To test the hypothesis that more stringent quality regulations contribute to better quality nursing home care and to assess their cost-effectiveness.
Primary and secondary data from all states and U.S. nursing homes in 2005–2006.
We estimated seven models, regressing quality measures on the Harrington Regulation Stringency Index and control variables. To account for endogeneity between regulation and quality, we used instrumental variables techniques. Quality was measured by staffing hours by type per case-mix adjusted day, hotel expenditures, and risk-adjusted decline in activities of daily living, high-risk pressure sores, and urinary incontinence.
All states' licensing and certification offices were surveyed to obtain data about deficiencies. Secondary data included the Minimum Data Set, Medicare Cost Reports, and the Economic Freedom Index.
Regulatory stringency was significantly associated with better quality for four out of the seven measures studied. The cost-effectiveness for the ADL measure was estimated at about $72,000 in 2011 $/QALY.
Quality regulations lead to better quality in nursing homes along some dimensions, but not all. Our estimates of cost-effectiveness suggest that increased regulatory stringency is in the ballpark of other acceptable cost-effective practices.
nursing homes; quality of care; regulation; cost-effectiveness; comparative effectiveness
Mentally ill people may face barriers to receiving elective surgical procedures due to societal stigma, and the cognitive, behavioral, and interpersonal deficits associated with metal illness. Using data from a cohort of elderly Medicare beneficiaries in 2007, we examined whether the mentally ill have less access than persons without mental illness to several common procedures that are typically non-emergent and performed at the discretion of the provider and patient. Results suggest that Medicare patients with mental illness are between 30 and 70 percent less likely to receive these “referral-sensitive” surgical procedures. Those who did undergo an elective procedure generally experienced poorer outcomes both in the hospital and after discharge. Efforts to improve the access and outcomes of nonpsychiatric care for mentally ill patients are warranted.
To track the trend of the ability of U.S. nursing homes to provide on-site mental health services after the Omnibus Budget Reconciliation Act (OBRA) mandated mental illness detection and treatment for nursing home patients, and to determine cross-sectional correlates of service availability and models of services.
Retrospective analyses of the 1995-2004 National Nursing Home Surveys (NNHS) periodically conducted by the Centers for Disease Control and Prevention. Longitudinal trend of mental health service provision was analyzed for all and subgroups of facilities. Multivariate regression determined facility and geographic correlates in 2004.
Representing the nation’s approximately 17,000 nursing homes, the NNHS suggested that roughly 80% of facilities provided on-site mental health services each year and over time. In 2004, roughly a quarter of all facilities provided each model of services – regular (25%), on call (28%), or both regular and on call (24%) services – with the remaining 23% facilities providing no on-site mental health services. Multivariate analyses found that largest facilities (≥200 beds) were more able to serve the mentally ill (odds ratio=3.80, p=.024) than small facilities (<100 beds); facilities with mass coverage by Medicare/Medicaid programs, in the northeast region, or in metropolitan areas were more likely than their counterparts to provide on-site services. Similar correlates were found for alternative service models available.
The overall availability of nursing home-based mental health services did not improve over time during the post-OBRA era. Service availability is more problematic for certain facilities such as small or rural ones. Financial, regulatory, and system-level efforts are needed to address this issue.
nursing home; mental health services; OBRA; NNHS
Patients diagnosed with serious mental illness (SMI) who qualify for nursing home placement tend to require high levels of both psychiatric and nursing care. It is unknown, however, whether they are equally likely to be admitted to nursing homes with adequate quality of care compared to other patients.
We analyzed a national cohort of over 1.3 million new nursing home admissions in 2007 using the Minimum Data Set. The total and healthcare-related deficiency citations for each facility were obtained from the Online Survey, Certification, and Reporting file. Bivariate and multivariate regression analyses determined the association of schizophrenia or bipolar disorder with admissions to facilities with higher deficiencies.
