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1.  Extrapyramidal signs by dementia severity in Alzheimer’s disease and dementia with Lewy bodies 
Alzheimer’s disease (AD) and dementia with Lewy bodies (DLB) are common etiologies of dementia with overlapping clinical features. Our objective was to determine which extrapyramidal signs (EPS) are most helpful in identifying DLB. We analyzed data from the National Alzheimer’s Coordinating Center, including demographics, Unified Parkinson’s Disease Rating Scale (UPDRS) scores, Mini Mental State Exam (MMSE) scores, and clinical diagnosis. The subjects were divided into three groups: AD, DLB or LBV (Lewy body variant). The UPDRS motor scores were totaled and analyzed within and across MMSE strata using regression techniques. Next, we divided UPDRS subscores into 9 EPS, dichotomized as either present or absent. Logistic regression analysis was used to compare each of the EPS in the AD and LB (DLB+LBV) groups. DLB subjects (n=130) were more likely to be male, younger, and have higher MMSE scores (p<0.001) than AD (n=1,826) or LBV (n=105) subjects. Differences were found for total UPDRS score and number of EPS (p<0.001), after controlling for age, gender and MMSE. Logistic regression models demonstrated that masked facies best differentiated AD from LB (OR=6.5, p<0.001, 95% CI: 3.8–11.1). If these findings are neuropathologically validated, then the presence of specific EPS may help clinicians better differentiate AD and DLB.
doi:10.1097/WAD.0b013e31826f040d
PMCID: PMC3562426  PMID: 23023095
2.  Variations in the PDCD6 Gene Are Associated with Increased Uterine Leiomyoma Risk in the Chinese 
Programmed cell death 6 (PDCD6) participates in T cell receptor, Fas, and glucocorticoid—induced programmed cell death. To test the relationship between PDCD6 polymorphisms and uterine leiomyomas (UL) risk, we investigated the association of two SNPs (rs4957014 and rs3756712) in PDCD6 with UL risk in a case–control study of 295 unrelated premenopausal UL patients and 436 healthy postmenopausal control subjects in a population of China. Genotypes of the two SNPs were determined with the use of PCR-restriction fragment length polymorphism assay. Significantly increased UL risks were found to be associated with the T allele of rs4957014 and the T allele of rs3756712 (p=0.016, odds ratio [OR]=1.325, 95% confidence intervals [CI]=1.053–1.668 for rs4957014; p<0.0001, OR=1.898, 95% CI=1.457–2.474 for rs3756712, respectively). Increased UL risks were associated with them in different genetic models. The present study provided evidence that rs4957014 and rs3756712 are associated with UL risk, the results indicated that genetic polymorphisms in PDCD6 may contribute to the development of UL.
doi:10.1089/gtmb.2012.0461
PMCID: PMC3700461  PMID: 23551056
3.  miRNAs in Human Cancer 
MicroRNAs (miRNAs) are small (~18–25 nucleotides), endogenous, noncoding RNAs that regulate gene expression in a sequence-specific manner via the degradation of target mRNAs or the inhibition of protein translation. miRNAs are predicted to target up to one-third of all human mRNAs. Each miRNA can target hundreds of transcripts and proteins directly or indirectly, and more than one miRNA can converge on a single target transcript; thus, the potential regulatory circuitry afforded by miRNAs is enormous. Increasing evidence is revealing that the expression of miRNAs is deregulated in cancer. High-throughput miRNA quantification technologies provide powerful tools to study global miRNA profiles. It has become progressively more apparent that, although the number of miRNAs (~1,000) is much smaller than the number of protein-coding genes (~22,000), miRNA expression signatures more accurately reflect the developmental lineage and tissue origin of human cancers. Large-scale studies in human cancer have further demonstrated that miRNA expression signatures are associated not only with specific tumor subtypes but also with clinical outcomes.
doi:10.1007/978-1-61779-427-8_21
PMCID: PMC4076826  PMID: 22144208
MicroRNA; Noncoding RNA; Cancer
4.  Receptor Interactive Protein Kinase 3 Promotes Cisplatin-Triggered Necrosis in Apoptosis-Resistant Esophageal Squamous Cell Carcinoma Cells 
PLoS ONE  2014;9(6):e100127.
Cisplatin-based chemotherapy is currently the standard treatment for locally advanced esophageal cancer. Cisplatin has been shown to induce both apoptosis and necrosis in cancer cells, but the mechanism by which programmed necrosis is induced remains unknown. In this study, we provide evidence that cisplatin induces necrotic cell death in apoptosis-resistant esophageal cancer cells. This cell death is dependent on RIPK3 and on necrosome formation via autocrine production of TNFα. More importantly, we demonstrate that RIPK3 is necessary for cisplatin-induced killing of esophageal cancer cells because inhibition of RIPK1 activity by necrostatin or knockdown of RIPK3 significantly attenuates necrosis and leads to cisplatin resistance. Moreover, microarray analysis confirmed an anti-apoptotic molecular expression pattern in esophageal cancer cells in response to cisplatin. Taken together, our data indicate that RIPK3 and autocrine production of TNFα contribute to cisplatin sensitivity by initiating necrosis when the apoptotic pathway is suppressed or absent in esophageal cancer cells. These data provide new insight into the molecular mechanisms underlying cisplatin-induced necrosis and suggest that RIPK3 is a potential marker for predicting cisplatin sensitivity in apoptosis-resistant and advanced esophageal cancer.
doi:10.1371/journal.pone.0100127
PMCID: PMC4069059  PMID: 24959694
5.  Impacts of a Nanosized Ceria Additive on Diesel Engine Emissions of Particulate and Gaseous Pollutants 
Environmental science & technology  2013;47(22):13077-13085.
