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1.  Cassava genome from a wild ancestor to cultivated varieties 
Nature Communications  2014;5:5110.
Cassava is a major tropical food crop in the Euphorbiaceae family that has high carbohydrate production potential and adaptability to diverse environments. Here we present the draft genome sequences of a wild ancestor and a domesticated variety of cassava and comparative analyses with a partial inbred line. We identify 1,584 and 1,678 gene models specific to the wild and domesticated varieties, respectively, and discover high heterozygosity and millions of single-nucleotide variations. Our analyses reveal that genes involved in photosynthesis, starch accumulation and abiotic stresses have been positively selected, whereas those involved in cell wall biosynthesis and secondary metabolism, including cyanogenic glucoside formation, have been negatively selected in the cultivated varieties, reflecting the result of natural selection and domestication. Differences in microRNA genes and retrotransposon regulation could partly explain an increased carbon flux towards starch accumulation and reduced cyanogenic glucoside accumulation in domesticated cassava. These results may contribute to genetic improvement of cassava through better understanding of its biology.
Cassava is a major source of food in tropical and subtropical regions. Here the authors sequence the genomes of wild and domesticated cassava varieties and identify genes that have been selected for and against during the evolution and domestication of this economically important crop.
PMCID: PMC4214410  PMID: 25300236
2.  Radiotherapy for asymptomatic brain metastasis in epidermal growth factor receptor mutant non-small cell lung cancer without prior tyrosine kinase inhibitors treatment: a retrospective clinical study 
Non-small cell lung cancer (NSCLC) with brain metastasis (BM) harboring an epidermal growth factor receptor (EGFR) mutation shows good response to tyrosine kinase inhibitors (TKIs). This study is to assess the appropriate timing of brain radiotherapy (RT) for asymptomatic BM in EGFR mutant NSCLC patients.
There were 628 patients diagnosed with EGFR mutant NSCLC between October 2005 and December 2011. Treatment outcomes had been retrospectively evaluated in 96 patients with asymptomatic BM without prior TKI treatment. 39 patients received first-line brain RT, 23 patients received delayed brain RT, and 34 patients did not receive brain RT.
With a median follow-up of 26 months, the 2-year OS was 40.6 %. Univariate analyses revealed that ECOG performance status (p = 0.006), other distant metastases (p = 0.002) and first line systemic treatment (p = 0.032) were significantly associated with overall survival (OS). Multivariate analyses revealed that other sites of distant metastases (p = 0.030) were prognostic factor. The timing of brain RT was not significantly related to OS (p = 0.246). The 2-year BM progression-free survival (PFS) was 26.9 %. Brain RT as first-line therapy failed to demonstrate a significant association with BM PFS (p = 0.643).
First-line brain RT failed to improve long-term survival in TKI-naïve EGFR mutant NSCLC patients with asymptomatic BM. Prospective studies are needed to validate these clinical findings.
PMCID: PMC4490723  PMID: 26014133
Asymptomatic brain metastasis; Radiotherapy; Chemotherapy; Epidermal growth factor receptor mutation; Tyrosine kinase inhibitor
3.  Scoring the correlation of genes by their shared properties using OScal, an improved overlap quantification model 
Scientific Reports  2015;5:10583.
Scoring the correlation between two genes by their shared properties is a common and basic work in biological study. A prospective way to score this correlation is to quantify the overlap between the two sets of homogeneous properties of the two genes. However the proper model has not been decided, here we focused on studying the quantification of overlap and proposed a more effective model after theoretically compared 7 existing models. We defined three characteristic parameters (d, R, r) of an overlap, which highlight essential differences among the 7 models and grouped them into two classes. Then the pros and cons of the two groups of model were fully examined by their solution space in the (d, R, r) coordinate system. Finally we proposed a new model called OScal (Overlap Score calculator), which was modified on Poisson distribution (one of 7 models) to avoid its disadvantages. Tested in assessing gene relation using different data, OScal performs better than existing models. In addition, OScal is a basic mathematic model, with very low computation cost and few restrictive conditions, so it can be used in a wide-range of research areas to measure the overlap or similarity of two entities.
PMCID: PMC4445036  PMID: 26015386
5.  Construction and Analysis of High-Density Linkage Map Using High-Throughput Sequencing Data 
PLoS ONE  2014;9(6):e98855.
Linkage maps enable the study of important biological questions. The construction of high-density linkage maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. However, the marker number explosion and genotyping errors from NGS data challenge the computational efficiency and linkage map quality of linkage study methods. Here we report the HighMap method for constructing high-density linkage maps from NGS data. HighMap employs an iterative ordering and error correction strategy based on a k-nearest neighbor algorithm and a Monte Carlo multipoint maximum likelihood algorithm. Simulation study shows HighMap can create a linkage map with three times as many markers as ordering-only methods while offering more accurate marker orders and stable genetic distances. Using HighMap, we constructed a common carp linkage map with 10,004 markers. The singleton rate was less than one-ninth of that generated by JoinMap4.1. Its total map distance was 5,908 cM, consistent with reports on low-density maps. HighMap is an efficient method for constructing high-density, high-quality linkage maps from high-throughput population NGS data. It will facilitate genome assembling, comparative genomic analysis, and QTL studies. HighMap is available at
PMCID: PMC4048240  PMID: 24905985
6.  Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx) 
Science (New York, N.Y.)  2009;326(5951):433-436.
