMCID: PMC3924720  PMID: 23750464
college students; marijuana; intervention; prevention; marijuana related-consequences
5.  Research Progress on Expansive Soil Cracks under Changing Environment 
The Scientific World Journal  2014;2014:816759.
Engineering problems shunned previously rise to the surface gradually with the activities of reforming the natural world in depth, the problem of expansive soil crack under the changing environment becoming a control factor of expansive soil slope stability. The problem of expansive soil crack has gradually become a research hotspot, elaborates the occurrence and development of cracks from the basic properties of expansive soil, and points out the role of controlling the crack of expansive soil strength. We summarize the existing research methods and results of expansive soil crack characteristics. Improving crack measurement and calculation method and researching the crack depth measurement, statistical analysis method, crack depth and surface feature relationship will be the future direction.
PMCID: PMC4075004  PMID: 25013869
6.  Expansive Soil Crack Depth under Cumulative Damage 
The Scientific World Journal  2014;2014:498437.
The crack developing depth is a key problem to slope stability of the expansive soil and its project governance and the crack appears under the roles of dry-wet cycle and gradually develops. It is believed from the analysis that, because of its own cohesion, the expansive soil will have a certain amount of deformation under pulling stress but without cracks. The soil body will crack only when the deformation exceeds the ultimate tensile strain that causes cracks. And it is also believed that, due to the combined effect of various environmental factors, particularly changes of the internal water content, the inherent basic physical properties of expansive soil are weakened, and irreversible cumulative damages are eventually formed, resulting in the development of expansive soil cracks in depth. Starting from the perspective of volumetric strain that is caused by water loss, considering the influences of water loss rate and dry-wet cycle on crack developing depth, the crack developing depth calculation model which considers the water loss rate and the cumulative damages is established. Both the proposal of water loss rate and the application of cumulative damage theory to the expansive soil crack development problems try to avoid difficulties in matrix suction measurement, which will surely play a good role in promoting and improving the research of unsaturated expansive soil.
PMCID: PMC3967709  PMID: 24737974
7.  A tutorial on count regression and zero-altered count models for longitudinal substance use data 
Critical research questions in the study of addictive behaviors concern how these behaviors change over time - either as the result of intervention or in naturalistic settings. The combination of count outcomes that are often strongly skewed with many zeroes (e.g., days using, number of total drinks, number of drinking consequences) with repeated assessments (e.g., longitudinal follow-up after intervention or daily diary data) present challenges for data analyses. The current article provides a tutorial on methods for analyzing longitudinal substance use data, focusing on Poisson, zero-inflated, and hurdle mixed models, which are types of hierarchical or multilevel models. Two example datasets are used throughout, focusing on drinking-related consequences following an intervention and daily drinking over the past 30 days, respectively. Both datasets as well as R, SAS, Mplus, Stata, and SPSS code showing how to fit the models are available on a supplemental website.
PMCID: PMC3513584  PMID: 22905895
8.  A Randomized Controlled Trial of Event Specific Prevention Strategies for Reducing Problematic Drinking Associated with 21st Birthday Celebrations 
While research has documented heavy drinking practices and associated negative consequences of college students turning 21, few studies have examined prevention efforts aimed to reduce high-risk drinking during 21st birthday celebrations. The present study evaluated the comparative efficacy of a general prevention effort (i.e., BASICS) and event specific prevention in reducing 21st birthday drinking and related negative consequences. Furthermore, this study evaluated inclusion of peers in interventions and mode of intervention delivery (i.e., in-person vs. web).
Participants included 599 college students (46% male) who intended to consume at least five/four drinks (men/women respectively) on their 21st birthday. After completing a screening/baseline assessment approximately one week before turning 21, participants were randomly assigned to one of six conditions: 21st birthday in-person BASICS, 21st birthday web BASICS, 21st birthday in-person BASICS plus friend intervention, 21st birthday web BASICS plus friend intervention, BASICS, or an attention control. A follow-up assessment was completed approximately one week after students’ birthdays.
Results indicated a significant intervention effect for BASICS in reducing blood alcohol content reached and number of negative consequences experienced. All three in-person interventions reduced negative consequences experienced. Results for the web-based interventions varied by drinking outcome and whether or not a friend was included.
Overall, results provide support for both general intervention and ESP approaches across modalities for reducing extreme drinking and negative consequences associated with turning 21. These results suggest there are several promising options for campuses seeking to reduce both use and consequences associated with 21st birthday celebrations.
