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1.  A G-Protein β Subunit, AGB1, Negatively Regulates the ABA Response and Drought Tolerance by Down-Regulating AtMPK6-Related Pathway in Arabidopsis 
PLoS ONE  2015;10(1):e0116385.
Heterotrimeric G-proteins are versatile regulators involved in diverse cellular processes in eukaryotes. In plants, the function of G-proteins is primarily associated with ABA signaling. However, the downstream effectors and the molecular mechanisms in the ABA pathway remain largely unknown. In this study, an AGB1 mutant (agb1-2) was found to show enhanced drought tolerance, indicating that AGB1 might negatively regulate drought tolerance in Arabidopsis. Data showed that AGB1 interacted with protein kinase AtMPK6 that was previously shown to phosphorylate AtVIP1, a transcription factor responding to ABA signaling. Our study found that transcript levels of three ABA responsive genes, AtMPK6, AtVIP1 and AtMYB44 (downstream gene of AtVIP1), were significantly up-regulated in agb1-2 lines after ABA or drought treatments. Other ABA-responsive and drought-inducible genes, such as RD29A (downstream gene of AtMYB44), were also up-regulated in agb1-2 lines. Furthermore, overexpression of AtVIP1 resulted in hypersensitivity to ABA at seed germination and seedling stages, and significantly enhanced drought tolerance in transgenic plants. These results suggest that AGB1 was involved in the ABA signaling pathway and drought tolerance in Arabidopsis through down-regulating the AtMPK6, AtVIP1 and AtMYB44 cascade.
doi:10.1371/journal.pone.0116385
PMCID: PMC4312036  PMID: 25635681
2.  Genome-wide analysis of the Hsf family in soybean and functional identification of GmHsf-34 involvement in drought and heat stresses 
BMC Genomics  2014;15(1):1009.
Background
High temperature affects organism growth and metabolic activity. Heat shock transcription factors (Hsfs) are key regulators in heat shock response in eukaryotes and prokaryotes. Under high temperature conditions, Hsfs activate heat shock proteins (Hsps) by combining with heat stress elements (HSEs) in their promoters, leading to defense of heat stress. Since the first plant Hsf gene was identified in tomato, several plant Hsf family genes have been thoroughly characterized. Although soybean (Glycine max), an important oilseed crops, genome sequences have been available, the Hsf family genes in soybean have not been characterized accurately.
Result
We analyzed the Hsf genetic structures and protein function domains using the GSDS, Pfam, SMART, PredictNLS, and NetNES online tools. The genome scanning of dicots (soybean and Arabidopsis) and monocots (rice and maize) revealed that the whole-genome replication occurred twice in soybean evolution. The plant Hsfs were classified into 3 classes and 16 subclasses according to protein structure domains. The A8 and B3 subclasses existed only in dicots and the A9 and C2 occurred only in monocots. Thirty eight soybean Hsfs were systematically identified and grouped into 3 classes and 12 subclasses, and located on 15 soybean chromosomes. The promoter regions of the soybean Hsfs contained cis-elements that likely participate in drought, low temperature, and ABA stress responses. There were large differences among Hsfs based on transcriptional levels under the stress conditions. The transcriptional levels of the A1 and A2 subclass genes were extraordinarily high. In addition, differences in the expression levels occurred for each gene in the different organs and at the different developmental stages. Several genes were chosen to determine their subcellular localizations and functions. The subcellular localization results revealed that GmHsf-04, GmHsf-33, and GmHsf-34 were located in the nucleus. Overexpression of the GmHsf-34 gene improved the tolerances to drought and heat stresses in Arabidopsis plants.
Conclusions
This present investigation of the quantity, structural features, expression characteristics, subcellular localizations, and functional roles provides a scientific basis for further research on soybean Hsf functions.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1009) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-1009
PMCID: PMC4253008  PMID: 25416131
Hsfs; Genome-wide identification; Expression pattern; Subcellular localization; Functional identification; Soybean
3.  A Soybean C2H2-Type Zinc Finger Gene GmZF1 Enhanced Cold Tolerance in Transgenic Arabidopsis 
PLoS ONE  2014;9(10):e109399.