A single–base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ∼16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.
PMCID: PMC3951477  PMID: 19713493
7.  Three-dimensional conformal radiotherapy with concurrent chemotherapy for postoperative recurrence of esophageal squamous cell carcinoma: clinical efficacy and failure pattern 
To assess the therapeutic outcome and failure pattern of three-dimensional conformal radiotherapy (3D-CRT)-based concurrent chemoradiotherapy (CCRT) for recurrence of esophageal squamous cell carcinoma (SCC) after radical surgery.
Treatment outcome and failure pattern were retrospectively evaluated in 83 patients with localized cervical and thoracic recurrences after radical surgery for thoracic esophageal SCC. All patients were treated with 3DCRT-based CCRT (median radiation dose 60 Gy), in which 39 received concurrent cisplatin plus 5-fluorouracil (PF), and 44 received concurrent docetaxel plus cisplatin (TP). Treatment response was evaluated at 1–3 months after CCRT.
With a median follow-up of 34 months (range, 2–116 months), the 3-year overall survival (OS) of all the patients was 51.8% and the median OS time was 43.0 months. The overall tumor response rate was 75.9% (63/83), with a complete remission (CR) rate of 44.6% (37/83). In univariate analysis, tumor response after CCRT (p = 0.000), recurrence site (p = 0.028) and concurrent chemotherapy (p = 0.090) showed a trend favoring better OS. Multivariate analysis revealed that tumor response after CCRT (p = 0.000) and concurrent chemotherapy (p = 0.010) were independent predictors of OS. Forty-seven patients had progressive diseases after CCRT, 27 had local failure (27/47, 57.4%), 18 had distant metastasis (18/47, 38.3%) and 2 had both local and distant failures (2/47, 4.3%).
3DCRT-based CCRT is effective in postoperatively recurrent esophageal SCC. Patients that obtained complete remission after CCRT appeared to achieve long-term OS and might benefit from concurrent TP regimen. Local and distant failures remained high and prospective studies are needed to validate these factors.
PMCID: PMC3816598  PMID: 24139225
Esophageal squamous cell carcinoma; Postoperative recurrence; Concurrent chemoradiotherapy
8.  Identification and Characterization of Long Non-Coding RNAs Related to Mouse Embryonic Brain Development from Available Transcriptomic Data 
PLoS ONE  2013;8(8):e71152.
Long non-coding RNAs (lncRNAs) as a key group of non-coding RNAs have gained widely attention. Though lncRNAs have been functionally annotated and systematic explored in higher mammals, few are under systematical identification and annotation. Owing to the expression specificity, known lncRNAs expressed in embryonic brain tissues remain still limited. Considering a large number of lncRNAs are only transcribed in brain tissues, studies of lncRNAs in developmental brain are therefore of special interest. Here, publicly available RNA-sequencing (RNA-seq) data in embryonic brain are integrated to identify thousands of embryonic brain lncRNAs by a customized pipeline. A significant proportion of novel transcripts have not been annotated by available genomic resources. The putative embryonic brain lncRNAs are shorter in length, less spliced and show less conservation than known genes. The expression of putative lncRNAs is in one tenth on average of known coding genes, while comparable with known lncRNAs. From chromatin data, putative embryonic brain lncRNAs are associated with active chromatin marks, comparable with known lncRNAs. Embryonic brain expressed lncRNAs are also indicated to have expression though not evident in adult brain. Gene Ontology analysis of putative embryonic brain lncRNAs suggests that they are associated with brain development. The putative lncRNAs are shown to be related to possible cis-regulatory roles in imprinting even themselves are deemed to be imprinted lncRNAs. Re-analysis of one knockdown data suggests that four regulators are associated with lncRNAs. Taken together, the identification and systematic analysis of putative lncRNAs would provide novel insights into uncharacterized mouse non-coding regions and the relationships with mammalian embryonic brain development.
PMCID: PMC3743905  PMID: 23967161
9.  Epithelial Mesenchymal Transition Is Required for Acquisition of Anoikis Resistance and Metastatic Potential in Adenoid Cystic Carcinoma 
PLoS ONE  2012;7(12):e51549.
