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1.  Complete Genome Sequence of vB_EcoM_112, a T-Even-Type Bacteriophage Specific for Escherichia coli O157:H7 
Genome Announcements  2014;2(6):e00393-14.
Bacteriophage vB_EcoM_112 (formerly e11/2) is an Escherichia coli phage with specificity for the O157:H7 serotype. The vB_EcoM_112 genome sequence shares high degrees of similarity with the phage T4 genome sequence.
doi:10.1128/genomeA.00393-14
PMCID: PMC4241651  PMID: 25395625
2.  In Vivo and Ex Vivo Evaluations of Bacteriophages e11/2 and e4/1c for Use in the Control of Escherichia coli O157:H7▿  
Applied and Environmental Microbiology  2010;76(21):7210-7216.
This study investigated the effect of bacteriophages (phages) e11/2 and e4/1c against Escherichia coli O157:H7 in an ex vivo rumen model and in cattle in vivo. In the ex vivo rumen model, samples were inoculated with either 103 or 106 CFU/ml inoculum of E. coli O157:H7 and challenged separately with each bacteriophage. In the presence of phage e11/2, the numbers of E. coli O157:H7 bacteria were significantly (P < 0.05) reduced to below the limit of detection within 1 h. Phage e4/1c significantly (P < 0.05) reduced E. coli O157:H7 numbers within 2 h of incubation, but the number of surviving E. coli O157:H7 bacteria then remained unchanged over a further 22-h incubation period. The ability of a phage cocktail of e11/2 and e4/1c to reduce the fecal shedding of E. coli O157:H7 in experimentally inoculated cattle was then investigated in two cattle trials. Cattle (yearlings, n = 20 for trial one; adult fistulated cattle, n = 2 for trial two) were orally inoculated with 1010 CFU of E. coli O157:H7. Animals (n = 10 for trial one; n = 1 for trial two) were dosed daily with a bacteriophage cocktail of 1011 PFU for 3 days postinoculation. E. coli O157:H7 and phage numbers in fecal and/or rumen samples were determined over 7 days postinoculation. E. coli O157:H7 numbers rapidly declined in all animals within 24 to 48 h; however, there was no significant difference (P > 0.05) between the numbers of E. coli O157:H7 bacteria shed by the phage-treated or control animals. Phages were recovered from the rumen but not from the feces of the adult fistulated animal in trial two but were recovered from the feces of the yearling animals in trial one. While the results from the rumen model suggest that phages are effective in the rumen, further research is required to improve the antimicrobial effectiveness of phages for the elimination of E. coli O157:H7 in vivo.
doi:10.1128/AEM.01530-10
PMCID: PMC2976219  PMID: 20851992
3.  Unusual Case of Fibromyoma Uteri 
California and Western Medicine  1936;45(4):355-356.
Images
PMCID: PMC1761394  PMID: 18743836
4.  The Feasibility of Formation and Kinetics of NMR Signal Amplification by Reversible Exchange (SABRE) at High Magnetic Field (9.4 T) 
1H NMR signal amplification by reversible exchange (SABRE) was observed for pyridine and pyridine-d5 at 9.4 T, a field that is orders of magnitude higher than what is typically utilized to achieve the conventional low-field SABRE effect. In addition to emissive peaks for the hydrogen spins at the ortho positions of the pyridine substrate (both free and bound to the metal center), absorptive signals are observed from hyperpolarized orthohydrogen and Ir-complex dihydride. Real-time kinetics studies show that the polarization build-up rates for these three species are in close agreement with their respective 1H T1 relaxation rates at 9.4 T. The results suggest that the mechanism of the substrate polarization involves cross-relaxation with hyperpolarized species in a manner similar to the spin-polarization induced nuclear Overhauser effect. Experiments utilizing pyridine-d5 as the substrate exhibited larger enhancements as well as partial H/D exchange for the hydrogen atom in the ortho position of pyridine and concomitant formation of HD molecules. While the mechanism of polarization enhancement does not explicitly require chemical exchange of hydrogen atoms of parahydrogen and the substrate, the partial chemical modification of the substrate via hydrogen exchange means that SABRE under these conditions cannot rigorously be referred to as a non-hydrogenative parahydrogen induced polarization process.
doi:10.1021/ja501052p
PMCID: PMC3985893  PMID: 24528143
5.  Research on Emissions, Air quality, Climate, and Cooking Technologies in Northern Ghana (REACCTING): study rationale and protocol 
BMC Public Health  2015;15:126.
