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1.  Comparison between better and poorly differentiated locally advanced gastric cancer in preoperative chemotherapy: a retrospective, comparative study at a single tertiary care institute 
Background
Gastric cancer is the third leading cause of cancer-related mortality in China, and the long-term survival for locally advanced gastric cancer is very poor. Simple surgery cannot yield an ideal result because of the high recurrence rate after tumor resection. Preoperative chemotherapy could help to reduce tumor volume, improve the R0 resection rate (no residual tumor after surgery), and decrease the risk of local tumor recurrence. The aim of this study was to evaluate the influence of pathological differentiation in the effect of preoperative chemotherapy for patients with locally advanced gastric cancer.
Methods
Patients with locally advanced gastric cancer (n = 32) received preoperative chemotherapy under the XELOX (capecitabine plus oxaliplatin) regimen. According to pathological examination, patients’ tumors were classified into better (well and moderate) and poorly differentiated (lower differentiated and undifferentiated) groups, and the clinical response rate, type of gastrectomy, and negative tumor residual rate were compared between the two groups of patients. Morphological changes and toxic reactions were monitored after chemotherapy.
Results
The results showed that the clinical response rate in the better differentiated group was significantly higher than that in the poorly differentiated group (100% versus 25%, P = 0.000). The partial gastrectomy rate in the better differentiated group was significantly higher than that in the poorly differentiated group (87.5% versus 25% P = 0.000). A significant shrinking of tumor and necrosis of tumor tissues caused by chemotherapy could be observed.
Conclusions
In conclusion, the better differentiated group with locally advanced gastric cancer is suitable for preoperative chemotherapy under the XELOX regimen, and as a result of effective preoperative chemotherapy, much more gastric tissue can be preserved for the better differentiated group.
doi:10.1186/1477-7819-12-280
PMCID: PMC4177253  PMID: 25200958
locally advanced gastric cancer; pathological differentiation; preoperative chemotherapy; surgery
2.  Oral health survey and oral health questionnaire for high school students in Tibet, China 
Head & Face Medicine  2014;10:17.
Objectives
The aim of this study is to identify the oral health status as well as oral health practices and access for care of graduating senior high school Tibetan students in Shannan prefecture of Tibet.
Methods
Based on standards of the 3rd Chinese National Oral Epidemiological Survey and WHO Oral Health Surveys, 1907 graduating students from three senior high schools were examined for caries, periodontitis, dental fluorosis, and oral hygiene status. The questionnaire to the students addressed oral health practices and present access to oral medical services.
Results
Dental caries prevalence (39.96%) and mean DMFT (0.97) were high in Tibetan students. In community periodontal indexes, the detection rate of gingivitis and dental calculus were 59.50% and 62.64%, respectively. Oral hygiene index-simplified was 0.69, with 0.36 and 0.33 in debris index-simplified and calculus index-simplified, respectively. Community dental fluorosis index was 0.29, with 8.13% in prevalence rate. The questionnaire showed students had poor oral health practices and unawareness for their needs for oral health services. It was also noted that the local area provides inadequate oral medical services.
Conclusions
Tibetan students had higher prevalence of dental diseases and lower awareness of oral health needs. The main reasons were geographical environment, dietary habit, students’ attitude to oral health, and lack of oral health promotion and education. Oral health education and local dentists training should be strengthened to get effective prevention of dental diseases.
doi:10.1186/1746-160X-10-17
PMCID: PMC4049488  PMID: 24884668
Oral health; Questionnaire; Epidemiology; Tibet; Plateau
3.  Genome-Wide Analysis of DNA Methylation in Five Tissues of Zhikong Scallop, Chlamys farreri 
PLoS ONE  2014;9(1):e86232.
