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1.  Chitosan oligosaccharides block LPS-induced O-GlcNAcylation of NF-κB and endothelial inflammatory response 
Carbohydrate polymers  2013;99:10.1016/j.carbpol.2013.08.082.
It is known that chitosan oligosaccharides (COS) suppress LPS-induced vascular endothelial inflammatory response by mechanism involving NF-κB blockade. It remains unknown how COS inhibit NF-κB. We provided evidence both in cultured endothelial cells and mouse model supporting a new mechanism. Regardless of the endothelial cell types, the LPS-induced NF-κB-dependent inflammatory gene expression was suppressed by COS, which was associated with reduced NF-κB nucleus translocation. LPS enhanced O-GlcNAc modification of NF-κB/p65 and activated NF-κB pathway, which could be prevented either by siRNA knockdown of O-GlcNAc transferase (OGT) or pretreatment with COS. Inhibition of either mitogen-activated protein kinase or superoxide generation abolishes LPS-induced NF-κB O-GlcNAcylation. Consistently, aortic tissues from LPS-treated mice presented enhanced NF-κB/p65 O-GlcNAcylation in association with upregulated gene expression of inflammatory cytokines in vascular tissues; however, pre-administration of COS prevented these responses. In conclusion, COS decreased OGT-dependent O-GlcNAcylation of NF-κB and thereby attenuated LPS-induced vascular endothelial inflammatory response.
doi:10.1016/j.carbpol.2013.08.082
PMCID: PMC3843148  PMID: 24274545
Chitosan oligosaccharides; LPS (Lipopolysaccharides); Endothelial cells; O-GlcNAcylation; NF-κB (nuclear factor kappa-light-chain-enhancer of activated B cells); Inflammatory response
2.  Dissemination of Cephalosporin Resistance Genes between Escherichia coli Strains from Farm Animals and Humans by Specific Plasmid Lineages 
PLoS Genetics  2014;10(12):e1004776.
Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli. Worryingly, the incidence of human infections caused by third-generation cephalosporin-resistant E. coli is increasing worldwide. Recent studies have suggested that these E. coli strains, and their antibiotic resistance genes, can spread from food-producing animals, via the food-chain, to humans. However, these studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these strains. We therefore used whole-genome sequencing (WGS) to study the relatedness of cephalosporin-resistant E. coli from humans, chicken meat, poultry and pigs. One strain collection included pairs of human and poultry-associated strains that had previously been considered to be identical based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance gene sequencing. The second collection included isolates from farmers and their pigs. WGS analysis revealed considerable heterogeneity between human and poultry-associated isolates. The most closely related pairs of strains from both sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome. In contrast, epidemiologically linked strains from humans and pigs differed by only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types. The plasmid backbones within each lineage were virtually identical and were shared by genetically unrelated human and animal isolates. Plasmid reconstructions from short-read sequencing data were validated by long-read DNA sequencing for two strains. Our findings failed to demonstrate evidence for recent clonal transmission of cephalosporin-resistant E. coli strains from poultry to humans, as has been suggested based on traditional, low-resolution typing methods. Instead, our data suggest that cephalosporin resistance genes are mainly disseminated in animals and humans via distinct plasmids.
Author Summary
The rapid global rise of infections caused by Escherichia coli that are resistant to clinically relevant antimicrobials, including third-generation cephalosporins, is cause for concern. The intestinal tract of livestock, in particular poultry, is an important reservoir for drug resistant E. coli, but it is unknown to what extent these bacteria can spread to humans. Food is thought to be an important source because drug-resistant E. coli have been detected in animals raised for meat consumption and in meat products. Previous studies that used traditional, low-resolution, genetic typing methods found that drug resistant E. coli present in humans and poultry were indistinguishable from each other, suggesting dissemination of these bacteria through the food-chain to humans. However, by applying high-resolution, whole-genome sequencing methods, we did not find evidence for such transmission of bacteria through the food-chain. Instead, by employing a novel approach for the reconstruction of mobile genetic elements from whole-genome sequence data, we discovered that genetically unrelated E. coli isolates from both humans and animal sources carried nearly identical plasmids that encode third-generation cephalosporin resistance determinants. Our data suggest that cephalosporin resistance is mainly disseminated via the transfer of mobile genetic elements between animals and humans.
