Cytosine methylation, an epigenetic modification of DNA, is a target of growing interest for developing high throughput profiling technologies. Here we introduce two new, complementary techniques for cytosine methylation profiling utilizing next generation sequencing technology: bisulfite padlock probes (BSPPs) and methyl sensitive cut counting (MSCC). In the first method, we designed a set of ~10,000 BSPPs distributed over the ENCODE pilot project regions to take advantage of existing expression and chromatin immunoprecipitation data. We observed a pattern of low promoter methylation coupled with high gene body methylation in highly expressed genes. Using the second method, MSCC, we gathered genome-scale data for 1.4 million HpaII sites and confirmed that gene body methylation in highly expressed genes is a consistent phenomenon over the entire genome. Our observations highlight the usefulness of techniques which are not inherently or intentionally biased in favor of only profiling particular subsets like CpG islands or promoter regions.

OBJECTIVE:

To evaluate the incremental cost-effectiveness of a system-based approach for the management of neonatal jaundice and the prevention of kernicterus in term and late-preterm (≥35 weeks) infants, compared with the traditional practice based on visual inspection and selected bilirubin testing.

STUDY DESIGN:

Two hypothetical cohorts of 150,000 term and late-preterm neonates were used to compare the costs and outcomes associated with the use of a system-based or traditional practice approach. Data for the evaluation were obtained from the case costing centre at a large teaching hospital in Ontario, supplemented by data from the literature.

RESULTS:

The per child cost for the system-based approach cohort was $176, compared with $173 in the traditional practice cohort. The higher cost associated with the system-based cohort reflects increased costs for predischarge screening and treatment and increased postdischarge follow-up visits. These costs are partially offset by reduced costs from fewer emergency room visits, hospital readmissions and kernicterus cases. Compared with the traditional approach, the cost to prevent one kernicterus case using the system-based approach was $570,496, the cost per life year gained was $26,279, and the cost per quality-adjusted life year gained was $65,698.

CONCLUSION:

The cost to prevent one kernicterus case using the system-based approach is much lower than previously reported in the literature.

Right heart failure is the cause of death of most patients with severe pulmonary arterial hypertensive (PAH) disorders, yet little is known about the cellular and molecular causes of right ventricular failure (RVF). We first showed a differential gene expression pattern between normal rat right and left ventricles, and postulated the existence of a molecular right heart failure program that distinguishes RVF from adaptive right ventricular hypertrophy (RVH), and that may differ in some respects from a left heart failure program. By means of microarrays and transcriptional sequencing strategies, we used two models of adaptive RVH to characterize a gene expression pattern reflective of growth and the maintenance of myocardial structure. Moreover, two models of RVF were associated with fibrosis, capillary rarefaction, the decreased expression of genes encoding the angiogenesis factors vascular endothelial growth factor, insulin-like growth factor 1, apelin, and angiopoeitin-1, and the increased expression of genes encoding a set of glycolytic enzymes. The treatment of established RVF with a β-adrenergic receptor blocker reversed RVF, and partly reversed the molecular RVF program. We conclude that normal right and left ventricles demonstrate clearly discernable differences in the expression of mRNA and microRNA, and that RVH and RVF are characterized by distinct patterns of gene expression that relate to cell growth, angiogenesis, and energy metabolism.

Here, we report the draft genome sequence of Antarctic sea ice bacterium Glaciecola punicea ACAM 611T, the type species of the genus Glaciecola. A blue-light-absorbing proteorhodopsin gene is present in the 3.08-Mb genome. This genome sequence can facilitate the study of the physiological metabolisms and ecological roles of sea ice bacteria.