Human adenoid cystic carcinoma (ACC) is characterized by diffused invasion of the tumor into adjacent organs and early distant metastasis. Anoikis resistance and epithelial mesenchymal transition (EMT) are considered prerequisites for cancer cells to metastasize. Exploring the relationship between these processes and their underlying mechanism of action is a promising way to better understand ACC tumors. We initially established anoikis-resistant sublines of ACC cells; the variant cells revealed a mesenchymal phenotype through Slug-mediated EMT-like transformation and displayed enhanced metastatic potential both in vitro and in vivo. Suppression of EMT by knockdown of Slug significantly impaired anoikis resistance, migration, and invasion of the variant cells. With overexpression of Slug and Twist, we determined that induction of EMT in normal ACC cells could prevent anoikis, albeit partially. These findings strongly suggest that EMT is indispensable in anoikis resistance, at least in ACC cells. Furthermore, we found that the EGFR/PI3K/Akt pathway acts as the common regulator for EMT-like transformation and anoikis resistance, as confirmed by their specific inhibitors. Gefitinib and LY294003 restored the sensibilities of anoikis-resistant cells to anoikis and simultaneously impaired their metastatic potential. In addition, the results from our in vivo model of metastasis suggest that pretreatment with gefitinib promotes mouse survival by alleviating pulmonary metastasis. Most importantly, immunohistochemistry of human ACC specimens showed a correlation between the overexpression of Slug and EGFR staining. This study has demonstrated that Slug-mediated EMT-like transformation is required by human ACC cells to achieve anoikis resistance and their metastatic potential. Targeting the EGFR/PI3K/Akt pathway holds potential as a preventive strategy against distant metastasis of ACC.
PMCID: PMC3522696  PMID: 23272116
10.  Optimization of fatty alcohol biosynthesis pathway for selectively enhanced production of C12/14 and C16/18 fatty alcohols in engineered Escherichia coli 
With the increasing stress from oil price and environmental pollution, aroused attention has been paid to the microbial production of chemicals from renewable sources. The C12/14 and C16/18 alcohols are important feedstocks for the production of surfactants and detergents, which are widely used in the most respected consumer detergents, cleaning products and personal care products worldwide. Though bioproduction of fatty alcohols has been carried out in engineered E. coli, several key problems have not been solved in earlier studies, such as the quite low production of C16/18 alcohol, the lack of optimization of the fatty alcohol biosynthesis pathway, and the uncharacterized performance of the engineered strains in scaled-up system.
We improved the fatty alcohol production by systematically optimizing the fatty alcohol biosynthesis pathway, mainly targeting three key steps from fatty acyl-acyl carrier proteins (ACPs) to fatty alcohols, which are sequentially catalyzed by thioesterase, acyl-coenzyme A (CoA) synthase and fatty acyl-CoA reductase. By coexpression of thioesterase gene BTE, acyl-CoA synthase gene fadD and fatty acyl-CoA reductase gene acr1, 210.1 mg/L C12/14 alcohol was obtained. A further optimization of expression level of BTE, fadD and acr1 increased the C12/14 alcohol production to 449.2 mg/L, accounting for 75.0% of the total fatty alcohol production (598.6 mg/L). In addition, by coexpression of thioesterase gene ‘tesA, acyl-CoA synthase gene fadD and fatty acyl-CoA reductase gene FAR, 101.5 mg/L C16/18 alcohol was obtained, with C16/18 alcohol accounting for 89.2% of the total fatty alcohol production.
To our knowledge, this is the first report on selective production of C12/14 and C16/18 alcohols by microbial fermentation. This work achieved high-specificity production of both C12/14 and C16/18 alcohols. The encouraging 598.6 mg/L of fatty alcohols represents the highest titer reported so far. In addition, the 101.5 mg/L 89.2% C16/18 alcohol suggests an important breakthrough in C16/18 alcohol production. A more detailed optimization of the expression level of fatty alcohol biosynthesis pathway may contribute to a further improvement of fatty alcohol production.
PMCID: PMC3439321  PMID: 22607313
Fatty alcohol; Escherichia coli; Pathway optimization; Selective production; Fermentation
11.  First Report on Co-Occurrence Knockdown Resistance Mutations and Susceptibility to Beta-Cypermethrin in Anopheles sinensis from Jiangsu Province, China 
PLoS ONE  2012;7(1):e29242.
The increasing prevalence of insecticide resistance in Anopheles sinensis, a major vector of malaria in Jiangsu province in eastern China, threatens to compromise the successful use of insecticides in malaria control strategies. It is therefore vital to understand the insecticide resistance status of An. sinensis in the region. This study examined the nucleotide diversity of the para-sodium channel and knockdown resistance (kdr) in five field populations of adult An. sinensis mosquitoes collected in Jiangsu province, identifying the L1014F and L1014C substitutions for the first time. Competitive polymerase chain reaction (PCR) amplification of specific allele (cPASA) and polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) for resistance diagnosis were developed and validated. Comparing the results with direct sequencing revealed that the PCR-RFLP method was more sensitive and specific whereas the cPASA method was more convenient and suitable. The significant positive correlation between kdr allele frequency and bioassay-based resistance phenotype demonstrates that the frequency of L1014F and L1014C substitutions in the kdr gene provides a useful molecular marker for monitoring beta-cypermethrin resistance in natural populations of An. sinensis. Our results point to the L1014F substitution as the key mutation associated with beta-cypermethrin resistance. The high resistance and mutation frequency detected in the five populations also suggest cross-resistance with other pyrethroids may occur in An. sinensis, highlighting the need for further surveys to map insecticide resistance in China and the adoption of a rational management of insecticide application for resistance management and mosquito vector control.