doi:10.1371/journal.pgen.1004776
PMCID: PMC4270446  PMID: 25522320
3.  Characterization and Expression of Genes Encoding Three Small Heat Shock Proteins in Sesamia inferens (Lepidoptera: Noctuidae) 
The pink stem borer, Sesamia inferens (Walker), is a major pest of rice and is endemic in China and other parts of Asia. Small heat shock proteins (sHSPs) encompass a diverse, widespread class of stress proteins that have not been characterized in S. inferens. In the present study, we isolated and characterized three S. inferens genes that encode members of the α-crystallin/sHSP family, namely, Sihsp21.4, Sihsp20.6, and Sihsp19.6. The three cDNAs encoded proteins of 187, 183 and 174 amino acids with calculated molecular weights of 21.4, 20.6 and 19.6 kDa, respectively. The deduced amino acid sequences of the three genes showed strong similarity to sHSPs identified in other lepidopteran insects. Sihsp21.4 contained an intron, but Sihsp20.6 and Sihsp19.6 lacked introns. Real-time quantitative PCR analyses revealed that Sihsp21.4 was most strongly expressed in S. inferens heads; Whereas expression of Sihsp20.6 and Sihsp19.6 was highest in eggs. The three S. inferens sHSP genes were up-regulated during low temperature stress. In summary, our results show that S. inferens sHSP genes have distinct regulatory roles in the physiology of S. inferens.
doi:10.3390/ijms151223196
PMCID: PMC4284760  PMID: 25514417
Sesamia inferens; small heat shock protein; cloning; expression pattern
4.  Evaluation and Validation of Reference Genes for qRT-PCR Normalization in Frankliniella occidentalis (Thysanoptera:Thripidae) 
PLoS ONE  2014;9(10):e111369.
Quantitative real time PCR (qRT-PCR) has emerged as a reliable and reproducible technique for studying gene expression analysis. For accurate results, the normalization of data with reference genes is particularly essential. Once the transcriptome sequencing of Frankliniella occidentalis was completed, numerous unigenes were identified and annotated. Unfortunately, there are no studies on the stability of reference genes used in F. occidentalis. In this work, seven candidate reference genes, including actin, 18S rRNA, H3, tubulin, GAPDH, EF-1 and RPL32, were evaluated for their suitability as normalization genes under different experimental conditions using the statistical software programs BestKeeper, geNorm, Normfinder and the comparative ΔCt method. Because the rankings of the reference genes provided by each of the four programs were different, we chose a user-friendly web-based comprehensive tool RefFinder to get the final ranking. The result demonstrated that EF-1 and RPL32 displayed the most stable expression in different developmental stages; RPL32 and GAPDH showed the most stable expression at high temperatures, while 18S and EF-1 exhibited the most stable expression at low temperatures. In this study, we validated the suitable reference genes in F. occidentalis for gene expression profiling under different experimental conditions. The choice of internal standard is very important in the normalization of the target gene expression levels, thus validating and selecting the best genes will help improve the quality of gene expression data of F. occidentalis. What is more, these validated reference genes could serve as the basis for the selection of candidate reference genes in other insects.
doi:10.1371/journal.pone.0111369
PMCID: PMC4214748  PMID: 25356721
5.  ML297 (VU0456810), the First Potent and Selective Activator of the GIRK Potassium Channel, Displays Antiepileptic Properties in Mice 
ACS Chemical Neuroscience  2013;4(9):1278-1286.
The G-protein activated, inward-rectifying potassium (K+) channels, “GIRKs”, are a family of ion channels (Kir3.1-Kir3.4) that has been the focus of intense research interest for nearly two decades. GIRKs are comprised of various homo- and heterotetrameric combinations of four different subunits. These subunits are expressed in different combinations in a variety of regions throughout the central nervous system and in the periphery. The body of GIRK research implicates GIRK in processes as diverse as controlling heart rhythm, to effects on reward/addiction, to modulation of response to analgesics. Despite years of GIRK research, very few tools exist to selectively modulate GIRK channels’ activity and until now no tools existed that potently and selectively activated GIRKs. Here we report the development and characterization of the first truly potent, effective, and selective GIRK activator, ML297 (VU0456810). We further demonstrate that ML297 is active in two in vivo models of epilepsy, a disease where up to 40% of patients remain with symptoms refractory to present treatments. The development of ML297 represents a truly significant advancement in our ability to selectively probe GIRK’s role in physiology as well as providing the first tool for beginning to understand GIRK’s potential as a target for a diversity of therapeutic indications.
doi:10.1021/cn400062a
PMCID: PMC3778424  PMID: 23730969
GIRK; G-protein; inward rectifier; potassium channel; epilepsy; activator
6.  The catalytic region and PEST domain of PTPN18 distinctly regulate the HER2 phosphorylation and ubiquitination barcodes 
Cell Research  2014;24(9):1067-1090.