Background
Cooking over open fires using solid fuels is both common practice throughout much of the world and widely recognized to contribute to human health, environmental, and social problems. The public health burden of household air pollution includes an estimated four million premature deaths each year. To be effective and generate useful insight into potential solutions, cookstove intervention studies must select cooking technologies that are appropriate for local socioeconomic conditions and cooking culture, and include interdisciplinary measurement strategies along a continuum of outcomes.
Methods/Design
REACCTING (Research on Emissions, Air quality, Climate, and Cooking Technologies in Northern Ghana) is an ongoing interdisciplinary randomized cookstove intervention study in the Kassena-Nankana District of Northern Ghana. The study tests two types of biomass burning stoves that have the potential to meet local cooking needs and represent different “rungs” in the cookstove technology ladder: a locally-made low-tech rocket stove and the imported, highly efficient Philips gasifier stove. Intervention households were randomized into four different groups, three of which received different combinations of two improved stoves, while the fourth group serves as a control for the duration of the study. Diverse measurements assess different points along the causal chain linking the intervention to final outcomes of interest. We assess stove use and cooking behavior, cooking emissions, household air pollution and personal exposure, health burden, and local to regional air quality. Integrated analysis and modeling will tackle a range of interdisciplinary science questions, including examining ambient exposures among the regional population, assessing how those exposures might change with different technologies and behaviors, and estimating the comparative impact of local behavior and technological changes versus regional climate variability and change on local air quality and health outcomes.
Discussion
REACCTING is well-poised to generate useful data on the impact of a cookstove intervention on a wide range of outcomes. By comparing different technologies side by side and employing an interdisciplinary approach to study this issue from multiple perspectives, this study may help to inform future efforts to improve health and quality of life for populations currently relying on open fires for their cooking needs.
doi:10.1186/s12889-015-1414-1
PMCID: PMC4336492
Cookstoves; Household air pollution; Global health; Study protocol; Randomized intervention study
6.  Trafficking of Epidermal Growth Factor Receptor Ligands in Polarized Epithelial Cells 
Annual review of physiology  2013;76:275-300.
A largely unilamellar epithelial layer lines body cavities and organ ducts such as the digestive tract and kidney tubules. This polarized epithelium is composed of biochemically and functionally separate apical and basolateral surfaces. The epidermal growth factor receptor (EGFR) signaling pathway is a critical regulator of epithelial homeostasis and is perturbed in a number of epithelial disorders. It is underappreciated that in vivo EGFR signaling is most often initiated by cell-surface delivery and processing of one of seven transmembrane ligands, resulting in release of the soluble form that binds EGFR. In polarized epithelial cells, EGFR is restricted largely to the basolateral surface, and apical or basolateral ligand delivery therefore has important biological consequences. In vitro approaches have been used to study the biosynthesis, cell-surface delivery, proteolytic processing, and release of soluble EGFR ligands in polarized epithelial cells. We review these results, discuss their relevance to normal physiology, and demonstrate the pathophysiological consequences of aberrant trafficking. These studies have uncovered a rich diversity of apico-basolateral trafficking mechanisms among the EGFR ligands, provided insights into the pathogenesis of an inherited magnesium-wasting disorder of the kidney (isolated renal hypomagnesemia), and identified a new mode of EGFR ligand signaling via exosomes.
doi:10.1146/annurev-physiol-021113-170406
PMCID: PMC4180094  PMID: 24215440
EGFR; basolateral; polarized trafficking; epithelial polarity; cancer
7.  Evidence for Alterations in Stimulatory G proteins and Oxytocin Levels in Children with Autism 
Psychoneuroendocrinology  2013;40:159-169.