Compared to other patients, patients with schizophrenia (n=23,767) tended to enter nursing homes with both more total deficiencies (13.3 vs 11.2, p<0.001) and more healthcare-related deficiencies (8.6 vs 7.2, p<0.001); and patients with bipolar disorder (n=19,741) were more likely to enter facilities with more problematic care too (12.5 vs 11.2, p<0.001 for total deficiencies; and 8.2 vs 7.2, p<0.001 for healthcare-related deficiencies). After sequentially controlling for the within-county choice of facilities, patient characteristics, and facility covariates, the association of SMI with admitting to higher-deficiency nursing homes persisted.
Patients diagnosed with schizophrenia or bipolar disorder (ie, SMI) were more likely than other patients to be admitted to nursing homes with higher deficiency citations for both overall quality and clinical care quality. Future research is necessary to understand the reasons behind the disparity in quality of nursing home care associated with SMI.
serious mental illness; deficiency citations; nursing home quality; schizophrenia; bipolar disorder
To improve nursing home quality, many states developed “Technical Assistance Programs” that provide on-site consultation and training for nursing facility staff.
We conducted a national survey on these state programs to collect data on program design, operations, financing, and perceived effectiveness.
As of 2010, 17 states have developed such programs. Compared to existing state nursing home quality regulations, these programs represent a collaborative, rather than enforcement-oriented, approach to quality. However, existing programs vary substantially in key structural features such as staffing patterns, funding levels, and relationship with state survey and certification agencies. Perceived effectiveness by program officials on quality was high, although few states have performed formal evaluations. Perceived barriers to program effectiveness included lack of appropriate staff and funding, among others.
State “Technical Assistance Programs” for nursing homes varies in program design and perceived effectiveness. Future comparative evaluations are needed to inform evidence-based quality initiatives.
state regulations; technical assistance program; nursing home; quality improvement; long-term care
Nursing home residents with serious mental illness need a high level of general medical and end-of-life services. This study tested whether persons with serious mental illness are as likely as other nursing home residents to make informed choices about treatments through medical advance care plans.
Secondary analyses were conducted with data from a 2004 national survey of nursing home residents with serious mental illness (N=1,769) and without (N=11,738). Bivariate and multivariate analyses determined differences in documented advance care plans, including living wills; “do not resuscitate” and “do not hospitalize” orders; and orders concerning restriction of feeding tube, medication, or other treatments.
The overall rates of having any of the four advance care plans were 57% and 68% for residents with and without serious mental illness, respectively (p<.001). Residents with serious mental illness also showed lower rates for individual advance care plans. In a multivariate analysis that adjusted for resident and facility characteristics (N=1,174 nursing homes) as well as survey procedures, serious mental illness was associated with a 24% reduced odds of having any advance directives (adjusted odds ratio=.76, 95% confidence interval=.66–.87, p<.001). Similar results were found for individual documented plans.
Among U.S. nursing home residents, those with serious mental illness were less likely than others to have written medical advance directives. Future research is needed to help understand both resident factors (such as inappropriate behaviors, impaired communication skills, and disrupted family support) and provider factors (including training, experience, and attitude) that underlie this finding.
This study determined whether higher patient volume of skilled nursing facility (SNF) care was associated with a lower hospital transfer rate. Using the nursing home Minimum Data Set and the On-line Survey, Certification, and Reporting file, we assembled a national cohort of Medicare SNF post-acute care admissions between January and September of 2008. Multivariable analyses based on Cox proportional hazards models found that patients admitted to high-volume SNFs (annual number of admissions in the top tertile group) showed an approximately 15% reduced risk for 30-day rehospitalization and an approximately 25% reduced risk for 90-day rehospitalization, compared to patients admitted to low-volume SNFs (annual number of admissions in the bottom tertile group, or<45). Similar patterns of volume-outcome associations were found for hospital-based and freestanding facilities separately. The inverse volume-outcome association in post-acute SNF care may reflect a “practice makes perfect” effect, a “selective referral” effect, or both.
