Citation counts for peer-reviewed articles and the impact factor of journals have long been indicators of article importance or quality. In the Web 2.0 era, growing numbers of scholars are using scholarly social network tools to communicate scientific ideas with colleagues, thereby making traditional indicators less sufficient, immediate, and comprehensive. In these new situations, the altmetric indicators offer alternative measures that reflect the multidimensional nature of scholarly impact in an immediate, open, and individualized way. In this direction of research, some studies have demonstrated the correlation between altmetrics and traditional metrics with different samples. However, up to now, there has been relatively little research done on the dimension and interaction structure of altmetrics.
Our goal was to reveal the number of dimensions that altmetric indicators should be divided into and the structure in which altmetric indicators interact with each other.
Because an article-level metrics dataset is collected from scholarly social media and open access platforms, it is one of the most robust samples available to study altmetric indicators. Therefore, we downloaded a large dataset containing activity data in 20 types of metrics present in 33,128 academic articles from the application programming interface website. First, we analyzed the correlation among altmetric indicators using Spearman rank correlation. Second, we visualized the multiple correlation coefficient matrixes with graduated colors. Third, inputting the correlation matrix, we drew an MDS diagram to demonstrate the dimension for altmetric indicators. For correlation structure, we used a social network map to represent the social relationships and the strength of relations.
We found that the distribution of altmetric indicators is significantly non-normal and positively skewed. The distribution of downloads and page views follows the Pareto law. Moreover, we found that the Spearman coefficients from 91.58% of the pairs of variables indicate statistical significance at the .01 level. The non-metric MDS map divided the 20 altmetric indicators into three clusters: traditional metrics, active altmetrics, and inactive altmetrics. The social network diagram showed two subgroups that are tied to each other but not to other groups, thus indicating an intersection between altmetrics and traditional metric indicators.
Altmetrics complement, and most correlate significantly with, traditional measures. Therefore, in future evaluations of the social impact of articles, we should consider not only traditional metrics but also active altmetrics. There may also be a transfer phenomenon for the social impact of academic articles. The impact transfer path has transfer, or intermediate, stations that transport and accelerate article social impact from active altmetrics to traditional metrics and vice versa. This discovery will be helpful to explain the impact transfer mechanism of articles in the Web 2.0 era. Hence, altmetrics are in fact superior to traditional filters for assessing scholarly impact in multiple dimensions and in terms of social structure.
altmetrics; article-level metrics; scholarly social network tools; indicator; dimension; structure
This retrospective study evaluated trends and association between resistance of Pseudomonas aeruginosa isolated from patients with hospital-acquired infections (HAIs) and hospital antimicrobial usage from 2003 through 2011 in a tertiary care hospital in northeast China. HAI was defined as occurrence of infection after hospital admission, without evidence that infection was present or incubating (≦48 h) on admission. In vitro susceptibilities were determined by disk diffusion test and susceptibility profiles were determined using zone diameter interpretive criteria, as recommended by Clinical and Laboratory Standards Institute (CLSI). Data on usage of various antimicrobial agents, expressed as defined daily dose (DDD) per 1,000 patients-days developed by WHO Anatomical Therapeutical Chemical (ATC)/DDD index 2011, were collected from hospital pharmacy computer database. Most of 747 strains of P. aeruginosa were collected from respiratory samples (201 isolates, 26.9%), blood (179, 24.0%), secretions and pus (145, 19.4%) over the years. Time series analysis demonstrated a significant increase in resistance rates of P. aeruginosa to ticarcillin/clavulanic acid, piperacillin/tazobactam, cefoperazone/sulbactam, piperacillin, imipenem, meropenem, ceftazidime, cefepime, ciprofloxacin, and levofloxacin except aminoglycosides over time in the hospital (P<0.001). The rates of carbapenem-resistant P. aeruginosa (CRPA) isolated from patients with HAIs were 14.3%, 17.1%, 21.1%, 24.6%, 37.0%, 48.8%, 56.4%, 51.2%, and 54.1% over time. A significant increase in usage of anti-pseudomonal carbapenems (P<0.001) was seen. ARIMA models demonstrated that anti-pseudomonal carbapenems usage was strongly correlated with the prevalence of imipenem and meropenem-resistant P. aeruginosa (P<0.001). Increasing of quarterly CRPA was strongly correlated at one time lag with quarterly use of anti-pseudomonal carbapenems (P<0.001). Our data demonstrated positive correlation between anti-pseudomonal antimicrobial usage and P. aeruginosa resistance to several classes of antibiotics, but not all antimicrobial agents in the hospital.