The neurotransmitter oxytocin plays an important role in social affiliation. Low oxytocin levels and defects in the oxytocin receptor have been reported in childhood autism. However, little is known about oxytocin’s post-receptor signaling pathways in autism. Oxytocin signals via stimulatory and inhibitory G proteins. c-fos mRNA expression has been used as a marker of OT signaling as well as of G protein signaling. Herein, we hypothesized that oxytocin and its signaling pathways would be altered in children with autism. We measured plasma oxytocin levels by ELISA, G-protein and c-fos mRNA by PCR, and G proteins by immunoblot in cultured peripheral blood mononuclear cells (PBMCs) in children with autism and in age-matched controls. Males with autism displayed elevated oxytocin levels compared to controls (p<0.05). Children with autism displayed significantly higher mRNA for stimulatory G proteins compared to controls (p<0.05). Oxytocin levels correlated strongly positively with c-fos mRNA levels, but only in control participants (p<0.01). Oxytocin, G-protein, and c-fos mRNA levels correlated inversely with measures of social and emotional behaviors, but only in control participants. These data suggest that children with autism may exhibit a dysregulation in oxytocin and/or its signaling pathways.
doi:10.1016/j.psyneuen.2013.11.014
PMCID: PMC4259400  PMID: 24485488
8.  A 3D-Printed High Power Nuclear Spin Polarizer 
Three-dimensional printing with high-temperature plastic is used to enable spin exchange optical pumping (SEOP) and hyperpolarization of xenon-129 gas. The use of 3D printed structures increases the simplicity of integration of the following key components with a variable temperature SEOP probe: (i) in situ NMR circuit operating at 84 kHz (Larmor frequencies of 129Xe and 1H nuclear spins), (ii) <0.3 nm narrowed 200 W laser source, (iii) in situ high-resolution near-IR spectroscopy, (iv) thermoelectric temperature control, (v) retroreflection optics, and (vi) optomechanical alignment system. The rapid prototyping endowed by 3D printing dramatically reduces production time and expenses while allowing reproducibility and integration of “off-the-shelf” components and enables the concept of printing on demand. The utility of this SEOP setup is demonstrated here to obtain near-unity 129Xe polarization values in a 0.5 L optical pumping cell, including ~74 ± 7% at 1000 Torr xenon partial pressure, a record value at such high Xe density. Values for the 129Xe polarization exponential build-up rate [(3.63 ± 0.15) × 10−2 min−1] and in-cell 129Xe spin−lattice relaxation time (T1 = 2.19 ± 0.06 h) for 1000 Torr Xe were in excellent agreement with the ratio of the gas-phase polarizations for 129Xe and Rb (PRb ~ 96%). Hyperpolarization-enhanced 129Xe gas imaging was demonstrated with a spherical phantom following automated gas transfer from the polarizer. Taken together, these results support the development of a wide range of chemical, biochemical, material science, and biomedical applications.
doi:10.1021/ja412093d
PMCID: PMC4287367  PMID: 24400919
9.  Repeated stimuli elicit diminished high-gamma electrocorticographic responses 
NeuroImage  2013;85(0 2):10.1016/j.neuroimage.2013.07.006.
In the phenomenon of repetition suppression (RS), when a person views a stimulus, the neural activity involved in processing that item is relatively diminished if that stimulus had been previously viewed. Previous noninvasive imaging studies mapped the prevalence of RS for different stimulus types to identify brain regions involved in representing a range of cognitive information. However, these noninvasive findings are challenging to interpret because they do not provide information on how RS relates to the brain's electrophysiological activity. We examined the electrophysiological basis of RS directly using brain recordings from implanted electrocorticographic (ECoG) electrodes in neurosurgical patients. Patients performed a memory task during ECoG recording and we identified high-gamma signals (65–128 Hz) that distinguished the neuronal representation of specific memory items. We then compared the neural representation of each item between novel and repeated viewings. This revealed the presence of RS, in which the neuronal representation of a repeated item had a significantly decreased amplitude and duration compared with novel stimuli. Furthermore, the magnitude of RS was greatest for the stimuli that initially elicited the largest activation at each site. These results have implications for understanding the neural basis of RS and human memory by showing that individual cortical sites exhibit the largest RS for the stimuli that they most actively represent.
doi:10.1016/j.neuroimage.2013.07.006
PMCID: PMC3859728  PMID: 23867555
electrocorticography; gamma band; repetition suppression
10.  Efficient Transformation of Parahydrogen Spin Order into Heteronuclear Magnetization 
The journal of physical chemistry. B  2013;117(5):1219-1224.