skilled nursing facilities; post-acute care; volume-outcome association; rehospitalization; Minimum Data Set
To understand the dynamics of brain edema in different areas after traumatic brain injury (TBI) in rabbit, we used dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) and diffusion-weighted imaging (DWI) to monitor blood–brain barrier (BBB) permeability and cytotoxic brain edema after weight drop-induced TBI in rabbit. The dynamics of BBB permeability and brain edema were quantified using Ktrans and apparent diffusion coefficient (ADC) in the focal and perifocal lesion areas, as well as the area contralateral to the lesion. In the focal lesion area, Ktrans began to increase at 3 h post-TBI, peaked at 3 days, and decreased gradually while remaining higher than sham injury animals at 7 and 30 days. ADC was more variable, increased slightly at 3 h, decreased to its lowest value at 7 days, then increased to a peak at 30 days. In the perifocal lesion area, Ktrans began to increase at 1 day, peaked at 3–7 days, and returned to control level by 30 days. ADC showed a trend to increase at 1 day, followed by a continuous increase thereafter. In the contralateral area, no changes in Ktrans and ADC were observed at any time-point. These data demonstrate that different types of brain edema predominate in the focal and perifocal lesion areas. Specifically cytotoxic edema was predominant in the focal lesion area while vasogenic edema predominated in the perifocal area in acute phase. Furthermore, secondary opening of the BBB after TBI may appear if secondary injury is not controlled. BBB damage may be a driving force for cytotoxic brain edema and could be a new target for TBI intervention.
blood-brain barrier; cytotoxic edema; diffusion-weighted imaging; dynamic contrast-enhanced MRI; rabbit; traumatic brain injury; vasogenic edema
The “Notch-sparing” γ-secretase inhibitor (GSI) BMS-708,163 (Avagacestat) is currently in phase II clinical trials for Alzheimer’s disease. Unlike previously failed GSIs, BMS-708,163 is considered to be a promising drug candidate due to its reported Notch-sparing activity for the inhibition of Aβ production over Notch cleavage. We now report that BMS-708,163 binds directly to PS1-NTF, and that binding can be competed by other pan-GSIs, but not by γ-secretase modulators (GSMs). Furthermore, BMS-708,163 blocks the binding of four different active site-directed GSI photoaffinity probes. We therefore report that this compound acts as a non-selective γ-secretase inhibitor.
Streptococcussuis serotype 2 (SS 2) is an important zoonotic pathogen that has caused two major infectious outbreaks of streptococcal toxic shock syndrome (STSS) in China. A novel gene located in the 89K pathogenicity island (PAI) encoding a putative hemolysin-III-related protein (Hhly3) has been previously characterized. In this study, the SS2 deletion mutant of the exogenous gene hhly3 was constructed by homologous recombination. This protein was found to exhibit cytolytic activity, and hemolytic activity of the hhly3 gene knockout mutant (Δhhly3) was significantly lower than that in the wild-type strain ZY05719. In addition, qRT-PCR revealed that Hhly3 played an important role in the expression of the secreted hemolysin SLY, which may be the key reason for the decreased hemolytic activity. Consequently, compared with the WT strain, the infection and pathogenicity of Δhhly3 was also decreased, as evidenced by in vitro bacterial growth in whole blood and by the in vivo zebrafish test, suggesting that hhly3 is a novel exogenous hemolysis-related gene in SS2 strains.