Oral ibuprofen has demonstrated good effects on symptomatic patent ductus arteriosus (PDA) but with many contraindications and potential side-effects. In the past two years, oral paracetamol administration to several preterm infants with PDA has been reported. Here, a randomized, non-blinded, parallel-controlled and non-inferiority trial was designed to evaluate the efficacy and safety profiles of oral paracetamol to those of standard ibuprofen for PDA closure in premature infants.
One hundred and sixty infants (gestational age ≤34 weeks) with echocardiographically confirmed PDA were randomly assigned to receive either oral paracetamol (n = 80) or ibuprofen (n = 80). After the initial treatment course in both groups, the need for a second course was determined by echocardiographic evaluation. The main outcome was rate of ductal closure, and secondary outcomes were adverse effects and complications.
The ductus was closed in 65 (81.2%) infants of the paracetamol group compared with 63 (78.8%) of the ibuprofen group. The 95% confidence interval of the difference between these groups was [−0.080,0.128], demonstrating that the effectiveness of paracetamol treatment was not inferior to that of ibuprofen. In fact, the incidence of hyperbilirubinemia or gastrointestinal bleeding in the paracetamol group was significantly lower than that of the ibuprofen group. No significant differences in other clinical side effects or complications were noted.
This comparison of drug efficacy and safety profiles in premature infants with PDA revealed that oral paracetamol was comparable to ibuprofen in terms of the rate of ductal closure and even showed a decreased risk of hyperbilirubinemia or gastrointestinal bleeding. Therefore, paracetamol may be accepted as a first-line drug treatment for PDA in preterm infants.
Mature microRNAs (miRNAs) are a class of small non-coding RNAs involved in posttranslational gene silencing. Previous studies found that downregulation of miRNAs is a common feature observed in solid tumors, including hepatocellular carcinoma (HCC). We employed a genome-wide approach to test the hypothesis that DNA methylation alterations in miRNA host genes may cause deregulated miRNA expression in HCC. We analyzed tumor and adjacent non-tumor tissues from 62 Taiwanese HCC cases using Infinium HumanMethylation27 DNA Analysis BeadChips that include 254 CpG sites covering 110 miRNAs from 64 host genes. Expression levels of three identified miRNAs (miR-10a, miR-10b and miR-196b) were measured in a subset of 37 HCC tumor and non-tumor tissues. After Bonferroni adjustment, a total of 54 CpG sites from 27 host genes significantly differed in DNA methylation levels between tumor and adjacent non-tumor tissues with 53 sites significantly hypermethylated in tumor tissues. Among the 54 significant CpG sites, 15 sites had more than 2-fold tumor/non-tumor changes, 17 sites had differences > 10%, and 10 sites had both features [including 8 significantly hypermethylated CpG sites in the host genes of miR-10a, miR-10b and miR-196b (HOXB4, HOXD4 and HOXA9, respectively)]. Significant downregulation of miR-10a was observed in tumor compared with non-tumor tissues (0.50 vs. 1.73, p = 0.031). The concordance for HOXB4 methylation alteration and dysregulation of miR-10a was 73.5%. No significant change was observed for miR-10b expression. Unexpectedly, miR-196b was significantly upregulated in tumor compared with non-tumor tissues (p = 0.0001). These data suggest that aberrant DNA methylation may lead to dysregulation of miR-10a in HCC tumor tissues.
HCC; genome-wide; host gene; microRNA; DNA methylation
Serine-rich repeat glycoproteins (SRRPs) are important bacterial adhesins conserved in streptococci and staphylococci. Fap1, a SRRP identified in Streptococcus parasanguinis, is the major constituent of bacterial fimbriae and is required for adhesion and biofilm formation. An 11-gene cluster is required for Fap1 glycosylation and secretion; however, the exact mechanism of Fap1 biogenesis remains a mystery. Two glycosylation-associated proteins within this cluster—Gap1 and Gap3—function together in Fap1 biogenesis. Here we report the role of the third glycosylation-associated protein, Gap2. A gap2 mutant exhibited the same phenotype as the gap1 and gap3 mutants in terms of Fap1 biogenesis, fimbrial assembly, and bacterial adhesion, suggesting that the three proteins interact. Indeed, all three proteins interacted with each other independently and together to form a stable protein complex. Mechanistically, Gap2 protected Gap3 from degradation by ClpP protease, and Gap2 required the presence of Gap1 for expression at the wild-type level. Gap2 augmented the function of Gap1 in stabilizing Gap3; this function was conserved in Gap homologs from Streptococcus agalactiae. Our studies demonstrate that the three Gap proteins work in concert in Fap1 biogenesis and reveal a new function of Gap2. This insight will help us elucidate the molecular mechanism of SRRP biogenesis in this bacterium and in pathogenic species.