Fuel additives incorporating nanosized ceria have been increasingly used in diesel engines as combustion promoters. However, few studies have assessed the impact of these nanotechnology-based additives on pollutant emissions. Here, we systematically compare emission rates of particulate and gaseous pollutants from a single-cylinder, four-cycle diesel engine using fuel mixes containing nanoceria of varying concentrations. The test fuels were made by adding different amounts of a commercial fuel additive Envirox into an ultralow-sulfur diesel fuel at 0 (base fuel), 0.1-, 1-, and 10-fold the manufacturer-recommended concentration of 0.5 mL Envirox per liter of fuel. The addition of Envirox resulted in ceria-concentration-dependent emission reductions of CO2, CO, total particulate mass, formaldehyde, acetaldehyde, acrolein, and several polycyclic aromatic hydrocarbons. These reductions at the manufacturer-recommended doping concentration, however, were accompanied by a substantial increase of certain other air pollutants, specifically the number of ultrafine particles (+32%), NOx (+9.3%), and the particle-phase benzo[a]pyrene toxic equivalence quotient (+35%). Increasing fuel ceria concentrations also led to decreases in the size of emitted particles. Given health concerns related to ultrafine particles and NOx, our findings call for additional studies to further evaluate health risks associated with the use of nanoceria additives in various engines under various operating conditions.
doi:10.1021/es402140u
PMCID: PMC4066369  PMID: 24144266
6.  3D Face Recognition Based on Multiple Keypoint Descriptors and Sparse Representation 
PLoS ONE  2014;9(6):e100120.
Recent years have witnessed a growing interest in developing methods for 3D face recognition. However, 3D scans often suffer from the problems of missing parts, large facial expressions, and occlusions. To be useful in real-world applications, a 3D face recognition approach should be able to handle these challenges. In this paper, we propose a novel general approach to deal with the 3D face recognition problem by making use of multiple keypoint descriptors (MKD) and the sparse representation-based classification (SRC). We call the proposed method 3DMKDSRC for short. Specifically, with 3DMKDSRC, each 3D face scan is represented as a set of descriptor vectors extracted from keypoints by meshSIFT. Descriptor vectors of gallery samples form the gallery dictionary. Given a probe 3D face scan, its descriptors are extracted at first and then its identity can be determined by using a multitask SRC. The proposed 3DMKDSRC approach does not require the pre-alignment between two face scans and is quite robust to the problems of missing data, occlusions and expressions. Its superiority over the other leading 3D face recognition schemes has been corroborated by extensive experiments conducted on three benchmark databases, Bosphorus, GavabDB, and FRGC2.0. The Matlab source code for 3DMKDSRC and the related evaluation results are publicly available at http://sse.tongji.edu.cn/linzhang/3dmkdsrcface/3dmkdsrc.htm.
doi:10.1371/journal.pone.0100120
PMCID: PMC4062431  PMID: 24940876
7.  Searching for the Definition of Macrosomia through an Outcome-Based Approach 
PLoS ONE  2014;9(6):e100192.
Background
Macrosomia has been defined in various ways by obstetricians and researchers. The purpose of the present study was to search for a definition of macrosomia through an outcome-based approach.
Methods
In a study of 30,831,694 singleton term live births and 38,053 stillbirths in the U.S. Linked Birth-Infant Death Cohort datasets (1995–2004), we compared the occurrence of stillbirth, neonatal death, and 5-min Apgar score less than four in subgroups of birthweight (4000–4099 g, 4100–4199 g, 4200–4299 g, 4300–4399 g, 4400–4499 g, 4500–4999 g vs. reference group 3500–4000 g) and birthweight percentile for gestational age (90th–94th percentile, 95th-96th, and ≥97th percentile, vs. reference group 75th–90th percentile).
Results
There was no significant increase in adverse perinatal outcomes until birthweight exceeded the 97th percentile. Weight-specific odds ratios (ORs) elevated substantially to 2 when birthweight exceeded 4500 g in Whites. In Blacks and Hispanics, the aORs exceeded 2 for 5-min Apgar less than four when birthweight exceeded 4300 g. For vaginal deliveries, the aORs of perinatal morbidity and mortality were larger for most of the subgroups, but the patterns remained the same.
Conclusions
A birthweight greater than 4500 g in Whites, or 4300 g in Blacks and Hispanics regardless of gestational age is the optimal threshold to define macrosomia. A birthweight greater than the 97th percentile for a given gestational age, irrespective of race is also reasonable to define macrosomia. The former may be more clinically useful and simpler to apply.
doi:10.1371/journal.pone.0100192
PMCID: PMC4062533  PMID: 24941024
8.  Diabetic cardiomyopathy is associated with defective myocellular copper regulation and both defects are rectified by divalent copper chelation 
Background
Heart disease is the leading cause of death in diabetic patients, and defective copper metabolism may play important roles in the pathogenesis of diabetic cardiomyopathy (DCM). The present study sought to determine how myocardial copper status and key copper-proteins might become impaired by diabetes, and how they respond to treatment with the Cu (II)-selective chelator triethylenetetramine (TETA) in DCM.
