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1.  Soybean (Glycine max) SWEET gene family: insights through comparative genomics, transcriptome profiling and whole genome re-sequence analysis 
BMC Genomics  2015;16(1):520.
Background
SWEET (MtN3_saliva) domain proteins, a recently identified group of efflux transporters, play an indispensable role in sugar efflux, phloem loading, plant-pathogen interaction and reproductive tissue development. The SWEET gene family is predominantly studied in Arabidopsis and members of the family are being investigated in rice. To date, no transcriptome or genomics analysis of soybean SWEET genes has been reported.
Results
In the present investigation, we explored the evolutionary aspect of the SWEET gene family in diverse plant species including primitive single cell algae to angiosperms with a major emphasis on Glycine max. Evolutionary features showed expansion and duplication of the SWEET gene family in land plants. Homology searches with BLAST tools and Hidden Markov Model-directed sequence alignments identified 52 SWEET genes that were mapped to 15 chromosomes in the soybean genome as tandem duplication events. Soybean SWEET (GmSWEET) genes showed a wide range of expression profiles in different tissues and developmental stages. Analysis of public transcriptome data and expression profiling using quantitative real time PCR (qRT-PCR) showed that a majority of the GmSWEET genes were confined to reproductive tissue development. Several natural genetic variants (non-synonymous SNPs, premature stop codons and haplotype) were identified in the GmSWEET genes using whole genome re-sequencing data analysis of 106 soybean genotypes. A significant association was observed between SNP-haplogroup and seed sucrose content in three gene clusters on chromosome 6.
Conclusion
Present investigation utilized comparative genomics, transcriptome profiling and whole genome re-sequencing approaches and provided a systematic description of soybean SWEET genes and identified putative candidates with probable roles in the reproductive tissue development. Gene expression profiling at different developmental stages and genomic variation data will aid as an important resource for the soybean research community and can be extremely valuable for understanding sink unloading and enhancing carbohydrate delivery to developing seeds for improving yield.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1730-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1730-y
PMCID: PMC4499210  PMID: 26162601
SWEET; Effluxer; Sugar transport; Sink; Whole genome re-sequencing; Soybean
2.  Compound antimalarial ethosomal cataplasm: preparation, evaluation, and mechanism of penetration enhancement 
Malaria is still a serious public health problem in some parts of the world. The problems of recurrence and drug resistance are increasingly more serious. Thus, it is necessary to develop a novel antimalarial agent. The objectives of this study were to construct a novel compound antimalarial transdermal nanosystem–ethosomal cataplasm, to investigate its characteristics and efficiency, and to systematically explore the penetration-enhancing mechanisms of ethosomal cataplasm. Artesunate-loaded ethosomes and febrifugine-loaded ethosomes were prepared, and their characteristics were evaluated. Drug-loaded ethosomes were incorporated in the matrix of cataplasm to form the compound antimalarial ethosomal cataplasm. With the help of ethosomal technology, the accumulated permeation quantity of artesunate significantly increased at 8 hours after administration, which was 1.57 times as much as that of conventional cataplasm. Soon after administration, the ethosomal cataplasm could make a large quantity of antimalarial drug quickly penetrate through skin, then the remaining drug in the ethosomal cataplasm could be steadily released. These characteristics of ethosomal cataplasm are favorable for antimalarial drugs to kill Plasmodium spp. quickly and prevent the resurgence of Plasmodium spp. As expected, the ethosomal cataplasm showed good antimalarial efficiency in this experiment. The negative conversion rates were 100% and the recurrence rates were 0% at all dosages. The mechanism of penetration enhancement of the ethosomal cataplasm was systematically explored using an optics microscope, polarization microscope, and transmission electron microscopy. The microstructure, ultrastructure, and birefringent structure in skin were observed. Data obtained in this study showed that the application of ethosomal technology to antimalarial cataplasm could improve the transdermal delivery of drug, enhance the efficacy, and facilitate practical application in clinic.
doi:10.2147/IJN.S83402
PMCID: PMC4494185  PMID: 26170661
ethosomes; transdermal drug-delivery systems; artesunate; febrifugine
3.  Overexpression of the Large-Conductance, Ca2+-Activated K+ (BK) Channel Shortens Action Potential Duration in HL-1 Cardiomyocytes 
PLoS ONE  2015;10(6):e0130588.
Long QT syndrome is characterized by a prolongation of the interval between the Q wave and the T wave on the electrocardiogram. This abnormality reflects a prolongation of the ventricular action potential caused by a number of genetic mutations or a variety of drugs. Since effective treatments are unavailable, we explored the possibility of using cardiac expression of the large-conductance, Ca2+-activated K+ (BK) channel to shorten action potential duration (APD). We hypothesized that expression of the pore-forming α subunit of human BK channels (hBKα) in HL-1 cells would shorten action potential duration in this mouse atrial cell line. Expression of hBKα had minimal effects on expression levels of other ion channels with the exception of a small but significant reduction in Kv11.1. Patch-clamped hBKα expressing HL-1 cells exhibited an outward voltage- and Ca2+-sensitive K+ current, which was inhibited by the BK channel blocker iberiotoxin (100 nM). This BK current phenotype was not detected in untransfected HL-1 cells or in HL-1 null cells sham-transfected with an empty vector. Importantly, APD in hBKα-expressing HL-1 cells averaged 14.3 ± 2.8 ms (n = 10), which represented a 53% reduction in APD compared to HL-1 null cells lacking BKα expression. APD in the latter cells averaged 31.0 ± 5.1 ms (n = 13). The shortened APD in hBKα-expressing cells was restored to normal duration by 100 nM iberiotoxin, suggesting that a repolarizing K+ current attributed to BK channels accounted for action potential shortening. These findings provide initial proof-of-concept that the introduction of hBKα channels into a cardiac cell line can shorten APD, and raise the possibility that gene-based interventions to increase hBKα channels in cardiac cells may hold promise as a therapeutic strategy for long QT syndrome.
doi:10.1371/journal.pone.0130588
PMCID: PMC4474436  PMID: 26091273
4.  Increased Tim-3 expression on peripheral T lymphocyte subsets and association with higher disease activity in systemic lupus erythematosus 
Diagnostic Pathology  2015;10:71.