The mechanism for the observed association of alcohol consumption breast cancer risk is not known; understanding that mechanism could improve understanding of breast carcinogenesis and optimize prevention strategies. Alcohol may impact breast malignancies or tumor progression by altering DNA methylation. We examined promoter methylation of three genes, the E- cadherin, p16, and RAR-β2 genes in archived breast tumor tissues from participants in a population-based case-control study. Real time methylation-specific PCR was performed on 803 paraffin-embedded samples; and lifetime alcohol consumption was queried. Unordered polytomous and unconditional logistic regression were used to derive adjusted odds ratios (OR) and 95% confidence intervals (CI). RAR-β2 methylation was not associated with drinking. Among premenopausal women, alcohol consumption was also not associated with promoter methylation for E- cadherin and p16 genes. In case-case comparisons of postmenopausal breast cancer, compared to lifetime never drinkers, promoter methylation likelihood was increased for higher alcohol intake for E - cadherin (OR = 2.39, 95% CI, 1.15–4.96), in particular for those with ER-negative tumors (OR = 4.13, 95% CI, 1.16–14.72), and decreased for p16 (OR = 0.52, 95% CI, 0.29-0.92). There were indications that the association with p16 was stronger for drinking at younger ages. Methylation was also associated with drinking intensity independent of total consumption for both genes. We found alcohol consumption was associated with DNA methylation in postmenopausal breast tumors, suggesting that the association of alcohol and breast cancer may be related, at least in part, to altered methylation, and may differ by drinking pattern.

There are over 30 species in the marine bacterial genus Pseudoalteromonas. However, our knowledge about this genus is still limited. We sequenced the genomes of type strains of seven species in the genus, facilitating the study of the physiology, adaptation, and evolution of this genus.

Background

A 21-gene recurrence score (RS) assay may inform adjuvant systematic treatment decisions in women with early stage breast cancer. We sought to investigate the cost effectiveness of using the RS-assay versus current clinical practice (CCP) in women with early-stage estrogen- or progesterone-receptor-positive, axilliary lymph-node negative breast cancer (ER+/ PR + LN- ESBC) from the perspective of the Canadian public healthcare system.

Methods

We developed a Markov model to project the lifetime clinical and economic consequences of ESBC. We evaluated adjuvant therapy separately in post- and pre-menopausal women with ER+/ PR + LN- ESBC. We assumed that the RS-assay would reclassify pre- and post-menopausal women among risk levels (low, intermediate and high) and guide adjuvant systematic treatment decisions. The model was parameterized using 7 year follow up data from the Manitoba Cancer Registry, cost data from Manitoba administrative databases, and secondary sources. Costs are presented in 2010 CAD. Future costs and benefits were discounted at 5%.

Results

The RS-assay compared to CCP generated cost-savings in pre-menopausal women and had an ICER of $60,000 per QALY gained in post-menopausal women. The cost effectiveness was most sensitive to the proportion of women classified as intermediate risk by the RS-assay who receive adjuvant chemotherapy and the risk of relapse in the RS-assay model.

Conclusions

The RS-assay is likely to be cost effective in the Canadian healthcare system and should be considered for adoption in women with ER+/ PR + LN- ESBC. However, ongoing assessment and validation of the assay in real-world clinical practice is warranted.

Objectives

To investigate Hepatitis C Virus (HCV) knowledge and alcohol consumption among patients (N=114) in a Methadone Maintenance Treatment (MMT) clinic in Shanghai.

Methods

A cross-sectional survey was carried out in an MMT clinic. Structured questionnaires (HCV Knowledge Scale, Alcohol Use Disorders Identification Test (AUDIT)) and some open-ended questions were used to assess (1) HCV knowledge; (2) HCV treatment received, (3) awareness of HCV status; and (4) alcohol consumption.

Results

Findings revealed the HCV-positive rate was 57.0%. There were significant gaps in knowledge about HCV and HCV treatment received. The group mean score of HCV knowledge was 11.3 out of 20 (SD=2.1) and the mean score on the AUDIT was 3.2 (SD=5.4). Most participants (68.4%) reported not knowing their HCV status. Among HCV-positive participants, only 15.3% had received HCV anti-virus treatment, and 18.4% expressed a need for counseling about HCV infection.