PMCID: PMC3260143  PMID: 22272229
12.  Chinese Culture, Homosexuality Stigma, Social Support and Condom Use: A Path Analytic Model 
Stigma research and action  2011;1(1):27-35.
The objective of this study was to examine the interrelationships among individualism, collectivism, homosexuality-related stigma, social support, and condom use among Chinese homosexual men.
A cross-sectional study using the respondent-driven sampling approach was conducted among 351 participants in Shenzhen, China. Path analytic modeling was used to analyze the interrelationships.
The results of path analytic modeling document the following statistically significant associations with regard to homosexuality: (1) higher levels of vertical collectivism were associated with higher levels of public stigma [β (standardized coefficient) = 0.12] and self stigma (β = 0.12); (2) higher levels of vertical individualism were associated with higher levels self stigma (β = 0.18); (3) higher levels of horizontal individualism were associated with higher levels of public stigma (β = 0.12); (4) higher levels of self stigma were associated with higher levels of social support from sexual partners (β = 0.12); and (5) lower levels of public stigma were associated with consistent condom use (β = −0.19).
The findings enhance our understanding of how individualist and collectivist cultures influence the development of homosexuality-related stigma, which in turn may affect individuals’ decisions to engage in HIV-protective practices and seek social support. Accordingly, the development of HIV interventions for homosexual men in China should take the characteristics of Chinese culture into consideration.
PMCID: PMC3124705  PMID: 21731850
collectivism; HIV/AIDS; homosexuality; individualism
13.  CADgene: a comprehensive database for coronary artery disease genes 
Nucleic Acids Research  2010;39(Database issue):D991-D996.
Coronary artery disease (CAD) is a complex, multifactorial disease and a leading cause of mortality world wide. Over the past decades, great efforts have been made to elucidate the underlying genetic basis of CAD and massive data have been accumulated. To integrate these data together and to provide a useful resource for researchers, we developed the CADgene, a comprehensive database for CAD genes. We manually extracted CAD-related evidence for more than 300 candidate genes for CAD from over 1300 publications of genetic studies. We classified these candidate genes into 12 functional categories based on their roles in CAD. For each gene, we extracted detailed information from related studies (e.g. the size of case–control, population, SNP, odds ratio, P-value, etc.) and made useful annotations, which include general gene information, Gene Ontology annotations, KEGG pathways, protein–protein interactions and others. Besides the statistical number of studies for each gene, CADgene also provides tools to search and show the most frequently studied candidate genes. In addition, CADgene provides cumulative data from 11 publications of CAD-related genome-wide association studies. CADgene has a user-friendly web interface with multiple browse and search functions. It is freely available at
PMCID: PMC3013698  PMID: 21045063
14.  LPS-induced down-regulation of signal regulatory protein α contributes to innate immune activation in macrophages 
The Journal of Experimental Medicine  2007;204(11):2719-2731.
Activation of the mitogen-activated protein kinases (MAPKs) and nuclear factor κB (NF-κB) cascades after Toll-like receptor (TLR) stimulation contributes to innate immune responses. Signal regulatory protein (SIRP) α, a member of the SIRP family that is abundantly expressed in macrophages, has been implicated in regulating MAPK and NF-κB signaling pathways. In addition, SIRPα can negatively regulate the phagocytosis of host cells by macrophages, indicating an inhibitory role of SIRPα in innate immunity. We provide evidences that SIRPα is an essential endogenous regulator of the innate immune activation upon lipopolysaccharide (LPS) exposure. SIRPα expression was promptly reduced in macrophages after LPS stimulation. The decrease in SIRPα expression levels was required for initiation of LPS-induced innate immune responses because overexpression of SIRPα reduced macrophage responses to LPS. Knockdown of SIRPα caused prolonged activation of MAPKs and NF-κB pathways and augmented production of proinflammatory cytokines and type I interferon (IFN). Mice transferred with SIRPα-depleted macrophages were highly susceptible to endotoxic shock, developing multiple organ failure and exhibiting a remarkable increase in mortality. SIRPα may accomplish this mainly through its association and sequestration of the LPS signal transducer SHP-2. Thus, SIRPα functions as a biologically important modulator of TLR signaling and innate immunity.
PMCID: PMC2118489  PMID: 17954568
15.  Elevated Levels of Serum Tumor Markers CEA and CA15-3 Are Prognostic Parameters for Different Molecular Subtypes of Breast Cancer 
PLoS ONE  2015;10(7):e0133830.
Background & Aims
The utility of measuring carcinoembryonic antigen(CEA) and cancer antigen 15-3 (CA15-3) levels in patients with breast cancer remains controversial. The present study aims to investigate the prognostic value of preoperative serum CEA and CA15-3 levels in breast cancer patients.