Background
Both the T cell immunoglobulin domain- and mucin domain-containing molecule-3 (Tim-3) and the death receptor Fas contribute to the pathogenesis of various autoimmune diseases, including systemic lupus erythematosus (SLE). The aim of the present study was to determine whether Tim-3 and Fas are co-expressed on certain peripheral T lymphocyte subsets, and whether this expression is associated with greater disease activity in SLE.
Methods
Peripheral blood mononuclear cells were isolated from 46 patients newly diagnosed with SLE and 28 age- and sex-matched healthy controls (HCs). Expression of Tim-3 and Fas on T subsets was analyzed by flow cytometry, while mRNA levels of the Tim-3 ligand galectin-9 and Fas ligand FasL were assayed using real-time RT-PCR.
Results
The proportions of CD3+CD4+ and CD3+CD4- T cells expressing Tim-3+ and Tim+Fas+ were significantly higher in patients than in HCs (p < 0.05), while the proportions of these subtypes expressing Fas were similar for the two groups. Patients with active SLE, as defined by their score on the SLE Disease Activity Index, had lower proportions of CD3+CD4+ T cells and higher proportions of CD3+CD4+Tim-3+ and CD3+CD4+Tim-3+Fas+ T cells than did patients with stable SLE. Serum levels of complement C3 and C4 proteins, considered as a marker of SLE activity, correlated negatively with proportions of CD3+CD4+ and CD3+CD4- T cells expressing Tim-3.
Conclusions
Expression of Tim-3 and co-expression of Tim-3 and Fas on certain peripheral T subsets are associated with disease activity in SLE patients. Future research should examine whether the same is true of other T subsets implicated in SLE, and should explore the potential role(s) of Tim-3 in the disease pathway.
Virtual slides
http://www.diagnosticpathology.diagnomx.eu/vs/1855527845145188
doi:10.1186/s13000-015-0306-0
PMCID: PMC4469310  PMID: 26076826
Systemic lupus erythematosus; Tim-3; Fas; T lymphocyte subset; Disease activity
5.  Tongxinluo (TXL), a Traditional Chinese Medicinal Compound, Improves Endothelial Function After Chronic Hypoxia Both In Vivo and In Vitro 
Abstract:
Vascular injury after chronic hypoxia leads to endothelial injury and structural damage to tight junctions (TJs), thereby resulting in a variety of cardiovascular diseases. Thus, attenuating hypoxia-induced damage has great significance for the prevention and treatment of cardiovascular disease. The aim of this study was to investigate whether the endothelial protection conferred by tongxinluo (TXL), a traditional Chinese medicinal compound, is related to its regulation of TJ protein expression. In vivo, we found that TXL could promote hypoxia-induced angiogenesis in lung and liver tissue. In vitro, we found that CoCl2 treatment significantly reduced the expression of the TJ proteins occludin, claudin-1, VE-cadherin, and beta-catenin in cultured human cardiac microvascular endothelial cells. TXL pretreatment abrogated the CoCl2-induced downregulation of these TJ proteins. Conversely, overexpression of Krüppel-like factor 4 (KLF4) inhibited the expression of TJ proteins in human cardiac microvascular endothelial cells, an effect that was reversed by TXL pretreatment. Further experiments showed that TXL could promote endothelial cell proliferation by increasing KLF4 phosphorylation, thereby reversing the effect of KLF4 on the expression of TJ proteins. These findings provide a new molecular mechanism for the TXL-induced increase in TJ protein expression.
doi:10.1097/FJC.0000000000000226
PMCID: PMC4461393  PMID: 26065642
TXL; human cardiac microvascular endothelial cells; chronic hypoxia; tight junction protein; KLF4
6.  A porcine reproductive and respiratory syndrome virus (PRRSV) vaccine candidate based on the fusion protein of PRRSV glycoprotein 5 and the Toll-like Receptor-5 agonist Salmonella Typhimurium FljB 
BMC Veterinary Research  2015;11:121.
Background
Porcine reproductive and respiratory syndrome (PRRS) is characterized by severe reproductive failure and severe pneumonia in neonatal pigs and is caused by PRRS virus (PRRSV). Glycoprotein 5 (GP5) from PRRSV is a key inducer of neutralizing antibodies. Flagellin, a toll-like receptor 5 (TLR-5) agonist, is an effective inducer of innate immune responses. This study presents a novel PRRSV vaccine candidate based on the adjuvant effect of Salmonella Typhimurium FljB fused with PRRSV GP5.