Zinc finger proteins were involved in response to different environmental stresses in plant species. A typical Cys2/His2-type (C2H2-type) zinc finger gene GmZF1 from soybean was isolated and was composed of 172 amino acids containing two conserved C2H2-type zinc finger domains. Phylogenetic analysis showed that GmZF1 was clustered on the same branch with six C2H2-type ZFPs from dicotyledonous plants excepting for GsZFP1, and distinguished those from monocotyledon species. The GmZF1 protein was localized at the nucleus, and has specific binding activity with EP1S core sequence, and nucleotide mutation in the core sequence of EPSPS promoter changed the binding ability between GmZF1 protein and core DNA element, implying that two amino acid residues, G and C boxed in core sequence TGACAGTGTCA possibly play positive regulation role in recognizing DNA-binding sites in GmZF1 proteins. High accumulation of GmZF1 mRNA induced by exogenous ABA suggested that GmZF1 was involved in an ABA-dependent signal transduction pathway. Over-expression of GmZF1 significantly improved the contents of proline and soluble sugar and decreased the MDA contents in the transgenic lines exposed to cold stress, indicating that transgenic Arabidopsis carrying GmZF1 gene have adaptive mechanisms to cold stress. Over-expression of GmZF1 also increased the expression of cold-regulated cor6.6 gene by probably recognizing protein-DNA binding sites, suggesting that GmZF1 from soybean could enhance the tolerance of Arabidopsis to cold stress by regulating expression of cold-regulation gene in the transgenic Arabidopsis.
doi:10.1371/journal.pone.0109399
PMCID: PMC4186855  PMID: 25286048
4.  Gr-1+CD11b+ Immature Myeloid Cells (IMC) Promote Resistance of Pro-Inflammatory T Cells to Suppression by Regulatory T Cells in Atherosclerotic Apo E- Deficient Mice 
PLoS ONE  2014;9(9):e108620.
Accumulating evidence indicates that both defects in Treg numbers and/or function as well as resistance of effector T cells to suppression may contribute to the development of human chronic inflammatory diseases. However, which mechanism involved in the progression of atherosclerosis remains unclear. In this study, we evaluated the production and function of CD4+ inflammatory and regulatory T cells in atherosclerosis-prone mice. We found that the hyperactivity and unresponsiveness to Treg-mediated suppression of inflammatory CD4+ T cells occurred in the progression of atherosclerosis, though Treg cells were present in very large numbers and fully functional. We further found that Gr-1+CD11b+ immature myeloid cells were significantly accumulated in atherosclerotic Apo E−/− mice, and they promoted resistance of inflammatory CD4+ T cells to Treg-mediated suppression in vitro and in vivo. we further confirmed that Gr-1+CD11b+ immature myeloid cells produced high level of interleukin 6 which was at least partially responsible for inducing unresponsiveness of inflammatory CD4+ T cells to suppression via activation of Jak/Stat signaling pathway. Taken together, these findings might provide new insights to explore potential targets for immune therapeutic intervention in atherosclerosis.
doi:10.1371/journal.pone.0108620
PMCID: PMC4182509  PMID: 25269085
5.  Surgical management of multilevel cervical spinal stenosis and spinal cord injury complicated by cervical spine fracture 
Background
There are few reports regarding surgical management of multilevel cervical spinal stenosis with spinal cord injury. Our purpose is to evaluate the safety and feasibility of open-door expansive laminoplasty in combination with transpedicular screw fixation for the treatment of multilevel cervical spinal stenosis and spinal cord injury in the trauma population.
Methods
This was a retrospective study of 21 patients who had multilevel cervical spinal stenosis and spinal cord injury with unstable fracture. An open-door expansive posterior laminoplasty combined with transpedicular screw fixation was performed under persistent intraoperative skull traction. Outcome measures included postoperative improvement in Japanese Orthopedic Association (JOA) score and incidence of complications.
Results
The average operation time was 190 min, with an average blood loss of 437 ml. A total of 120 transpedicular screws were implanted into the cervical vertebrae between vertebral C3 and C7, including 20 into C3, 34 into C4, 36 into C5, 20 into C6, and 10 into C7. The mean preoperative JOA score was 3.67 ± 0.53. The patients were followed for an average of 17.5 months, and the average JOA score improved to 8.17 ± 1.59, significantly higher than the preoperative score (t = 1.798, P < 0.05), with an average improvement of 44.7 ± 11.7%. Postoperative complications in four patients included cerebrospinal fluid leakage, delayed wound healing, pulmonary infection, and urinary system infection. All four patients were responsive to antibiotic treatment; one died from respiratory failure 3 months postoperatively.
Conclusions
The open-door expansive laminoplasty combined with posterior transpedicular screw fixation is feasible for treating multilevel cervical spinal stenosis and spinal cord injury complicated by unstable fracture. Its advantages include minimum surgical trauma, less intraoperative blood loss, and satisfactory stable supportive effect for reduction of fracture.