The tyrosine phosphorylation barcode encoded in C-terminus of HER2 and its ubiquitination regulate diverse HER2 functions. PTPN18 was reported as a HER2 phosphatase; however, the exact mechanism by which it defines HER2 signaling is not fully understood. Here, we demonstrate that PTPN18 regulates HER2-mediated cellular functions through defining both its phosphorylation and ubiquitination barcodes. Enzymologic characterization and three crystal structures of PTPN18 in complex with HER2 phospho-peptides revealed the molecular basis for the recognition between PTPN18 and specific HER2 phosphorylation sites, which assumes two distinct conformations. Unique structural properties of PTPN18 contribute to the regulation of sub-cellular phosphorylation networks downstream of HER2, which are required for inhibition of HER2-mediated cell growth and migration. Whereas the catalytic domain of PTPN18 blocks lysosomal routing and delays the degradation of HER2 by dephosphorylation of HER2 on pY1112, the PEST domain of PTPN18 promotes K48-linked HER2 ubiquitination and its rapid destruction via the proteasome pathway and an HER2 negative feedback loop. In agreement with the negative regulatory role of PTPN18 in HER2 signaling, the HER2/PTPN18 ratio was correlated with breast cancer stage. Taken together, our study presents a structural basis for selective HER2 dephosphorylation, a previously uncharacterized mechanism for HER2 degradation and a novel function for the PTPN18 PEST domain. The new regulatory role of the PEST domain in the ubiquitination pathway will broaden our understanding of the functions of other important PEST domain-containing phosphatases, such as LYP and PTPN12.
doi:10.1038/cr.2014.99
PMCID: PMC4152746  PMID: 25081058
phosphatase; receptor; ubiquitination; HER2; PTPN18; EGFR
7.  The Diagnosis Accuracy of PLA2R-AB in the Diagnosis of Idiopathic Membranous Nephropathy: A Meta-Analysis 
PLoS ONE  2014;9(8):e104936.
Background
The presence of antibodies against the M-type phospholipase A2 receptor (PLA2R-AB) is considered to be a promising serological diagnostic biomarker of idiopathic membranous nephropathy (iMN). However, controversy remains about the diagnostic accuracy of serum PLA2R-AB testing. Here, we performed a comprehensive meta-analysis to assess the overall diagnostic value of serum PLA2R-AB testing in iMN detection.
Methods
PubMed, Embase, and CNKI (Chinese National Knowledge Infrastructure) were searched for relevant original articles through January 31, 2014. The summary sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and diagnostic odds ratio (DOR) were estimated using the bivariate model. The heterogeneity among studies was explored by subgroup and meta-regression analysis.
Results
9 articles, including 15 studies, were eventually identified with a total of 2212 patients. The summary sensitivity of all studies is 78% (95% CI: 66% to 87%) and the specificity is 99% (95% CI: 96% to 100%). The summary positive and negative likelihood ratios are 96.1 (95% CI, 19.5 to 472.1) and 0.22 (95% CI: 0.14 to 0.35), respectively. The DOR is 437 (95%CI, 74 to 2592). The subgroup analysis and meta-regression suggest the test interval is the main source of heterogeneity.
Conclusions
Serum PLA2R-AB testing is a useful tool to detect iMN. In addition, considering the high heterogeneity and potential publication bias, further high quality studies are needed in the future.
doi:10.1371/journal.pone.0104936
PMCID: PMC4138154  PMID: 25136841
8.  Discovery of ‘molecular switches’ within a GIRK activator scaffold that afford selective GIRK inhibitors 
Bioorganic & medicinal chemistry letters  2013;23(16):10.1016/j.bmcl.2013.06.023.
This letter describes a multi-dimensional SAR campaign based on a potent, efficacious and selective GIRK1/2 activator (~10-fold versus GIRK1/4 and inactive on nonGIRK 1-containing GIRKs, GIRK 2 or GIRK2/3). Further chemical optimization through an iterative parallel synthesis effort identified multiple ‘molecular switches’ that modulated the mode of pharmacology from activator to inhibitor, as well as engendering varying selectivity profiles for GIRK1/2 and GIRK1/4. Importantly, these compounds were all inactive on nonGIRK1 containing GIRK channels. However, SAR was challenging as subtle structural modifications had large effects on both mode of pharmacology and GIRK1/2 and GIRK1/4 channel selectivity.
doi:10.1016/j.bmcl.2013.06.023
PMCID: PMC3816575  PMID: 23838260
GIRK; Kir3.x; Activators; Inhibitors; Thallium flux
9.  Effects of ear-canal pressurization on middle-ear bone- and air-conduction responses 
Hearing research  2009;263(0):204-215.
In extremely loud noise environments, it is important to not only protect one’s hearing against noise transmitted through the air-conduction (AC) pathway, but also through the bone-conduction (BC) pathways. Much of the energy transmitted through the BC pathways is concentrated in the mid-frequency range around 1.5–2 kHz, which is likely due to the structural resonance of the middle ear. One potential approach for mitigating this mid-frequency BC noise transmission is to introduce a positive or negative static pressure in the ear canal, which is known to reduce BC as well as AC hearing sensitivity. In the present study, middle-ear ossicular velocities at the umbo and stapes were measured using human cadaver temporal bones in response to both BC and AC excitations, while static air pressures of ±400 mm H2O were applied in the ear canal. For the maximum negative pressure of −400 mm H2O, mean BC stapes-velocity reductions of about 5–8 dB were observed in the frequency range from 0.8 to 2.5 kHz, with a peak reduction of 8.6(± 4.7) dB at 1.6 kHz. Finite-element analysis indicates that the peak BC-response reduction tends to be in the mid-frequency range because the middle-ear BC resonance, which is typically around 1.5–2 kHz, is suppressed by the pressure-induced stiffening of the middle-ear structure. The measured data also show that the BC responses are reduced more for negative static pressures than for positive static pressures. This may be attributable to a difference in the distribution of the stiffening among the middle-ear components depending on the polarity of the static pressure. The characteristics of the BC-response reductions are found to be largely consistent with the available psychoacoustic data, and are therefore indicative of the relative importance of the middle-ear mechanism in BC hearing.