Flaviviruses deliver their genome into the cell by fusing the viral lipid membrane to an endosomal membrane. The sequence and kinetics of the steps required for nucleocapsid delivery into the cytoplasm remain unclear. Here we dissect the cell entry pathway of virions and virus-like particles from two flaviviruses using single-particle tracking in live cells, a biochemical membrane fusion assay and virus infectivity assays. We show that the virus particles fuse with a small endosomal compartment in which the nucleocapsid remains trapped for several minutes. Endosomal maturation inhibitors inhibit infectivity but not membrane fusion. We propose a flavivirus cell entry mechanism in which the virus particles fuse preferentially with small endosomal carrier vesicles and depend on back-fusion of the vesicles with the late endosomal membrane to deliver the nucleocapsid into the cytoplasm. Virus entry modulates intracellular calcium release and phosphatidylinositol-3-phosphate kinase signaling. Moreover, the broadly cross-reactive therapeutic antibody scFv11 binds to virus-like particles and inhibits fusion.
Many viruses package their genetic material into a lipid envelope. In order to deliver their genome into the host-cell cytoplasm, where it can be replicated, viruses must fuse their envelope with a cellular lipid membrane. This fusion event is therefore a critical step in the entry of an enveloped virus into the cell. In this study, we used various cell biological and biochemical approaches to map precisely the cell entry pathway of two major human pathogens from the flavivirus family, yellow fever virus and Japanese encephalitis virus. We discovered that these viruses co-opt cellular phospholipid signaling to promote the fusion of their envelope with the lipid envelope of small compartments inside the host-cell endosomes. The viral genome remains trapped in these compartments for several minutes until the compartments fuse with the surrounding endosomal membrane. It is this second membrane fusion event that delivers the viral genome into the cytoplasm. We also showed that the antibody fragment scFv11 inhibits the fusion of the viral envelope with small lipid compartments, explaining the therapeutic activity of the scFv11 antibody. Our work identifies new vulnerabilities in the entry pathway of flaviviruses, including the formation of small endosomal compartments and two distinct membrane fusion events involving these compartments.
Previous methods for Kupffer cells (KCs) isolation require sophisticated skills and tedious procedures. Few studies have attempted to explore the self-renewal capacity of KCs in vitro. Therefore, the aim of this study was to establish a simple method for rat KCs isolation and further investigate the mitotic potential of KCs in vitro.
KCs were obtained by performing one-step perfusion, enzymatic tissue treatment, differential centrifugation and selective adherence. The proliferation ability of cultured KCs was determined by MTT assay and Propidium Iodide FACS analysis. Phagocytic assay and ED-1, ED-2 immunofluorescence were used to identify cell phenotype. After stimulation with LPS, the expression of surface antigens (MHCII, CD40, CD80, and CD86) and the production of cytokines (NF-κB, TNF-α, IL-6 and IL-10) were measured for cell function identification.
KCs were isolated with certain numbers and reasonable purities. The KCs were able to survive until at least passage 5 (P5), and at P3 showed equally strong phagocytic activity as primary KCs (P0). After stimulation with LPS, the change in the expression of surface antigens and the production of cytokines for P3 cells was similar to that for P0 cells.
Our study provides a simple and efficient method for KCs isolation, and reveals that self-renewing KCs have the same phagocytic activity and functions as primary KCs.
Extremely low-frequency magnetic field (ELF-MF) has been reported to be of potential pathogenetic relevance to Alzheimer's disease (AD) for years. However, evidence confirming this function remains inconclusive. Chronic Al treatment has been identified as a contributing factor to cognitive function impairment in AD. This study aims to examine whether or not ELF-MF and Al have synergistic effects toward AD pathogenesis by investigating the effects of ELF-MF with or without chronic Al treatment on SD rats.
Sprague-Dawley (SD) rats were subjected one of the following treatments: sham (control group), oral Al (Al group), ELF-MF (100 µT at 50 Hz) with oral Al (MF+Al group), or ELF-MF (100 µT at 50 Hz) without oral Al (MF group).
After 12 wk of treatment, oral Al treatment groups (Al and MF+Al groups) showed learning and memory impairment as well as morphological hallmarks, including neuronal cell loss and high density of amyloid-β (Aβ) in the hippocampus and cerebral cortex. ELF-MF without Al treatment showed no significant effect on AD pathogenesis. ELF-MF+Al treatment induced no more damage than Al treatment did.