doi:10.1186/s13018-014-0077-4
PMCID: PMC4143576  PMID: 25142353
Laminoplasty; Spinal cord injury; Spinal stenosis
6.  Monocyte chemotactic protein-1 expression as a prognosic biomarker in patients with solid tumor: a meta analysis 
Purpose: A great deal of studies have been performed on the prognostic value of monocyte chemotactic protein-1 (MCP-1) in solid tumors in recent years. However, no consistent outcomes are reported. Therefore, the prognostic value of MCP-1 still remains controversial in patients with solid tumors. Here we aimed to evaluate the prognostic value of MCP-1 expression for patients with solid tumors. Methods: Comprehensive literature was selected from PUBMED and EMBASE and clinical studies which reported analysis of survival data about MCP-1 in solid tumors were included. Stata 11.0 was used for performing a meta-analysis on evaluating the relation between MCP-1 and clinical staging, overall survival (OS) and disease free survival (DFS). Results: Eleven studies with a total of 1324 patients with solid tumors were included into our meta-analysis. The result showed that high concentration of MCP-1 was related to a worse OS (HR = 1.95, 95% CI 1.32-2.88). The subgroup analysis on different location of tumors showed that high concentration of MCP-1 meant bad prognosis in patients with digestive cancer (HR = 2.66, 95% CI 1.44-4.91) and urogenital cancer (HR = 2.23, 95% CI 1.61-3.10), even head and neck cancer (HR = 1.99, 95% CI 0.95-4.18) other than respiratory cancer (HR = 1.10, 95% CI 0.39-3.11). Another subgroup analysed on different sites of cancer and indicated a poor prognosis on adenocarcinoma (HR = 2.10, 95% CI 1.63-2.69). Conclusions: Our findings suggest that MCP-1 can be regarded as a poor prognostic maker for solid tumors and may represent important new therapeutic targets.
PMCID: PMC4128999  PMID: 25120764
Monocyte chemotactic protein-1; meta-analysis; cancer; prognosis; overall survival
7.  Multi-Agent Cooperative Target Search 
Sensors (Basel, Switzerland)  2014;14(6):9408-9428.
This paper addresses a vision-based cooperative search for multiple mobile ground targets by a group of unmanned aerial vehicles (UAVs) with limited sensing and communication capabilities. The airborne camera on each UAV has a limited field of view and its target discriminability varies as a function of altitude. First, by dividing the whole surveillance region into cells, a probability map can be formed for each UAV indicating the probability of target existence within each cell. Then, we propose a distributed probability map updating model which includes the fusion of measurement information, information sharing among neighboring agents, information decay and transmission due to environmental changes such as the target movement. Furthermore, we formulate the target search problem as a multi-agent cooperative coverage control problem by optimizing the collective coverage area and the detection performance. The proposed map updating model and the cooperative control scheme are distributed, i.e., assuming that each agent only communicates with its neighbors within its communication range. Finally, the effectiveness of the proposed algorithms is illustrated by simulation.
doi:10.3390/s140609408
PMCID: PMC4118349  PMID: 24865884
UAV; multi-agent network; target search; cooperative control
8.  Endoscopic papillary large balloon dilation vs endoscopic sphincterotomy for retrieval of common bile duct stones: A meta-analysis 
AIM: To compare the efficacy and safety of endoscopic papillary large balloon dilation (EPLBD) with endoscopic sphincterotomy (EST) in retrieval of common bile duct stones (≥ 10 mm).
METHODS: PubMed, Web of Knowledge, EBSCO, the Cochrane Library, and EMBASE were searched for eligible studies. Randomized controlled trials (RCTs) that compared EPLBD with EST were identified. Data extraction and quality assessment were performed by two independent reviewers using the same criteria. Any disagreement was discussed with a third reviewer until a final consensus was reached. Pooled outcomes of complete bile duct stone clearance, stone clearance in one session, requirement for mechanical lithotripsy, and overall complication rate were determined using relative risk and 95%CI. The separate post-endoscopic retrograde cholangiopancreatography complications were pooled and determined with the Peto odds ratio and 95%CI because of the small number of events. Heterogeneity was evaluated with the chi-squared test with P ≤ 0.1 and I2 with a cutoff of ≥ 50%. A fixed effects model was used primarily. A random effects model was applied when significant heterogeneity was detected. Sensitivity analysis was applied to explore the potential bias.
RESULTS: Five randomized controlled trials with 621 participants were included. EPLBD compared with EST had similar outcomes with regard to complete stone removal rate (93.7% vs 92.5%, P = 0.54) and complete duct clearance in one session (82.2% vs 77.7%, P = 0.17). Mechanical lithotripsy was performed less in EPLBD in the retrieval of whole stones (15.5% vs 25.2%, P = 0.003), as well as in the stratified subgroup of stones larger than 15 mm (24.2% vs 40%, P = 0.001). There was no statistically significant difference in the incidence of overall adverse events (7.9% vs 10.7%, P = 0.25), post-ERCP pancreatitis (4.0% vs 5.0%, P = 0.54), hemorrhage (1.7% vs 2.8%, P = 0.32), perforation (0.3% vs 0.9%, P = 0.35) or acute cholangitis (1.3% vs 1.3%, P = 0.92).