Methods
Experiments were performed in Wistar rats with streptozotocin (STZ)-induced diabetes with or without TETA treatment. Cardiac function was analyzed in isolated-perfused working hearts, and myocardial total copper content measured by particle-induced x-ray emission spectroscopy (PIXE) coupled with Rutherford backscattering spectrometry (RBS). Quantitative expression (mRNA and protein) and/or activity of key proteins that mediate LV-tissue-copper binding and transport, were analyzed by combined RT-qPCR, western blotting, immunofluorescence microscopy, and enzyme activity assays. Statistical analysis was performed using Student’s t-tests or ANOVA and p-values of < 0.05 have been considered significant.
Results
Left-ventricular (LV) copper levels and function were severely depressed in rats following 16-weeks’ diabetes, but both were unexpectedly normalized 8-weeks after treatment with TETA was instituted. Localized myocardial copper deficiency was accompanied by decreased expression and increased polymerization of the copper-responsive transition-metal-binding metallothionein proteins (MT1/MT2), consistent with impaired anti-oxidant defences and elevated susceptibility to pro-oxidant stress. Levels of the high-affinity copper transporter-1 (CTR1) were depressed in diabetes, consistent with impaired membrane copper uptake, and were not modified by TETA which, contrastingly, renormalized myocardial copper and increased levels and cell-membrane localization of the low-affinity copper transporter-2 (CTR2). Diabetes also lowered indexes of intracellular (IC) copper delivery via the copper chaperone for superoxide dismutase (CCS) to its target cuproenzyme, superoxide dismutase-1 (SOD1): this pathway was rectified by TETA treatment, which normalized SOD1 activity with consequent bolstering of anti-oxidant defenses. Furthermore, diabetes depressed levels of additional intracellular copper-transporting proteins, including antioxidant-protein-1 (ATOX1) and copper-transporting-ATPase-2 (ATP7B), whereas TETA elevated copper-transporting-ATPase-1 (ATP7A).
Conclusions
Myocardial copper deficiency and defective cellular copper transport/trafficking are revealed as key molecular defects underlying LV impairment in diabetes, and TETA-mediated restoration of copper regulation provides a potential new class of therapeutic molecules for DCM.
doi:10.1186/1475-2840-13-100
PMCID: PMC4070334  PMID: 24927960
Diabetic cardiomyopathy; Copper-deficiency cardiomyopathy; Left-ventricular dysfunction; Myocellular copper; Copper transporters; Superoxide dismutase 1; Copper chaperones; Cu (II)-chelation; Copper metalation; Heart failure
9.  Self-Sterility in Camellia oleifera May Be Due to the Prezygotic Late-Acting Self-Incompatibility 
PLoS ONE  2014;9(6):e99639.
In this report, self-sterility in Camellia oleifera was explored by comparing structural and statistical characteristics following self-pollination (SP) and cross-pollination (CP). Although slightly delayed pollen germination and pollen tube growth in selfed ovaries compared to crossed ovaries was observed, there was no significant difference in the percentages of pollen that germinated and pollen tubes that grew to the base of the style. There was also no difference in morphological structure after the two pollination treatments. However, the proportions of ovule penetration and double fertilization in selfed ovules were significantly lower than in crossed ovules, indicating that a prezygotic late-acting self-incompatible mechanism may exist in C. oleifera. Callose deposition was observed in selfed abortive ovules, but not in normal. Ovules did not show differences in anatomic structure during embryonic development, whereas significant differences were observed in the final fruit and seed set. In addition, aborted ovules in selfed ovaries occurred within 35 days after SP and prior to zygote division. However, this process did not occur continuously throughout the life cycle, and no zygotes were observed in the selfed abortive ovules. These results indicated that the self-sterility in C. oleifera may be caused by prezygotic late-acting self-incompatibility (LSI).
doi:10.1371/journal.pone.0099639
PMCID: PMC4057179  PMID: 24926879
10.  Quantification of 1-aminopyrene in human urine after a controlled exposure to diesel exhaust 
Diesel exhaust (DE) is a significant source of air pollution that has been linked to respiratory and cardiovascular morbidity and mortality. Many components in DE, such as polycyclic aromatic hydrocarbons, are present in the environment from other sources. 1-Nitropyrene appears to be a more specific marker of DE exposure. 1-Nitropyrene is partially metabolized to 1-aminopyrene and excreted in urine. We developed a practical, sensitive method for measuring 1-aminopyrene in human urine using a HPLC-fluorescence technique. We measured 1-aminopyrene concentrations in spot urine samples collected prior to and during 24 h following the start of 1 h controlled exposures to DE (target concentration 300 μg m−3 as PM10) and clean air control. Time-weighted-average concentrations of urinary 1-aminopyrene were significantly greater following the DE exposure compared to the control (median 138.7 ng g−1 creatinine vs. 21.7 ng g−1 creatinine, p < 0.0001). Comparing DE to control exposures, we observed significant increases in 1-aminopyrine concentration from pre-exposure to either first post-exposure void or peak spot urine concentration following exposure (p = 0.027 and p = 0.0026, respectively). Large inter-individual variability, in both the concentration of urinary 1-aminopyrene and the time course of appearance in the urine following the standardized exposure to DE, suggests the need to explore subject variables that may affect conversion of inhaled 1-nitropyrene to urinary excretion of 1-aminopyrene.