DNA methylation plays a vital role in tissue development and differentiation in eukaryotes. Epigenetic studies have been seldom conducted in the extremely diverse and evolutionarily highly successful bilaterian lineage Mollusca. In the present study, we conducted the genome-wide profiling of DNA methylation for five tissues of a bivalve mollusc, Chlamys farreri using the methylation-sensitive amplification polymorphism (MSAP) technique. The methylation levels were quite similar among tissues, ranging from 20.9% to 21.7%. CG methylation was the dominant type (14.9%–16.5%) in the C. farreri genome, but CHG methylation also accounted for a substantial fraction of total methylation (5.1%–6.3%). Relatively high methylation diversity was observed within tissues. Methylation differentiation between tissues was evaluated and 460 tissue-specific epiloci were identified. Kidney differs from the other tissues in DNA methylation profiles. Our study presents the first look at the tissue-specific DNA methylation patterns in a bivalve mollusc and represents an initial step towards understanding of epigenetic regulatory mechanism underlying tissue development and differentiation in bivalves.
doi:10.1371/journal.pone.0086232
PMCID: PMC3891877  PMID: 24454962
4.  Large-Scale Development of Gene-Associated Single-Nucleotide Polymorphism Markers for Molluscan Population Genomic, Comparative Genomic, and Genome-Wide Association Studies 
Mollusca is the second most diverse group of animals in the world. Despite their perceived importance, omics-level studies have seldom been applied to this group of animals largely due to a paucity of genomic resources. Here, we report the first large-scale gene-associated marker development and evaluation for a bivalve mollusc, Chlamys farreri. More than 21,000 putative single-nucleotide polymorphisms (SNPs) were identified from the C. farreri transcriptome. Primers and probes were designed and synthesized for 4500 SNPs, and 1492 polymorphic markers were successfully developed using a high-resolution melting genotyping platform. These markers are particularly suitable for population genomic analysis due to high polymorphism within and across populations, a low frequency of null alleles, and conformation to neutral expectations. Unexpectedly, high cross-species transferability was observed, suggesting that the transferable SNPs may largely represent ancestral genetic variations that have been preserved differentially among subfamilies of Pectinidae. Gene annotations were available for 73% of the markers, and 65% could be anchored to the recently released Pacific oyster genome. Large-scale association analysis revealed key candidate genes responsible for scallop growth regulation, and provided markers for further genetic improvement of C. farreri in breeding programmes.
doi:10.1093/dnares/dst048
PMCID: PMC3989488  PMID: 24277739
mollusca; single-nucleotide polymorphism (SNP); transcriptome; high resolution melting (HRM); genome-wide association (GWAS)
5.  Validation of the European Organization for Research and Treatment of Cancer cervical cancer module for Chinese patients with cervical cancer 
Purpose
The aim of our study was to assess, for the first time, the validity, reliability, and acceptability of the European Organization for Research and Treatment of Cancer (EORTC) Quality of Life questionnaire (QLQ) cervical cancer module (CX24) in Chinese cervical cancer patients.
Patients and methods
One hundred fifteen outpatients with cervical cancer in the First Affiliated Hospital of Xinxiang Medical University from May 2013 to July 2013 were included in this study. All participants self-administered the EORTC QLQ-CX24 and the core questionnaire (EORTC QLQ-C30), and the Karnofsky Performance Scale was performed to evaluate scores. Data were analyzed with Cronbach’s α coefficient, Pearson correlation test, multitrait scaling analysis, and Mann–Whitney U test.
Results
Scale reliability was confirmed by Cronbach’s α coefficients for internal consistency, which ranged from 0.71 to 0.82. Convergent and discriminant validity were confirmed by multitrait scaling analysis, which revealed three (3.4%) scaling errors for symptom experience scales and zero (0%) for body image as well as sexual/vaginal functioning scales. Higher missing value rate occurred in sexuality-related items. The clinical validity of the Chinese version of the EORTC QLQ-CX24 was demonstrated by the ability to discriminate among patients in different International Federation of Gynecology and Obstetrics stages.
Conclusion
The EORTC QLQ-CX24 was proved to be a reliable and valid instrument with which to measure the quality of life in cervical cancer patients in the People’s Republic of China.
doi:10.2147/PPA.S52498
PMCID: PMC3804534  PMID: 24204125
cervical cancer; quality of life; EORTC QLQ-CX24; People’s Republic of China
6.  The MAT Locus Genes Play Different Roles in Sexual Reproduction and Pathogenesis in Fusarium graminearum 
PLoS ONE  2013;8(6):e66980.