PMCID: PMC3458124  PMID: 22823855
Alcohol; alcohol-related problems; college students; event-specific drinking; event-specific prevention; 21st birthday
9.  Hierarchical LiFePO4 with a controllable growth of the (010) facet for lithium-ion batteries 
Scientific Reports  2013;3:2788.
Hierarchically structured LiFePO4 was successfully synthesized by ionic liquid solvothermal method. These hierarchically structured LiFePO4 samples were constructed from nanostructured platelets with their (010) facets mainly exposed. To the best of our knowledge, facet control of a hierarchical LiFePO4 crystal has not been reported yet. Based on a series of experimental results, a tentative mechanism for the formation of these hierarchical structures was proposed. After these hierarchically structured LiFePO4 samples were coated with a thin carbon layer and used as cathode materials for lithium-ion batteries, they exhibited excellent high-rate discharge capability and cycling stability. For instance, a capacity of 95% can be maintained for the LiFePO4 sample at a rate as high as 20 C, even after 1000 cycles.
PMCID: PMC3784946  PMID: 24071818
10.  Laparoscopic adjustable gastric banding: a report of 228 cases 
Gastroenterology Report  2013;1(2):144-148.
Objective: To evaluate the surgical outcomes and complications after laparoscopic adjustable gastric banding (LAGB) in obese patients.
Methods: This retrospective study included 228 patients (73 males and 155 females, mean age, 32.5 ± 10.3 years) who underwent LAGB at the Changhai Hospital of the Second Military Medical University from June 2003 to June 2011. The body weight and postoperative complications were followed up.
Results: The pre-operative mean body mass index (BMI) was 39.5 ± 6.3 kg/m2. Except in one case of inadequate exposure of the stomach, all laparoscopic procedures were successfully accomplished, with no conversion to open surgery. The mean operation time was 65.0 ± 20.3 min. The mean hospital stay was 2.7 ± 0.9 days. Early postoperative complications (<30 days) occurred in five cases (2.2%) and late complications (>30 days) occurred in 75 cases (32.9%), including 56 cases (24.6%) with band-associated complications. The percentage of excess weight loss (EWL%) at 1, 3 and 5 years was 40.5 ± 30.5%, 59.5 ± 41.5% and 58.9 ± 46.4%, respectively. The percentages of patients with EWL% >25%, >50% and >75% were, respectively, 60%, 33% and 0% at 1 year follow-up, 43%, 39%, and 16% at 3 years follow-up and 40%, 34% and 16% at 5 years follow-up.
Conclusion Although LAGB has low peri-operative mortality and morbidity rates, it is associated with a high late complication rate and unsatisfactory weight loss. It may be optional, but not the first choice, for the treatment of obesity.
PMCID: PMC3938002  PMID: 24759820
obesity; gastric banding; laparoscopy; complications; percentage of excess weight loss
11.  NFYA1 Is Involved in Regulation of Postgermination Growth Arrest Under Salt Stress in Arabidopsis 
PLoS ONE  2013;8(4):e61289.
The nuclear factor Y (NF-Y), which is a ubiquitous transcription factor found in eukaryotes, is composed of three distinct subunits, namely, NF-YA, NF-YB, and NF-YC. Here, we firstly characterized the detailed function of the Arabidopsis NFYA1 factor. It is found that the 35S::AtNFYA1-overexpressed lines were hypersensitive to salt stress and Abscisic acid (ABA) during the early-postgermination growth stages. The transgenic lines exhibited a severe postgermination growth arrest compared with the wild-type (WT) under salt stress and ABA treatment. Interestingly, sodium tungstate, which is an ABA synthesis inhibitor, restored the salt-sensitive phenotype of the 35S::AtNFYA1 lines. Results of the qRT-PCR analysis showed that the mRNA levels of ABI3 and ABI5, as well as their downstream genes AtEM1 and AtEM6, were more greatly upregulated under salt stress during seed germination in the transgenic lines compared with those in WT. On the other hand, the NFYA1-RNAi lines were found to be insensitive to salt stress and exhibited decreased levels of ABI3, ABI5, EM1, and EM6 transcripts. Our results provide clear evidence supporting a role of AtNFYA1 in regulating postgermination growth arrest under salt stress.