Serum preoperative CEA and CA 15-3 concentration levels were measured in a total of 432 breast cancer patients. The association of tumor markers levels with clinicopathological parameters and outcomes were analyzed.
Elevated serum levels of CEA and CA15-3 were identified in 47 (10.9%) and 60(13.9%) patients, respectively. Larger tumor size, advanced axillary lymph nodal and TNM stage exhibited higher proportion of elevated CEA and CA15-3 levels. The elevation of CEA levels was significantly greater in patients with HER2 positive tumors, and the elevation of CA15-3 levels was significantly greater in ER negative breast patients. Univariate and multivariate Cox’s regression analysis revealed that elevated preoperative CEA and CA 15-3 levels were independent prognostic factors for DFS and OS. When considering the combination of both markers levels, patients with both elevated markers presented the worst survival. Independent prognostic significance of elevated preoperative serum CEA and CA15-3 levels were reconfirmed in Luminal B breast cancer.
Preoperative serum levels of CEA and CA15-3 are independent prognostic parameters for breast cancer.
PMCID: PMC4514648  PMID: 26207909
16.  Anterior D-rod and titanium mesh fixation for acute mid-lumbar burst fracture with incomplete neurologic deficits: A prospective study of 56 consecutive patients 
Indian Journal of Orthopaedics  2015;49(4):471-477.
Anterior decompression and reconstruction have gained wide acceptance as viable alternatives for unstable mid-lumbar burst fracture, but there are no mid and long term prospective studies regarding clinical and radiologic results of mid-lumbar burst fractures.
Materials and Methods:
An Institutional Review Board-approved prospective study of 56 consecutive patients of mid-lumbar burst fractures with a load-sharing score of 7 or more treated with anterior plating was carried out. All patients were evaluated for radiologic and clinical outcomes. The fusion status, spinal canal compromise, segmental kyphotic angle (SKA), vertebral body height loss (VBHL), and adjacent segment degeneration was examined for radiologic outcome, whereas the American Spinal Injury Association scale, the visual analog scale (VAS), and the employment status were used for clinical evaluation.
The patients underwent clinical and radiologic followup for at least 5 years after the surgery. At the last followup, there was no case of internal fixation failure, adjacent segment degeneration, and other complications. Interbody fusion was achieved in all cases. The average fusion time was 4.5 months. No patient suffered neurological deterioration and the average neurologic recovery was 1.3 grades on final observation. Based on VAS pain scores, canal compromise, percentage of VBHL and SKA, the difference was statistically significant between the preoperative period and postoperative or final followup (P < 0.05). Results at postoperative and final followup were better than the preoperative period. However, the difference was not significant between postoperative and final followup (P > 0.05). Thirty-four patients who were employed before the injury returned to work after the operation, 15 had changed to less strenuous work.
Good mid term clinicoradiological results of anterior decompression with D-rod and titanium mesh fixation for suitable patients with mid-lumbar burst fractures with incomplete neurologic deficits can be achieved. The incident rate of complications was low. D-rod is a reliable implant and has some potential advantages in L4 vertebral fractures.
PMCID: PMC4510804
Anterior lumbar fusion; internal fixation; lumbar burst fractures; mesh cage; neurologic deficit; Lumbar vertebrae; fracture fixation; spinal cord compression; neurologic deficits
17.  Surgical induced astigmatism correlated with corneal pachymetry and intraocular pressure: transconjunctival sutureless 23-gauge versus 20-gauge sutured vitrectomy in diabetes mellitus 
To determine the difference of surgical induced astigmatism between conventional 20-gauge sutured vitrectomy and 23-gauge transconjunctival sutureless vitrectomy, and the influence of corneal pachymetry and intraocular pressure (IOP) on surgical induced astigmatism in diabetic patients.
This retrospective, consecutive case series consisted of 40 eyes of 38 diabetic subjects who underwent either 20-gauge or 23-gauge vitrectomy. The corneal curvature and thickness were measured with Scheimpflug imaging before surgery and 1wk; 1, 3mo after surgery. We compared the surgical induced astigmatism (SIA) on the true net power in 23-gauge group with that in 20-gauge group. We determined the correlation between corneal thickness change ratio, IOP and SIA measured by Pentacam.
The mean SIAs were 1.082±0.085 D (mean±SEM), 0.689±0.070 D and 0.459±0.063 D at postoperative 1wk; 1, 3mo respectively in diabetic subjects. The vitrectomy induced astigmatisms were declined significantly with time (F2,36=33.629, P=0.000) postoperatively. The 23-gauge surgery group induced significantly less astigmatism than 20-gauge surgery group (F-1,37=11.046, P=0.020). Corneal thickness in diabetes elevated after surgery (F3,78=10.532, P=0.000). The linear regression analysis at postoperatively 1wk went as: SIA=-4.519+4.931 change ratio (Port3) +0.026 IOP (R2=0.46, P=0.000), whereas the rate of corneal thickness change and IOP showed no correlation with the change of astigmatism at postoperatively 1 and 3mo.