doi:10.1039/b810039j
PMCID: PMC4049318  PMID: 19137151
11.  Malondialdehyde in exhaled breath condensate and urine as a biomarker of air pollution induced oxidative stress 
Underlying mechanisms by which air pollutants adversely affect human health remain poorly understood. Oxidative stress has been considered as a potential mechanism that may promote lipid peroxidation by reactive oxygen species, leading to the formation of malondialdehyde (MDA) that is excreted in biofluids (e.g., urine and exhaled breath condensate (EBC)). A panel study was conducted to examine whether concentrations of MDA in EBC and urine were associated, respectively, with changes in air pollution levels brought by the Beijing Olympic air pollution control measures. EBC and urine samples from 125 healthy adults were collected twice in each of the pre-, during-, and post-Olympic periods. Period-specific means of MDA and changes in MDA levels associated with increases in 24-h average pollutant concentrations were estimated using linear mixed-effects models. From the pre- to the during-Olympic period, when concentrations of most pollutants decreased, EBC MDA and urinary MDA significantly decreased by 24% (P < 0.0001) and 28% (P = 0.0002), respectively. From the during-Olympic to the post-Olympic period, when concentrations of most pollutants increased, EBC MDA and urinary MDA increased by 28% (P = 0.094) and 55% (P = 0.046), respectively. Furthermore, the largest increases in EBC MDA associated with one interquartile range (IQR) increases in all pollutants but ozone ranged from 10% (95% CI: 2%, 18%) to 19% (95% CI: 14%, 25%). The largest increases in urinary MDA associated with IQR increases in pollutant concentration ranged from 9% (95%: 0.3%, 19%) to 15% (95% CI: 3%, 28%). These findings support the utility of EBC MDA as a biomarker of oxidative stress in the respiratory tract and urinary MDA as a biomarker of systemic oxidative stress in relation to air pollution exposure in healthy young adults. Both EBC and urine samples can be collected noninvasively in the general population.
doi:10.1038/jes.2012.127
PMCID: PMC4049321  PMID: 23321859
The Beijing Olympics; lipid peroxidation; malondialdehyde; oxidative stress; exhaled breath condensate
12.  Exploring the Electron Transfer Pathway in the Oxidation of Avermectin by CYP107Z13 in Streptomyces ahygroscopicus ZB01 
PLoS ONE  2014;9(6):e98916.
Streptomyces ahygroscopicus ZB01 can effectively oxidize 4″-OH of avermectin to form 4″-oxo-avermectin. CYP107Z13 is responsible for this site-specific oxidation in ZB01. In the present study, we explored the electron transfer pathway in oxidation of avermectin by CYP107Z13 in ZB01. A putative [3Fe-4S] ferredoxin gene fd68 and two possible NADH-dependent ferredoxin reductase genes fdr18 and fdr28 were cloned from the genomic DNA of ZB01. fd68 gene disruption mutants showed no catalytic activity in oxidation of avermectin to form 4″-oxo-avermectin. To clarify whether FdR18 and FdR28 participate in the electron transfer during avermectin oxidation by CYP107Z13, two whole-cell biocatalytic systems were designed in E. coli BL21 (DE3), with one co-expressing CYP107Z13, Fd68 and FdR18 and the other co-expressing CYP107Z13, Fd68 and FdR28. Both of the two biocatalytic systems were found to be able to mediate the oxidation of avermectin to form 4″-oxo-avermectin. Thus, we propose an electron transfer pathway NADH→FdR18/FdR28→Fd68→CYP107Z13 for oxidation of avermectin to form 4″-oxo-avermectin in ZB01.
doi:10.1371/journal.pone.0098916
PMCID: PMC4048220  PMID: 24905717
13.  MicroRNAs: New therapeutic targets for intestinal barrier dysfunction 
Defects in intestinal barrier function characterized by an increase in intestinal permeability contribute to intestinal inflammation. Growing evidence has shown that an increase in intestinal permeability has a pathogenic role in diseases such as inflammatory bowel disease (IBD) and celiac disease, and functional bowel disorders such as irritable bowel syndrome. Therefore, clarification of the inflammatory responses, the defense pathway and the corresponding regulatory system is essential and may lead to the development of new therapies. MicroRNAs (miRNAs) are small (19-22 nt) noncoding RNA molecules that regulate genes at the post-transcriptional level by base-pairing to specific messenger RNAs for degradation to repress translation. Recent studies suggested that miRNAs are important in the immune response and mediate a critical role in multiple immune response-related disorders. Based on these discoveries, attention has been focused on understanding the role of miRNAs in regulating intestinal barrier dysfunction, especially in IBD. Here, we provide a review of the most recent state-of-the-art research on miRNAs in intestinal barrier dysfunction.
doi:10.3748/wjg.v20.i19.5818
PMCID: PMC4024791  PMID: 24914342
MicroRNAs; Intestinal barrier dysfunction; Inflammatory bowel disease; Celiac disease; Therapeutic target
14.  Global Analysis of Gene Expression Profiles in Physic Nut (Jatropha curcas L.) Seedlings Exposed to Salt Stress 
PLoS ONE  2014;9(5):e97878.