CONCLUSION: EPLBD could be advocated as an alternative to EST in the retrieval of large common bile duct stones.
doi:10.3748/wjg.v20.i18.5548
PMCID: PMC4017071  PMID: 24833886
Endoscopic papillary large balloon dilation; Endoscopic sphincterotomy; Mechanical lithotripsy; Common bile duct stones; Meta analysis.
9.  Training Set Selection for the Prediction of Essential Genes 
PLoS ONE  2014;9(1):e86805.
Various computational models have been developed to transfer annotations of gene essentiality between organisms. However, despite the increasing number of microorganisms with well-characterized sets of essential genes, selection of appropriate training sets for predicting the essential genes of poorly-studied or newly sequenced organisms remains challenging. In this study, a machine learning approach was applied reciprocally to predict the essential genes in 21 microorganisms. Results showed that training set selection greatly influenced predictive accuracy. We determined four criteria for training set selection: (1) essential genes in the selected training set should be reliable; (2) the growth conditions in which essential genes are defined should be consistent in training and prediction sets; (3) species used as training set should be closely related to the target organism; and (4) organisms used as training and prediction sets should exhibit similar phenotypes or lifestyles. We then analyzed the performance of an incomplete training set and an integrated training set with multiple organisms. We found that the size of the training set should be at least 10% of the total genes to yield accurate predictions. Additionally, the integrated training sets exhibited remarkable increase in stability and accuracy compared with single sets. Finally, we compared the performance of the integrated training sets with the four criteria and with random selection. The results revealed that a rational selection of training sets based on our criteria yields better performance than random selection. Thus, our results provide empirical guidance on training set selection for the identification of essential genes on a genome-wide scale.
doi:10.1371/journal.pone.0086805
PMCID: PMC3899339  PMID: 24466248
10.  Correction: Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.) 
PLoS ONE  2014;9(1):10.1371/annotation/e3307d0c-bb59-4f75-89b4-8e0d5af087d5.
doi:10.1371/annotation/e3307d0c-bb59-4f75-89b4-8e0d5af087d5
PMCID: PMC3894297
11.  Effectiveness of YouTube as a Source of Medical Information on Heart Transplantation 
Background
In this digital era, there is a growing tendency to use the popular Internet site YouTube as a new electronic-learning (e-learning) means for continuing medical education. Heart transplantation (HTx) remains the most viable option for patients with end-stage heart failure or severe coronary artery disease. There are plenty of freely accessible YouTube videos providing medical information about HTx.
Objective
The aim of the present study is to determine the effectiveness of YouTube as an e-learning source on HTx.
Methods
In order to carry out this study, YouTube was searched for videos uploaded containing surgical-related information using the four keywords: (1) “heart transplantation”, (2) “cardiac transplantation”, (3) “heart transplantation operation”, and (4) “cardiac transplantation operation”. Only videos in English (with comments or subtitles in English language) were included. Two experienced cardiac surgeons watched each video (N=1800) and classified them as useful, misleading, or recipients videos based on the HTx-relevant information. The kappa statistic was used to measure interobserver variability. Data was analyzed according to six types of YouTube characteristics including “total viewership”, “duration”, “source”, “days since upload”, “scores” given by the viewers, and specialized information contents of the videos.
Results
A total of 342/1800 (19.00%) videos had relevant information about HTx. Of these 342 videos, 215 (62.8%) videos had useful information about specialized knowledge, 7/342 (2.0%) were found to be misleading, and 120/342 (35.1%) only concerned recipients’ individual issues. Useful videos had 56.09% of total viewership share (2,175,845/3,878,890), whereas misleading had 35.47% (1,375,673/3,878,890). Independent user channel videos accounted for a smaller proportion (19% in total numbers) but might have a wider impact on Web viewers, with the highest mean views/day (mean 39, SD 107) among four kinds of channels to distribute HTx-related information.
Conclusions
YouTube videos on HTx benefit medical professionals by providing a substantial amount of information. However, it is a time-consuming course to find high-quality videos. More authoritative videos by trusted sources should be posted for dissemination of reliable information. With an improvement of ranking system and content providers in future, YouTube, as a freely accessible outlet, will help to meet the huge informational needs of medical staffs and promote medical education on HTx.
doi:10.2196/ijmr.2669
PMCID: PMC3841345  PMID: 24263225
heart transplantation; Internet; medical informatics; online videos; YouTube; e-learning
12.  Two Wheat Glutathione Peroxidase Genes Whose Products Are Located in Chloroplasts Improve Salt and H2O2 Tolerances in Arabidopsis 
PLoS ONE  2013;8(10):e73989.