Our results showed no evidence of any association between ELF-MF exposure (100 µT at 50 Hz) and AD, and ELF-MF exposure does not influence the pathogenesis of AD induced by Al overload.
The aim of this study was to investigate the clinical value of serum cytokeratin 19 fragment (CYFRA21-1) and carcinoembryonic antigen (CEA) in the prediction of chemotherapy response and prognosis in patients with advanced non-small cell lung cancer (NSCLC). Serum CYFRA21-1 and CEA levels of 98 patients with advanced NSCLC were measured using immunoradiometric kits prior to and after 2 cycles of chemotherapy. After 2 cycles of chemotherapy, 45 patients achieved a radiological objective response (OR), 30 patients achieved stable disease (SD) and 23 patients had progressive disease (PD). Serum CYFRA21-1 and CEA were significantly decreased compared to baseline levels (P<0.001). By ROC curve analysis, a ≥60% reduction in CYFRA21-1 and a ≥25% reduction in CEA were the optimal cut-off levels with best sensitivity and specificity for the diagnosis of radiologic OR. The median survival of all patients was 10.2 months (range 2.6–26.3). Univariate survival analysis showed that the Eastern Cooperative Oncology Group (ECOG) performance status (PS) score, radiologic OR, a ≥60% reduction in CYFRA21-1 and a ≥25% reduction in CEA were significant prognostic factors for better overall survival. The median overall survival time in patients with a ≥60% reduction in CYFRA21-1 was significantly longer than in those with a <60% reduction (P<0.001). Similarly, the median overall survival time in patients with a ≥25% reduction in CEA was also significantly longer than in those with a <25% reduction (P<0.001). Multivariate analysis showed that ECOG PS score, a ≥60% reduction in CYFRA21-1 and a ≥25% reduction in CEA were independent prognostic factors of survival, while radiologic OR was not. In conclusion, a ≥60% reduction in CYFRA21-1 and a ≥25% reduction in CEA may be reliable surrogate markers for the prediction of chemothrapy response and prognosis, especially for the diagnosis of radiologic OR.
cytokeratin 19 fragment; carcinoembryonic antigen; non-small cell lung cancer; chemotherapy response; prognosis
Access to health care is a major requirement in improving health and fostering socioeconomic development. In the People's Republic of China (P.R. China), considerable changes have occurred in the social, economic, and health systems with a shift from a centrally planned to a socialist market economy. This brought about great benefits and new challenges, particularly for vertical disease control programs, including schistosomiasis. We explored systemic barriers in access to equitable and effective control of schistosomiasis.
Between August 2002 and February 2003, 66 interviews with staff from anti-schistosomiasis control stations and six focus group discussions with health personnel were conducted in the Dongting Lake area, Hunan Province. Additionally, 79 patients with advanced schistosomiasis japonica were interviewed. The health access livelihood framework was utilized to examine availability, accessibility, affordability, adequacy, and acceptability of schistosomiasis-related health care.
We found sufficient availability of infrastructure and human resources at most control stations. Many patients with advanced schistosomiasis resided in non-endemic or moderately endemic areas, however, with poor accessibility to disease-specific knowledge and specialized health services. Moreover, none of the patients interviewed had any form of health insurance, resulting in high out-of-pocket expenditure or unaffordable care. Reports on the adequacy and acceptability of care were mixed.
There is a need to strengthen health awareness and schistosomiasis surveillance in post-transmission control settings, as well as to reduce diagnostic and treatment costs. Further studies are needed to gain a multi-layered, in-depth understanding of remaining barriers, so that the ultimate goal of schistosomiasis elimination in P.R. China can be reached.