Conclusions

Considering the limited HCV knowledge and low level of HCV treatment received, effective HCV education and intervention strategies should be developed to target patients in China’s MMT clinics. Moreover, alcohol screening also should be part of the routine assessments within MMT programs. Scientific Significance: The current study reveals the importance of HCV testing and education among drug users in MMT clinics.

Objective

To determine sustained effectiveness in reducing depression symptoms and improving depression care one year following intervention completion.

Method

Of 387 low-income, predominantly Hispanic diabetes patients with major depression symptoms randomized to 12-month socio-culturally adapted collaborative care (psychotherapy and/or antidepressants, telephone symptom monitoring/relapse prevention) or enhanced usual care, 264 patients completed two-year follow-up. Depression symptoms (SCL-20, PHQ-9), treatment receipt, diabetes symptoms, and quality of life were assessed 24 months post-enrollment using intent-to-treat analyses.

Results

At 24 months, more intervention patients received ongoing antidepressant treatment (38% v 25%, chi-square=5.11, df=1, P=0.02); sustained depression symptom improvement (SCL-20<0.5 (adjusted OR=2.06, 95%CI=1.09–3.90, P=0.03), SCL-20 score (adjusted mean difference −0.22, P=0.001), and PHQ-9 ≥50% reduction (adjusted OR=1.87, 95%CI=1.05–3.32, P=0.03). Over 2 years, improved effects were found in significant study group by time interaction for SF-12 mental health, SDS functional impairment, diabetes symptoms, anxiety, and socioeconomic stressors (P=0.02 for SDS, P<0.0001 for all others); however, group differences narrowed over time and were no longer significant at 24 months.

Conclusions

Socio-culturally tailored collaborative care that included maintenance antidepressant medication, ongoing symptom monitoring and behavioral activation relapse prevention was associated with depression improvement over 24 months for predominantly Hispanic patients in primary safety net care.

The cycloprodigiosin biosynthetic gene cluster has not been reported. We sequenced the genome of a cycloprodigiosin-producing bacterial strain, Pseudoalteromonas rubra ATCC 29570T. Analysis revealed a probable cycloprodigiosin biosynthetic cluster, providing a good model for the study of cycloprodigiosin synthesis and regulation.

Yu et al. (Polar Biol. 32:1539–1547, 2009) isolated 199 Pseudoalteromonas strains from Arctic sea ice. We sequenced the genomes of six of these strains, which are affiliated to different Pseudoalteromonas species based on 16S rRNA gene sequences, facilitating the study of physiology and adaptation of Arctic sea ice Pseudoalteromonas strains.

SUMMARY

Both splicing factors and microRNAs are important regulatory molecules that play key roles in post-transcriptional gene regulation. By miRNA deep sequencing, we identified 40 miRNAs that are differentially expressed upon ectopic overexpression of the splicing factor SF2/ASF. Here we show that SF2/ASF and one of its upregulated microRNAs (miR-7) can form a negative feedback loop: SF2/ASF promotes miR-7 maturation, and mature miR-7 in turn targets the 3′UTR of SF2/ASF to repress its translation. Enhanced microRNA expression is mediated by direct interaction between SF2/ASF and the primary miR-7 transcript to facilitate Drosha cleavage and is independent of SF2/ASF’s function in splicing. Other miRNAs, including miR-221 and miR-222, may also be regulated by SF2/ASF through a similar mechanism. These results underscore a function of SF2/ASF in pri-miRNA processing and highlight the potential coordination between splicing control and miRNA-mediated gene repression in gene regulatory networks.

Objective

This article describes design elements of the Multifaceted Depression and Diabetes Program (MDDP) randomized clinical trial. The MDDP trial hypothesizes that a socioculturally adapted collaborative care depression management intervention will reduce depressive symptoms and improve patient adherence to diabetes self-care regimens, glycemic control, and quality-of-life. In addition, baseline data of 387 low-income, 96% Hispanic, enrolled patients with major depression and diabetes are examined to identify study population characteristics consistent with trial design adaptations.