Results
A truncated rGP5 gene lacking the signal peptide and transmembrane sequences was amplified and inserted into prokaryotic expression vectors, pColdI or pGEX-6p-1. Salmonella Typhimurium flagellin fljB was amplified and inserted into the plasmid pCold-rGP5, generating recombinant plasmid pCold-rGP5-fljB. Histidine (His)-tagged rGP5 and fusion protein rGP5-FljB were induced with isopropyl-β-d-thiogalactoside, verified by SDS-PAGE and western blotting, and purified via Ni-NTA affinity columns. The TLR-5-specific bioactivity of fusion protein rGP5-FljB was determined by detecting the expression levels of the cytokine IL-8 in HEK293-mTLR5 cells by sandwich ELISA. The purified endotoxin-free proteins were administered intraperitoneally in a C3H/HeJ mouse model. The results show that immunization with the fusion protein rGP5-FljB induced a significantly enhanced GP5-specific and PRRSV-specific IgG response that persisted for almost 5 weeks. Co-administration of the rGP5 with R848 or Alum also yielded a higher IgG response than administration of rGP5 alone. The IgG1/IgG2a ratio in the rGP5-FljB immunization group was significantly higher (9-fold) than that in the rGP5 alone group and was equivalent to the response in the rGP5 + Alum immunization group, suggesting a strong Th2 immune response was induced by the fusion protein.
Conclusions
Purified fusion protein rGP5-FljB is capable of activating the innate immune response, as demonstrated by the results of our TLR-5-specific bioactivity assay, and FljB has adjuvant activity, as shown by the results from our administration of rGP5-FljB in a mouse model. Our findings confirm that FljB could serve as an excellent adjuvant for the production of GP5-specific and PRRSV-specific IgG antibodies as part of an induction of a robust humoral immune response.
doi:10.1186/s12917-015-0439-0
PMCID: PMC4489122  PMID: 26001608
PRRSV; Glycoprotein 5; Flagellin; Fusion protein; Vaccine
7.  Midazolam Exacerbates Morphine Tolerance and Morphine-induced Hyperactive Behaviors in Young Rats with Burn Injury 
Brain research  2014;1564:52-61.
Midazolam and morphine are often used in pediatric intensive care unit (ICU) for analgesia and sedation. However, how these two drugs interact behaviorally remains unclear. Here, we examined whether 1) co-administration of midazolam with morphine would exacerbate morphine tolerance and morphine-induced hyperactive behaviors, and 2) protein kinase C (PKC) would contribute to these behavioral changes. Male rats of 3 to 4 weeks old were exposed to a hindpaw burn injury. In Experiment 1, burn-injured young rats received once daily saline or morphine (10 mg/kg, subcutaneous, s.c.), followed 30 min later by either saline or midazolam (2 mg/kg, intraperitoneal, i.p.), for 14 days beginning 3 days after burn injury. In Experiment 2, young rats with burn injury were administered with morphine (10 mg/kg, s.c.), midazolam (2 mg/kg, i.p.), and chelerythrine chloride (a non-specific PKC inhibitor 10 nmol, intrathecal) for 14 days. For both experiments, cumulative morphine anti-nociceptive dose-response (ED50) was tested and hyperactive behaviors such as jumping and scratching were recorded. Following 2 weeks of each treatment, ED50 dose was significantly increased in rats receiving morphine alone as compared with rats receiving saline or midazolam alone. The ED50 dose was further increased in rats receiving both morphine and midazolam. Co-administration of morphine and midazolam also exacerbated morphine-induced hyperactive behaviors. Expression of the NR1 subunit of the N-methyl-D-aspartate (NMDA) receptor and PKCγ in the spinal cord dorsal horn (immunohistochemistry; Western blot) was upregulated in burn-injured young rats receiving morphine alone or in combination with midazolam, and chelerythrine prevented the development of morphine tolerance. These results indicate that midazolam exacerbated morphine tolerance through a spinal NMDA/PKC-mediated mechanism.
doi:10.1016/j.brainres.2014.03.047
PMCID: PMC4042400  PMID: 24713351
Midazolam; Morphine tolerance; Hyperactivity; Young rats; Burn injury; NMDA; NR1; PKC
8.  Genetic diversity of male and female Chinese bayberry (Myrica rubra) populations and identification of sex-associated markers 
BMC Genomics  2015;16(1):394.
Background
Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important subtropical evergreen fruit tree in southern China. Generally dioecious, the female plants are cultivated for fruit and have been studied extensively, but male plants have received very little attention. Knowledge of males may have a major impact on conservation and genetic improvement as well as on breeding. Using 84 polymorphic SSRs, we genotyped 213 M. rubra individuals (99 male individuals, 113 female varieties and 1 monoecious) and compared the difference in genetic diversity between the female and the male populations.
Results
Neighbour-joining cluster analysis separated M. rubra from three related species, and the male from female populations within M. rubra. By structure analysis, 178 M. rubra accessions were assigned to two subpopulations: Male dominated (98) and Female dominated (80). The well-known cultivars ‘Biqi’ and ‘Dongkui’, and the landraces ‘Fenhong’ are derived from three different gene pools. Female population had a slightly higher values of genetic diversity parameters (such as number of alleles and heterozygosity) than the male population, but not significantly different. The SSR loci ZJU062 and ZJU130 showed an empirical Fst value of 0.455 and 0.333, respectively, which are significantly above the 95 % confidence level, indicating that they are outlier loci related to sex separation.
Conclusion
The male and female populations of Chinese bayberry have similar genetic diversity in terms of average number of alleles and level of heterozygosity, but were clearly separated by genetic structure analysis due to two markers associated with sex type, ZJU062 and ZJU130. Zhejiang Province China could be the centre of diversity of M. rubra in China, with wide genetic diversity coverage; and the two representative cultivars ‘Biqi’ and ‘Dongkui’, and one landrace ‘Fenhong’ in three female subpopulations. This research provides genetic information on male and female Chinese bayberry and will act as a reference for breeding programs.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1602-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1602-5
PMCID: PMC4436740  PMID: 25986380
9.  Validation of the Chinese Version of the Quality of Nursing Work Life Scale 
PLoS ONE  2015;10(5):e0121150.