doi:10.1016/j.heares.2009.11.013
PMCID: PMC4103952  PMID: 19944139
Bone conduction; Hearing protection; Middle-ear response; Middle-ear dynamics; Ear-canal air pressure; Auditory biomechanics
10.  Frequent mutation of the PI3K pathway in head and neck cancer defines predictive biomarkers 
Cancer discovery  2013;3(7):761-769.
Genomic findings underscore the heterogeneity of head and neck squamous cell carcinoma (HNSCC)(1, 2). Identification of mutations that predict therapeutic response would be a major advance. We determined the mutationally altered, targetable mitogenic pathways in a large HNSCC cohort. Analysis of whole-exome sequencing data from 151 tumors revealed the PI3K pathway to be the most frequently mutated oncogenic pathway (30.5%). PI3K pathway-mutated HNSCC tumors harbored a significantly higher rate of mutations in known cancer genes. In a subset of HPV-positive tumors, PIK3CA or PIK3R1 was the only mutated cancer gene. Strikingly, all tumors with concurrent mutation of multiple PI3K pathway genes were advanced (stage IV), implicating concerted PI3K pathway aberrations in HNSCC progression. Patient-derived tumorgrafts with canonical and non-canonical PIK3CA mutations were sensitive to an m-TOR/PI3K inhibitor (BEZ-235) in contrast to PIK3CA wildtype tumorgrafts. These results suggest that PI3K pathway mutations may serve as predictive biomarkers for treatment selection.
doi:10.1158/2159-8290.CD-13-0103
PMCID: PMC3710532  PMID: 23619167
PI3K; mutation; BEZ-235; head and neck cancer
11.  Five small heat shock protein genes from Chilo suppressalis: characteristics of gene, genomic organization, structural analysis, and transcription profiles 
Cell Stress & Chaperones  2013;19(1):91-104.
Small heat shock proteins (sHSPs) are the most diverse but also the most poorly known family of molecular chaperones, and they play essential roles in various biological processes. The striped stem borer, Chilo suppressalis (Insecta: Lepidoptera: Pyralidae), is one of the most serious pests of rice, causing extensive damage and yield loss. In this study, we isolated and characterized five members of the sHSPs family—Cshsp19.8, Cshsp21.4, Cshsp21.5, Cshsp21.7a, and Cshsp21.7b—from C. suppressalis. The cDNAs of these genes encoded proteins of 177, 187, 191, 191, and 191 amino acids with isoelectric points of 7.0, 5.6, 6.1, 6.3, and 6.3, respectively. While Cshsp19.8, Cshsp21.5, and Cshsp21.7b had no introns, Cshsp21.4 and Cshsp21.7a contained one and two introns, respectively. Structural analysis indicated that all five Cshsps possessed conserved arginine and a V/IXI/V motif, which is related to hydrophobic characteristics of sHSPs. The five heat shock proteins can be classified into two main groups: an orthologous type (Cshsp21.4 and Cshsp21.7a) and a species-specific type (Cshsp19.8, Cshsp21.5, and Cshsp21.7b). Real-time quantitative PCR analyses revealed that Cshsp19.8, Cshsp21.5, Cshsp21.7a, and Cshsp21.7b all exhibited their highest expression levels within Malpighian tubules or the hindgut, while such levels were found in the head for Cshsp21.4. The expression of Csshsps at different developmental stages revealed that the mRNA levels of Cshsp19.8, Cshsp21.4, Cshsp21.5, and Cshsp21.7b peaked in adults, whereas the highest level of Cshsp21.7a was observed in first instar larvae. Cshsp19.8 and Cshsp21.7b were both upregulated dramatically by heat and cold, and Cshsp21.5 could be induced by cold stress. Neither Cshsp21.4 nor Cshsp21.7a responded to heat or cold. These results demonstrated that different Csshsps play distinctive roles in the regulation of the physiological activities in C. suppressalis.