China has made great strides toward reducing the burden of schistosomiasis, facilitated by sustained political commitment and a multi-faceted, integrated control strategy. The ultimate goal is disease elimination, which might be challenging due to high rates of re-infection, clusters of re-emergence, and growing health disparities. Market-oriented reforms and system-wide policies within the health care system offer new opportunities, but also entail challenges for the national schistosomiasis control program. Few studies have examined systemic barriers to equitable and effective schistosomiasis control in China. We explored the five core dimensions of access to health care, placing emphasis on schistosomiasis in the Dongting Lake area of Hunan Province. We collected and analyzed perspectives from staff working at local anti-schistosomiasis control stations and designated schistosomiasis hospitals, and from patients with advanced schistosomiasis. Our data suggest that a lack of affordability and high out-of-pocket expenditure posed a major barrier to the health care users, as did a lack of relevant health-information, and poorly accessible diagnostic and specialized surgical services. The lessons learned from this work are important in the design and development of disease control programs and entail key policy implications for schistosomiasis elimination.
The bacterial type IV pilus (T4P) is the strongest biological motor known to date as its retraction can generate forces well over 100 pN. Myxococcus xanthus, a δ-proteobacterium, provides a good model for T4P investigations because its social (S) gliding motility is powered by T4P. In this study, the interactions among M. xanthus T4P proteins were investigated using genetics and the yeast two-hybrid (Y2H) system. Our genetic analysis suggests that there is an integrated T4P structure that crosses the inner membrane (IM), periplasm and the outer membrane (OM). Moreover, this structure exists in the absence of the pilus filament. A systematic Y2H survey provided evidence for direct interactions among IM and OM proteins exposed to the periplasm. For example, the IM lipoprotein PilP interacted with its cognate OM protein PilQ. In addition, interactions among T4P proteins from the thermophile Thermus thermophilus were investigated by Y2H. The results indicated similar protein-protein interactions in the T4P system of this non-proteobacterium despite significant sequence divergence between T4P proteins in T. thermophilus and M. xanthus. The observations here support the model of an integrated T4P structure in the absence of a pilus in diverse bacterial species.
Palynomorphs extracted from the mud coffins and plant remains preserved at the archaeological site of Xiaohe Cemetery (Cal. 3980 to 3540 years BP) in Lop Nur Desert of Xinjiang, China were investigated for the reconstruction of the ancient environments at the site. The results demonstrate that the Xiaohe People lived at a well-developed oasis, which was surrounded by extensive desert. The vegetation in the oasis consisted of Populus, Phragmites, Typha and probably of Gramineae, while the desert surrounding the oasis had some common drought-resistant plants dominated by Ephedra, Tamarix, Artemisia and Chenopodiaceae. This present work provides the first data of the environmental background at this site for further archaeological investigation.
In China, several species (Hedysarum polybotrys Hand.-Mazz., Hedysarum limprichtii Hlbr., Hedysarum vicioider Turcz. var. Taipeicum Hand.-Mazz. Liu, Hedysarum smithianum, et al.) of genus Hedysarum have a long history of use in traditional Chinese medicine (TCM). In TCM, these plants are used to increase the energy of the body. To date, 155 compounds, including flavonoids, triterpenes, coumarins, lignanoids, nitrogen compounds, sterols, carbohydrates, fatty compounds, and benzofuran, have been isolated from plants of the genus Hedysarum. Various chemical constituents contribute to the antioxidant, anti-tumor, anti-aging, anti-diabetic, and anti-hypertensive properties of these plants. Hedysarum species are used to treat infestation with gastrointestinal nematodes and may support the immune system and peripheral nervous system. In the present review, we summarize the research on the phytochemistry and pharmacology of Hedysarum species, which will be useful for better utilization of these important species in TCM.