Quality of Nursing Work Life (QNWL) serves as a predictor of a nurse’s intent to leave and hospital nurse turnover. However, QNWL measurement tools that have been validated for use in China are lacking. The present study evaluated the construct validity of the QNWL scale in China. A cross-sectional study was conducted conveniently from June 2012 to January 2013 at five hospitals in Guangzhou, which employ 1938 nurses. The participants were asked to complete the QNWL scale and the World Health Organization Quality of Life abbreviated version (WHOQOL-BREF). A total of 1922 nurses provided the final data used for analyses. Sixty-five nurses from the first investigated division were re-measured two weeks later to assess the test-retest reliability of the scale. The internal consistency reliability of the QNWL scale was assessed using Cronbach’s α. Test-retest reliability was assessed using the intra-class correlation coefficient (ICC). Criterion-relation validity was assessed using the correlation of the total scores of the QNWL and the WHOQOL-BREF. Construct validity was assessed with the following indices: χ2 statistics and degrees of freedom; relative mean square error of approximation (RMSEA); the Akaike information criterion (AIC); the consistent Akaike information criterion (CAIC); the goodness-of-fit index (GFI); the adjusted goodness of fit index; and the comparative fit index (CFI). The findings demonstrated high internal consistency (Cronbach’s α = 0.912) and test-retest reliability (interclass correlation coefficient = 0.74) for the QNWL scale. The chi-square test (χ2 = 13879.60, df [degree of freedom] = 813 P = 0.0001) was significant. The RMSEA value was 0.091, and AIC = 1806.00, CAIC = 7730.69, CFI = 0.93, and GFI = 0.74. The correlation coefficient between the QNWL total scores and the WHOQOL-BREF total scores was 0.605 (p<0.01). The QNWL scale was reliable and valid in Chinese-speaking nurses and could be used as a clinical and research instrument for measuring work-related factors among nurses in China.
doi:10.1371/journal.pone.0121150
PMCID: PMC4423946  PMID: 25950838
10.  Molecular Signatures of Major Depression 
Current Biology  2015;25(9):1146-1156.
Summary
Adversity, particularly in early life, can cause illness. Clues to the responsible mechanisms may lie with the discovery of molecular signatures of stress, some of which include alterations to an individual’s somatic genome. Here, using genome sequences from 11,670 women, we observed a highly significant association between a stress-related disease, major depression, and the amount of mtDNA (p = 9.00 × 10−42, odds ratio 1.33 [95% confidence interval [CI] = 1.29–1.37]) and telomere length (p = 2.84 × 10−14, odds ratio 0.85 [95% CI = 0.81–0.89]). While both telomere length and mtDNA amount were associated with adverse life events, conditional regression analyses showed the molecular changes were contingent on the depressed state. We tested this hypothesis with experiments in mice, demonstrating that stress causes both molecular changes, which are partly reversible and can be elicited by the administration of corticosterone. Together, these results demonstrate that changes in the amount of mtDNA and telomere length are consequences of stress and entering a depressed state. These findings identify increased amounts of mtDNA as a molecular marker of MD and have important implications for understanding how stress causes the disease.
Highlights
•Amount of mtDNA is increased, and telomeric DNA is shortened in major depression•Both changes can be induced with stress but are contingent on the depressed state•Changes are tissue specific and in part due to glucocorticoid secretion•Changes are in part reversible and represent switches in metabolic strategy
Cai et al. found increases in mtDNA and a reduction in telomeric DNA in cases of major depression using whole-genome sequencing. Both changes are depression state dependent. Mice exposed to chronic stress or glucorticoids showed that these changes reflect switches in metabolic strategy and are tissue specific and partial reversible.
doi:10.1016/j.cub.2015.03.008
PMCID: PMC4425463  PMID: 25913401
11.  Antimicrobial Resistance Profile and Genotypic Characteristics of Streptococcus suis Capsular Type 2 Isolated from Clinical Carrier Sows and Diseased Pigs in China 
BioMed Research International  2015;2015:284303.
Streptococcus suis serotype 2 is an important zoonotic pathogen. Antimicrobial resistance phenotypes and genotypic characterizations of S. suis 2 from carrier sows and diseased pigs remain largely unknown. In this study, 96 swine S. suis type 2, 62 from healthy sows and 34 from diseased pigs, were analyzed. High frequency of tetracycline resistance was observed, followed by sulfonamides. The lowest resistance of S. suis 2 for β-lactams supports their use as the primary antibiotics to treat the infection of serotype 2. In contrast, 35 of 37 S. suis 2 with MLSB phenotypes were isolated from healthy sows, mostly encoded by the ermB and/or the mefA genes. Significantly lower frequency of mrp+/epf+/sly+ was observed among serotype 2 from healthy sows compared to those from diseased pigs. Furthermore, isolates from diseased pigs showed more homogeneously genetic patterns, with most of them clustered in pulsotypes A and E. The data indicate the genetic complexity of S. suis 2 between herds and a close linkage among isolates from healthy sows and diseased pigs. Moreover, many factors, such as extensive use of tetracycline or diffusion of Tn916 with tetM, might have favored for the pathogenicity and widespread dissemination of S. suis serotype 2.