Sexual reproduction plays a critical role in the infection cycle of Fusarium graminearum because ascospores are the primary inoculum. As a homothallic ascomycete, F. graminearum contains both the MAT1-1 and MAT1-2-1 loci in the genome. To better understand their functions and regulations in sexual reproduction and pathogenesis, in this study we assayed the expression, interactions, and mutant phenotypes of individual MAT locus genes. Whereas the expression of MAT1-1-1 and MAT12-1 rapidly increased after perithecial induction and began to decline after 1 day post-perithecial induction (dpi), the expression of MAT1-1-2 and MAT1-1-3 peaked at 4 dpi. MAT1-1-2 and MAT1-1-3 had a similar expression profile and likely are controlled by a bidirectional promoter. Although none of the MAT locus genes were essential for perithecium formation, all of them were required for ascosporogenesis in self-crosses. In outcrosses, the mat11-1-2 and mat11-1-3 mutants were fertile but the mat1-1-1 and mat1-2-1 mutants displayed male- and female-specific defects, respectively. The mat1-2-1 mutant was reduced in FgSO expression and hyphal fusion. Mat1-1-2 interacted with all other MAT locus transcription factors, suggesting that they may form a protein complex during sexual reproduction. Mat1-1-1 also interacted with FgMcm1, which may play a role in controlling cell identity and sexual development. Interestingly, the mat1-1-1 and mat1-2-1 mutants were reduced in virulence in corn stalk rot assays although none of the MAT locus genes was important for wheat infection. The MAT1-1-1 and MAT1-2-1 genes may play a host-specific role in colonization of corn stalks.
doi:10.1371/journal.pone.0066980
PMCID: PMC3691137  PMID: 23826182
7.  Expression of Lewis y antigen and integrin αv, β3 in ovarian cancer and their relationship with chemotherapeutic drug resistance 
Objective
This study investigates the expression of Lewis y antigen, integrin αv, β3 in epithelial ovarian cancer tissues. We further evaluate the relationship between their expression and chemotherapy resistance of ovarian cancer and its possible clinical significance.
Methods
Tissues of 92 patients with ovarian cancer meeting the inclusion criteria with complete follow-up data were enrolled and divided into chemotherapy resistant group and sensitive group. The expression and relationship of Lewis y antigen and integrin αv, β3 are assessed in paraffin sections using immunohistochemistry and double-labeling immunofluorescence method. Multivariate logistic regression analysis was used to investigate the relationship between age, clinical stage, differentiation, histologic subtype, Lewis y antigen and integrin αv, β3 expression in ovarian cancer patients.
Results
The expression rates of Lewis y antigen and integrin αv in the resistant group, significantly higher than the rates found in the sensitive group (p <0.05). Multivariate analysis showed that the expression of Lewis y antigen, integrin αv and ovarian cancer’s clinical stage were independent, drug resistance-related risk factors. The expression levels of Lewis y antigen and integrin αv, β3 were positively correlated with each other.
Conclusions
A close correlation between Lewis y antigen, integrin αv, β3 and ovarian cancer was observed. Lewis y antigen can influence the biological behavior of a tumor cell as an important composition of integrin αv, β3 by some signal pathway. And the expression of Lewis y antigen, integrin αv and ovarian cancer’s clinical stage are both independent, drug resistance-related risk factors.
doi:10.1186/1756-9966-32-36
PMCID: PMC3699420  PMID: 23725446
Ovarian Cancer; Lewis y Antigen; Integrin αv, β3; Chemotherapeutic Drug Resistance
8.  Chemoresistance Is Associated with MUC1 and Lewis y Antigen Expression in Ovarian Epithelial Cancers 
Objective
The aim of this study was to analyze the correlation and clinical significance between the expression of Mucin-1 (MUC1) and the Lewis y antigen with chemoresistance in ovarian epithelial cancers.
Methods
Ovarian cancer patients (n = 92) treated at our hospital from May 2005 to July 2009 were divided, according to their treatment and follow-up outcomes, into a resistant group (n = 37) or sensitive group (n = 55). The expression of MUC1 and Lewis y antigen in ovarian cancer tissues was detected using immunohistochemistry and correlated with chemoresistance.