Methods

The PHQ-9 depression scale was used to identify patients meeting criteria for major depressive disorder (1 cardinal depression symptom + a PHQ-9 score of ≥ 10) from two community safety net clinics. Design elements included sociocultural adaptations in recruitment and efforts to reduce attrition and collaborative depression care management.

Results

Of 1,803 diabetes patients screened, 30.2% met criteria for major depressive disorder. Of 387 patients enrolled in the clinical trial, 98% had Type 2 diabetes, and 83% had glycated hemoglobin (HbA1c) levels ≥ 7%. Study recruitment rates and baseline data analyses identified socioeconomic and clinical factors that support trial design and intervention adaptations. Depression severity was significantly associated with diabetes complications, medical comorbidity, greater anxiety, dysthymia, financial worries, social stress, and poorer quality-of-life.

Conclusion

Low-income Hispanic patients with diabetes experience high prevalence of depressive disorder and depression severity is associated with socioeconomic stressors and clinical severity. Improving depression care management among Hispanic patients in public sector clinics should include intervention components that address self-care of diabetes and socioeconomic stressors.

Glaciecola nitratireducens strain FR1064T was isolated from seawater and described as a new species by Baik et al. in 2006. The genome size is about 1.01 to 1.26 Mb smaller than two reported Glaciecola genomes, indicating the gain or loss of large genome segments in the evolution of Glaciecola strains.

E495 is the most abundant protease secreted by the Arctic sea-ice bacterium Pseudoalteromonas sp. SM495. As a thermolysin family metalloprotease, E495 was found to have multiple active forms in the culture of strain SM495. E495-M (containing only the catalytic domain) and E495-M-C1 (containing the catalytic domain and one PPC domain) were two stable mature forms, and E495-M-C1-C2 (containing the catalytic domain and two PPC domains) might be an intermediate. Compared to E495-M, E495-M-C1 had similar affinity and catalytic efficiency to oligopeptides, but higher affinity and catalytic efficiency to proteins. The PPC domains from E495 were expressed as GST-fused proteins. Both of the recombinant PPC domains were shown to have binding ability to proteins C-phycocyanin and casein, and domain PPC1 had higher affinity to C-phycocyanin than domain PPC2. These results indicated that the domain PPC1 in E495-M-C1 could be helpful in binding protein substrate, and therefore, improving the catalytic efficiency. Site-directed mutagenesis on the PPC domains showed that the conserved polar and aromatic residues, D26, D28, Y30, Y/W65, in the PPC domains played key roles in protein binding. Our study may shed light on the mechanism of organic nitrogen degradation in the Arctic sea ice.

DNA methylation has been traditionally viewed as a highly stable epigenetic mark in post-mitotic cells, however, postnatal brains appear to exhibit stimulus-induced methylation changes, at least in a few identified CpG dinucleotides. How extensively the neuronal DNA methylome is regulated by neuronal activity is unknown. Using a next-generation sequencing-based method for genome-wide analysis at a single-nucleotide resolution, we quantitatively compared the CpG methylation landscape of adult mouse dentate granule neurons in vivo before and after synchronous neuronal activation. About 1.4% of 219,991 CpGs measured show rapid active demethylation or de novo methylation. Some modifications remain stable for at least 24 hours. These activity-modified CpGs exhibit a broad genomic distribution with significant enrichment in low-CpG density regions, and are associated with brain-specific genes related to neuronal plasticity. Our study implicates modification of the neuronal DNA methylome as a previously under-appreciated mechanism for activity-dependent epigenetic regulation in the adult nervous system.