PMCID: PMC3634844  PMID: 23637805
12.  “Add to Subtract”: A Simple Method to Remove Complex Background Signals from the 1H Nuclear Magnetic Resonance Spectra of Mixtures 
Analytical Chemistry  2011;84(2):994-1002.
Due to its highly reproducible and quantitative nature, and minimal requirements for sample preparation or separation, 1H nuclear magnetic resonance (NMR) spectroscopy is widely used for profiling small-molecule metabolites in biofluids. However 1H NMR spectra contain many overlapped peaks. In particular, blood serum/plasma and diabetic urine samples contain high concentrations of glucose, which produce strong peaks between 3.2 ppm – 4.0 ppm. Signals from most metabolites in this region are overwhelmed by the glucose background signals and become invisible. We propose a simple “Add to Subtract” background subtraction method, and show that it can reduce the glucose signals by 98% to allow retrieval of the hidden information. This procedure includes adding a small drop of concentrated glucose solution to the sample in the NMR tube, mixing, waiting for an equilibration time, and acquisition of a second spectrum. The glucose-free spectra are then generated by spectral subtraction using Bruker Topspin software. Subsequent multivariate statistical analysis can then be used to identify biomarker candidate signals for distinguishing different types of biological samples. The principle of this approach is generally applicable for all quantitative spectral data and should find utility in a variety of NMR-based mixture analyses as well as in metabolite profiling.
PMCID: PMC3282557  PMID: 22221170
1H NMR; metabolomics; metabolite profiling; glucose; signal suppression; mixture analysis; blood; urine
13.  An Integrative Computational Framework Based on a Two-Step Random Forest Algorithm Improves Prediction of Zinc-Binding Sites in Proteins 
PLoS ONE  2012;7(11):e49716.
Zinc-binding proteins are the most abundant metalloproteins in the Protein Data Bank where the zinc ions usually have catalytic, regulatory or structural roles critical for the function of the protein. Accurate prediction of zinc-binding sites is not only useful for the inference of protein function but also important for the prediction of 3D structure. Here, we present a new integrative framework that combines multiple sequence and structural properties and graph-theoretic network features, followed by an efficient feature selection to improve prediction of zinc-binding sites. We investigate what information can be retrieved from the sequence, structure and network levels that is relevant to zinc-binding site prediction. We perform a two-step feature selection using random forest to remove redundant features and quantify the relative importance of the retrieved features. Benchmarking on a high-quality structural dataset containing 1,103 protein chains and 484 zinc-binding residues, our method achieved >80% recall at a precision of 75% for the zinc-binding residues Cys, His, Glu and Asp on 5-fold cross-validation tests, which is a 10%-28% higher recall at the 75% equal precision compared to SitePredict and zincfinder at residue level using the same dataset. The independent test also indicates that our method has achieved recall of 0.790 and 0.759 at residue and protein levels, respectively, which is a performance better than the other two methods. Moreover, AUC (the Area Under the Curve) and AURPC (the Area Under the Recall-Precision Curve) by our method are also respectively better than those of the other two methods. Our method can not only be applied to large-scale identification of zinc-binding sites when structural information of the target is available, but also give valuable insights into important features arising from different levels that collectively characterize the zinc-binding sites. The scripts and datasets are available at
PMCID: PMC3499040  PMID: 23166753
14.  Effect of the cord pretension of the Dynesys dynamic stabilisation system on the biomechanics of the lumbar spine: a finite element analysis 
European Spine Journal  2011;20(11):1850-1858.
The Dynesys dynamics stabilisation system was developed to maintain the mobility of motion segment of the lumbar spine in order to reduce the incidence of negative effects at the adjacent segments. However, the magnitude of cord pretension may change the stiffness of the Dynesys system and result in a diverse clinical outcome, and the effects of Dynesys cord pretension remain unclear. Displacement-controlled finite element analysis was used to evaluate the biomechanical behaviour of the lumbar spine after insertion of Dynesys with three different cord pretensions. For the implanted level, increasing the cord pretension from 100 to 300 N resulted in an increase in flexion stiffness from 19.0 to 64.5 Nm/deg, a marked increase in facet contact force (FCF) of 35% in extension and 32% in torsion, a 40% increase of the annulus stress in torsion, and an increase in the high-stress region of the pedicle screw in flexion and lateral bending. For the adjacent levels, varying the cord pretension from 100 to 300 N only had a minor influence on range of motion (ROM), FCF, and annulus stress, with changes of 6, 12, and 9%, respectively. This study found that alteration of cord pretension affects the ROM and FCF, and annulus stress within the construct but not the adjacent segment. In addition, use of a 300 N cord pretension causes a much higher stiffness at the implanted level when compared with the intact lumbar spine.