Spin order obtained in the strong coupling regime of protons from parahydrogen-induced hyperpolarization (PHIP) is initially captured as an ensemble of singlet states. For biomedical applications of PHIP, locking this spin order on long-lived heteronuclear storage nuclei increases spectral dispersion, reduces background interference from water protons, and eliminates the need to synchronize subsequent detection pulse sequences to accrued singlet-state evolution. A variety of traditional sequences such as INEPT or HMQC are available to interconvert heteronuclear single quantum coherences at high field, but new approaches are required for converting singlet states into heteronuclear single quantum coherences at low field in the strong coupling regime of protons. Described here is a consolidated pulse sequence that achieves this transformation of singlet-state spin order into heteronuclear magnetization across a wide range of scalar couplings in AA′X spin systems. Analytic solutions to the spin evolution are presented, and performance was validated experimentally in the parahydrogen addition product, 2-hydroxyethyl 1-13C-propionate-d3. Hyperpolarized carbon-13 signals were enhanced by a factor of several million relative to Boltzmann polarization in a static magnetic field of 47.5 mT (~13% polarization). We anticipate that this pulse sequence will provide efficient conversion of parahydrogen spin order over a broad range of emerging PHIP agents that feature AA′X spin systems.
doi:10.1021/jp3089462
PMCID: PMC4287364  PMID: 23214962
11.  Enhanced arbovirus surveillance with deep sequencing: identification of novel rhabdoviruses and bunyaviruses in Australian mosquitoes 
Virology  2013;448:10.1016/j.virol.2013.09.026.
Viral metagenomics characterizes known and identifies unknown viruses based on sequence similarities to any previously sequenced viral genomes. A metagenomics approach was used to identify virus sequences in Australian mosquitoes causing cytopathic effects in inoculated mammalian cell cultures. Sequence comparisons revealed strains of Liao Ning virus (Reovirus, Seadornavirus), previously detected only in China, livestock-infecting Stretch Lagoon virus (Reovirus, Orbivirus), two novel dimarhabdoviruses, named Beaumont and North Creek viruses, and two novel orthobunyaviruses, named Murrumbidgee and Salt Ash viruses. The novel virus proteomes diverged by ≥50% relative to their closest previously genetically characterized viral relatives. Deep sequencing also generated genomes of Warrego and Wallal viruses, orbiviruses linked to kangaroo blindness, whose genomes had not been fully characterized. This study highlights viral metagenomics in concert with traditional arbovirus surveillance to characterize known and new arboviruses in field-collected mosquitoes. Follow-up epidemiological studies are required to determine whether the novel viruses infect humans.
doi:10.1016/j.virol.2013.09.026
PMCID: PMC3870893  PMID: 24314645
virus discovery; deep sequencing; arbovirus surveillance; bunyavirus; rhabdovirus; reovirus; novel virus; mosquito; Australia
12.  A genome-wide association study and biological pathway analysis of epilepsy prognosis in a prospective cohort of newly treated epilepsy 
Human Molecular Genetics  2013;23(1):247-258.
We present the analysis of a prospective multicentre study to investigate genetic effects on the prognosis of newly treated epilepsy. Patients with a new clinical diagnosis of epilepsy requiring medication were recruited and followed up prospectively. The clinical outcome was defined as freedom from seizures for a minimum of 12 months in accordance with the consensus statement from the International League Against Epilepsy (ILAE). Genetic effects on remission of seizures after starting treatment were analysed with and without adjustment for significant clinical prognostic factors, and the results from each cohort were combined using a fixed-effects meta-analysis. After quality control (QC), we analysed 889 newly treated epilepsy patients using 472 450 genotyped and 6.9 × 106 imputed single-nucleotide polymorphisms. Suggestive evidence for association (defined as Pmeta < 5.0 × 10−7) with remission of seizures after starting treatment was observed at three loci: 6p12.2 (rs492146, Pmeta = 2.1 × 10−7, OR[G] = 0.57), 9p23 (rs72700966, Pmeta = 3.1 × 10−7, OR[C] = 2.70) and 15q13.2 (rs143536437, Pmeta = 3.2 × 10−7, OR[C] = 1.92). Genes of biological interest at these loci include PTPRD and ARHGAP11B (encoding functions implicated in neuronal development) and GSTA4 (a phase II biotransformation enzyme). Pathway analysis using two independent methods implicated a number of pathways in the prognosis of epilepsy, including KEGG categories ‘calcium signaling pathway’ and ‘phosphatidylinositol signaling pathway’. Through a series of power curves, we conclude that it is unlikely any single common variant explains >4.4% of the variation in the outcome of newly treated epilepsy.