Hedysarum; Chemical constituents; Pharmacology; Utilization; TCM
6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK), a key enzyme in the folate biosynthesis pathway catalyzing the pyrophosphoryl transfer from ATP to 6-hydroxymethyl-7,8-dihydropterin, is an attractive target for developing novel antimicrobial agents. Previously, we studied the mechanism of HPPK action, synthesized bisubstrate analogue inhibitors by linking 6-hydroxymethylpterin to adenosine through phosphate groups, and developed a new generation of bisubstrate inhibitors by replacing the phosphate bridge with a piperidine-containing linkage. To further improve linker properties, we have synthesized a new compound, characterized its protein binding/inhibiting properties, and determined its structure in complex with HPPK. Surprisingly, this inhibitor exhibits a new binding mode in that the adenine base is flipped when compared to previously reported structures. Furthermore, the side chain of amino acid residue E77 is involved in protein-inhibitor interaction, forming hydrogen bonds with both 2' and 3' hydroxyl groups of the ribose moiety. Residue E77 is conserved among HPPK sequences, but interacts only indirectly with the bound MgATP via water molecules. Never observed before, the E77-ribose interaction is compatible only with the new inhibitor-binding mode. Therefore, this compound represents a new direction for further development.
Antibacterial; Bisubstrate; Folate; HPPK; Pterin
Nursing homes found to be not meeting quality standards are cited for deficiencies. Before 1995, their only recourse was a formal appeal process, which is lengthy and costly. In 1995, the Centers for Medicare & Medicaid Services (CMS) instituted the Informal Dispute Resolution (IDR) process. This study presents for the first time national statistics about the IDR process and an analysis of the factors that influence nursing homes’ decisions to request an IDR.
Retrospective study including descriptive statistics and multivariate logistic hierarchical models.
U.S. nursing homes in 2005 to 2008.
15,916 Medicaid and Medicare certified nursing homes nationally, with 94,188 surveys and 9,388 IDRs.
The unit of observation was an annual survey or a complaint survey that generated at least one deficiency. The dependent variable was dichotomous and indicated whether the annual or a complaint survey triggered an IDR request. Independent variables included characteristics of the nursing home, the deficiency, the market, and the state regulatory environment.
Ten percent of all annual surveys and complaint surveys resulted in IDRs. There was substantial variation across states, which persisted over time. Multivariate results suggest that nursing homes’ decisions to request an IDR depend on their assessment of the probability of success and assessment of the benefits of the submission.
Nursing homes avail themselves of the IDR process. Their propensity to do so depends on a number of factors, including the state regulatory system and the market environment in which they operate.
nursing homes; quality; deficiencies; regulation; appeal
Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in cattle. The complex, multifaceted interaction of M. avium subsp. paratuberculosis with its host includes dampening the ability of infected cells to respond to stimuli that promote M. avium subsp. paratuberculosis clearance. By disrupting host defenses, M. avium subsp. paratuberculosis creates an intracellular environment that favors the establishment and maintenance of infection. Toll-like receptors (TLRs) are important sensors that initiate innate immune responses to microbial challenge and are also immunotherapeutic targets. For example, TLR9 contributes to host defense against M. avium subsp. paratuberculosis, and its agonists (CpG oligodeoxynucleotides [ODNs]) are under investigation for treatment of Johne's disease and other infections. Here we demonstrate that M. avium subsp. paratuberculosis infection changes the responsiveness of bovine monocytes to TLR9 stimulation. M. avium subsp. paratuberculosis inhibits classical TLR9-mediated responses despite a 10-fold increase in TLR9 expression and maintained uptake of CpG ODNs. Other TLR9-mediated responses, such as oxidative burst, which occur through noncanonical signaling, remain functional. Kinome analysis verifies that classic TLR9 signaling is blocked by M. avium subsp. paratuberculosis infection and that signaling instead proceeds through a Pyk2-mediated mechanism. Pyk2-mediated signaling does not hinder infection, as CpG ODNs fail to promote M. avium subsp. paratuberculosis clearance. Indeed, Pyk2 signaling appears to be an important aspect of M. avium subsp. paratuberculosis infection, as Pyk2 inhibitors significantly reduce the number of intracellular M. avium subsp. paratuberculosis bacteria. The actions of M. avium subsp. paratuberculosis on TLR9 signaling may represent a strategy to generate a host environment which is better suited for infection, revealing potential new targets for therapeutic intervention.