Results
The positive rates of MUC1 and Lewis y antigen in the resistant group were both 91.89%, significantly higher than their positive rates in the sensitive group (65.45% and 69.09%, respectively, and both p < 0.05). MUC1 or Lewis y expression and the pathological stage of the tissue were independent risk factors for chemoresistance (all p < 0.05).
Conclusion
The increased expression of MUC1 and the Lewis y antigen is a significant risk factor for chemoresistance in patients with ovarian epithelial cancer.
doi:10.3390/ijms140611024
PMCID: PMC3709716  PMID: 23708102
ovarian epithelial cancer; MUC1; Lewis y antigen; chemoresistance; immunohistochemistry
9.  Transcriptome Sequencing of Zhikong Scallop (Chlamys farreri) and Comparative Transcriptomic Analysis with Yesso Scallop (Patinopecten yessoensis) 
PLoS ONE  2013;8(5):e63927.
Background
Bivalves play an important role in the ecosystems they inhabit and represent an important food source all over the world. So far limited genetic research has focused on this group of animals largely due to the lack of sufficient genetic or genomic resources. Here, we performed de novo transcriptome sequencing to produce the most comprehensive expressed sequence tag resource for Zhikong scallop (Chlamys farreri), and conducted the first transcriptome comparison for scallops.
Results
In a single 454 sequencing run, 1,033,636 reads were produced and then assembled into 26,165 contigs. These contigs were then clustered into 24,437 isotigs and further grouped into 20,056 isogroups. About 47% of the isogroups showed significant matches to known proteins based on sequence similarity. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified through Gene ontology (GO) and KEGG pathway analyses. Transcriptome comparison with Yesso scallop (Patinopecten yessoensis) revealed similar patterns of GO representation. Moreover, 38 putative fast-evolving genes were identified through analyzing the orthologous gene pairs between the two scallop species. More than 46,000 single nucleotide polymorphisms (SNPs) and 350 simple sequence repeats (SSRs) were also detected.
Conclusion
Our study provides the most comprehensive transcriptomic resource currently available for C. farreri. Based on this resource, we performed the first large-scale transcriptome comparison between the two scallop species, C. farreri and P. yessoensis, and identified a number of putative fast-evolving genes, which may play an important role in scallop speciation and/or local adaptation. A large set of single nucleotide polymorphisms and simple sequence repeats were identified, which are ready for downstream marker development. This transcriptomic resource should lay an important foundation for future genetic or genomic studies on C. farreri.
doi:10.1371/journal.pone.0063927
PMCID: PMC3646770  PMID: 23667690
10.  The AMT1 Arginine Methyltransferase Gene Is Important for Plant Infection and Normal Hyphal Growth in Fusarium graminearum 
PLoS ONE  2012;7(5):e38324.
Arginine methylation of non-histone proteins by protein arginine methyltransferase (PRMT) has been shown to be important for various biological processes from yeast to human. Although PRMT genes are well conserved in fungi, none of them have been functionally characterized in plant pathogenic ascomycetes. In this study, we identified and characterized all of the four predicted PRMT genes in Fusarium graminearum, the causal agent of Fusarium head blight of wheat and barley. Whereas deletion of the other three PRMT genes had no obvious phenotypes, the Δamt1 mutant had pleiotropic defects. AMT1 is a predicted type I PRMT gene that is orthologous to HMT1 in Saccharomyces cerevisiae. The Δamt1 mutant was slightly reduced in vegetative growth but normal in asexual and sexual reproduction. It had increased sensitivities to oxidative and membrane stresses. DON mycotoxin production and virulence on flowering wheat heads also were reduced in the Δamt1 mutant. The introduction of the wild-type AMT1 allele fully complemented the defects of the Δamt1 mutant and Amt1-GFP fusion proteins mainly localized to the nucleus. Hrp1 and Nab2 are two hnRNPs in yeast that are methylated by Hmt1 for nuclear export. In F. graminearum, AMT1 is required for the nuclear export of FgHrp1 but not FgNab2, indicating that yeast and F. graminearum differ in the methylation and nucleo-cytoplasmic transport of hnRNP components. Because AMT2 also is a predicted type I PRMT with limited homology to yeast HMT1, we generated the Δamt1 Δamt2 double mutants. The Δamt1 single and Δamt1 Δamt2 double mutants had similar defects in all the phenotypes assayed, including reduced vegetative growth and virulence. Overall, data from this systematic analysis of PRMT genes suggest that AMT1, like its ortholog in yeast, is the predominant PRMT gene in F. graminearum and plays a role in hyphal growth, stress responses, and plant infection.