PMCID: PMC3207341  PMID: 21523456
Lumbar spine; Biomechanics; Dynesys dynamic stabilisation system; Finite element method; Cord pretension
15.  Identification and quantification of metabolites in 1H NMR spectra by Bayesian model selection 
Bioinformatics  2011;27(12):1637-1644.
Motivation: Nuclear magnetic resonance (NMR) spectroscopy is widely used for high-throughput characterization of metabolites in complex biological mixtures. However, accurate interpretation of the spectra in terms of identities and abundances of metabolites can be challenging, in particular in crowded regions with heavy peak overlap. Although a number of computational approaches for this task have recently been proposed, they are not entirely satisfactory in either accuracy or extent of automation.
Results: We introduce a probabilistic approach Bayesian Quantification (BQuant), for fully automated database-based identification and quantification of metabolites in local regions of 1H NMR spectra. The approach represents the spectra as mixtures of reference profiles from a database, and infers the identities and the abundances of metabolites by Bayesian model selection. We show using a simulated dataset, a spike-in experiment and a metabolomic investigation of plasma samples that BQuant outperforms the available automated alternatives in accuracy for both identification and quantification.
Availability: The R package BQuant is available at:
Supplementary Information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3106181  PMID: 21398670
16.  A Multifunctional Protein Encoded by Turkey Herpesvirus Suppresses RNA Silencing in Nicotiana benthamiana▿ 
Journal of Virology  2011;85(23):12792-12803.
Many plant and animal viruses counteract RNA silencing-mediated defense by encoding diverse RNA silencing suppressors. We characterized HVT063, a multifunctional protein encoded by turkey herpesvirus (HVT), as a silencing suppressor in coinfiltration assays with green fluorescent protein transgenic Nicotiana benthamiana line 16c. Our results indicated that HVT063 could strongly suppress both local and systemic RNA silencing induced by either sense RNA or double-stranded RNA (dsRNA). HVT063 could reverse local silencing, but not systemic silencing, in newly emerging leaves. The local silencing suppression activity of HVT063 was also verified using the heterologous vector PVX. Further, single alanine substitution of arginine or lysine residues of the HVT063 protein showed that each selected single amino acid contributed to the suppression activity of HVT063 and region 1 (residues 138 to 141) was more important, because three of four single amino acid mutations in this region could abolish the silencing suppressor activity of HVT063. Moreover, HVT063 seemed to induce a cell death phenotype in the infiltrated leaf region, and the HVT063 dilutions could decrease the silencing suppressor activity and alleviate the cell death phenotype. Collectively, these results suggest that HVT063 functions as a viral suppressor of RNA silencing that targets a downstream step of the dsRNA formation in the RNA silencing process. Positively charged amino acids in HVT063, such as arginine and lysine, might contribute to the suppressor activity by boosting the interaction between HVT063 and RNA, since HVT063 has been demonstrated to be an RNA binding protein.
PMCID: PMC3209371  PMID: 21957299
17.  Control of Pain After Surgical Debridement of Burn Wounds 
Archives of Trauma Research  2012;1(2):79-80.
PMCID: PMC3876528  PMID: 24396749
Burns; Debridement; Pain
18.  The Interaction between Bamboo Mosaic Virus Replication Protein and Coat Protein Is Critical for Virus Movement in Plant Hosts ▿ 
Journal of Virology  2011;85(22):12022-12031.