Electronic supplementary material
The online version of this article (doi:10.1007/s12192-013-0437-8) contains supplementary material, which is available to authorized users.
doi:10.1007/s12192-013-0437-8
PMCID: PMC3857428  PMID: 23702967
sHSPs; Chilo suppressalis; Genome; Structure; Expression; Temperature
12.  Discovery and SAR of a novel series of GIRK1/2 and GIRK1/4 activators 
This Letter describes a novel series of GIRK activators identified through an HTS campaign. The HTS lead was a potent and efficacious dual GIRK1/2 and GIRK1/4 activator. Further chemical optimization through both iterative parallel synthesis and fragment library efforts identified dual GIRK1/2 and GIRK1/4 activators as well as the first examples of selective GIRK1/4 activators. Importantly, these compounds were inactive on GIRK2 and other non-GIRK1 containing GIRK channels, and SAR proved shallow.
doi:10.1016/j.bmcl.2013.07.002
PMCID: PMC4066871  PMID: 23916258
GIRK; Kir3.x; Activators; Thallium flux
13.  Combination of ranibizumab with photodynamic therapy vs ranibizumab monotherapy in the treatment of age-related macular degeneration: a systematic review and meta-analysis of randomized controlled trials 
AIM
To compare the efficacy and safety of combination of ranibizumab with photodynamic therapy (PDT) vs ranibizumab monotherapy in the treatment of age-related macular degeneration (AMD).
METHODS
The Cochrane Central Register of Controlled Trials (CENTRAL) in the Cochrane Library, Pubmed, and Embase were searched. There were no language or data restrictions in the search for trials. Only randomized controlled trials (RCTs) were included. Methodological quality of the literatures was evaluated according to the Jadad Score. RevMan 5.2.6 software was used to do the meta-analysis.
RESULTS
Seven studies were included in our systematic review, among which four of them were included in quantitative analysis. The result shows that the ranibizumab monotherapy group had a better mean best corrected visual acuity (BCVA) change vs baseline at month 12 compared with that of the combination treatment group, and the statistical difference was significant (WMD, -2.61; 95% CI, -5.08 to -0.13; P=0.04). However, after the removal of one study, the difference between the two groups showed no significant difference (WMD, -2.29; 95% CI, -4.81 to 0.23; P=0.07). Meanwhile, no significant central retinal thickness (CRT) reduction was found in the combination treatment group and the ranibizumab monotherapy group at 12 months follow-up. Nevertheless, the combination group tended to have a greater reduction in CRT (WMD, -4.13µm; 95%CI, -25.88 to 17.63, P=0.71). The proportion of patients gaining more than 3 lines at month 12 in the ranibizumab group was higher than in the combination group and there was a significant difference (RR, 0.72; 95% CI, 0.54 to 0.95; P=0.02). Whereas there was no significant difference for the proportion of patients gaining more than 0 line at month 12 between the two groups (RR, 0.93; 95% CI, 0.76 to 1.15; P=0.52). The general tendency shows a reduction in ranibizumab retreatment number in the combination treatment group compared with the ranibizumab monotherapy group. As major adverse events, the differences in the number of eye pain, endophthalmitis, hypertension and arterial thromboembolic events were not significant between the two groups, and the incidence of serious adverse events in the two groups was very low.
CONCLUSION
For the maintenance of vision, the comparison of the combination of ranibizumab with PDT vs ranibizumab monotherapy shows no apparent difference. Compared with the combination of ranibizumab and PDT, patients treated with ranibizumab monothearpy may gain more visual acuity (VA) improvement. The combination treatment group had a tendency to reduce the number of ranibizumab retreatment. Both the two treatment strategies were well tolerated.
doi:10.3980/j.issn.2222-3959.2014.03.28
PMCID: PMC4067674  PMID: 24967206
ranibizumab; photodynamic therapy; age-related macular degeneration; meta-analysis
14.  Metformin inhibits histone H2B monoubiquitination and downstream gene transcription in human breast cancer cells 
Oncology Letters  2014;8(2):809-812.
Metformin, one of the most widely prescribed antihyperglycemic drugs, has recently received increasing attention for its potential effects with regard to cancer prevention and treatment. However, the mechanisms behind the suppression of cancer cell growth by metformin remain far from completely understood. The aim of the present study was to investigate whether metformin could regulate histone modification and its downstream gene transcription, and its potential function in inhibiting breast cancer cell proliferation. A T47D cell proliferation curve was determined by cell counting following metformin treatment with differing doses or time courses. The cell cycle was analyzed by flow cytometry with propidium iodide staining. Histone H2B monoubiquitination was evaluated by western blotting subsequent to histone extraction. The histone H2B monoubiquitination downstream gene expression level was determined by quantitative PCR. The results showed that metformin changed the cell-cycle check-point and inhibited breast cancer cell proliferation in a dose-dependent manner. AMPK was activated and histone H2B monoubiquitination and downstream gene transcription were inhibited following metformin treatment in the T47D cells. The effect of metformin on T47D cell proliferation was dependent on AMPK activity. It was concluded that metformin can suppress breast cancer cell growth by the activation of AMPK and the inhibition of histone H2B monoubiquitination and downstream gene transcription. This study reveals a novel potential mechanism of cancer cell growth suppression by metformin.
doi:10.3892/ol.2014.2158
PMCID: PMC4081422  PMID: 25009658
metformin; histone H2B; breast cancer; AMPK
15.  Two new species of the stonefly genus Amphinemura (Insecta, Plecoptera, Nemouridae) from China 
ZooKeys  2014;23-30.