doi:10.1371/journal.pone.0038324
PMCID: PMC3365026  PMID: 22693618
11.  Network Analysis of Oyster Transcriptome Revealed a Cascade of Cellular Responses during Recovery after Heat Shock 
PLoS ONE  2012;7(4):e35484.
Oysters, as a major group of marine bivalves, can tolerate a wide range of natural and anthropogenic stressors including heat stress. Recent studies have shown that oysters pretreated with heat shock can result in induced heat tolerance. A systematic study of cellular recovery from heat shock may provide insights into the mechanism of acquired thermal tolerance. In this study, we performed the first network analysis of oyster transcriptome by reanalyzing microarray data from a previous study. Network analysis revealed a cascade of cellular responses during oyster recovery after heat shock and identified responsive gene modules and key genes. Our study demonstrates the power of network analysis in a non-model organism with poor gene annotations, which can lead to new discoveries that go beyond the focus on individual genes.
doi:10.1371/journal.pone.0035484
PMCID: PMC3329459  PMID: 22530030
12.  Ethyl 2-[4,5-bis­(butyl­sulfan­yl)-1,3-dithiol-2-yl­idene]-1,3-dithiolo[4,5-c]pyrrole-4-carboxyl­ate 
In the title mol­ecule, C19H25NO2S6, the butyl chains are each disordered over two conformations in a 0.689 (10):0.311 (10) ratio. In the crystal, pairs of N—H⋯O hydrogen bonds link mol­ecules into centrosymmetric dimers. Short S⋯S contacts of 3.553 (4) Å are observed.
doi:10.1107/S1600536812015309
PMCID: PMC3344526  PMID: 22590288
13.  1-(1,3-Benzothia­zol-2-yl)-3-phenyl-2-pyrazoline 
In the title compound, C16H13N3S, the pyrazoline ring forms dihedral angles of 6.89 (14) and 4.96 (11)° with the benzene ring and the benzothia­zole group, respectively. In the crystal, weak C—H⋯N inter­actions link the mol­ecules into chains extending along the b-axis direction.
doi:10.1107/S1600536812013219
PMCID: PMC3344177  PMID: 22606180
14.  Transcriptome Sequencing and Characterization for the Sea Cucumber Apostichopus japonicus (Selenka, 1867) 
PLoS ONE  2012;7(3):e33311.
Background
Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquaculture species in Asian countries. Many efforts have been devoted to increasing the number of expressed sequence tags (ESTs) for A. japonicus, but a comprehensive characterization of its transcriptome remains lacking. Here, we performed the large-scale transcriptome profiling and characterization by pyrosequencing diverse cDNA libraries from A. japonicus.
Results
In total, 1,061,078 reads were obtained by 454 sequencing of eight cDNA libraries representing different developmental stages and adult tissues in A. japonicus. These reads were assembled into 29,666 isotigs, which were further clustered into 21,071 isogroups. Nearly 40% of the isogroups showed significant matches to known proteins based on sequence similarity. Gene ontology (GO) and KEGG pathway analyses recovered diverse biological functions and processes. Candidate genes that were potentially involved in aestivation were identified. Transcriptome comparison with the sea urchin Strongylocentrotus purpuratus revealed similar patterns of GO term representation. In addition, 4,882 putative orthologous genes were identified, of which 202 were not present in the non-echinoderm organisms. More than 700 simple sequence repeats (SSRs) and 54,000 single nucleotide polymorphisms (SNPs) were detected in the A. japonicus transcriptome.