The structural evolution of low-molecular-weight poly(ethylene oxide)-block-polystyrene (PEO-b-PS) diblock copolymer thin film with various initial film thicknesses on silicon substrate under thermal annealing was investigated by atomic force microscopy, optical microscopy, and contact angle measurement. At film thickness below half of the interlamellar spacing of the diblock copolymer (6.2 nm), the entire silicon is covered by a polymer brush with PEO blocks anchored on the Si substrate due to the substrate-induced effect. When the film is thicker than 6.2 nm, a dense polymer brush which is equal to half of an interlamellar layer was formed on the silicon, while the excess material dewet this layer to form droplets. The droplet surface was rich with PS block and the PEO block crystallized inside the bigger droplet to form spherulite.
Global decreases in DNA methylation, particularly in repetitive elements, have been associated with genomic instability and human cancer. Emerging, though limited, data suggest that in white blood cell (WBC) DNA levels of methylation, overall or in repetitive elements, may be associated with cancer risk. We measured methylation levels of three repetitive elements [Satellite 2 (Sat2)], long interspersed nuclear element-1 (LINE-1) and Alu) by MethyLight, and LINE-1 by pyrosequencing in a total of 282 breast cancer cases and 347 unaffected sisters from the New York site of the Breast Cancer Family Registry (BCFR) using DNA from both granulocytes and total WBC. We found that methylation levels in all markers were correlated between sisters (Spearman correlation coefficients ranged from 0.17 to 0.55). Sat2 methylation was statistically significantly associated with increased breast cancer risk [odds ratio (OR) = 2.09, 95% confidence interval (CI) = 1.09–4.03; for each unit decrease in the natural log of the methylation level, OR = 2.12, 95% CI = 0.88–5.11 for the lowest quartile compared with the highest quartile]. These associations were only observed in total WBC but not granulocyte DNA. There was no association between breast cancer and LINE-1 and Alu methylation. If replicated in larger prospective studies, these findings support that selected markers of epigenetic changes measured in WBC, such as Sat2, may be potential biomarkers of breast cancer risk.
Levels of kynurenic acid (KYNA), an endogenous product of tryptophan degradation, are elevated in the brain and cerebrospinal fluid of individuals with schizophrenia (SZ). This increase has been implicated in the cognitive dysfunctions seen in the disease since KYNA is an antagonist of the α7 nicotinic acetylcholine receptor and the NMDA receptor, both of which are critically involved in cognitive processes and in a defining neurodevelopmental period in the pathophysiology of SZ. We tested the hypothesis that early developmental increases in brain KYNA synthesis might cause biochemical and functional impairments in adulthood. To this end, we stimulated KYNA formation by adding the KYNA precursor kynurenine (100 mg/day) to the chow fed to rat dams from gestational day 15 to postnatal day 21 (PD 21). This treatment raised brain KYNA levels in the offspring by 341% on PD 2 and 210% on PD 21. Rats were then fed normal chow until adulthood (PD 56-PD 80). In the adult animals, basal levels of extracellular KYNA, measured in the hippocampus by in vivo microdialysis, were elevated (+12%), whereas extracellular glutamate levels were significantly reduced (−13%). In separate adult animals, early kynurenine treatment was shown to impair performance in two behavioral tasks linked to hippocampal function, the passive avoidance test and the Morris water maze test. Collectively, these studies introduce a novel, naturalistic rat model of SZ and also suggest that increases in brain KYNA during a vulnerable period in brain development may play a significant role in the pathophysiology of the disease.
Rats; Cognition; Hippocampus; Kynurenic acid; Schizophrenia
Burnout has been a major concern in the field of occupational health. However, there is a paucity of research exploring the factors related to burnout among Chinese doctors. Investigation of these factors is important to improve the health of doctors and the quality of healthcare services in China.
The study population consisted of 1,618 registered hospital doctors from Liaoning province of China. Burnout was measured using the Chinese version of the Maslach Burnout Inventory-General Survey. Occupational stress was measured using the Chinese versions of the Job Content Questionnaire and the Effort-Reward Imbalance Questionnaire. Data were collected on the respondents’ demographic characteristics and work situations. Of the doctors solicited for enrollment, 1,202 returned the completed questionnaire (555 men, 647 women), giving a response rate of 74.3%. A general linear regression model was applied to analyze the factors associated with burnout.