There are significant serial changes in both 20-gauge and 23-gauge group in diabetic subjects. 23-gauge induce less astigmatism than 20-gauge and become stable more rapidly than 20-gauge. The elevation of corneal thickness and IOP was associated with increased astigmatim at the early postoperative stage both in 23-gauge and 20-gauge surgery group.
PMCID: PMC4458657  PMID: 26086002
astigmatism; corneal pachymetry; vitrectomy; intraocular pressure; diabetes mellitus
18.  Low Serum Testosterone Levels Are Associated with Elevated Urinary Mandelic Acid, and Strontium Levels in Adult Men According to the US 2011–2012 National Health and Nutrition Examination Survey 
PLoS ONE  2015;10(5):e0127451.
Little is known regarding the effects of environmental exposure of chemicals on androgenic system in the general population. We studied 5,107 subjects included in the National Health and Nutrition Examination Survey (2011–2012).
Urinary, serum, and blood levels of 15 subclasses comprising 110 individual chemicals were analyzed for their association with serum testosterone levels. The subjects were divided into high and low testosterone groups according to the median testosterone concentration (374.51 ng/dL). Odds ratios (ORs) of individual chemicals in association with testosterone were estimated using logistic regression after adjusting for age, ethnicity, cotinine, body mass index, creatinine, alcohol, and the poverty income ratio.
Adjusted ORs for the highest versus lowest quartiles of exposure were 2.12 (95% CI: 1.07, 4.21; Ptrend = 0.044), 1.84 (95% CI: 1.02, 3.34; Ptrend = 0.018) for the association between urinary mandelic acid, and strontium quartiles with low testosterone concentrations in adult men, respectively. However, no association was observed for the remaining chemicals with testosterone.
The National Health and Nutrition Examination Survey data suggest that elevations in urinary mandelic acid, and strontium levels are negatively related to low serum testosterone levels in adult men.
PMCID: PMC4440739  PMID: 25996772
19.  Physiological and Comparative Proteomic Analysis Reveals Different Drought Responses in Roots and Leaves of Drought-Tolerant Wild Wheat (Triticum boeoticum) 
PLoS ONE  2015;10(4):e0121852.
To determine the proteomic-level responses of drought tolerant wild wheat (Triticum boeoticum), physiological and comparative proteomic analyses were conducted using the roots and the leaves of control and short term drought-stressed plants. Drought stress was imposed by transferring hydroponically grown seedlings at the 3-leaf stage into 1/2 Hoagland solution containing 20% PEG-6000 for 48 h. Root and leaf samples were separately collected at 0 (control), 24, and 48 h of drought treatment for analysis. Physiological analysis indicated that abscisic acid (ABA) level was greatly increased in the drought-treated plants, but the increase was greater and more rapid in the leaves than in the roots. The net photosynthetic rate of the wild wheat leaves was significantly decreased under short-term drought stress. The deleterious effects of drought on the studied traits mainly targeted photosynthesis. Comparative proteomic analysis identified 98 and 85 differently changed protein spots (DEPs) (corresponding to 87 and 80 unique proteins, respectively) in the leaves and the roots, respectively, with only 6 mutual unique proteins in the both organs. An impressive 86% of the DEPs were implicated in detoxification and defense, carbon metabolism, amino acid and nitrogen metabolism, proteins metabolism, chaperones, transcription and translation, photosynthesis, nucleotide metabolism, and signal transduction. Further analysis revealed some mutual and tissue-specific responses to short-term drought in the leaves and the roots. The differences of drought-response between the roots and the leaves mainly included that signal sensing and transduction-associated proteins were greatly up-regulated in the roots. Photosynthesis and carbon fixation ability were decreased in the leaves. Glycolysis was down-regulated but PPP pathway enhanced in the roots, resulting in occurrence of complex changes in energy metabolism and establishment of a new homeostasis. Protein metabolism was down-regulated in the roots, but enhanced in the leaves. These results will contribute to the existing knowledge on the complexity of root and leaf protein changes that occur in response to drought, and also provide a framework for further functional studies on the identified proteins.
PMCID: PMC4393031  PMID: 25859656
20.  Abnormal immunomodulatory ability on memory T cells in humans with severe aplastic anemia 
Severe aplastic anemia (SAA) is a bone marrow failure disease induced by hyperfunctional autoimmunic Th1 lymphocytes. Memory T cells (TM) are a component of the adaptive immune system. They ensure the host of more aggressive and faster immune response to efficiently eliminate the specific antigens after re-exposure and thus play a key role in T-cell functions. In this study we investigate the quantities and functions of memory T cells in SAA patients before and after immunosuppressive therapy (IST) to further clarify the mechanism of SAA apoptosis of bone marrow hematopoietic cells. Results showed that the percentage of CD4+ effector T cells in peripheral blood and bone marrow lymphocytes was decreased in SAA patients. The ratio of CD4+ memory T lymphocytes to CD8+ memory T subsets (CD4+/CD8+TM) in SAA patients was also lower. The percentage of CD8+ effector T cells in peripheral blood and CD8+ central memory T cells in the bone marrow lymphocytes was significantly higher in newly diagnosed patients. Furthermore, the median expressions of perforin and granzyme B on memory T cells were higher in SAA patients compared to those in normal controls. After IST, the quantities and functions of memory T cells return to normal level. Therefore, we concluded that the abnormal immunomodulatory ability on memory T cells may contribute to the imbalance of Th1/Th2 subsets and thus lead to over-function of T lymphocytes and hematopoiesis failure in SAA.