Bamboo mosaic virus (BaMV) is a positive-sense RNA virus belonging to the genus Potexvirus. Open reading frame 1 (ORF1) encodes the viral replication protein that consists of a capping enzyme domain, a helicase-like domain (HLD), and an RNA-dependent RNA polymerase domain from the N to C terminus. ORF5 encodes the viral coat protein (CP) required for genome encapsidation and the virus movement in plants. In this study, application of a yeast-two hybrid assay detected an interaction between the viral HLD and CP. However, the interaction did not affect the NTPase activity of the HLD. To identify the critical amino acids of CP interacting with the HLD, a random mutational library of CP was created using error-prone PCR, and the mutations adversely affecting the interaction were screened by a bacterial two-hybrid system. As a result, the mutations A209G and N210S in CP were found to weaken the interaction. To determine the significance of the interaction, the mutations were introduced into a BaMV infectious clone, and the mutational effects on viral replication, movement, and genome encapsidation were investigated. There was no effect on accumulations of BaMV CP and genomic RNAs within protoplasts; however, the virus cell-to-cell movement in plants was restricted. Sequence alignment revealed that A209 of BaMV CP is conserved in many potexviruses. Mutation of the corresponding residue in Foxtail mosaic virus CP also reduced the viral HLD-CP interaction and restricted the virus movement, suggesting that interaction between CP and a widely conserved HLD in the potexviral replication protein is crucial for viral trafficking through plasmodesmata.
PMCID: PMC3209275  PMID: 21917973
19.  Multivariate Statistical Identification of Human Bladder Carcinomas Using Ambient Ionization Imaging Mass Spectrometry 
Diagnosis of human bladder cancer in untreated tissue sections is achieved by using imaging data from desorption electrospray ionization mass spectrometry (DESI-MS) combined with multivariate statistical analysis. We use the distinctive DESI-MS glycerophospholipid (GP) mass spectral profiles to visually characterize and formally classify twenty pairs (40 tissue samples) of human cancerous and adjacent normal bladder tissue samples. The individual ion images derived from the acquired profiles correlate with standard histological hematoxylin and eosin (H&E)-stained serial sections. The profiles allow us to classify the disease status of the tissue samples with high accuracy as judged by reference histological data. To achieve this, the data from the twenty pairs were divided into a training set and a validation set. Spectra from the tumor and normal regions of each of the tissue sections in the training set were used for orthogonal projection to latent structures (O-PLS) treated partial least-square discriminate analysis (PLS-DA). This predictive model was then validated by using the validation set and showed a 5% error rate for classification and a misclassification rate of 12%. It was also used to create synthetic images of the tissue sections showing pixel-by-pixel disease classification of the tissue and these data agreed well with the independent classification that uses histological data by a certified pathologist. This represents the first application of multivariate statistical methods for classification by ambient ionization although these methods have been applied previously to other MS imaging methods. The results are encouraging in terms of the development of a method that could be utilized in a clinical setting through visualization and diagnosis of intact tissue.
PMCID: PMC3050580  PMID: 21284043
cancer; desorption electrospray ionization; lipidomics; molecular imaging; multivariate statistics; mass spectrometry
20.  Genotypic differences in Al resistance and the role of cell-wall pectin in Al exclusion from the root apex in Fagopyrum tataricum 
Annals of Botany  2010;107(3):371-378.
Background and Aims
Aluminium (Al) toxicity is one of the factors limiting crop production on acid soils. However, genotypic differences exist among plant species or cultivars in response to Al toxicity. This study aims to investigate genotypic differences among eight cultivars of tatary buckwheat (Fagopyrum tataricum) for Al resistance and explore the possible mechanisms of Al resistance.
Al resistance was evaluated based on relative root elongation (root elongation with Al/root elongation without Al). Root apex Al content, pectin content and exudation of root organic acids were determined and compared.
Key Results
Genotypic differences among the eight cultivars were correlated with exclusion of Al from the root apex. However, there was a lack of correlation between Al exclusion and Al-induced oxalate secretion. Interestingly, cell-wall pectin content of the root apex was generally lower in Al-resistant cultivars than in Al-sensitive cultivars. Although we were unable to establish a significant correlation between Al exclusion and pectin content among the eight cultivars, a strong correlation could be established among six cultivars, in which the pectin content in the most Al-resistant cultivar ‘Chuan’ was significantly lower than that in the most Al-sensitive cultivar ‘Liuku2’. Furthermore, root apex cell-wall pectin methylesterase activity (PME) was similar in ‘Chuan’ and ‘Liuku2’ in the absence of Al, but Al treatment resulted in increased PME activity in ‘Liuku2’ compared with ‘Chuan’. Immunolocalization of pectins also showed that the two cultivars had similar amounts of either low-methyl-ester pectins or high-methyl-ester pectins in the absence of Al, but Al treatment resulted in a more significant increase of low-methyl-ester pectins and decrease of high-methyl-ester pectins in ‘Liuku2’.
Cell-wall pectin content may contribute, at least in part, to differential Al resistance among tatary buckwheat cultivars.