Oxidative stress caused by accumulation of reactive oxygen species (ROS) is capable of damaging effects on numerous cellular components. Glutathione peroxidases (GPXs, EC 1.11.1.9) are key enzymes of the antioxidant network in plants. In this study, W69 and W106, two putative GPX genes, were obtained by de novo transcriptome sequencing of salt-treated wheat (Triticum aestivum) seedlings. The purified His-tag fusion proteins of W69 and W106 reduced H2O2 and t-butyl hydroperoxide (t-BHP) using glutathione (GSH) or thioredoxin (Trx) as an electron donor in vitro, showing their peroxidase activity toward H2O2 and toxic organic hydroperoxide. GFP fluorescence assays revealed that W69 and W106 are localized in chloroplasts. Quantitative real-time PCR (Q-RT-PCR) analysis showed that two GPXs were differentially responsive to salt, drought, H2O2, or ABA. Isolation of the W69 and W106 promoters revealed some cis-acting elements responding to abiotic stresses. Overexpression of W69 and W106 conferred strong tolerance to salt, H2O2, and ABA treatment in Arabidopsis. Moreover, the expression levels of key regulator genes (SOS1, RbohD and ABI1/ABI2) involved in salt, H2O2 and ABA signaling were altered in the transgenic plants. These findings suggest that W69 and W106 not only act as scavengers of H2O2 in controlling abiotic stress responses, but also play important roles in salt and ABA signaling.
doi:10.1371/journal.pone.0073989
PMCID: PMC3788784  PMID: 24098330
13.  3,3-Bis(methyl­sulfan­yl)-1-(4-nitro­phen­yl)prop-2-en-1-one 
In the title compound, C11H11NO3S2, the S—Csp 2 bonds are shorter [1.746 (3) and 1.750 (2) Å] than the S—CH3 bonds [1.794 (3) and 1.806 (3) Å], which we attribute to d–π inter­actions between the S atoms and the C=C bond. The 1,1-bis­(methyl­sulfan­yl)-3-oxo­propyl­ene fragment and the 4-nitro­phenyl group are both almost planar, with the largest deviations from their mean planes being 0.053 (1) and 0.017 (2) Å, respectively. The dihedral angle between the two planes is 35.07 (7)°. Mol­ecules in the crystal are linked into a three-dimensional network by C—H⋯S and C—H⋯O hydrogen bonds.
doi:10.1107/S1600536813014542
PMCID: PMC3772470  PMID: 24046613
14.  [6-(Furan-2-yl)-7-nitro-2,3,4,6,7,8-hexa­hydro-1H-pyrido[1,2-a]pyrimidin-9-yl](phen­yl)methanone 
The asymmetric unit of the title compound, C19H19N3O4, contains two mol­ecules with very few conformational differences; a C atom in the pyrimidine ring in one of the mol­ecules is disordered in a 0.688 (15):0.312 (15) ratio. In both mol­ecules, the fused pyridine and pyrimidine rings adopt half-chair conformations. The dihedral angles between the furan and benzene rings are 81.00 (13) and 84.99 (10)° in the two mol­ecules. The mol­ecular structure is consolidated by intra­molecular N—H⋯O hydrogen bonding. In the crystal, C—H⋯O hydrogen bonds connect the molecules into a three-dimensional network.
doi:10.1107/S160053681301386X
PMCID: PMC3685119  PMID: 23795138
15.  1-(4-Chloro­phen­yl)-2-(1,3-diazepan-2-yl­idene)ethanone 
In the title compound, C13H15ClN2O, there are two crystallographically independent but conformationally similar (E)-mol­ecules in the asymmetric unit [dihedral angles between the phenyl ring and a common planar fragment of the 1,3-diazepane moiety = 47.34 (16) and 48.00 (16)°]. The seven-membered ring system adopts a chair conformation in both molecules. In the crystal, N—H⋯O hydrogen bonds lead to chains extending along the b-axis direction.
doi:10.1107/S1600536813013858
PMCID: PMC3685108  PMID: 23795127
16.  A wheat PI4K gene whose product possesses threonine autophophorylation activity confers tolerance to drought and salt in Arabidopsis  
Journal of Experimental Botany  2013;64(10):2915-2927.