PMCID: PMC4466934  PMID: 26097547
Severe aplastic anemia; memory T cells; perforin; ganzyme B
21.  Comparative transcriptome analyses on silk glands of six silkmoths imply the genetic basis of silk structure and coloration 
BMC Genomics  2015;16(1):203.
Silk has numerous unique properties that make it a staple of textile manufacturing for several thousand years. However, wider applications of silk in modern have been stalled due to limitations of traditional silk produced by Bombyx mori. While silk is commonly produced by B. mori, several wild non-mulberry silkmoths--especially members of family Saturniidae--produce silk with superior properties that may be useful for wider applications. Further utilization of such silks is hampered by the non-domestication status or limited culturing population of wild silkworms. To date there is insufficient basic genomic or transcriptomic data on these organisms or their silk production.
We sequenced and compared the transcriptomes of silk glands of six Saturniidae wild silkmoth species through next-generation sequencing technology, identifying 37758 ~ 51734 silkmoth unigenes, at least 36.3% of which are annotated with an e-value less than 10−5. Sequence analyses of these unigenes identified a batch of genes specific to Saturniidae that are enriched in growth and development. Analyses of silk proteins including fibroin and sericin indicate intra-genus conservation and inter-genus diversification of silk protein features among the wild silkmoths, e.g., isoelectric points, hydrophilicity profile and amino acid composition in motifs of silk H-fibroin. Interestingly, we identified p25 in two of the silkmoths, which were previously predicted to be absent in Saturniidae. There are rapid evolutionary changes in sericin proteins, which might account for the highly heterogeneity of sericin in Saturniidae silkmoths. Within the six sikmoths, both colored-cocoon silkmoth specific transcripts and differentially expressed genes between the colored-cocoon and non-colored-cocoon silkmoths are significantly enriched in catalytic activity, especially transferase activity, suggesting potentially viable targets for future gene mining or genetic manipulation.
Our results characterize novel and potentially valuable gene resources of saturniid silkmoths that may facilitate future genetic improvement and modification of mulberry silkworms. Our results suggest that the disparate features of silk--coloration, retention, strength, etc. --are likely not only due to silk proteins, but also to the environment of silk assembly, and more specifically, that stable silk coloration exhibited by some Saturniidae silkmoths may be attributable to active catalytic progress in pigmentation.
Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1420-9) contains supplementary material, which is available to authorized users.
PMCID: PMC4372302  PMID: 25886738
Silkmoths; Comparative transcriptomics; Silk proteins; Silk coloration
22.  Mouse SIRT3 Attenuates Hypertrophy-Related Lipid Accumulation in the Heart through the Deacetylation of LCAD 
PLoS ONE  2015;10(3):e0118909.
Cardiac hypertrophy is an adaptive response to pressure, volume stress, and loss of contractile mass from prior infarction. Metabolic changes in cardiac hypertrophy include suppression of fatty acid oxidation and enhancement of glucose utilization, which could result in lipid accumulation in the heart. SIRT3, a mitochondrial NAD+-dependent deacetylase, has been demonstrated to play a crucial role in controlling the acetylation status of many enzymes participating in energy metabolism. However, the role of SIRT3 in the pathogenesis of hypertrophy-related lipid accumulation remains unclear. In this study, hypertrophy-related lipid accumulation was investigated using a mouse cardiac hypertrophy model induced by transverse aortic constriction (TAC). We showed that mice developed heart failure six weeks after TAC. Furthermore, abnormal lipid accumulation and decreased palmitate oxidation rates were observed in the hypertrophic hearts, and these changes were particularly significant in SIRT3-KO mice. We also demonstrated that the short form of SIRT3 was downregulated in wild-type (WT) hypertrophic hearts and that this change was accompanied by a higher acetylation level of long-chain acyl CoA dehydrogenase (LCAD), which is a key enzyme participating in fatty acid oxidation. In addition, SIRT3 may play an essential role in attenuating lipid accumulation in the heart through the deacetylation of LCAD.
PMCID: PMC4351969  PMID: 25748450
23.  Day 3 ET, single blastocyst transfer (SBT) or frozen-thawed embryo transfer (FET): which is preferable for high responder patients in IVF/ICSI cycles? 