doi:10.1093/hmg/ddt403
PMCID: PMC3857947  PMID: 23962720
13.  Designing Clinical Trials for Dystonia 
Neurotherapeutics  2013;11(1):117-127.
With advances in the understanding of the pathophysiology of dystonia, novel therapeutics are being developed. Such therapies will require clinical investigation ranging from exploratory studies to examine safety, tolerability, dosage selection, and preliminary efficacy to confirmatory studies to evaluate efficacy definitively. As dystonia is a rare and complex disorder with clinical and etiological heterogeneity, clinical trials will require careful consideration of the trial design, including enrollment criteria, concomitant medication use, and outcome measures. Given the complexities of designing and implementing efficient clinical trials, it is important for clinicians and statisticians to collaborate closely throughout the clinical development process and that each has a basic understanding of both the clinical and statistical issues that must be addressed. To facilitate designing appropriate clinical trials in this field, we review important general clinical trial and regulatory principles, and discuss the critical components of trials with an emphasis on considerations specific to dystonia. Additionally, we discuss designs used in early exploratory, late exploratory, and confirmatory phases, including adaptive designs.
Electronic supplementary material
The online version of this article (doi:10.1007/s13311-013-0221-6) contains supplementary material, which is available to authorized users.
doi:10.1007/s13311-013-0221-6
PMCID: PMC3899487  PMID: 24282121
Dystonia; Clinical trials; Exploratory trials; Confirmatory trials; Adaptive designs
14.  Diffuse pulmonary ossification as a rare cause of interstitial lung disease 
Diffuse pulmonary ossification (DPO) is a rare form of interstitial lung disease. The present article describes a case of DPO in an elderly man who presented with progressive dyspnea on exertion and an isolated reduction in diffusing capacity for carbon monoxide. DPO may occur as sequelae of mitral stenosis, left heart failure, idiopathic pulmonary fibrosis, recurrent aspiration pneumonia, solid organ transplant, adult respiratory distress syndrome or may arise idiopathically. In the absence of other findings of interstitial lung disease, a lung biopsy is unlikely to be helpful in the management of these patients.
PMCID: PMC3938233  PMID: 24046820
Computed tomography; Interstitial lung disease; Pulmonary ossification; Restrictive lung disease
15.  A Person-Centered Analysis of Posttraumatic Stress Disorder Symptoms Following a Natural Disaster: Predictors of Latent Class Membership 
Journal of anxiety disorders  2013;28(1):16-24.
The present study applied latent class analysis to a sample of 810 participants residing in southern Mississippi at the time of Hurricane Katrina to determine if people would report distinct, meaningful PTSD symptom classes following a natural disaster. We found a four-class solution that distinguished persons on the basis of PTSD symptom severity/pervasiveness (Severe, Moderate, Mild, and Negligible Classes). Multinomial logistic regression models demonstrated that membership in the Severe and Moderate Classes was associated with potentially traumatic hurricane-specific experiences (e.g., being physically injured, seeing dead bodies), pre-hurricane traumatic events, co-occurring depression symptom severity and suicidal ideation, certain religious beliefs, and post-hurricane stressors (e.g., social support). Collectively, the findings suggest that more severe/pervasive typologies of natural disaster PTSD may be predicted by the frequency and severity of exposure to stressful/traumatic experiences (before, during, and after the disaster), co-occurring psychopathology, and specific internal beliefs.