doi:10.1155/2015/284303
PMCID: PMC4434170  PMID: 26064892
12.  Non-coding RNAs and LRRFIP1 Regulate TNF Expression1 
Non-coding RNAs have been implicated in the regulation of expression of numerous genes, however, the mechanism is not fully understood. We identified bidirectional, long non-coding RNAs upstream of the TNF gene using five different methods. They arose in a region where the repressors LRRFIP1, EZH2, and SUZ12 were demonstrated to bind, suggesting a role in repression. The non-coding RNAs were polyadenylated, capped, and chromatin-associated. Knock-down of the non-coding RNAs was associated with de-repression of TNF mRNA and diminished binding of LRRFIP1 to both RNA targets and chromatin. Over-expression of the non-coding RNAs led to diminished expression of TNF and recruitment of repressor proteins to the locus. One repressor protein, LRRFIP1, bound directly to the non-coding RNAs. These data place the non-coding RNAs upstream of TNF gene as central to the transcriptional regulation. They appear to serve as a platform for the assembly of a repressive complex.
doi:10.4049/jimmunol.1302063
PMCID: PMC3965610  PMID: 24567534
13.  Identification and Immune Functional Characterization of Pigeon TLR7 
Toll-like receptor 7 (TLR7) is activated by single-stranded RNA and synthetic imidazoquinoline components, and induces interferon production. In this study, we cloned the TLR7 gene from King pigeon (Columba livia). The TLR7 open reading frame is 3144 bp and encodes a 1047-amino acid protein, consisting of a canonical TLR composition with 15 leucine-rich repeats (LRRs). Amino acid-inserting modifications were found at position 15 of LRR2, LRR11, LRR13, and LRR14 and position 10 of LRR10. The tissue distribution of pigeon TLR7 suggests that immune-associated tissues, especially the spleen and liver, have high TLR7 expression. HEK293T cells transfected with pigeon TLR7 plasmid responded to the agonist R848, indicating a functional TLR7 homolog. Following R848 stimulation of pigeon peripheral blood mononuclear cells, the levels of IFN-γ, IL-6, IL-8, CCL5, and IL-10 mRNA, assessed using quantitative real-time PCR, were significantly up-regulated. After Newcastle disease virus vaccine strain LaSota inoculation and agonist R848 injection, the level of TLR7 mRNA in the spleen of pigeons increased significantly in the R848-injected group, but decreased in the LaSota-inoculated group at three day post-infection (d.p.i.). The mRNA levels of inflammatory cytokines and chemokines were significantly upregulated in both LaSota-inoculated and R848-injected groups. Triggering pigeon TLR7 leads to robust up-regulation of inflammatory cytokines and chemokines, suggesting an important role in the innate immune response.
doi:10.3390/ijms16048364
PMCID: PMC4425086  PMID: 25874762
TLR7; pigeon; identification; characterization; immune function
14.  Identification of Novel QTL Governing Root Architectural Traits in an Interspecific Soybean Population 
PLoS ONE  2015;10(3):e0120490.
Cultivated soybean (Glycine max L.) cv. Dunbar (PI 552538) and wild G. soja (PI 326582A) exhibited significant differences in root architecture and root-related traits. In this study, phenotypic variability for root traits among 251 BC2F5 backcross inbred lines (BILs) developed from the cross Dunbar/PI 326582A were identified. The root systems of the parents and BILs were evaluated in controlled environmental conditions using a cone system at seedling stage. The G. max parent Dunbar contributed phenotypically favorable alleles at a major quantitative trait locus on chromosome 8 (Satt315-I locus) that governed root traits (tap root length and lateral root number) and shoot length. This QTL accounted for >10% of the phenotypic variation of both tap root and shoot length. This QTL region was found to control various shoot- and root-related traits across soybean genetic backgrounds. Within the confidence interval of this region, eleven transcription factors (TFs) were identified. Based on RNA sequencing and Affymetrix expression data, key TFs including MYB, AP2-EREBP and bZIP TFs were identified in this QTL interval with high expression in roots and nodules. The backcross inbred lines with different parental allelic combination showed different expression pattern for six transcription factors selected based on their expression pattern in root tissues. It appears that the marker interval Satt315–I locus on chromosome 8 contain an essential QTL contributing to early root and shoot growth in soybean.
doi:10.1371/journal.pone.0120490
PMCID: PMC4355624  PMID: 25756528
15.  Genetic variants in root architecture-related genes in a Glycine soja accession, a potential resource to improve cultivated soybean 
BMC Genomics  2015;16(1):132.
Background
Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja.
Results
Wild and cultivated soybean both contributed alleles towards significant additive large effect QTLs on chromosome 6 and 7 for a longer total root length and root distribution, respectively. Epistatic effect QTLs were also identified for taproot length, average diameter, and root distribution. These root traits will influence the water and nutrient uptake in soybean. Two cell division-related genes (D type cyclin and auxin efflux carrier protein) with insertion/deletion variations might contribute to the shorter root phenotypes observed in G. soja compared with cultivated soybean. Based on the location of the QTLs and sequence information from a second G. soja accession, three genes (slow anion channel associated 1 like, Auxin responsive NEDD8-activating complex and peroxidase), each with a non-synonymous single nucleotide polymorphism mutation were identified, which may also contribute to changes in root architecture in the cultivated soybean. In addition, Apoptosis inhibitor 5-like on chromosome 7 and slow anion channel associated 1-like on chromosome 15 had epistatic interactions for taproot length QTLs in soybean.
Conclusion
Rare alleles from a G. soja accession are expected to enhance our understanding of the genetic components involved in root architecture traits, and could be combined to improve root system and drought adaptation in soybean.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1334-6) contains supplementary material, which is available to authorized users.
doi:10.1186/s12864-015-1334-6
PMCID: PMC4354765  PMID: 25765991
Root; Quantitative trait locus; Soybean; Wild soybean; Root architecture; Non-synonymous SNP; Microarray; Single feature polymorphism; DNA sequencing
16.  Melatonin prevents morphine-induced hyperalgesia and tolerance in rats: role of protein kinase C and N-methyl-D-aspartate receptors 
BMC Anesthesiology  2015;15:12.