Background
Salt stress interferes with plant growth and production. Plants have evolved a series of molecular and morphological adaptations to cope with this abiotic stress, and overexpression of salt response genes reportedly enhances the productivity of various crops. However, little is known about the salt responsive genes in the energy plant physic nut (Jatropha curcas L.). Thus, excavate salt responsive genes in this plant are informative in uncovering the molecular mechanisms for the salt response in physic nut.
Methodology/Principal Findings
We applied next-generation Illumina sequencing technology to analyze global gene expression profiles of physic nut plants (roots and leaves) 2 hours, 2 days and 7 days after the onset of salt stress. A total of 1,504 and 1,115 genes were significantly up and down-regulated in roots and leaves, respectively, under salt stress condition. Gene ontology (GO) analysis of physiological process revealed that, in the physic nut, many “biological processes” were affected by salt stress, particular those categories belong to “metabolic process”, such as “primary metabolism process”, “cellular metabolism process” and “macromolecule metabolism process”. The gene expression profiles indicated that the associated genes were responsible for ABA and ethylene signaling, osmotic regulation, the reactive oxygen species scavenging system and the cell structure in physic nut.
Conclusions/Significance
The major regulated genes detected in this transcriptomic data were related to trehalose synthesis and cell wall structure modification in roots, while related to raffinose synthesis and reactive oxygen scavenger in leaves. The current study shows a comprehensive gene expression profile of physic nut under salt stress. The differential expression genes detected in this study allows the underling the salt responsive mechanism in physic nut with the aim of improving its salt resistance in the future.
doi:10.1371/journal.pone.0097878
PMCID: PMC4023963  PMID: 24837971
15.  Variability in Bioreactivity Linked to Changes in Size and Zeta Potential of Diesel Exhaust Particles in Human Immune Cells 
PLoS ONE  2014;9(5):e97304.
Acting as fuel combustion catalysts to increase fuel economy, cerium dioxide (ceria, CeO2) nanoparticles have been used in Europe as diesel fuel additives (Envirox™). We attempted to examine the effects of particles emitted from a diesel engine burning either diesel (diesel exhaust particles, DEP) or diesel doped with various concentrations of CeO2 (DEP-Env) on innate immune responses in THP-1 and primary human peripheral blood mononuclear cells (PBMC). Batches of DEP and DEP-Env were obtained on three separate occasions using identical collection and extraction protocols with the aim of determining the reproducibility of particles generated at different times. However, we observed significant differences in size and surface charge (zeta potential) of the DEP and DEP-Env across the three batches. We also observed that exposure of THP-1 cells and PBMC to identical concentrations of DEP and DEP-Env from the three batches resulted in statistically significant differences in bioreactivity as determined by IL-1β, TNF-α, IL-6, IFN-γ, and IL-12p40 mRNA (by qRT-PCR) and protein expression (by ELISPOT assays). Importantly, bioreactivity was noted in very tight ranges of DEP size (60 to 120 nm) and zeta potential (−37 to −41 mV). Thus, these physical properties of DEP and DEP-Env were found to be the primary determinants of the bioreactivity measured in this study. Our findings also point to the potential risk of over- or under- estimation of expected bioreactivity effects (and by inference of public health risks) from bulk DEP use without taking into account potential batch-to-batch variations in physical (and possibly chemical) properties.
doi:10.1371/journal.pone.0097304
PMCID: PMC4019517  PMID: 24825358
16.  Crizotinib induces PUMA-dependent apoptosis in colon cancer cells 
Molecular cancer therapeutics  2013;12(5):777-786.
Oncogenic alterations in MET or ALK have been identified in a variety of human cancers. Crizotinib (PF02341066) is a dual MET and ALK inhibitor and approved for the treatment of a subset of non-small-cell lung carcinoma; and in clinical development for other malignancies. Crizotinib can induce apoptosis in cancer cells while the underlying mechanisms are not well understood. In this study, we found that crizotinib induces apoptosis in colon cancer cells through the BH3-only protein PUMA. In cells with wild-type p53, crizotinib induces rapid induction of PUMA and Bim accompanied by p53 stabilization and DNA damage response. The induction of PUMA and Bim is mediated largely by p53, and deficiency in PUMA or p53, but not Bim, blocks crizotinib-induced apoptosis. Interestingly, MET knockdown led to selective induction of PUMA, but not Bim or p53. Crizotinib also induced PUMA-dependent apoptosis in p53-deficient colon cancer cells, and synergized with gefitinib or sorafenib to induce marked apoptosis via PUMA in colon cancer cells. Furthermore, PUMA deficiency suppressed apoptosis and therapeutic responses to crizotinib in xenograft models. These results establish a critical role of PUMA in mediating apoptotic responses of colon cancer cells to crizotinib, and suggest that mechanisms of oncogenic addiction to MET/ALK-mediated survival might be cell-type specific. These findings have important implications for future clinical development of crizotinib.