Phosphoinositides are involved in regulation of recruitment and activity of signalling proteins in cell membranes. Phosphatidylinositol (PI) 4-kinases (PI4Ks) generate PI4-phosphate the precursor of regulatory phosphoinositides. No type II PI4K research on the abiotic stress response has previously been reported in plants. A stress-inducible type II PI4K gene, named TaPI4KIIγ, was obtained by de novo transcriptome sequencing of drought-treated wheat (Triticum aestivum). TaPI4KIIγ, localized on the plasma membrane, underwent threonine autophosphorylation, but had no detectable lipid kinase activity. Interaction of TaPI4KIIγ with wheat ubiquitin fusion degradation protein (TaUDF1) indicated that it might be hydrolysed by the proteinase system. Overexpression of TaPI4KIIγ revealed that it could enhance drought and salt stress tolerance during seed germination and seedling growth. A ubdkγ7 mutant, identified as an orthologue of TaPI4KIIγ in Arabidopsis, was sensitive to salt, polyethylene glycol (PEG), and abscisic acid (ABA), and overexpression of TaPI4KIIγ in the ubdkγ7 mutant compensated stress sensitivity. TaPI4KIIγ promoted root growth in Arabidopsis, suggesting that TaPI4KIIγ might enhance stress resistance by improving root growth. Overexpression of TaPI4KIIγ led to an altered expression level of stress-related genes and changes in several physiological traits that made the plants more tolerant to stress. The results provided evidence that overexpression of TaPI4KIIγ could improve drought and salt tolerance.
doi:10.1093/jxb/ert133
PMCID: PMC3741686  PMID: 23682116
Kinase activity; overexpression; PI4K; protein interaction; stress response; Triticum aestivum.
17.  Research on Zheng Classification Fusing Pulse Parameters in Coronary Heart Disease 
This study was conducted to illustrate that nonlinear dynamic variables of Traditional Chinese Medicine (TCM) pulse can improve the performances of TCM Zheng classification models. Pulse recordings of 334 coronary heart disease (CHD) patients and 117 normal subjects were collected in this study. Recurrence quantification analysis (RQA) was employed to acquire nonlinear dynamic variables of pulse. TCM Zheng models in CHD were constructed, and predictions using a novel multilabel learning algorithm based on different datasets were carried out. Datasets were designed as follows: dataset1, TCM inquiry information including inspection information; dataset2, time-domain variables of pulse and dataset1; dataset3, RQA variables of pulse and dataset1; and dataset4, major principal components of RQA variables and dataset1. The performances of the different models for Zheng differentiation were compared. The model for Zheng differentiation based on RQA variables integrated with inquiry information had the best performance, whereas that based only on inquiry had the worst performance. Meanwhile, the model based on time-domain variables of pulse integrated with inquiry fell between the above two. This result showed that RQA variables of pulse can be used to construct models of TCM Zheng and improve the performance of Zheng differentiation models.
doi:10.1155/2013/602672
PMCID: PMC3657409  PMID: 23737839
18.  Genome-Wide Sequence Characterization and Expression Analysis of Major Intrinsic Proteins in Soybean (Glycine max L.) 
PLoS ONE  2013;8(2):e56312.
Water is essential for all living organisms. Aquaporin proteins are the major facilitator of water transport activity through cell membranes of plants including soybean. These proteins are diverse in plants and belong to a large major intrinsic (MIP) protein family. In higher plants, MIPs are classified into five subfamilies including plasma membrane intrinsic proteins (PIP), tonoplast intrinsic proteins (TIP), NOD26-like intrinsic proteins (NIP), small basic intrinsic proteins (SIP), and the recently discovered X intrinsic proteins (XIP). This paper reports genome wide assembly of soybean MIPs, their functional prediction and expression analysis. Using a bioinformatic homology search, 66 GmMIPs were identified in the soybean genome. Phylogenetic analysis of amino acid sequences of GmMIPs divided the large and highly similar multi-gene family into 5 subfamilies: GmPIPs, GmTIPs, GmNIPs, GmSIPs and GmXIPs. GmPIPs consisted of 22 genes and GmTIPs 23, which showed high sequence similarity within subfamilies. GmNIPs contained 13 and GmSIPs 6 members which were diverse. In addition, we also identified a two member GmXIP, a distinct 5th subfamily. GmMIPs were further classified into twelve subgroups based on substrate selectivity filter analysis. Expression analyses were performed for a selected set of GmMIPs using semi-quantitative reverse transcription (semi-RT-qPCR) and qPCR. Our results suggested that many GmMIPs have high sequence similarity but diverse roles as evidenced by analysis of sequences and their expression. It can be speculated that GmMIPs contains true aquaporins, glyceroporins, aquaglyceroporins and mixed transport facilitators.
doi:10.1371/journal.pone.0056312
PMCID: PMC3577755  PMID: 23437113
19.  A Novel Role for Arabidopsis CBL1 in Affecting Plant Responses to Glucose and Gibberellin during Germination and Seedling Development 
PLoS ONE  2013;8(2):e56412.