Two new species of the genus Amphinemura Ris from China are described and illustrated, i.e. A. annulata Du & Ji, sp. n. from Zhejiang, Shanxi, Shaanxi and Guizhou Province, and A. lingulata Du & Wang, sp. n. from Shaanxi and Sichuan Province. A. annulata is similar to A. tricintusidens Wang & Zhu in having an apical cavity of the epiproct, but the epiproct ventral sclerite and the median paraproct lobe of the two species are different. A. lingulata is related to A. didyma Zhu & Yang in having the similar epiproct, but they differ mostly in paraproct median and outer lobes.
doi:10.3897/zookeys.404.7067
PMCID: PMC4023258  PMID: 24843269
Amphinemura; Nemouridae; Plecoptera; new species; China
16.  AMPK regulates histone H2B O-GlcNAcylation 
Nucleic Acids Research  2014;42(9):5594-5604.
Histone H2B O-GlcNAcylation is an important post-translational modification of chromatin during gene transcription. However, how this epigenetic modification is regulated remains unclear. Here we found that the energy-sensing adenosine-monophosphate-activated protein kinase (AMPK) could suppress histone H2B O-GlcNAcylation. AMPK directly phosphorylates O-linked β-N-acetylglucosamine (O-GlcNAc) transferase (OGT). Although this phosphorylation does not regulate the enzymatic activity of OGT, it inhibits OGT–chromatin association, histone O-GlcNAcylation and gene transcription. Conversely, OGT also O-GlcNAcylates AMPK and positively regulates AMPK activity, creating a feedback loop. Taken together, these results reveal a crosstalk between the LKB1-AMPK and the hexosamine biosynthesis (HBP)-OGT pathways, which coordinate together for the sensing of nutrient state and regulation of gene transcription.
doi:10.1093/nar/gku236
PMCID: PMC4027166  PMID: 24692660
17.  Draft Genome Sequence of Serratia marcescens Strain LCT-SM166, a Space Flight Strain with a Specific Carbon Source Utilization Pattern 
Genome Announcements  2014;2(1):e00069-14.
Serratia marcescens has been detected in space habitats. To explore the influence of the space flight environment on this bacterium, we investigated the genome sequence of LCT-SM166, which was isolated after space flight and has a specific carbon source utilization pattern.
doi:10.1128/genomeA.00069-14
PMCID: PMC3924376  PMID: 24526644
18.  Objective assessment of urban built environment related to physical activity — development, reliability and validity of the China Urban Built Environment Scan Tool (CUBEST) 
BMC Public Health  2014;14:109.
Background
Some aspects of the neighborhood built environment may influence residents’ physical activity, which in turn, affects their health. This study aimed to develop an urban built environment evaluation tool and conduct necessary reliability and validity tests.
Methods
A 41-item urban built environment scan tool was developed to objectively assess the neighborhood built environment features related to physical activity. Six neighborhoods in Hangzhou were selected from three types of administrative planning units. A pair of auditors independently assessed all of the 205 street segments at the same time. Half of the segments (n = 104) were audited twice by the same auditor after a two-week time interval. Inter-rater reliability was assessed by comparing the audits of paired observers, while intra-rater reliability was evaluated by comparing an auditor’s repeated assessments of the same segments. The construct validity was tested using factor analysis.
Results
The inter-rater reliability for most items was above 0.8. The intra-rater reliability for most items was above 0.4, and was lower than corresponding inter-rater reliability. Six factors were extracted by factor analysis and the factor loading matrix showed good construct validity.
Conclusions
The CUBEST is a reliable and valid instrument that can be used to assess the physical activity-related built environment in Hangzhou, and potentially other cities in China.
doi:10.1186/1471-2458-14-109
PMCID: PMC3916581  PMID: 24495676
Environmental scan; Physical activity; Reliability; Validity
19.  Diapause, signal and molecular characteristics of overwintering Chilo suppressalis (Insecta: Lepidoptera: Pyralidae) 
Scientific Reports  2013;3:3211.
Diapause is a complex and dynamic process. Chilo suppressalis, an important rice pest in Asia enters facultative diapause as larvae. Our results demonstrated in Yangzhou, China, diapause was initiated between September 4 and 12, 2010. After diapause termination, C. suppressalis remained in quiescence in the field for as long as three months. The average time between collection of field larvae of C. suppressalis and their pupation decreased as the season progressed from fall to next spring. Unexpectedly, the pupated ratio of female to male in the initiation of diapause was 0.22. The abundance of hsp90, hsp70, hsp60 and CsAQP1 all peaked on January 8 or 15, 2011. Nitric oxide (NO) is a secondary messenger that is positively correlated with the diapause of C. suppressalis. Among several geographically separated populations of C. suppressalis, there are no significant differences in the mRNA levels of hsp70, hsp60 or CsAQP1.
doi:10.1038/srep03211
PMCID: PMC3827604  PMID: 24226906
20.  MicroRNAs 185, 96, and 223 Repress Selective High-Density Lipoprotein Cholesterol Uptake through Posttranscriptional Inhibition 
Molecular and Cellular Biology  2013;33(10):1956-1964.