doi:10.1158/1535-7163.MCT-12-1146
PMCID: PMC3651803  PMID: 23427294
crizotinib; PUMA; p53; apoptosis; colon cancer
17.  Baicalin Inhibits Hypoxia-Induced Pulmonary Artery Smooth Muscle Cell Proliferation via the AKT/HIF-1α/p27-Associated Pathway 
Baicalin, a flavonoid compound purified from the dry roots of Scutellaria baicalensis Georgi, has been shown to possess various pharmacological actions. Previous studies have revealed that baicalin inhibits the growth of cancer cells through the induction of apoptosis. Pulmonary arterial hypertension (PAH) is a devastating disease characterized by enhanced pulmonary artery smooth muscle cell (PASMCs) proliferation and suppressed apoptosis. However, the potential mechanism of baicalin in the regulation of PASMC proliferation and the prevention of cardiovascular diseases remains unexplored. To test the effects of baicalin on hypoxia, we used rats treated with or without baicalin (100 mg·kg−1 each rat) at the beginning of the third week after hypoxia. Hemodynamic and pulmonary pathomorphology data showed that right ventricular systolic pressures (RVSP), the weight of the right ventricle/left ventricle plus septum (RV/LV + S) ratio and the medial width of pulmonary arterioles were much higher in chronic hypoxia. However, baicalin treatment repressed the elevation of RVSP, RV/LV + S and attenuated the pulmonary vascular structure remodeling (PVSR) of pulmonary arterioles induced by chronic hypoxia. Additionally, baicalin (10 and 20 μmol·L−1) treatment suppressed the proliferation of PASMCs and attenuated the expression of hypoxia-inducible factor-α (HIF-α) under hypoxia exposure. Meanwhile, baicalin reversed the hypoxia-induced reduction of p27 and increased AKT/protein kinase B phosphorylation p-AKT both in vivo and in vitro. These results suggested that baicalin could effectively attenuate PVSR and hypoxic pulmonary hypertension.
doi:10.3390/ijms15058153
PMCID: PMC4057725  PMID: 24821539
baicalin; pulmonary hypertension; pulmonary artery smooth muscle cells; proliferation
18.  Clusterin silencing inhibits proliferation and reduces invasion in human laryngeal squamous carcinoma cells 
Background
Clusterin is, in its major form, a secreted heterodimeric disulfide-linked glycoprotein (sCLU), which plays important roles in cell survival and death. In laryngeal squamous cell carcinomas (LSCC), sCLU is up-regulated and its expression is related to the invasiveness of these tumors. The purpose of this study was to explore the inhibiting role of sCLU gene silence in the invasive ability and growth of Hep-2 human laryngeal squamous carcinoma cells (Hep-2) by transfection of short hairpin RNA expression plasmids against sCLU (sCLU-shRNA) (in vivo) or small interference RNA (sCLU-siRNA) (in vitro).
Methods
sCLU-siRNA and the control siRNA were transfected into Hep-2 cells using Lipofectamine 2000. RT-PCR and Western blot were used to detect the effect of siRNA transfection on sCLU mRNA and sCLU protein expression. The invasive activity of sCLU-siRNA-transfected Hep-2 cells was measured with the modified Boyden chamber assay and wound healing assay. The effects of sCLU-siRNA on cell proliferation were evaluated by MTT assay. Apoptosis was measured by Annexin V-fluorescein isothiocyanate (FITC)/propidium iodide (PI) double-staining methods. We next evaluated the effects of sCLU silencing by sCLU-shRNA transfection in vivo on tumor growth and metastatic properties to the lung. Terminal deoxytransferase-mediated dUTP nick end labeling (TUNEL) staining was used to observe the apoptosis in the xenografts.
Results
It showed that siRNA-mediated down-regulation of sCLU expression in Hep-2 cells significantly inhibited cell proliferation and promoted apoptosis in vitro. Furthermore, siRNA-mediated down-regulation of sCLU expression decreases in vitro cell migration and invasion ability. In vivo, the average volume of tumors in the sCLU-shRNA transfected group was significantly lower than in the control group (P <0.01), and the significant apoptosis detected with TUNEL was indicated in the sCLU-shRNA transfected groups (P <0.05). Significantly, we found that sCLU-shRNA could exert marked inhibition of the lung metastasis of Hep-2 cells in nude mice in vivo.
Conclusions
sCLU gene silence can inhibit invasion and growth of LSCC. sCLU may provide a potential therapeutic target against human LSCC.
doi:10.1186/1477-7819-12-124
PMCID: PMC4016627  PMID: 24767179
Laryngeal squamous carcinoma; Clusterin; Proliferation; Apoptosis; Invasion; Gene treatment
19.  Cognitive, Anxiety, and Mood Disorders in the Fragile X-associated Tremor/Ataxia Syndrome (FXTAS) 
General hospital psychiatry  2007;29(4):349-356.
Objective
The authors evaluated patients with Fragile X-associated Tremor/Ataxia Syndrome (FXTAS), a neurodegenerative disorder associated with a CGG repeat expansion in the premutation range in the fragile X mental retardation 1 gene (FMR1).
Method
Neurological, psychiatric, and neuropsychological evaluations were completed on 15 males with FXTAS.
Results
Seven cases were diagnosed with dementia; seven were diagnosed with mood and/or anxiety disorders. Twelve subjects demonstrated deficits on neuropsychological testing.