The burnout mean scores were 11.46 (7.51) for emotional exhaustion, 6.93 (5.15) for cynicism, and 24.07 (9.50) for professional efficacy. In descending order of standardized estimates, variables that predicted a high level of emotional exhaustion included: high extrinsic effort, dissatisfaction with doctor-patient relationship, high overcommitment, working >40 h per week, low reward, and high psychological job demands. Variables that predicted a high level of cynicism included: high extrinsic effort, low reward, dissatisfaction with doctor-patient relationship, high overcommitment, low decision authority, low supervisor support, and low skill discretion. Variables that predicted a low perceived professional efficacy included: high psychological job demands, low coworker support, high extrinsic effort, low decision authority, low reward, and dissatisfaction with doctor-patient relationship.
These findings suggest that occupational stress is strongly related to burnout among hospital doctors in China. Strategies that aim to improve work situations and decrease occupational stress are necessary to reduce burnout, including health education, health promotion, and occupational training programs.
Burnout; Doctors; Maslach Burnout Inventory-General Survey; Occupational stress
The HIV-1 accessory factor Vif is necessary for efficient viral infection in non-permissive cells. Vif antagonizes the antiviral activity of human cytidine deaminase APOBEC3 proteins that confer the non-permissive phenotype by tethering them (APOBEC3DE/3F/3G) to the Vif-CBF-β-ElonginB-ElonginC-Cullin5-Rbx (Vif-CBF-β-EloB-EloC-Cul5-Rbx) E3 complex to induce their proteasomal degradation. EloB and EloC were initially reported as positive regulatory subunits of the Elongin (SIII) complex. Thereafter, EloB and EloC were found to be components of Cul-E3 complexes, contributing to proteasomal degradation of specific substrates. CBF-β is a newly identified key regulator of Vif function, and more information is needed to further clarify its regulatory mechanism. Here, we comprehensively investigated the functions of EloB (together with EloC) in the Vif-CBF-β-Cul5 E3 ligase complex.
The results revealed that: (1) EloB (and EloC) positively affected the recruitment of CBF-β to Vif. Both knockdown of endogenous EloB and over-expression of its mutant with a 34-residue deletion in the COOH-terminal tail (EloBΔC34/EBΔC34) impaired the Vif-CBF-β interaction. (2) Introduction of both the Vif SLQ → AAA mutant (VifΔSLQ, which dramatically impairs Vif-EloB-EloC binding) and the Vif PPL → AAA mutant (VifΔPPL, which is thought to reduce Vif-EloB binding) could reduce CBF-β binding. (3) EloB-EloC but not CBF-β could greatly enhance the folding of full-length Vif in Escherichia coli. (4) The over-expression of EloB or the N-terminal ubiquitin-like (UbL) domain of EloB could significantly improve the stability of Vif/VifΔSLQ/VifΔPPL through the region between residues 9 and 14.
Our results indicate that the Vif interaction with EloB-EloC may contribute to recruitment of CBF-β to Vif, demonstrating that the EloB C-teminus may play a role in improving Vif function and that the over-expression of EloB results in Vif stabilization.
CBF-β; Elongin BC complex; HIV-1; Protein binding; Ubiquitin-protein ligases; Vif
A lot of empirical studies have been conducted to evaluate the prevalence of depression and anxiety among Chinese adults with cancer. We aimed to conduct a meta-analysis in order to evaluate the prevalence and odds ratios of depression and anxiety in Chinese adults with cancer compared with those without.
The three most comprehensive computerized Chinese academic databases-CNKI, Wangfang and Vip databases-were systematically screened through September 2012. PubMed and Web of Science (SCIE) were also searched from their inception until September 2012 without language restrictions, and an internet search was also used. Case–control studies assessing the prevalence of depression and anxiety among Chinese adults with cancer were analyzed. Study selection and appraisal were conducted independently by three authors. The non-weighted prevalence, pooled random-effects estimates of odds ratio (OR) and 95% confidence intervals (CI) were all calculated.