PMCID: PMC3043930  PMID: 21183454
Aluminium resistance; cell wall; exclusion mechanism; Fagopyrum tataricum; pectin; pectin methylesterase; oxalate; toxicity
21.  Comprehensive Identification of Protein Substrates of the Dot/Icm Type IV Transporter of Legionella pneumophila 
PLoS ONE  2011;6(3):e17638.
A large number of proteins transferred by the Legionella pneumophila Dot/Icm system have been identified by various strategies. With no exceptions, these strategies are based on one or more characteristics associated with the tested proteins. Given the high level of diversity exhibited by the identified proteins, it is possible that some substrates have been missed in these screenings. In this study, we took a systematic method to survey the L. pneumophila genome by testing hypothetical orfs larger than 300 base pairs for Dot/Icm-dependent translocation. 798 of the 832 analyzed orfs were successfully fused to the carboxyl end of β-lactamase. The transfer of the fusions into mammalian cells was determined using the β-lactamase reporter substrate CCF4-AM. These efforts led to the identification of 164 proteins positive in translocation. Among these, 70 proteins are novel substrates of the Dot/Icm system. These results brought the total number of experimentally confirmed Dot/Icm substrates to 275. Sequence analysis of the C-termini of these identified proteins revealed that Lpg2844, which contains few features known to be important for Dot/Icm-dependent protein transfer can be translocated at a high efficiency. Thus, our efforts have identified a large number of novel substrates of the Dot/Icm system and have revealed the diverse features recognizable by this protein transporter.
PMCID: PMC3052360  PMID: 21408005
22.  Casticin, a flavonoid isolated from Vitex rotundifolia, inhibits prolactin release in vivo and in vitro 
Acta Pharmacologica Sinica  2010;31(12):1564-1568.
To investigate the anti-hyperprolactinemia activity of casticin, a flavonoid isolated from Vitex rotundifolia, and elucidate its molecular mechanism.
Hyperprolactinemia (MIHP) was induced by administration of metoclopramide dihydrochloride (50 mg/kg, tid, ip, for 10 d) in SD rats and the primary pituitary cells were prepared from the pituitary glands of the SD rats. Prolactin concentrations were measured using a radioimmunoassay. Cell viability was measured using an MTT assay. The mRNA expression of estrogen receptor alpha and beta in rat pituitary cells was measured using semi-quantitative RT-PCR analysis.
The level of serum prolactin in the MIHP model group was 2.1 fold higher than that in the untreated control group (P<0.01). Casticin (10, 20, and 40 mg/kg, ip, for 7 d) reduced serum prolactin levels by 33.9%, 54.3%, and 64.7%, respectively (P<0.01). The positive control drug bromocriptine 1 mg/kg decreased the serum prolactin concentration in MIHP rats by 44.9%. 17β-Estradiol (E2) significantly increased the proliferation of pituitary cells and casticin (1 and 10 μmol/L) markedly inhibited E2-induced pituitary cell proliferation by 27.7% and 42.1%, respectively. Stimulation of pituitary cells with E2 increased prolactin secretion into the cell culture supernatants, and casticin (0.1, 1, and 10 μmol/L) significantly inhibited the prolactin release stimulated by E2 in a concentration-dependent manner. Casticin (1 and 10 μmol/L) significantly inhibited ERα mRNA expression in pituitary cells stimulated with E2 (P<0.01) but increased ERβ mRNA expression at a concentration of 10 μmol/L (P<0.01). However, casticin had no effects on proliferation and prolectin release of the unstimulated primary pituitary cells in vitro.
Casticin inhibited the release of prolactin from pituitary cells of SD rats stimulated with E2 in vivo and in vitro. These effects might be related with inhibiting the ERα mRNA expression and increasing the ERβ mRNA expression.
PMCID: PMC4002951  PMID: 21042288
casticin; premenstrual syndrome; prolactin; estrogen; estrogen receptors
23.  Interdependence of Signal Processing and Analysis of Urine 1H NMR Spectra for Metabolic Profiling 
Analytical chemistry  2009;81(15):6080-6088.