Glucose and phytohormones such as abscisic acid (ABA), ethylene, and gibberellin (GA) coordinately regulate germination and seedling development. However, there is still inadequate evidence to link their molecular roles in affecting plant responses. Calcium acts as a second messenger in a diverse range of signal transduction pathways. As calcium sensors unique to plants, calcineurin B-like (CBL) proteins are well known to modulate abiotic stress responses. In this study, it was found that CBL1 was induced by glucose in Arabidopsis. Loss-of-function mutant cbl1 exhibited hypersensitivity to glucose and paclobutrazol, a GA biosynthetic inhibitor. Several sugar-responsive and GA biosynthetic gene expressions were altered in the cbl1 mutant. CBL1 protein physically interacted with AKINβ1, the regulatory β subunit of the SnRK1 complex which has a central role in sugar signaling. Our results indicate a novel role for CBL1 in modulating responses to glucose and GA signals.
doi:10.1371/journal.pone.0056412
PMCID: PMC3577912  PMID: 23437128
20.  The Voltage-Dependent Anion Channel 1 (AtVDAC1) Negatively Regulates Plant Cold Responses during Germination and Seedling Development in Arabidopsis and Interacts with Calcium Sensor CBL1 
The voltage-dependent anion channel (VDAC), a highly conserved major mitochondrial outer membrane protein, plays crucial roles in energy metabolism and metabolite transport. However, knowledge about the roles of the VDAC family in plants is limited. In this study, we investigated the expression pattern of VDAC1 in Arabidopsis and found that cold stress promoted the accumulation of VDAC1 transcripts in imbibed seeds and mature plants. Overexpression of VDAC1 reduced tolerance to cold stress in Arabidopsis. Phenotype analysis of VDAC1 T-DNA insertion mutant plants indicated that a vdac1 mutant line had faster germination kinetics under cold treatment and showed enhanced tolerance to freezing. The yeast two-hybrid system revealed that VDAC1 interacts with CBL1, a calcium sensor in plants. Like the vdac1, a cbl1 mutant also exhibited a higher seed germination rate. We conclude that both VDAC1 and CBL1 regulate cold stress responses during seed germination and plant development.
doi:10.3390/ijms14010701
PMCID: PMC3565290  PMID: 23344040
Arabidopsis; voltage-dependent anion channel; cold stress; germination; calcium; interaction protein
21.  Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study 
BMC Bioinformatics  2012;13:331.
Background
Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a challenge to uncover their functions.
Results
We present a computational pipeline for detecting novel lncRNAs from the RNA-Seq data. First, the genome-guided transcriptome reconstruction is used to generate initially assembled transcripts. The possible partial transcripts and artefacts are filtered according to the quantified expression level. After that, novel lncRNAs are detected by further filtering known transcripts and those with high protein coding potential, using a newly developed program called lncRScan. We applied our pipeline to a mouse Klf1 knockout dataset, and discussed the plausible functions of the novel lncRNAs we detected by differential expression analysis. We identified 308 novel lncRNA candidates, which have shorter transcript length, fewer exons, shorter putative open reading frame, compared with known protein-coding transcripts. Of the lncRNAs, 52 large intergenic ncRNAs (lincRNAs) show lower expression level than the protein-coding ones and 13 lncRNAs represent significant differential expression between the wild-type and Klf1 knockout conditions.
Conclusions
Our method can predict a set of novel lncRNAs from the RNA-Seq data. Some of the lncRNAs are showed differentially expressed between the wild-type and Klf1 knockout strains, suggested that those novel lncRNAs can be given high priority in further functional studies.
doi:10.1186/1471-2105-13-331
PMCID: PMC3577497  PMID: 23237380
22.  Uncovering the Salt Response of Soybean by Unraveling Its Wild and Cultivated Functional Genomes Using Tag Sequencing 
PLoS ONE  2012;7(11):e48819.
Soil salinity has very adverse effects on growth and yield of crop plants. Several salt tolerant wild accessions and cultivars are reported in soybean. Functional genomes of salt tolerant Glycine soja and a salt sensitive genotype of Glycine max were investigated to understand the mechanism of salt tolerance in soybean. For this purpose, four libraries were constructed for Tag sequencing on Illumina platform. We identify around 490 salt responsive genes which included a number of transcription factors, signaling proteins, translation factors and structural genes like transporters, multidrug resistance proteins, antiporters, chaperons, aquaporins etc. The gene expression levels and ratio of up/down-regulated genes was greater in tolerant plants. Translation related genes remained stable or showed slightly higher expression in tolerant plants under salinity stress. Further analyses of sequenced data and the annotations for gene ontology and pathways indicated that soybean adapts to salt stress through ABA biosynthesis and regulation of translation and signal transduction of structural genes. Manipulation of these pathways may mitigate the effect of salt stress thus enhancing salt tolerance.
doi:10.1371/journal.pone.0048819
PMCID: PMC3509101  PMID: 23209559
23.  Deficits in LTP Induction by 5-HT2A Receptor Antagonist in a Mouse Model for Fragile X Syndrome 
PLoS ONE  2012;7(10):e48741.