Seventeen eligible studies with a total of 3497 subjects were included. The prevalence of depression and anxiety were significantly higher in adults with cancer compared with those without (Depression: 54.90% vs. 17.50%, OR = 7.85, 95% CI = 5.56-11.07, P = 0.000; Anxiety: 49.69% vs. 18.37%, OR = 6.46, 95% CI = 4.36-9.55, P = 0.000), the same situation was also observed in subgroup of control groups, assessment methods and cancer types. Although no difference of depression was observed in studies utilizing clinical diagnosis compared with self-report, the OR of anxiety in adults with cancer compared with those without was higher in studies utilizing clinical diagnosis (OR = 8.42, 95% CI = 4.83-14.70) than self-reports (OR = 5.83, 95% CI = 3.64-9.34). The ORs of depression and anxiety in cancer patients compared with disease group (Depression: OR = 6.03, 95% CI = 4.23-8.61; Anxiety: OR = 4.40, 95% CI = 3.05-6.36) were lower than in those compared with normal group (Depression: OR = 13.58, 95% CI = 6.26-29.46; Anxiety: OR = 15.47, 95% CI = 10.00-23.95).
We identified high prevalence rates of depression and anxiety among Chinese adults with cancer. The findings support that the prevalence of depression and anxiety among adults with cancer should receive more attention in Chinese medical settings.
Lower global DNA methylation is associated with genomic instability and it is one of the epigenetic mechanisms relevant to carcinogenesis. Emerging evidence for several cancers suggests that lower overall levels of global DNA methylation in blood are associated with different cancer types, although less is known about breast cancer. We examined global DNA methylation levels using a sibling design in 273 sisters affected with breast cancer and 335 unaffected sisters from the New York site of the Breast Cancer Family Registry. We measured global DNA methylation in total white blood cell (WBC) and granulocyte DNA by two different methods, the [3H]-methyl acceptance assay and the luminometric methylation assay (LUMA). Global methylation levels were only modestly correlated between sisters discordant for breast cancer (Spearman correlation coefficients ranged from -0.08 to 0.24 depending on assay and DNA source). Using conditional logistic regression models, women in the quartile with the lowest DNA methylation levels (as measured by the [3H]-methyl acceptance assay) had a 1.8-fold (95% CI = 1.0–3.3) higher relative association with breast cancer than women in the quartile with the highest DNA methylation levels. When we examined the association on a continuous scale, we also observed a positive association (odds ratio, OR = 1.3, 95% CI = 1.0–1.7, for a one unit change in the natural logarithm of the DPM/μg of DNA). We observed no association between measures by the LUMA assay and breast cancer risk. If replicated in prospective studies, this study suggests that global DNA methylation levels measured in WBC may be a potential biomarker of breast cancer risk even within families at higher risk of cancer.
blood; breast cancer; epigenetics; global DNA methylation; global methylation; LUMA; luminometric methylation assay; methyl acceptance assay; white blood cell; [3H]-methyl acceptance assay
Global DNA hypomethylation is associated with genomic instability and human cancer and blood DNAs collected at the time of cancer diagnosis have been used to examine the relationship between global methylation and cancer risk. To test the hypothesis that global hypomethylation is associated with increased risk of hepatocellular carcinoma (HCC), we conducted a prospective case–control study nested within a community-based cohort with 16 years of follow-up. We measured methylation levels in Satellite 2 (Sat2) by MethyLight and LINE-1 by pyrosequencing using baseline white blood cell DNA from 305 HCC cases and 1254 matched controls. We found that Sat2 hypomethylation was associated with HCC risk [odds ratio (OR) per unit decrease in natural log Sat2 methylation = 1.77, 95% confidence interval (CI) = 1.06–2.95]. The association was significant among individuals diagnosed with HCC before age 62 (OR per unit decrease in natural log Sat2 methylation = 2.47, 95% CI = 1.06–5.73) but not after (OR = 1.67, 95% CI = 0.84–3.32). We did not observe an association of LINE-1 with HCC overall risk by age at diagnosis. Among carriers of hepatitis B virus surface antigen (HBsAg), with each 1U decrease in natural log Sat2 methylation level, the OR for HCC increased by 2.19 (95% CI = 1.00–4.89). LINE-1 hypomethylation was associated with about a 2-fold increased risk of HCC, with ORs (95% CI) of 2.39 (1.06–5.39), 2.09 (0.91–4.77) and 2.28 (0.95–5.51, P
trend = 0.14) for HBsAg carriers in the third, second and lowest quartile of LINE-1 methylation, respectively compared with carriers in the fourth. These results suggest that global hypomethylation may be a useful biomarker of HCC susceptibility.
The essential amino acid tryptophan is not only a precursor of serotonin but is also degraded to several other neuroactive compounds, including kynurenic acid, 3-hydroxykynurenine and quinolinic acid. The synthesis of these metabolites is regulated by an enzymatic cascade, known as the kynurenine pathway, that is tightly controlled by the immune system. Dysregulations of the pathway, causing hyper- or hypofunction of active metabolites, are associated with neurodegenerative and other neurological disorders, as well as psychiatric diseases such as depression and schizophrenia. With recently developed pharmacological agents, it is now possible to restore metabolic equilibrium and envisage novel therapeutic interventions.