Hepatic scavenger receptor class B type I (SR-BI) plays an important role in selective high-density lipoprotein cholesterol (HDL-C) uptake, which is a pivotal step of reverse cholesterol transport. In this study, the potential involvement of microRNAs (miRNAs) in posttranscriptional regulation of hepatic SR-BI and selective HDL-C uptake was investigated. The level of SR-BI expression was repressed by miRNA 185 (miR-185), miR-96, and miR-223, while the uptake of 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate (DiI)-HDL was decreased by 31.9% (P < 0.001), 23.9% (P < 0.05), and 15.4% (P < 0.05), respectively, in HepG2 cells. The inhibition of these miRNAs by their anti-miRNAs had opposite effects in these hepatic cells. The critical effect of miR-185 was further validated by the loss of regulation in constructs with mutated miR-185 target sites. In addition, these miRNAs directly targeted the 3′ untranslated region (UTR) of SR-BI with a coordinated effect. Interestingly, the decrease of miR-96 and miR-185 coincided with the increase of SR-BI in the livers of ApoE KO mice on a high-fat diet. These data suggest that miR-185, miR-96, and miR-223 may repress selective HDL-C uptake through the inhibition of SR-BI in human hepatic cells, implying a novel mode of regulation of hepatic SR-BI and an important role of miRNAs in modulating cholesterol metabolism.
doi:10.1128/MCB.01580-12
PMCID: PMC3647964  PMID: 23459944
21.  A facile approach to synthesize SiO2 · Re2O3 (Re = Y, Eu, La, Sm, Tb, Pr) hollow sphere and its application in drug release 
Nanoscale Research Letters  2013;8(1):435.
Multifunctional SiO2 · Re2O3 (Re = Y, Eu, La, Sm, Tb, Pr) hollow spheres (HSs) have been fabricated using an acidic Re3+ ion solution. Under ultraviolet radiation, functional HSs emit different colors of light according to the different rare-earth ions embedded into the shell of SiO2 hollow spheres. The as-prepared hollow capsules were characterized by X-ray diffraction, transmission electron microscopy, high-resolution transmission electron microscopy, Brunauer-Emmett-Teller method, scanning electron microscopy, and energy-dispersive spectrometry. Drug loading and release experiments have been carried out using SiO2 · Eu2O3 HSs that acted as drug carriers. The results demonstrate that the multifunctional HSs exhibit a high storage capacity and the ability of retaining drug stability and activity, which indicates that the as-synthesized fluorescent hollow capsules are a potential candidate as drug delivery materials.
doi:10.1186/1556-276X-8-435
PMCID: PMC3819671  PMID: 24144278
SiO2 · Re2O3; Hollow spheres (HSs); Fluorescence
22.  An enthalpic basis of additivity in biphenyl hydroxamic acid ligands for stromelysin-1 
Fragment based drug discovery remains a successful tool for pharmaceutical lead discovery. Although based upon the principle of thermodynamic additivity, the underlying thermodynamic basis is poorly understood. A thermodynamic additivity analysis was performed using stromelysin-1 and a series of biphenyl hydroxamate ligands identified through fragment additivity. Our studies suggest that, in this instance, additivity arises from enthalpic effects, while interaction entropies are unfavorable; this thermodynamic behavior is masked by proton transfer. Evaluation of the changes in constant pressure heat capacities during binding suggest that solvent exclusion from the binding site does not account for the dramatic affinity enhancements observed.
doi:10.1016/j.bmcl.2012.05.032
PMCID: PMC3763901  PMID: 22985855
Additivity; Fragment based drug design; Stromelysin-1; Matrix metalloproteinase-3
23.  Latent Abnormal Pathology Affects Long-Term Graft Function in Elder Living Renal Allograft Recipients 
Objective. This study evaluated the long-term effects and clinical significance of latent abnormal pathology on elder living donor kidney graft function after renal transplantation in China. Methods. One-hundred and thirty-eight living donor renal transplantations have been carried out at our hospital in recent years. Of these, 72 Time-Zero biopsies were performed and used in this analysis. Clinical data were retrospectively measured at 3, 6, 12, and 24 months after renal transplants. Relationships and effects from biopsy results taken from implanted donor kidney grafts were analyzed. Results. Time-Zero biopsy pathology results from donor kidneys showed that 48.61% of donor kidneys had latent abnormal changes; arterial lesions of donor kidneys had significant effects on the renal function of grafts after 2 years' transplantation; correlations between donor age and arterial lesions were significant; and Time-Zero biopsy pathology results could help predict the long-term function of a renal graft. Conclusions. Existing latent pathological changes of an elder living donor kidney before transplantation could affect long-term renal function. Whether a senior donor is used should be very carefully considered.
doi:10.1155/2013/605704
PMCID: PMC3792505  PMID: 24171033
24.  A Chinese patient with relapsed and refractory Hodgkin lymphoma treated with brentuximab vedotin 
Chinese Journal of Cancer  2013;32(9):520-523.