Conclusions
Physicians assessing dementia patients are urged to consider this newly-described syndrome, especially in patients with dementia associated with a movement disorder and in patients with family history of mental retardation. If FXTAS is a possible diagnosis, the physician may obtain FMR1 DNA testing; patients who are positive on DNA testing should have an MRI, be referred to neurology, and receive genetic counseling
doi:10.1016/j.genhosppsych.2007.03.003
PMCID: PMC3991490  PMID: 17591512
FXTAS; fragile X premutation; dementia; anxiety disorder; mood disorder
20.  3D Ear Identification Based on Sparse Representation 
PLoS ONE  2014;9(4):e95506.
Biometrics based personal authentication is an effective way for automatically recognizing, with a high confidence, a person’s identity. Recently, 3D ear shape has attracted tremendous interests in research field due to its richness of feature and ease of acquisition. However, the existing ICP (Iterative Closet Point)-based 3D ear matching methods prevalent in the literature are not quite efficient to cope with the one-to-many identification case. In this paper, we aim to fill this gap by proposing a novel effective fully automatic 3D ear identification system. We at first propose an accurate and efficient template-based ear detection method. By utilizing such a method, the extracted ear regions are represented in a common canonical coordinate system determined by the ear contour template, which facilitates much the following stages of feature extraction and classification. For each extracted 3D ear, a feature vector is generated as its representation by making use of a PCA-based local feature descriptor. At the stage of classification, we resort to the sparse representation based classification approach, which actually solves an l1-minimization problem. To the best of our knowledge, this is the first work introducing the sparse representation framework into the field of 3D ear identification. Extensive experiments conducted on a benchmark dataset corroborate the effectiveness and efficiency of the proposed approach. The associated Matlab source code and the evaluation results have been made publicly online available at http://sse.tongji.edu.cn/linzhang/ear/srcear/srcear.htm.
doi:10.1371/journal.pone.0095506
PMCID: PMC3989323  PMID: 24740247
21.  RNA Sequencing Analysis Reveals Transcriptomic Variations in Tobacco (Nicotiana tabacum) Leaves Affected by Climate, Soil, and Tillage Factors 
The growth and development of plants are sensitive to their surroundings. Although numerous studies have analyzed plant transcriptomic variation, few have quantified the effect of combinations of factors or identified factor-specific effects. In this study, we performed RNA sequencing (RNA-seq) analysis on tobacco leaves derived from 10 treatment combinations of three groups of ecological factors, i.e., climate factors (CFs), soil factors (SFs), and tillage factors (TFs). We detected 4980, 2916, and 1605 differentially expressed genes (DEGs) that were affected by CFs, SFs, and TFs, which included 2703, 768, and 507 specific and 703 common DEGs (simultaneously regulated by CFs, SFs, and TFs), respectively. GO and KEGG enrichment analyses showed that genes involved in abiotic stress responses and secondary metabolic pathways were overrepresented in the common and CF-specific DEGs. In addition, we noted enrichment in CF-specific DEGs related to the circadian rhythm, SF-specific DEGs involved in mineral nutrient absorption and transport, and SF- and TF-specific DEGs associated with photosynthesis. Based on these results, we propose a model that explains how plants adapt to various ecological factors at the transcriptomic level. Additionally, the identified DEGs lay the foundation for future investigations of stress resistance, circadian rhythm and photosynthesis in tobacco.
doi:10.3390/ijms15046137
PMCID: PMC4013620  PMID: 24733065
climate factors; soil factors; tillage factors; tobacco leaves; transcriptome; RNA-seq
22.  Role of Bcl-xL/Beclin-1 in Interplay between Apoptosis and Autophagy in Oxaliplatin and Bortezomib-induced Cell Death 
Biochemical pharmacology  2014;88(2):178-188.
Recent studies indicate that a complex relationship exists between autophagy and apoptosis. In this study we investigated a regulatory relationship between autophagy and apoptosis in colorectal cancer cells utilizing molecular and biochemical approaches. For this study, human colorectal carcinoma HCT116 and CX-1 cells were treated with two chemotherapeutic agents—oxaliplatin, which induces apoptosis, and bortezomib, which triggers both apoptosis and autophagy. A combinatorial treatment of oxaliplatin and bortezomib caused a synergistic induction of apoptosis which was mediated through an increase in caspase activation. The combinational treatment of oxaliplatin and bortezomib promoted the JNK-Bcl-xL-Bax pathway which modulated the synergistic effect through the mitochondria-dependent apoptotic pathway. JNK signaling led to Bcl-xL phosphorylation at serine 62, oligomerization of Bax, alteration of mitochondrial membrane potential, and subsequent cytochrome c release. Overexpression of dominant-negative mutant of Bcl-xL (S62A), but not dominant-positive mutant of Bcl-xL (S62D), suppressed cytochrome c release and synergistic death effect. Interestingly, Bcl-xL also affected autophagy through alteration of interaction with Beclin-1. Beclin-1 was dissociated from Bcl-xL and initiated autophagy during treatment with oxaliplatin and bortezomib. However, activated caspase 8 cleaved Beclin-1 and suppressed Beclin-1-associated autophagy and enhanced apoptosis. A combinatorial treatment of oxaliplatin and bortezomib-induced Beclin-1 cleavage was abolished in Beclin-1 double mutant (D133AA/D149A) knock-in HCT116 cells, restoring the autophagy-promoting function of Beclin-1 and suppressing the apoptosis induced by the combination therapy. In addition, the combinatorial treatment significantly inhibited colorectal cancer xenografts’ tumor growth. An understanding of the molecular mechanisms of crosstalk between apoptosis and autophagy will support the application of combinatorial treatment to colorectal cancer.