Background
Morphine-induced hyperalgesia and tolerance significantly limits its clinical use in relieving acute and chronic pain. Melatonin, a pineal gland neurohormone, has been shown to participate in certain neuropsychopharmacological actions. The present study investigated the effect of melatonin on morphine-induced hyperalgesia and tolerance and possible involvement of protein kinase C (PKC)/N-methyl-D-aspartate (NMDA) pathway in melatonin-mediated.
Methods
Experiments were performed on adult, male Sprague–Dawley rats. Melatonin (10 mg/kg, intraperitoneal, i.p.) or saline was administrated 10 min after morphine injection (10 mg/kg, subcutaneous, s.c.) each day for consecutive 14 days. Withdrawal threshold of the hindpaw to mechanical and thermal stimulation was measured before any drug administration and one hour after melatonin or saline on each designated test day. On the 15th day, thermal withdrawal was measured after s.c. morphine (20 mg/kg), but not melatonin, and morphine tolerance was measured and expressed by MPAE% (percent of maximal possible anti-nociceptive effect) of morphine. Levels of expression of protein kinase C gamma (PKCγ) and NMDA receptor subtype NR1 in spinal cord were detected by Western blotting.
Results
The mechanical withdrawal threshold and thermal withdrawal latency decreased and shortened significantly (i.e., threshold decreased) in rats that received morphine treatment for two weeks compared with that in rats receiving saline. This morphine-induced mechanical and thermal hyperalgesia were greatly attenuated by co-administration of morphine with melatonin. The MPAE% representing morphine analgesic effect was reduced approximately 60% in rats that received morphine treatment. However, following the treatment of morphine with melatonin, the MPAE% was reduced only about 30%, comparing with those that received saline treatment as control. Administration of morphine alone resulted in significantly increased expression of PKCγ and NR1 proteins in the spinal cord. These increased levels of expression of PKCγ and NR1 were significantly inhibited by co-administration of morphine with melatonin.
Conclusions
Our findings demonstrate that melatonin have potential to attenuate repetitive morphine-induced hyperalgesia and tolerance, possibly by inhibiting PKCγ and NR1 activities in the spinal cord.
doi:10.1186/1471-2253-15-12
PMCID: PMC4350305  PMID: 25745356
Melatonin; Morphine-induced hyperalgesia; Morphine tolerance; PKCγ; NR1
17.  Integrated prevention of mother-to-child transmission for human immunodeficiency virus, syphilis and hepatitis B virus in China 
Abstract
Problem
China continues to face challenges in eliminating mother-to-child transmission of human immunodeficiency virus (HIV), syphilis and hepatitis B virus (HBV).
Approach
In 2010, a programme that integrated and standardized prevention of mother-to-child transmission (PMTCT) efforts for HIV, syphilis and HBV was implemented in 1156 counties. At participating antenatal care clinics, pregnant women were offered all three tests concurrently and free of charge. Further interventions such as free treatment, prophylaxis and testing for mothers and their children were provided for HIV and syphilis.
Local setting
China’s national PMTCT HIV programme started in 2003, at which time there were no national programmes for perinatal syphilis and HBV. In 2009, the rate of maternal-to-child transmission of HIV was 8.1% (57/702). Reported congenital syphilis was 60.8 per 100 000 live births. HBV infection was 7.2% of the overall population infected.
Relevant changes
Between 2010 and 2013 the number of pregnant women attending antenatal care clinics with integrated PMTCT services increased from 5.5 million to 13.1 million. In 2013, 12.7 million pregnant women were tested for HIV, 12.6 million for syphilis and 12.7 million for HBV. Mother-to-child transmission of HIV fell to 6.7% in 2013. Data on syphilis transmission are not yet available.
Lessons learnt
Integrated PMTCT services proved to be feasible and effective, and they are now part of the routine maternal and child health services provided to infected women. The services are provided through a collaboration between maternal and child health clinics, the national and local Centers for Disease Control and Prevention, and general hospitals.
doi:10.2471/BLT.14.139626
PMCID: PMC4271682  PMID: 25558108
18.  Physiological response to drought stress in Camptotheca acuminata seedlings from two provenances 
Drought stress is a key environmental factor limiting the growth and productivity of plants. The purpose of this study was to investigate the physiological responses of Camptotheca acuminata (C. acuminata) to different drought stresses and compare the drought tolerance between the provenances Kunming (KM) and Nanchang (NC), which are naturally distributed in different rainfall zones with annual rainfalls of 1000–1100 mm and 1600–1700 mm, respectively. We determined relative water content (RWC), chlorophyll content [Chl(a+b)], net photosynthesis (Pn), gas exchange parameters, relative leakage conductivity (REC), malondialdehyde (MDA) content and superoxide dismutase (SOD) and peroxidase (POD) activities of C. acuminata seedlings under both moderate (50% of maximum field capacity) and severe drought stress (30% of maximum field capacity). As the degree of water stress increased, RWC, Chl(a+b) content, Pn, stomatal conductance (Gs), transpiration rate (Tr) and intercellular CO2 concentration (Ci) values decreased, but water use efficiency (WUE), REC, MDA content and SOD and POD activities increased in provenances KM and NC. Under moderate and severe drought stress, provenance KM had higher RWC, Chl(a+b), Pn, WUE, SOD, and POD and lower Gs, Tr, Ci, and REC in leaves than provenance NC. The results indicated that provenance KM may maintain stronger drought tolerance via improvements in water-retention capacity, antioxidant enzyme activity, and membrane integrity.
doi:10.3389/fpls.2015.00361
PMCID: PMC4440367  PMID: 26052334
Camptotheca acuminata; provenance; drought stress; physiological response; antioxidant enzyme
19.  Protective Efficacy of Vitamins C and E on p,p′-DDT-Induced Cytotoxicity via the ROS-Mediated Mitochondrial Pathway and NF-κB/FasL Pathway 
PLoS ONE  2014;9(12):e113257.