Conclusion
Pyrosequencing was proven to be efficient in rapidly identifying a large set of genes for the sea cucumber A. japonicus. Through the large-scale transcriptome sequencing as well as public EST data integration, we performed a comprehensive characterization of the A. japonicus transcriptome and identified candidate aestivation-related genes. A large number of potential genetic markers were also identified from the A. japonicus transcriptome. This transcriptome resource would lay an important foundation for future genetic or genomic studies on this species.
doi:10.1371/journal.pone.0033311
PMCID: PMC3299772  PMID: 22428017
15.  Lewis y Regulate Cell Cycle Related Factors in Ovarian Carcinoma Cell RMG-I in Vitro via ERK and Akt Signaling Pathways 
Objective
To investigate the effect of Lewis y overexpression on the expression of proliferation-related factors in ovarian cancer cells.
Methods
mRNA levels of cyclins, CDKs, and CKIs were measured in cells before and after transfection with the α1,2-fucosyltransferase gene by real-time PCR, and protein levels of cyclins, CDKs and CKIs were determined in cells before and after gene transfection by Western blot.
Results
Lewis y overexpression led to an increase in both mRNA and protein expression levels of cyclin A, cyclin D1 and cyclin E in ovarian cancer cells, decrease in both mRNA and protein expression levels of p16 and p21, and decrease of p27 at only the protein expression level without change in its mRNA level. There were no differences in proteins and the mRNA levels of CDK2, CDK4 and CDK6 before and after gene transfection. Anti-Lewis y antibody, ERK and PI3K pathway inhibitors PD98059 and LY294002 reduced the difference in cyclin and CKI expression caused by Lewis y overexpression.
Conclusion
Lewis y regulates the expression of cell cycle-related factors through ERK/MAPK and PI3K/Akt signaling pathways to promote cell proliferation.
doi:10.3390/ijms13010828
PMCID: PMC3269723  PMID: 22312289
Lewis(y) antigen; cell cycle; cyclin; cyclin-dependent kinases; cyclin-dependent kinase inhibitors
16.  Elevated Levels of Lewis Y and Integrin α5β1 Correlate with Chemotherapeutic Drug Resistance in Epithelial Ovarian Carcinoma 
Objective
To measure Lewis y and integrin α5β1 expression in epithelial ovarian carcinoma and to correlate the levels of these molecules with ovarian carcinoma chemotherapy and prognosis.
Methods
The study population included 34 ovarian carcinoma patients with chemotherapeutic drug-resistance, six partially drug-sensitive cases, and 52 drug-sensitive cases (92 total). Immunochemistry was used to determine expression of Lewis y antigen and integrin α5β1 in ovarian carcinoma tissues, and correlation of these molecules with chemotherapy resistance was further investigated, Multi-factor logistic regression analysis was applied to investigate: age, surgical stage, grade, subtype of patient cases, metastasis of lymph nodes, residual tumor size, expression levels of Lewis y antigen and integrin α5β1 correlation with ovarian carcinoma chemotherapy resistance.
Results
The expression rates of Lewis y antigen and integrins α5 and β1 were significantly greater in the drug-resistant group (91.17%, 85.29%, 88.24%) than the partially sensitive (50.00%, 33.33%, 50.00%) or sensitive groups (61.54%, 57.69%, 55.77%). Binary logistic regression analysis revealed that surgical stage, residual tumor size, and expression of integrin α5 and Lewis y in ovarian carcinoma tissues were independent risk factors for chemotherapeutic drug resistance.
Conclusions
Overexpression of Lewis y and integrin α5 are strong risk factors for chemotherapeutic drug resistance in ovarian carcinoma patients.
doi:10.3390/ijms131215588
PMCID: PMC3546651  PMID: 23443083
integrins; Lewis y antigen; ovarian caricinoma; chemoresistance
17.  Functional Analysis of the Kinome of the Wheat Scab Fungus Fusarium graminearum 
PLoS Pathogens  2011;7(12):e1002460.