doi:10.1016/j.bcp.2014.01.027
PMCID: PMC3969586  PMID: 24486574
Oxaliplatin; Bortezomib; Mitochondria-dependent pathway; Bcl-xL; Beclin-1
23.  Pulmonary lymphangitic carcinomatosis in liver carcinoma: a rare case report and literature review 
Primary liver carcinoma is the most important malignant disease. The nodular metastatic foci of liver carcinoma are usually found in the lung, adrenal gland or abdomen after resection or transplantation. Pulmonary lymphangitic carcinomatosis (PLC) accounts for approximately 6% to 8% of metastatic cancer in the lung. The occurrence of PLC is extremely rare in liver carcinoma. Herein we report the case of a patient with PLC after liver transplantation due to liver carcinoma. PLC was confirmed by clinical manifestations, imaging studies and cytologic examination of exfoliated cells in the pleural effusion.
doi:10.1186/1477-7819-12-66
PMCID: PMC3986917  PMID: 24669948
Liver carcinoma; Liver transplantation; Metastasis; Pulmonary lymphangitic carcinomatosis
24.  A Designed Experiments Approach to Optimization of Automated Data Acquisition during Characterization of Bacteria with MALDI-TOF Mass Spectrometry 
PLoS ONE  2014;9(3):e92720.
MALDI-TOF MS has been shown capable of rapidly and accurately characterizing bacteria. Highly reproducible spectra are required to ensure reliable characterization. Prior work has shown that spectra acquired manually can have higher reproducibility than those acquired automatically. For this reason, the objective of this study was to optimize automated data acquisition to yield spectra with reproducibility comparable to those acquired manually. Fractional factorial design was used to design experiments for robust optimization of settings, in which values of five parameters (peak selection mass range, signal to noise ratio (S:N), base peak intensity, minimum resolution and number of shots summed) commonly used to facilitate automated data acquisition were varied. Pseudomonas aeruginosa was used as a model bacterium in the designed experiments, and spectra were acquired using an intact cell sample preparation method. Optimum automated data acquisition settings (i.e., those settings yielding the highest reproducibility of replicate mass spectra) were obtained based on statistical analysis of spectra of P. aeruginosa. Finally, spectrum quality and reproducibility obtained from non-optimized and optimized automated data acquisition settings were compared for P. aeruginosa, as well as for two other bacteria, Klebsiella pneumoniae and Serratia marcescens. Results indicated that reproducibility increased from 90% to 97% (p-value0.002) for P. aeruginosa when more shots were summed and, interestingly, decreased from 95% to 92% (p-value 0.013) with increased threshold minimum resolution. With regard to spectrum quality, highly reproducible spectra were more likely to have high spectrum quality as measured by several quality metrics, except for base peak resolution. Interaction plots suggest that, in cases of low threshold minimum resolution, high reproducibility can be achieved with fewer shots. Optimization yielded more reproducible spectra than non-optimized settings for all three bacteria.
doi:10.1371/journal.pone.0092720
PMCID: PMC3963954  PMID: 24662978
25.  PEG-Farnesylthiosalicylate Conjugate as a Nanomicellar Carrier for Delivery of Paclitaxel 
Bioconjugate chemistry  2013;24(3):464-472.
S-trans, trans-farnesylthiosalicylic acid (FTS) is a synthetic small molecule that acts as a potent and especially nontoxic Ras antagonist. It inhibits both oncogenically activated Ras and growth factor receptor-mediated Ras activation, resulting in the inhibition of Ras-dependent tumor growth. In this work, a FTS conjugate with polyethylene glycol (PEG) through a labile ester linkage, PEG5K-FTS2(L), was developed. PEG5K-FTS2 conjugate readily forms micelles in aqueous solutions with a critical micelle concentration of 0.68 μM and hydrophobic drugs such as paclitaxel (PTX) could be effectively loaded into these particles. Both drug-free and PTX- loaded micelles were spherical in shape with a uniform size of 20 ~ 30 nm. The release of PTX from PTX-loaded PEG5K-FTS2 micelles was significantly slower than that from Taxol formulation. In vitro cytotoxicity studies with several tumor cell lines showed that PEG5K-FTS2(L) was comparable to FTS in antitumor activity. Western immunoblotting showed that total Ras levels were downregulated in several cancer cell lines treated with FTS or PEG5K-FTS2(L). The micellar formulation of PTX exhibited more in vitro cytotoxic activity against several tumor cell lines compared with free PTX, suggesting a possible synergistic effect between the carrier and the codelivered drug. The anti-tumor activity of the PTX loaded PEG5K-FTS2(L) micelles in a syngeneic murine breast cancer model was found to be significantly higher than that of Taxol, which may be attributed to their preferential tumor accumulation and a possible synergistic effect between PEG5K-FTS2 carrier and loaded PTX.
doi:10.1021/bc300608h
PMCID: PMC3623935  PMID: 23425093

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