Dichlorodiphenoxytrichloroethane (DDT) is a known persistent organic pollutant and liver damage toxicant. However, there has been little emphasis on the mechanism underlying liver damage toxicity of DDT and the relevant effective inhibitors. Hence, the present study was conducted to explore the protective effects of vitamin C (VC) and vitamin E (VE) on the cytotoxicity of DDT in HL-7702 cells and elaborate the specific molecular mechanisms. The results demonstrated that p,p′-DDT exposure at over 10 µM depleted cell viability of HL-7702 cells and led to cell apoptotic. p,p′-DDT treatment elevated the level of reactive oxygen species (ROS) generation, induced mitochondrial membrane potential, and released cytochrome c into the cytosol, with subsequent elevations of Bax and p53, along with suppression of Bcl-2. In addition, the activations of caspase-3 and -8 were triggered. Furthermore, p,p′-DDT promoted the expressions of NF-κB and FasL. When the cells were exposed to the NF-κB inhibitor (PDTC), the up-regulated expression of FasL was attenuated. Strikingly, these alterations caused by DDT treatment were prevented or reversed by the addition of VC or VE, and the protective effects of co-treatment with VC and VE were higher than the single supplement with p,p′-DDT. Taken together, these findings provide novel experimental evidences supporting that VC or/and VE could reduce p,p′-DDT-induced cytotoxicity of HL-7702 cells via the ROS-mediated mitochondrial pathway and NF-κB/FasL pathway.
doi:10.1371/journal.pone.0113257
PMCID: PMC4252254  PMID: 25464339
20.  Lighter: fast and memory-efficient sequencing error correction without counting 
Genome Biology  2014;15(11):509.
Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting k-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input k-mers and the other holding k-mers likely to be correct. As long as the sampling fraction is adjusted in inverse proportion to the depth of sequencing, Bloom filter size can be held constant while maintaining near-constant accuracy. Lighter is parallelized, uses no secondary storage, and is both faster and more memory-efficient than competing approaches while achieving comparable accuracy.
Electronic supplementary material
The online version of this article (doi:10.1186/s13059-014-0509-9) contains supplementary material, which is available to authorized users.
doi:10.1186/s13059-014-0509-9
PMCID: PMC4248469  PMID: 25398208
21.  Genome Sequence of Tumebacillus flagellatus GST4, the First Genome Sequence of a Species in the Genus Tumebacillus 
Genome Announcements  2014;2(6):e01189-14.
We present here the first genome sequence of a species in the genus Tumebacillus. The draft genome sequence of Tumebacillus flagellatus GST4 provides a genetic basis for future studies addressing the origins, evolution, and ecological role of Tumebacillus organisms, as well as a source of acid-resistant amylase-encoding genes for further studies.
doi:10.1128/genomeA.01189-14
PMCID: PMC4241674  PMID: 25395648
22.  p, p′-Dichlorodiphenyldichloroethylene Induces Colorectal Adenocarcinoma Cell Proliferation through Oxidative Stress 
PLoS ONE  2014;9(11):e112700.
p, p′-Dichlorodiphenyldichloroethylene (DDE), the major metabolite of Dichlorodiphenyltrichloroethane (DDT), is an organochlorine pollutant and associated with cancer progression. The present study investigated the possible effects of p,p′-DDE on colorectal cancer and the involved molecular mechanism. The results indicated that exposure to low concentrations of p,p′-DDE from 10−10 to 10−7 M for 96 h markedly enhanced proliferations of human colorectal adenocarcinoma cell lines. Moreover, p,p′-DDE exposure could activate Wnt/β-catenin and Hedgehog/Gli1 signaling cascades, and the expression level of c-Myc and cyclin D1 was significantly increased. Consistently, p,p′-DDE-induced cell proliferation along with upregulated c-Myc and cyclin D1 were impeded by β-catenin siRNA or Gli1 siRNA. In addition, p,p′-DDE was able to activate NADPH oxidase, generate reactive oxygen species (ROS) and reduce GSH content, superoxide dismutase (SOD) and calatase (CAT) activities. Treatment with antioxidants prevented p,p′-DDE-induced cell proliferation and signaling pathways of Wnt/β-catenin and Hedgehog/Gli1. These results indicated that p,p′-DDE promoted colorectal cancer cell proliferation through Wnt/β-catenin and Hedgehog/Gli1 signalings mediated by oxidative stress. The finding suggests an association between p,p′-DDE exposure and the risk of colorectal cancer progression.
doi:10.1371/journal.pone.0112700
PMCID: PMC4227882  PMID: 25386960
23.  Overexpression of ETV4 protein in triple-negative breast cancer is associated with a higher risk of distant metastasis 
OncoTargets and therapy  2014;7:1733-1742.
Background
Patients with triple-negative breast cancer (TNBC) present a higher probability of distant metastasis and lack of effective targeted therapy. ETS translocation variant 4 (ETV4) is an ETS (E-26) transcription factor and has been associated with tumor metastasis. However, the clinical and functional significance of ETV4 in TNBC still remains unclear.