Complex environmental conditions can significantly affect bacterial genome size by unknown mechanisms. The So0157-2 strain of Sorangium cellulosum is an alkaline-adaptive epothilone producer that grows across a wide pH range. Here, we show that the genome of this strain is 14,782,125 base pairs, 1.75-megabases larger than the largest bacterial genome from S. cellulosum reported previously. The total 11,599 coding sequences (CDSs) include massive duplications and horizontally transferred genes, regulated by lots of protein kinases, sigma factors and related transcriptional regulation co-factors, providing the So0157-2 strain abundant resources and flexibility for ecological adaptation. The comparative transcriptomics approach, which detected 90.7% of the total CDSs, not only demonstrates complex expression patterns under varying environmental conditions but also suggests an alkaline-improved pathway of the insertion and duplication, which has been genetically testified, in this strain. These results provide insights into and a paradigm for how environmental conditions can affect bacterial genome expansion.
Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors’ websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.
Circulating microRNA expression levels can serve as diagnostic/prognostic biomarkers in several types of malignant tumors; however, to our knowledge, there have been reports describing their value in cervical squamous cell carcinoma (SCC). In this study, we used hybridization arrays to compare the microRNA expression profiles in cervical squamous cell carcinomas (SCC) samples among patients with lymph node metastasis (LNM) or without LNM; 89 microRNAs were found to fit our inclusion criteria. Using quantitative PCR (qPCR), we examined the expression levels of these microRNAs in cervical cancer tissue, as well as in serum from patients and healthy women. We compared the expression levels between patients with LNM (n=40) and those without LNM (n=40) and healthy controls (n=20). Using regression analysis, we generated a comprehensive set of marker microRNAs and drew the fitted binormal receiver operating characteristic (ROC) curves to access the predictive value. We identified 6 serum microRNAs that can predict LNM in cervical SCC patients; these microRNAs were miR-1246, miR-20a, miR-2392, miR-3147, miR-3162-5p and miR-4484. The area under the curve (AUC) of the comprehensive set of serum microRNAs predicting LNM was 0.932 (sensitivity, 0.856; specificity, 0.850). The predictive value of the serum microRNAs was inferior to that in tissue (AUC 0.992; sensitivity, 0.967; specificity, 0.950; P=0.018). We compared the LNM predictive value of serum microRNAs and SCC antigen (SCC-Ag) by drawing fitted binormal ROC curves However, serum microRNA analysis is by far superior to serum SCC-Ag analysis (AUC 0.713; sensitivity, 0.612; specificity, 0.700; P<0.0001). Serum microRNAs are a good predictor of LNM with clinical value in early-stage cervical SCC.
cervical squamous cell carcinoma; microRNA; lymph node metastasis; serum marker
Imprinted genes form a special subset of the genome, exhibiting monoallelic expression in a parent-of-origin–dependent fashion. This monoallelic expression is controlled by parental-specific epigenetic marks, which are established in gametogenesis and early embryonic development and are persistent in all somatic cells throughout life. We define this specific set of cis-acting epigenetic regulatory elements as the imprintome, a distinct and specially tasked subset of the epigenome. Imprintome elements contain DNA methylation and histone modifications that regulate monoallelic expression by affecting promoter accessibility, chromatin structure, and chromatin configuration. Understanding their regulation is critical because a significant proportion of human imprinted genes are implicated in complex diseases. Significant species variation in the repertoire of imprinted genes and their epigenetic regulation, however, will not allow model organisms solely to be used for this crucial purpose. Ultimately, only the human will suffice to accurately define the human imprintome.
differential methylation. DNA methylation; histone modification; imprinted gene; imprintome; monoallelic expression