Metabolic profiling of urine presents challenges due to the extensive random variation of metabolite concentrations, and to dilution resulting from changes in the overall urine volume. Thus statistical analysis methods play a particularly important role, however appropriate choices of these methods are not straightforward. Here we investigate constant and variance-stabilization normalization of raw and peak picked spectra, for use with exploratory analysis (principal component analysis) and confirmatory analysis (ordinary and Empirical Bayes t-test) in 1H NMR-based metabolic profiling of urine. We compare the performance of these methods using urine samples spiked with known metabolites according to a Latin square design. We find that analysis of peak picked and log-transformed spectra is preferred, and that signal processing and statistical analysis steps are interdependent. While variance-stabilizing transformation is preferred in conjunction with principal component analysis, constant normalization is more appropriate for use with a t-test. Empirical Bayes t-test provides more reliable conclusions when the number of samples in each group is relatively small. Performance of these methods is illustrated using a clinical metabolomics experiment on patients with type 1 diabetes to evaluate the effect of insulin deprivation.
PMCID: PMC2789356  PMID: 19950923
Metabolomics; Metabolite profiling; NMR spectroscopy; Normalization; Moderated t-test; Logarithmic transformation; Urine; Diabetes
24.  Biomechanical analysis of the lumbar spine on facet joint force and intradiscal pressure - a finite element study 
Finite element analysis results will show significant differences if the model used is performed under various material properties, geometries, loading modes or other conditions. This study adopted an FE model, taking into account the possible asymmetry inherently existing in the spine with respect to the sagittal plane, with a more geometrically realistic outline to analyze and compare the biomechanical behaviour of the lumbar spine with regard to the facet force and intradiscal pressure, which are associated with low back pain symptoms and other spinal disorders. Dealing carefully with the contact surfaces of the facet joints at various levels of the lumbar spine can potentially help us further ascertain physiological behaviour concerning the frictional effects of facet joints under separate loadings or the responses to the compressive loads in the discs.
A lumbar spine model was constructed from processes including smoothing the bony outline of each scan image, stacking the boundary lines into a smooth surface model, and subsequent further processing in order to conform with the purpose of effective finite element analysis performance. For simplicity, most spinal components were modelled as isotropic and linear materials with the exception of spinal ligaments (bilinear). The contact behaviour of the facet joints and changes of the intradiscal pressure with different postures were analyzed.
The results revealed that asymmetric responses of the facet joint forces exist in various postures and that such effect is amplified with larger loadings. In axial rotation, the facet joint forces were relatively larger in the contralateral facet joints than in the ipsilateral ones at the same level. Although the effect of the preloads on facet joint forces was not apparent, intradiscal pressure did increase with preload, and its magnitude increased more markedly in flexion than in extension and axial rotation.
Disc pressures showed a significant increase with preload and changed more noticeably in flexion than in extension or in axial rotation. Compared with the applied preloads, the postures played a more important role, especially in axial rotation; the facet joint forces were increased in the contralateral facet joints as compared to the ipsilateral ones at the same level of the lumbar spine.
PMCID: PMC2913991  PMID: 20602783
25.  Companion Animals as Sentinels for Community Exposure to Industrial Chemicals: The Fairburn, GA, Propyl Mercaptan Case Study 
Public Health Reports  2008;123(3):333-342.
This study utilized the electronic medical records of six veterinary hospitals (operated by Banfield, The Pet Hospital®) in the vicinity of Fairburn, Georgia, to assess the health of dogs and cats following the unintentional release of propyl mercaptan from a waste-processing facility.
Standardized electronic medical records were used to define clinical syndromes (eye inflammation, gastrointestinal, respiratory, fever, general weakness/change in mental state) in dogs and cats. The frequency and geographic distribution of each syndrome was evaluated before, during, and after the chemical release, using control charts, density maps, change in average mean distance from a suspected point source of chemical release, space-time statistics, and autoregressive integrated moving averages.
No consistent pattern of change in syndromic events was observed following the suspected release of propyl mercaptan. Some syndromes, including respiratory syndrome in cats, gastrointestinal syndrome in dogs, and eye inflammation syndrome in both cats and dogs, showed a change in time and spatial patterns following the release of propyl mercaptan into the community. These changes were consistent with clinical signs observed in people during a previous propyl mercaptan release in California as well as the release in Fairburn.
A systematic review of electronic medical records of dogs and cats exposed to release of propyl mercaptan showed no conclusive and consistent evidence of adverse health effects. Methods for the use of medical records of pets for detecting environmental hazards require further development and evaluation.
PMCID: PMC2289986  PMID: 19006975

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