Purpose: Compulsive Internet Use (CIU) has increasingly become an area of research among process addictions. Largely based on data from cross-sectional studies, a positive association between CIU and substance use has previously been reported. This study presents gender and country-specific longitudinal findings on the relationships between CIU and substance use. Methods: Data were drawn from youth attending non-conventional high schools, recruited into two similarly implemented trials conducted in China and the USA. The Chinese sample included 1,761 students (49% male); the US sample included 1,182 students (57% male) with over half (65%) of the US youth being of Hispanic ethnicity. Path analyses were applied to detect the concurrent and predictive relationships between baseline and one-year follow-up measures of CIU level, 30-day cigarette smoking, and 30-day binge drinking. Results: (1) CIU was not positively related with substance use at baseline. (2) There was a positive predictive relationship between baseline CIU and change in substance use among female, but not male students. (3) Relationships between concurrent changes in CIU and substance use were also found among female, but not male students. (4) Baseline substance use did not predict an increase in CIU from baseline to 1-year follow-up. Conclusions: While CIU was found to be related to substance use, the relationship was not consistently positive. More longitudinal studies with better measures for Internet Addiction are needed to ascertain the detailed relationship between Internet addiction and substance use.

Objectives

To investigate associations of overweight status and perception with trajectories of psychological distress in adolescents.

Methods

Longitudinal data for 6,970 Chinese adolescents were included. The multivariate Curve-of-Factor Latent Growth Curve Models were adopted to examine trajectories of psychological distress symptoms and associations with overweight status and perception.

Results

After controlling for actual overweight status, psychological distress symptoms were weakly but significantly associated with overweight perception (γ=0.08 for boys and γ=0.10 for girls, P<0.05) and misperception (γ=0.06 for boys and γ=0.09 for girls, P<0.05).

Discussion

Our findings help understanding associations of overweight perception and psychological well being of adolescents.

In the crystal structure of the title compound, [Ni(C16H36N4)](C6H4O2PS2)2, the NiII cation is located on a center of inversion and is chelated by the folded tetra­amine macrocycle ligand in a slightly distorted NiN4 square-planar geometry. Two symmetry-related O,O′-(1,2-phenyl­ene)dithio­phosphate anions are located on either side of the NiII cation, with Ni⋯S of 3.9558 (5) Å, and link to the tetra­amine macrocycle ligand via N—H⋯S hydrogen bonding.

Metazoan transcription is controlled either through coordinated recruitment of transcription machinery to the gene promoter, or through regulated pausing of RNA polymerase II (Pol II) in early elongation. We report that a striking difference between genes that use these distinct regulatory strategies lies in the “default” chromatin architecture specified by their DNA sequences. Pol II pausing is prominent at highly-regulated genes whose sequences inherently disfavor nucleosome formation within the gene, but favor occlusion of the promoter by nucleosomes. In contrast, housekeeping genes that lack pronounced Pol II pausing show higher nucleosome occupancy downstream, but their promoters are deprived of nucleosomes regardless of polymerase binding. Our results indicate that a key role of paused Pol II is to compete with nucleosomes for occupancy of highly-regulated promoters, thereby preventing the formation of repressive chromatin architecture to facilitate further or future gene activation.

Studies have indicated that family meals may be a protective factor for childhood obesity; however, limited evidence is available in children with different racial, socioeconomic, and individual characteristics. The purpose of this study was to examine family meal frequency (FMF) as a protective factor for obesity in a US-based sample of non-Hispanic White, non-Hispanic Black, and Hispanic children aged 6 to 11, and to identify individual, familial, and socioeconomic factors that moderate this association. Data were from the 2003 National Survey of Children’s Health (n=16,770). Multinomial logistic regression analyses were used to test the association between FMF and weight status, and the moderating effects of household structure, education, poverty level, and sex, by racial group. Non-Hispanic White children who consumed family meals everyday were less likely to be obese than those eating family meals 0 or few days a week. A moderating effect for gender was observed in non-Hispanic Black children such that FMF was marginally protective in boys but not girls. Higher FMF was a marginal risk factor for obesity in Hispanic boys from low-education households, but not in girls from similar households. In conclusion, family meals appear to be protective of obesity in non-Hispanic White children, and non-Hispanic Black boys; whereas, they may put Hispanic boys living in low education households at risk. Greater emphasis is needed in future research on understanding why this association differs among different race/ethnic groups, and the influence of the quality in addition to the quantity of family meals on child obesity.