In a previous study, we showed that the cephalochordate amphioxus Branchiostoma floridae has localized maternal transcripts of conserved germ cell markers Vasa and Nanos in its early embryos. These results provided strong evidence to support a preformation mechanism for primordial germ cell (PGC) development in B. floridae.
In this study, we further characterize the expression of B. floridae homologs of Piwi and Tudor, which play important roles in germline development in diverse metazoan animals. We show that maternal mRNA of one of the identified Piwi-like homologs, Bf-Piwil1, also colocalizes with Vasa in the vegetal germ plasm and has zygotic expression in both the putative PGCs and the tail bud, suggesting it may function in both germline and somatic stem cells. More interestingly, one Tudor family gene, Bf-Tdrd7, is only expressed maternally and colocalizes with Vasa in germ plasm, suggesting that it may function exclusively in germ cell specification. To evaluate the conservation of the preformation mechanism among amphioxus species, we further analyze Vasa, Nanos, Piwil1, and Tdrd7 expression in two Asian amphioxus species, B. belcheri and B. japonicum. Their maternal transcripts all localize in similar patterns to those seen in B. floridae. In addition, we labeled putative PGCs with Vasa antibody to trace their dynamic distribution in developing larvae.
We identify additional germ plasm components in amphioxus and demonstrate the molecular distinction between the putative germline stem cells and somatic stem cells. Moreover, our results suggest that preformation may be a conserved mechanism for PGC specification among Branchiostoma species. Our Vasa antibody staining results suggest that after the late neurula stage, amphioxus PGCs probably proliferate with the tail bud cells during posterior elongation and are deposited near the forming myomere boundaries. Subsequently, these PGCs would concentrate at the ventral tip of the myoseptal walls to form the gonad anlagen.
Cephalochordate; Nanos; Piwi; Primordial germ cell; Tudor; Vasa
Autoimmune hepatitis (AIH) is a severe type of chronic liver disease. The lack of appropriate animal models has resulted in a limited understanding regarding the etiology of AIH. Here, we demonstrated that mice deficient in Tyro3, Axl and Mer (TAM) receptor tyrosine kinases (RTKs) developed persistent inflammatory liver damage resembling AIH. Tyro3−/−Axl−/−Mer−/− triple mutant (TAM−/−) mice exhibited chronic hepatitis, manifested by progressive appearance of interface hepatitis, immune cell infiltrations and elevated inflammatory cytokine levels in the liver. Accordingly, increased levels of transaminases were observed. Moreover, characteristic autoantibodies and high levels of plasma immunoglobulin G for AIH were detected as TAM−/− mice aged. Finally, we provided evidence that the liver damage in TAM−/− mice mainly result from bone marrow-derived cells and could be rescued by transplantation of WT bone marrow cells. Results suggest that TAM RTKs play an important role in maintaining immune tolerance of the liver.
Alterations in DNA methylation frequently occur in hepatocellular cancer (HCC). We have previously demonstrated that hypermethylation in candidate genes can be detected in plasma DNA prior to HCC diagnosis. To identify with a genome-wide approach additional genes hypermethylated in HCC that could be used for more accurate analysis of plasma DNA for early diagnosis, we analyzed tumor and adjacent non-tumor tissues from 62 Taiwanese HCC cases using Illumina methylation arrays that screen 26,486 autosomal CpG sites. After Bonferroni adjustment, a total of 2,324 CpG sites significantly differed in methylation level, with 684 CpG sites significantly hypermethylated and 1,640 hypomethylated in tumor compared to non-tumor tissues. Array data were validated with pyrosequencing in a subset of 5 of these genes; correlation coefficients ranged from 0.92 to 0.97. Analysis of plasma DNA from 38 cases demonstrated that 37% to 63% of cases had detectable hypermethylated DNA (≥5% methylation) for these 5 genes individually. At least one of these genes was hypermethylated in 87% of cases, suggesting that measurement of DNA methylation in plasma samples is feasible. The panel of methylated genes indentified in the current study will be further tested in large cohort of prospectively collected samples to determine their utility as early biomarkers of hepatocellular carcinoma.
Genome-wide; DNA mehtylation; Hepatocellular Carcinoma
Cognitive deficits represent a core symptom cluster in schizophrenia (SZ) that is predictive of functional outcome, but not effectively treated by current antipsychotics. Thus, there is a need for the development of validated animal models for testing potential cognition-enhancing drugs.