Methods
A human tumor metastasis polymerase chain reaction array was used to profile differential expression of tumor metastasis-related genes in TNBC tissue. Real-time reverse transcription and Western blot analyses were performed to verify ETV4 expression in TNBC cells and tissue. Immunohistochemistry was used to detect expression of ETV4 protein in 135 TNBC tissue samples for association between ETV4 protein expression and clinical outcomes.
Results
A total total of eight upregulated (CCL7, KISS1, MET, MMP7, NR4A3, ETV4, TIMP3, and TSHR) and three downregulated (ITGA7, SSTR, and MMP2) genes were identified between TNBC tissue and the luminal subtype of breast cancer tissue. ETV4 messenger ribonucleic acid was more than five-fold upregulated in TNBC tissue compared with the control tissue. ETV4 overexpression was found in 57.0% of 135 TNBC cases. Overexpression of ETV4 protein was associated with an advanced stage and a higher proportion of positive lymph node and lymphovascular invasion. Patients with an ETV4-overexpressed tumor had a significantly higher risk of developing distant metastasis (P<0.0001) and shorter overall survival and disease-free survival. Overexpression of ETV4 protein was an independent predictor of short disease-free survival of TNBC patients (P=0.021).
Conclusion
Overexpression of ETV4 protein increases risk of developing distant metastasis and results in a poor prognosis for TNBC patients. Thus, ETV4 might be a novel target for developing an alternative therapeutic strategy for prevention of TNBC distant metastasis.
doi:10.2147/OTT.S66692
PMCID: PMC4196788  PMID: 25328406
breast carcinoma; triple-negative; ETS translocation variant 4; ETV4; prognosis
24.  nDNA-prot: identification of DNA-binding proteins based on unbalanced classification 
BMC Bioinformatics  2014;15(1):298.
Background
DNA-binding proteins are vital for the study of cellular processes. In recent genome engineering studies, the identification of proteins with certain functions has become increasingly important and needs to be performed rapidly and efficiently. In previous years, several approaches have been developed to improve the identification of DNA-binding proteins. However, the currently available resources are insufficient to accurately identify these proteins. Because of this, the previous research has been limited by the relatively unbalanced accuracy rate and the low identification success of the current methods.
Results
In this paper, we explored the practicality of modelling DNA binding identification and simultaneously employed an ensemble classifier, and a new predictor (nDNA-Prot) was designed. The presented framework is comprised of two stages: a 188-dimension feature extraction method to obtain the protein structure and an ensemble classifier designated as imDC. Experiments using different datasets showed that our method is more successful than the traditional methods in identifying DNA-binding proteins. The identification was conducted using a feature that selected the minimum Redundancy and Maximum Relevance (mRMR). An accuracy rate of 95.80% and an Area Under the Curve (AUC) value of 0.986 were obtained in a cross validation. A test dataset was tested in our method and resulted in an 86% accuracy, versus a 76% using iDNA-Prot and a 68% accuracy using DNA-Prot.
Conclusions
Our method can help to accurately identify DNA-binding proteins, and the web server is accessible at http://datamining.xmu.edu.cn/~songli/nDNA. In addition, we also predicted possible DNA-binding protein sequences in all of the sequences from the UniProtKB/Swiss-Prot database.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2105-15-298) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2105-15-298
PMCID: PMC4165999  PMID: 25196432
DNA-binding protein; Ensemble classifier; Unbalanced dataset; Bioinformatics
25.  Transducin β-like 1 X-linked receptor 1 suppresses cisplatin sensitivity in Nasopharyngeal Carcinoma via activation of NF-κB pathway 
Molecular Cancer  2014;13:195.
Background
Transducin β-like 1 X-linked receptor 1 (TBL1XR1) is an important transcriptional cofactor involved in the regulation of many signaling pathways, and is associated with carcinogenesis and tumor progression. However, the precise role of TBL1XR1 in these processes is not well understood.
Methods
We detected the expression of TBL1XR1 protein and mRNA in nasopharyngeal carcinoma (NPC) cell lines and biopsies by western blotting, real-time PCR and immunohistochemical staining (IHC). Overexpression of TBL1XR1 in NPC enhanced chemoresistance to cisplatin using two NPC cell lines in vitro and in vivo.
Results
TBL1XR1 was upregulated in NPC cell lines and clinical samples. The expression of TBL1XR1 was correlated with several clinicopathological factors including clinical stage, T classification, N classification and patient survival. Univariate and multivariate analysis revealed that TBL1XR1 was an independent prognostic factor for patient survival. In vitro and in vivo studies demonstrated that TBL1XR1 high expression induced resistance to cisplatin-induced apoptosis in NPC cells. Furthermore, we found that TBL1XR1 activated the NF-κB pathway and promoted transcription of genes downstream of NF-κB, especially anti-apoptotic genes.
Conclusions
Upregulation of TBL1XR1 induces NPC cells resistance to cisplatin by activating the NF-κB pathway, and correlates with poor overall survival of NPC patients. TBL1XR1 has a pivotal role in NPC and could be a valuable prognostic factor as well as a novel biomarker for tailoring appropriate therapeutic regimes.
Electronic supplementary material
The online version of this article (doi:10.1186/1476-4598-13-195) contains supplementary material, which is available to authorized users.
doi:10.1186/1476-4598-13-195
PMCID: PMC4158072  PMID: 25145705
TBL1XR1; Nasopharyngeal carcinoma; Cisplatin; Chemotherapy; Anti-Apoptotic; NF-κB signalling

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