Objectives

To prospectively investigate associations between overweight and depressive symptoms in Asian and Hispanic adolescents.

Methods

Data included 780 Hispanic and 375 Asian students. Structural equation model was used to prospectively explore moderation effects of gender, ethnicity, and acculturation on associations of overweight, body image dissatisfaction, and depressive symptoms.

Results

Significant mediation effect was found only in Asian girls (mediation effect=0.16, P<0.05) and girls with high acculturation (mediation effect=0.17, P<0.05). Overweight significantly predicted higher body image dissatisfaction, which in turn was significantly related to depressive symptoms.

Conclusion

Our findings help understanding the association of overweight and experience of depressive symptoms.

Background

Providing emergency department (ED) wait time information to the public has been suggested as a mechanism to reduce lengthy ED wait times (by enabling patients to select the ED site with shorter wait time), but the effects of such a program have not been evaluated. We evaluated the effects of such a program in a community with two ED sites.

Methods

Descriptive statistics for wait times of the two sites before and after the publication of wait time information were used to evaluate the effects of the publication of wait time information on wait times. Multivariate logistical regression was used to test whether or not individual patients used published wait time to decide which site to visit.

Results

We found that the rates of wait times exceeding 4 h, and the 95th percentile of wait times in the two sites decreased after the publication of wait time information, even though the average wait times experienced a slight increase. We also found that after controlling for other factors, the site with shorter wait time had a higher likelihood of being selected after the publication of wait time information, but there was no such relationship before the publication.

Conclusions

These findings were consistent with the hypothesis that the publication of wait time information leads to patients selecting the site with shorter wait time. While publishing ED wait time information did not improve average wait time, it reduced the rates of lengthy wait times.

Objective

There have been few comparisons of the effectiveness of collaborative depression care between older versus younger adults with co-morbid illness, particularly among low-income populations.

Design

Intent-to-treat analyses are conducted on pooled data from three randomized controlled trials that tested collaborative care aimed at improving depression, quality of life and treatment receipt.

Settings

Trials were conducted in oncology and primary care safety net clinics and diverse home health care programs.

Participants

1,081 patients with major depressive symptoms and cancer, diabetes or other co-morbid illness.

Intervention

Similar intervention protocols included patient, provider, socio-cultural and organizational adaptations.

Measurements

The PHQ-9 depression, SF-12/20 quality-of-life, self-reported hospitalization, ER, ICU utilization, and antidepressant, psychotherapy treatment receipt are assessed at baseline, 6, 12 months.

Results

There are no significant differences in reducing depression symptoms (P ranged 0.18-0.58), improving quality-of-life (t=1.86, df=669, P=0.07 for physical functioning at 12 months; and P ranged 0.23-0.99 for all others) between patients ≥60 versus 18-59. Both age group intervention patients have significantly higher rates of a 50% PHQ-9 reduction (older: Wald χ2[df=1]=4.82, p=0.03; younger: Wald χ2[df=1]=6.47, p=0.02), greater reduction in major depression rates (older: Wald χ2[df=1]=7.72, p=0.01; younger: Wald χ2[df=1]=4.0, p=0.05) than enhanced-usual-care patients at 6 months, and are no significant age group differences in treatment type or intensity.

Conclusion

Collaborative depression care in individuals with co-morbid illness is as effective in reducing depression in older patients as younger patients, including among low-income, minority patients. Patient, provider, and organizational adaptations of depression care management models may contribute to positive outcomes.