As kynurenic acid (KYNA) levels are increased in the prefrontal cortex (PFC) of individuals with SZ, we acutely increased brain levels of this astrocyte-derived, negative modulator of the alpha7 nicotinic acetylcholine receptor (α7nAChR) by administration of its bioprecursor kynurenine (KYN) and measured the effects on KYNA and glutamate levels in PFC as well as performance in a set-shifting task.
Injections of KYN (100 mg/kg, i.p.) increased extracellular KYNA levels (1500% of baseline) and decreased glutamate levels (70% of baseline) in PFC. KYN also produced marked deficits in set-shifting. Saline- and KYN-treated rats similarly acquired the compound discrimination and the intra-dimensional shift (mean trials to criterion, saline: 7.0 and 6.3, respectively; KYN: 8.0 and 6.7). Both groups required more trials to acquire the initial reversal (saline: 15.3; KYN: 22.2). However, KYN-treated rats exhibited severe deficits in acquiring the extra-dimensional shift (saline: 8.2; KYN = 21.3). These deficits were normalized by an acute injection of the α7nAChR positive allosteric modulator galantamine (3.0 mg/kg, i.p) 5 min prior to KYN (100 mg/kg, i.p.). Thus, trials to criterion were comparable between galantamine + KYN (7.8) and controls (8.2). Finally, the KYN-induced impairment requires antagonism of prefrontal α7nAChRs, as bilateral local perfusion of galantamine (5.0 μM) attenuated the effects of systemic KYN.
These results validate the use of animals with elevated brain KYNA levels in SZ research and support continued studies on drugs that normalize brain KYNA levels and/or positively modulate α7nAChRs as pro-cognitve adjuncts for treating SZ.
cognition; schizophrenia; animal model; kynurenine; glutamate
Lactobacillus pobuzihii E100301T is a novel Lactobacillus species previously isolated from pobuzihi (fermented cummingcordia) in Taiwan. Phylogenetically, this strain is closest to Lactobacillus acidipiscis, but its phenotypic characteristics can be clearly distinguished from those of L. acidipiscis. We present the draft genome sequence of strain L. pobuzihii E100301T.
A preliminary study was conducted to investigate feasibility of using an oral cancer chemopreventive agent (−)-epigallocatechin-3-gallate (EGCG), the most biologically active component in the green tea extract, in a form of ‘swish-and-spit’ mouthwash. Such application of EGCG is beneficial as it maximizes exposure of the oral mucosa to the agent but minimizes systemic side effect.
The study was conducted on individuals suspected to have oral field cancerization who are at a high risk for developing recurrent oral precancerous and carcinomatous lesions. EGCG was used as a daily mouthwash for 7 days. EGCG’s ability to modulate target molecules implicated in oral carcinogenesis was assessed by measuring the change in expression level of biomarkers.
Immunohistochemical expression of phosphoactivated epidermal growth factor receptor (pEGFR), cyclooxygenase-2 (cox-2) and ki-67 were evaluated at baseline and at the endpoint (day 8). Although not statistically significant, overall decrease in expression levels of pEGFR (27.5%), cox-2 (15.9%) and ki-67 positive cells (51.8%) were observed following EGCG treatment. Moreover, a detectable level of EGCG was found in saliva but not in plasma after the one-week treatment regime, demonstrating local availability of EGCG in oral mucosa without significant systemic absorption.
To best of our knowledge this is the first study to explore use of oral cancer chemopreventive agent in a form of mouthwash in patients with oral field cancerization. Although a definitive conclusion was not reached due to limited sample size, if proven effective, EGCG therapy may offer a non-invasive preventive modality for oral field cancerization.