To compare the clinical outcomes after day 3 embryo transfer, day 5 single blastocyst transfer (SBT) and frozen-thawed embryo transfer (FET) in high responder patients (>15 retrieved oocytes) undergoing IVF/ICSI treatment.
A retrospective analysis of three embryo transfer strategies for the high responder patients in IVF/ICSI cycles. The 1041 high responder patients diagnosed as primary infertility with more than 15 oocytes retrieved were recruited in Day 3 ET group, 308 patients with more than 15 oocytes retrieved first transferred with one blastocyst in SBT group and 425 patients with more than 15 oocytes retrieved in fresh cycle, first transferred with one frozen-thawed blastocyst were assigned in FET group.
In the high responder patients, the clinical pregnancy rate after day 5 SBT was significantly lower than that of day 3 ET (43.18 % VS 57.16 %, p < 0.05). In addition, the clinical pregnant rate and implantation rate of FET cycles were significantly higher than SBT cycles (59.06 % vs. 43.18 % and 64.70 % vs. 47.40 %, p < 0.05). The multiple pregnancy rate in FET cycles was markedly lower than that of day 3 ET (2.35 % VS 34.97 %, p < 0.05).
FET was the preferable strategy for the high responder patients in IVF/ICSI cycles to obtain both desirable clinical outcome and lower multiple pregnancy rates.
PMCID: PMC3947074  PMID: 24390677
Day 3 embryo transfer; SBT; High responder patients; IVF/ICSI cycles
24.  Apparent diffusion coefficient measurements and Gd-DTPA enhanced-imaging in staging hepatic fibrosis in rats 
To evaluate the utility of ADC values and Gd-DTPA equilibrium phase MR imaging in staging hepatic fibrosis in rats. 48 rats were allocated into experimental and control groups. Experimental rats were subcutaneously injected with a mixture of CCl4. From 4th-12th weeks, MR images were obtained, which include pre-enhanced phase imaging, DWI and equilibrium phase imaging. Then the rat groups were subdivided according to the stages of fibrosis (S0, S1, S2, S3 and S4) after histopathological analysis. The original MRI data were forwarded to the workstation to obtain apparent diffusion coefficient (ADC) maps at b value of 500 s/mm2. Pre-enhanced phase and equilibrium phase signal intensities and relative contrast enhancement index (RCEI) were measured as well. Lastly, the ADC values and RCEI of the experimental group were compared with each other and with the control group. All statistical analyses were carried out with SPSS, where P < 0.05 is considered to represent a significant difference. Hepatic ADC values are significantly different between the experimental and control groups (P = 0). There is a statistically significant difference between the experimental and control groups on RCEI (P = 0). Comparing the S1, S2, S3 and S4 groups, there is a statistically significant difference between the mild group (S1 and S2) and the severe group (S4) in terms of ADC values and RCEI (all P < 0.05). A statistically significant difference is also found between the moderate group (S3) and the severe group in ADC values. As the degree of fibrosis increases, there are a reduction in ADC values and an increase in RCEI. Comparing the groups with ADC values and enhancement index, there are statistically significant differences in sensitivity and specificity on diagnosis of hepatic fibrosis. The ADC values have the best sensitivity (93.1%) and specificity (83.3%). Quantitative ADC values and RCEI may be helpful to the staging of rat fibrosis, but their application in human is controversial.
PMCID: PMC4402798  PMID: 25932151
Hepatic fibrosis staging; magnetic resonance imaging; apparent diffusion coefficient; equilibrium phase imaging; rat model
25.  Genetic alterations of histone lysine methyltransferases and their significance in breast cancer 
Oncotarget  2014;6(4):2466-2482.
Histone lysine methyltransferases (HMTs), a large class of enzymes that catalyze site-specific methylation of lysine residues on histones and other proteins, play critical roles in controlling transcription, chromatin architecture, and cellular differentiation. However, the genomic landscape and clinical significance of HMTs in breast cancer remain poorly characterized. Here, we conducted a meta-analysis of approximately 50 HMTs in breast cancer and identified associations among recurrent copy number alterations, mutations, gene expression, and clinical outcome. We identified 12 HMTs with the highest frequency of genetic alterations, including 8 with high-level amplification, 2 with putative homozygous deletion, and 2 with somatic mutation. Different subtypes of breast cancer have different patterns of copy number and expression for each HMT gene. In addition, chromosome 1q contains four HMTs that are concurrently or independently amplified or overexpressed in breast cancer. Copy number or mRNA expression of several HMTs was significantly associated with basal-like breast cancer and shorter patient survival. Integrative analysis identified 8 HMTs (SETDB1, SMYD3, ASH1L, SMYD2, WHSC1L1, SUV420H1, SETDB2, and KMT2C) that are dysregulated by genetic alterations, classifying them as candidate therapeutic targets. Together, our findings provide a strong foundation for further mechanistic research and therapeutic options using HMTs to treat breast cancer.
PMCID: PMC4385864  PMID: 25537518
breast cancer; histone lysine methyltransferase; gene amplification; deletion; mutation

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