As in other eukaryotes, protein kinases play major regulatory roles in filamentous fungi. Although the genomes of many plant pathogenic fungi have been sequenced, systematic characterization of their kinomes has not been reported. The wheat scab fungus Fusarium graminearum has 116 protein kinases (PK) genes. Although twenty of them appeared to be essential, we generated deletion mutants for the other 96 PK genes, including 12 orthologs of essential genes in yeast. All of the PK mutants were assayed for changes in 17 phenotypes, including growth, conidiation, pathogenesis, stress responses, and sexual reproduction. Overall, deletion of 64 PK genes resulted in at least one of the phenotypes examined, including three mutants blocked in conidiation and five mutants with increased tolerance to hyperosmotic stress. In total, 42 PK mutants were significantly reduced in virulence or non-pathogenic, including mutants deleted of key components of the cAMP signaling and three MAPK pathways. A number of these PK genes, including Fg03146 and Fg04770 that are unique to filamentous fungi, are dispensable for hyphal growth and likely encode novel fungal virulence factors. Ascospores play a critical role in the initiation of wheat scab. Twenty-six PK mutants were blocked in perithecia formation or aborted in ascosporogenesis. Additional 19 mutants were defective in ascospore release or morphology. Interestingly, F. graminearum contains two aurora kinase genes with distinct functions, which has not been reported in fungi. In addition, we used the interlog approach to predict the PK-PK and PK-protein interaction networks of F. graminearum. Several predicted interactions were verified with yeast two-hybrid or co-immunoprecipitation assays. To our knowledge, this is the first functional characterization of the kinome in plant pathogenic fungi. Protein kinase genes important for various aspects of growth, developmental, and infection processes in F. graminearum were identified in this study.
Author Summary
Fusarium head blight caused by Fusarium graminearum is one of the most important diseases on wheat and barley. Although protein kinases are known to play major regulatory roles in fungi, systematic characterization of fungal kinomes has not been reported in plant pathogens. In this study we generated deletion mutants for 96 protein kinase genes. All of the resulting knockout mutants were assayed for changes in 17 phenotypes, including growth, reproduction, stress responses, and plant infection. Overall, deletion of 64 kinase genes resulted in at least one of the phenotypes examined. In total, 42 kinase mutants were significantly reduced in virulence or non-pathogenic. A number of these protein kinase genes, including two that are unique to filamentous fungi, are dispensable for hyphal growth and likely encode novel fungal virulence factors. Ascospores are the primary inoculum for wheat scab. We identified 26 mutants blocked in ascospore. We also used the in silico approach to predict the kinase-kinase interactions and verified some of them by yeast two-hybrid or co-IP assays. Overall, in this study we functionally characterize the kinome of F. graminearum. Protein kinase genes that are important for various aspects of growth, developmental, and plant infection processes were identified.
doi:10.1371/journal.ppat.1002460
PMCID: PMC3245316  PMID: 22216007
18.  (E)-Methyl 3-(1H-indol-3-yl)acrylate 
In the title compound, C12H11NO2, the indole and methyl acrylate mean planes are inclined at an angle of 10.6 (1)°. In the crystal, N—H⋯π inter­actions link mol­ecules into chains along [010] and weak inter­molecular C—H⋯O hydrogen bonds further consolidate the crystal packing.
doi:10.1107/S1600536811046745
PMCID: PMC3238944  PMID: 22199793
19.  (E)-Methyl 3-(1H-indol-2-yl)acrylate 
The title compound, C12H11NO2, is close to being planar (r.m.s. deviation for the non-H atoms = 0.033 Å). In the crystal, mol­ecules are linked by N—H⋯O hydrogen bonds, generating C(7) chains running along the b axis. A weak C—H⋯O interaction helps to establish the packing.
doi:10.1107/S1600536811030121
PMCID: PMC3213627  PMID: 22091204
20.  2,3-Bis(ethyl­sulfan­yl)-1,4,5,8-tetra­thia­fulvalene-6,7-dicarbonitrile 
In the title compound, C12H10N2S6, all non-H atoms, except for those in the ethyl groups, lie in the same non-crystallographic plane, with a r.m.s. deviation of 0.0366 (5) Å. In the crystal structure, mol­ecules are linked through weak C—H⋯N hydrogen bonds between methyl and cyano groups, forming centrosymmetric dimers. The dimers are arranged along the a axis, due to inter­molecular N⋯S [3.337 (4) Å] inter­actions.