At present, approximately 20% of Hodgkin lymphomas (HL) are relapsed and refractory, and therapeutic methods including chemotherapy, radiotherapy, and even stem cell transplantation are unsatisfactory. Brentuximab vedotin, composed of CD30 antibody and a chemotherapeutic agent, is a new targeted drug that eradicates tumor cells by binding to the CD30 antigen on their surface. In clinical trials, the response rate and complete remission rate of this drug were 73% and 40%, respectively, for relapsed and refractory HL. Here we report a case of CD30-positive relapsed and refractory HL that was treated with brentuximab. Before the treatment with brentuximab, the patient underwent chemotherapy, radiotherapy, and autologous stem cell transplantation. However, the disease continued to progress, affecting multiple organs and prompting symptoms such as persistent fever. After the treatment with brentuximab, the patient's condition improved. Body temperature returned to normal after 4 days. Lung nodules were reduced in size and number after a single course of treatment, and PET/CT showed partial remission and complete remission after 3 and 6 courses of treatment, respectively. The entire treatment process progressed smoothly, though the patient experienced some symptoms due to chemotherapy, including peripheral neuritis of the limbs, irritating dry cough, and mild increase in aminotransferase. No serious adverse effects were observed. The current general condition of the patient is good; the continuous complete remission has amounted to 6 months.
doi:10.5732/cjc.012.10221
PMCID: PMC3845561  PMID: 23544448
Hodgkin lymphoma; treatment; brentuximab vedotin
25.  The complete mitochondrial genomes of two rice planthoppers, Nilaparvata lugens and Laodelphax striatellus: conserved genome rearrangement in Delphacidae and discovery of new characteristics of atp8 and tRNA genes 
BMC Genomics  2013;14:417.
Background
Nilaparvata lugens (the brown planthopper, BPH) and Laodelphax striatellus (the small brown planthopper, SBPH) are two of the most important pests of rice. Up to now, there was only one mitochondrial genome of rice planthopper has been sequenced and very few dependable information of mitochondria could be used for research on population genetics, phylogeographics and phylogenetic evolution of these pests. To get more valuable information from the mitochondria, we sequenced the complete mitochondrial genomes of BPH and SBPH. These two planthoppers were infected with two different functional Wolbachia (intracellular endosymbiont) strains (wLug and wStri). Since both mitochondria and Wolbachia are transmitted by cytoplasmic inheritance and it was difficult to separate them when purified the Wolbachia particles, concomitantly sequencing the genome of Wolbachia using next generation sequencing method, we also got nearly complete mitochondrial genome sequences of these two rice planthoppers. After gap closing, we present high quality and reliable complete mitochondrial genomes of these two planthoppers.
Results
The mitogenomes of N. lugens (BPH) and L. striatellus (SBPH) are 17, 619 bp and 16, 431 bp long with A + T contents of 76.95% and 77.17%, respectively. Both species have typical circular mitochondrial genomes that encode the complete set of 37 genes which are usually found in metazoans. However, the BPH mitogenome also possesses two additional copies of the trnC gene. In both mitochondrial genomes, the lengths of the atp8 gene were conspicuously shorter than that of all other known insect mitochondrial genomes (99 bp for BPH, 102 bp for SBPH). That two rearrangement regions (trnC-trnW and nad6-trnP-trnT) of mitochondrial genomes differing from other known insect were found in these two distantly related planthoppers revealed that the gene order of mitochondria might be conservative in Delphacidae. The large non-coding fragment (the A+T-rich region) putatively corresponding responsible for the control of replication and transcription of mitochondria contained a variable number of tandem repeats (VNTRs) block in different natural individuals of these two planthoppers. Comparison with a previously sequenced individual of SBPH revealed that the mitochondrial genetic variation within a species exists not only in the sequence and secondary structure of genes, but also in the gene order (the different location of trnH gene).
Conclusion
The mitochondrial genome arrangement pattern found in planthoppers was involved in rearrangements of both tRNA genes and protein-coding genes (PCGs). Different species from different genera of Delphacidae possessing the same mitochondrial gene rearrangement suggests that gene rearrangements of mitochondrial genome probably occurred before the differentiation of this family. After comparatively analyzing the gene order of different species of Hemiptera, we propose that except for some specific taxonomical group (e.g. the whiteflies) the gene order might have diversified in family level of this order. The VNTRs detected in the control region might provide additional genetic markers for studying population genetics, individual difference and phylogeographics of planthoppers.
doi:10.1186/1471-2164-14-417
PMCID: PMC3701526  PMID: 23799924

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