Fragile X syndrome is a common inherited form of mental retardation caused by the lack of fragile X mental retardation protein (FMRP) because of Fmr1 gene silencing. Serotonin (5-HT) is significantly increased in the null mutants of Drosophila Fmr1, and elevated 5-HT brain levels result in cognitive and behavioral deficits in human patients. The serotonin type 2A receptor (5-HT2AR) is highly expressed in the cerebral cortex; it acts on pyramidal cells and GABAergic interneurons to modulate cortical functions. 5-HT2AR and FMRP both regulate synaptic plasticity. Therefore, the lack of FMRP may affect serotoninergic activity. In this study, we determined the involvement of FMRP in the 5-HT modulation of synaptic potentiation with the use of primary cortical neuron culture and brain slice recording. Pharmacological inhibition of 5-HT2AR by R-96544 or ketanserin facilitated long-term potentiation (LTP) in the anterior cingulate cortex (ACC) of WT mice. The prefrontal LTP induction was dependent on the activation of NMDARs and elevation of postsynaptic Ca2+ concentrations. By contrast, inhibition of 5-HT2AR could not restore the induction of LTP in the ACC of Fmr1 knock-out mice. Furthermore, 5-HT2AR inhibition induced AMPA receptor GluR1 subtype surface insertion in the cultured ACC neurons of Fmr1 WT mice, however, GluR1 surface insertion by inhibition of 5-HT2AR was impaired in the neurons of Fmr1KO mice. These findings suggested that FMRP was involved in serotonin receptor signaling and contributed in GluR1 surface expression induced by 5-HT2AR inactivation.
doi:10.1371/journal.pone.0048741
PMCID: PMC3485341  PMID: 23119095
24.  Riluzole-Triggered GSH Synthesis via Activation of Glutamate Transporters to Antagonize Methylmercury-Induced Oxidative Stress in Rat Cerebral Cortex 
Objective. This study was to evaluate the effect of riluzole on methylmercury- (MeHg-) induced oxidative stress, through promotion of glutathione (GSH) synthesis by activating of glutamate transporters (GluTs) in rat cerebral cortex. Methods. Eighty rats were randomly assigned to four groups, control group, riluzole alone group, MeHg alone group, and riluzole + MeHg group. The neurotoxicity of MeHg was observed by measuring mercury (Hg) absorption, pathological changes, and cell apoptosis of cortex. Oxidative stress was evaluated via determining reactive oxygen species (ROS), 8-hydroxy-2-deoxyguanosine (8-OHdG), malondialdehyde (MDAs), carbonyl, sulfydryl, and GSH in cortex. Glutamate (Glu) transport was studied by measuring Glu, glutamine (Gln), mRNA, and protein of glutamate/aspartate transporter (GLAST) and glutamate transporter-1 (GLT-1). Result. (1) MeHg induced Hg accumulation, pathological injury, and apoptosis of cortex; (2) MeHg increased ROS, 8-OHdG, MDA, and carbonyl, and inhibited sulfydryl and GSH; (3) MeHg elevated Glu, decreased Gln, and downregulated GLAST and GLT-1 mRNA expression and protein levels; (4) riluzole antagonized MeHg-induced downregulation of GLAST and GLT-1 function and expression, GSH depletion, oxidative stress, pathological injury, and apoptosis obviously. Conclusion. Data indicate that MeHg administration induced oxidative stress in cortex and that riluzole could antagonize this situation through elevation of GSH synthesis by activating of GluTs.
doi:10.1155/2012/534705
PMCID: PMC3432391  PMID: 22966415
25.  Application of Multilabel Learning Using the Relevant Feature for Each Label in Chronic Gastritis Syndrome Diagnosis 
Background. In Traditional Chinese Medicine (TCM), most of the algorithms are used to solve problems of syndrome diagnosis that only focus on one syndrome, that is, single label learning. However, in clinical practice, patients may simultaneously have more than one syndrome, which has its own symptoms (signs). Methods. We employed a multilabel learning using the relevant feature for each label (REAL) algorithm to construct a syndrome diagnostic model for chronic gastritis (CG) in TCM. REAL combines feature selection methods to select the significant symptoms (signs) of CG. The method was tested on 919 patients using the standard scale. Results. The highest prediction accuracy was achieved when 20 features were selected. The features selected with the information gain were more consistent with the TCM theory. The lowest average accuracy was 54% using multi-label neural networks (BP-MLL), whereas the highest was 82% using REAL for constructing the diagnostic model. For coverage, hamming loss, and ranking loss, the values obtained using the REAL algorithm were the lowest at 0.160, 0.142, and 0.177, respectively. Conclusion. REAL extracts the relevant symptoms (signs) for each syndrome and improves its recognition accuracy. Moreover, the studies will provide a reference for constructing syndrome diagnostic models and guide clinical practice.
doi:10.1155/2012/135387
PMCID: PMC3376946  PMID: 22719781

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