doi:10.1107/S1600536811028601
PMCID: PMC3213538  PMID: 22091115
21.  Methyl 3-(1H-indol-3-yl)propano­ate 
The mol­ecule of the title compound, C12H13NO2, adopts an essentially planar conformation (r.m.s. deviation = 0.057 Å). In the crystal, the mol­ecules are linked by inter­molecular N—H⋯O hydrogen bonds, generating chains along [201].
doi:10.1107/S1600536811028595
PMCID: PMC3213562  PMID: 22091139
22.  Transcriptome Sequencing and De Novo Analysis for Yesso Scallop (Patinopecten yessoensis) Using 454 GS FLX 
PLoS ONE  2011;6(6):e21560.
Background
Bivalves comprise 30,000 extant species, constituting the second largest group of mollusks. However, limited genetic research has focused on this group of animals so far, which is, in part, due to the lack of genomic resources. The advent of high-throughput sequencing technologies enables generation of genomic resources in a short time and at a minimal cost, and therefore provides a turning point for bivalve research. In the present study, we performed de novo transcriptome sequencing to first produce a comprehensive expressed sequence tag (EST) dataset for the Yesso scallop (Patinopecten yessoensis).
Results
In a single 454 sequencing run, 805,330 reads were produced and then assembled into 32,590 contigs, with about six-fold sequencing coverage. A total of 25,237 unique protein-coding genes were identified from a variety of developmental stages and adult tissues based on sequence similarities with known proteins. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in growth, reproduction and stress/immune-response were identified. More than 49,000 single nucleotide polymorphisms (SNPs) and 2,700 simple sequence repeats (SSRs) were also detected.
Conclusion
Our data provide the most comprehensive transcriptomic resource currently available for P. yessoensis. Candidate genes potentially involved in growth, reproduction, and stress/immunity-response were identified, and are worthy of further investigation. A large number of SNPs and SSRs were also identified and ready for marker development. This resource should lay an important foundation for future genetic or genomic studies on this species.
doi:10.1371/journal.pone.0021560
PMCID: PMC3123371  PMID: 21720557
23.  2-[4,5-Bis(butyl­sulfan­yl)-1,3-dithiol-2-yl­idene]-5-methyl-5H-1,3-dithiolo[4,5-c]pyrrole-4-carbaldehyde 
In the title compound, C18H23NOS6, the dithiol­opyrrole ring is almost planar [r.m.s. deviation = 0.044 (3) Å] and makes a dihedral angle of 25.11 (7)° with the dithiole ring. In the crystal, pairs of neighboring mol­ecules are connected by weak inter­molecular C—H⋯O inter­actions. These dimers are further linked into a chain along [110] by C—H⋯O inter­actions.
doi:10.1107/S160053681004910X
PMCID: PMC3011525  PMID: 21589623
24.  2,3-(3,6,9-Trioxaundecane-1,11-diyl­disulfan­yl)-1,4,5,8-tetra­thia­fulvalene-6,7-dicarbonitrile 
In the title compound, C16H16N2O3S6, the two five-membered rings form a dihedral angle of 7.86 (9)°. Weak C—H⋯N hydrogen bonds link the mol­ecules to form a chain along c; the chains are further connected by weak C—H⋯O hydrogen bonds to form a three-dimensional supra­molecular network.
doi:10.1107/S1600536810017587
PMCID: PMC2979555  PMID: 21579460
25.  4,6,7,9,10,12,13,15,16,18-Decahydro-1,3-dithiolo[4,5-l][1,4,7,10,15]trioxadithia­cyclo­hepta­decine-2-thione 
The title compound, C13H20O3S5, is bis­ected by a crystallographic twofold rotation axis, which relates the two halves of the mol­ecule to one another: one S, one C and one O atom lie on the axis. The thione S atom lies in the plane of the five-membered rings with an r.m.s. deviation of 0.0042 (5) Å. Parts of the 17-membered macrocycle were refined using a two-part disorder model [occupancies of 0.553 (14) and 0.447 (14)]. There are no noteworthy inter­molecular inter­actions.
doi:10.1107/S1600536810016946
PMCID: PMC2979504  PMID: 21579425

Results 1-25 (32)