(−)-epigallocatechin-3-gallate; oral field cancerization; topical chemopreventive agent; feasibility trial
Multicopper oxidases (MCOs) are a family of enzymes that use copper ions as cofactors to oxidize various substrates. Previous research has demonstrated that several MCOs such as MnxG, MofA and MoxA can act as putative Mn(II) oxidases. Meanwhile, the endospore coat protein CotA from Bacillus species has been confirmed as a typical MCO. To study the relationship between CotA and the Mn(II) oxidation, the cotA gene from a highly active Mn(II)-oxidizing strain Bacillus pumilus WH4 was cloned and overexpressed in Escherichia coli strain M15. The purified CotA contained approximately four copper atoms per molecule and showed spectroscopic properties typical of blue copper oxidases. Importantly, apart from the laccase activities, the CotA also displayed substantial Mn(II)-oxidase activities both in liquid culture system and native polyacrylamide gel electrophoresis. The optimum Mn(II) oxidase activity was obtained at 53°C in HEPES buffer (pH 8.0) supplemented with 0.8 mM CuCl2. Besides, the addition of o-phenanthroline and EDTA both led to a complete suppression of Mn(II)-oxidizing activity. The specific activity of purified CotA towards Mn(II) was 0.27 U/mg. The Km, Vmax and kcat values towards Mn(II) were 14.85±1.17 mM, 3.01×10−6±0.21 M·min−1 and 0.32±0.02 s−1, respectively. Moreover, the Mn(II)-oxidizing activity of the recombinant E. coli strain M15-pQE-cotA was significantly increased when cultured both in Mn-containing K liquid medium and on agar plates. After 7-day liquid cultivation, M15-pQE-cotA resulted in 18.2% removal of Mn(II) from the medium. Furthermore, the biogenic Mn oxides were clearly observed on the cell surfaces of M15-pQE-cotA by scanning electron microscopy. To our knowledge, this is the first report that provides the direct observation of Mn(II) oxidation with the heterologously expressed protein CotA, Therefore, this novel finding not only establishes the foundation for in-depth study of Mn(II) oxidation mechanisms, but also offers a potential biocatalyst for Mn(II) removal.
The natural flavone acacetin has been demonstrated to inhibit transient outward potassium current (Ito) in human atrial myocytes. However, the molecular determinants of acacetin for blocking Ito are unknown. The present study was designed to investigate the properties and molecular determinants of this compound for blocking hKv4.3 channels (coding Ito) stably expressed in HEK 293 cells using the approaches of whole-cell patch voltage-clamp technique and mutagenesis. It was found that acacetin inhibited hKv4.3 current by binding to both the closed and open channels, and decreased the recovery from inactivation. The blockade of hKv4.3 channels by acacetin was use- and frequency-dependent, and IC50s of acacetin for inhibiting hKv4.3 were 7.9, 6.1, 3.9, and 3.2 µM, respectively, at 0.2, 0.5, 1, and 3.3 Hz. The mutagenesis study revealed that the hKv4.3 mutants T366A and T367A in the P-loop helix, and V392A, I395A and V399A in the S6-segment had a reduced channel blocking efficacy of acacetin (IC50, 44.5 µM for T366A, 25.8 µM for T367A, 17.6 µM for V392A, 16.2 µM for I395A, and 19.1 µM for V399A). These results demonstrate the novel information that acacetin may inhibit the closed channels and block the open state of the channels by binding to their P-loop filter helix and S6 domain. The use- and rate-dependent blocking of hKv4.3 by acacetin is likely beneficial for managing atrial fibrillation.
We have recently shown that hepatitis B virus (HBV) core antigen (HBcAg) is the major viral factor for HBV clearance using a hydrodynamics-based mouse model. Knockout of HBcAg hampers the development of antiviral immune responses and thus promotes HBV persistence. Here, we further demonstrated that only in the capsid form, but not the free or dimer form, can HBcAg exert its contributory role in HBV clearance. HBcAg is the main structural protein of HBV icosahedral nucleocapsid. A mutant HBV DNA which expresses an assembly-defective HBcAg, HBcAgY132A, surprisingly prolonged HBV surface antigenemia in both C57BL/6 and BALB/c mice without affecting viral transcription and translation. This result was not due to a loss of the possible immune epitope caused by the single-amino-acid substitution of HBcAg. Moreover, the particular HBV mutant failed to induce robust humoral and cellular immunity against HBV. These data revealed the requirement of capsid structure for inducing adequate immunity that leads to HBV clearance in mice.
The Ca2+/calmodulin (CaM) signaling pathway mediates the heat stress (HS) response and acquisition of thermotolerance in plants. We showed that the rice CaM1-1 isoform can interpret a Ca2+ signature difference in amplitude, frequency, and temporal–spatial properties in regulating transcription of nucleoplasmic small heat-shock protein gene (sHSPC/N) during HS. Ca2+ and A23187 treatments under HS generated an intense and sustained increase in [Ca2+]cyt and accelerated the expression of CaM1-1 and sHSPC/N genes, which suggests that HS-induced apoplastic Ca2+ influx was responsible for the [Ca2+]cyt transient and downstream HS signaling. Here, we discuss an emerging paradigm in the oscillation regulation of CaM1-1 expression during HS and highlight the areas that need further investigation.
Ca2+; calmodulin; heat shock signaling; temporal–spatial regulation; thermotolerance