doi:10.1016/j.janxdis.2013.11.002
PMCID: PMC3951614  PMID: 24334161
16.  Reovirus-associated reduction of microRNA-let-7d is related to the increased apoptotic death of cancer cells in clinical samples 
We analyzed the in situ molecular correlates of infection from cancer patients treated with reovirus. Melanoma, colorectal, and ovarian cancer samples from such patients showed variable infection of the cancer cells but not the intermingled benign cells. RT in situ PCR showed most cancer cells contained the viral genome with threefold less having productive viral infection as documented by either tubulin or reoviral protein co-expression. Productive infection in the cancer cells was strongly correlated with co-expression of p38 and caspase-3 as well as apoptosis-related death (P<0.001). The cancer cell apoptotic death was due to a marked viral-induced inhibition of microRNA-let-7d that, in turn, upregulated caspase-3 activity. In summary, reovirus shows a striking tropism to cancer cells in clinical samples. A rate-limiting factor of reovirus-induced cancer cell death is productive viral infection that operates via the marked reduction of microRNA-let-7d and concomitant elevated caspase-3 expression.
doi:10.1038/modpathol.2012.95
PMCID: PMC4275064  PMID: 22699519
apoptosis; caspase-3; microRNA-let-7d; PKR; Ras; reovirus
17.  The role of the Cronobacter sakazakii ProP C-terminal coiled coil domain in osmotolerance 
Gut Pathogens  2014;6(1):46.
Background
We investigate the role of the C-terminal coiled coil of the secondary proline porter ProP in contributing to Cronobacter sakazakii osmotolerance.
Findings
The extended C-terminal domain of ProP1 (encoded by ESA_02131) was spliced onto the truncated C-terminal end of ProP2 (encoded by ESA_01706); creating a chimeric protein (ProPc) which exhibits increased osmotolerance relative to the wild type.
Conclusions
It appears that the C-terminal coiled coil domain tunes ProP at low osmolality, whereas ProP transporters lacking the coiled coil domain are more active at a higher osmolality range.
doi:10.1186/s13099-014-0046-9
PMCID: PMC4272814  PMID: 25530808
18.  OX40 is a potent immune stimulating target in late stage cancer patients 
Cancer research  2013;73(24):7189-7198.
OX40 is a potent co-stimulatory receptor that can potentiate T cell receptor signaling on the surface of T lymphocytes, leading to their activation by a specifically recognized antigen. In particular, OX40 engagement by ligands present on dendritic cells dramatically increases the proliferation, effector function and survival of T cells. Preclinical studies have shown that OX40 agonists increase anti-tumor immunity and improve tumor-free survival. In this study, we performed a Phase I clinical trial using a mouse monoclonal antibody (mAb) that agonizes human OX40 signaling in patients with advanced cancer. Patients treated with one course of the anti-OX40 mAb showed an acceptable toxicity profile and regression of at least one metastatic lesion in 12/30 patients. Mechanistically, this treatment increased T and B cell responses to reporter antigen immunizations, led to preferential upregulation of OX40 on CD4+ FoxP3+ regulatory T cells in tumor-infiltrating lymphocytes and increased the anti-tumor reactivity of T and B cells in patients with melanoma. Our findings clinically validate OX40 as a potent immune-stimulating target for treatment in cancer patients, providing a generalizable tool to favorably influence the antitumor properties of circulating T cells, B cells and intratumoral regulatory T cells.
doi:10.1158/0008-5472.CAN-12-4174
PMCID: PMC3922072  PMID: 24177180
Immunotherapy; T lymphocytes; immune biomarkers; T cell co-stimulation; tumor specific T cell response
19.  Two TIR-like domain containing proteins in a newly emerging zoonotic Staphylococcus aureus strain sequence type 398 are potential virulence factors by impacting on the host innate immune response 
Staphylococcus aureus, sequence type (ST) 398, is an emerging pathogen and the leading cause of livestock-associated methicillin-resistant S. aureus infections in Europe and North America. This strain is characterized by high promiscuity in terms of host-species and also lacks several traditional S. aureus virulence factors. This does not, however, explain the apparent ease with which it crosses species-barriers. Recently, TIR-domain containing proteins (Tcps) which inhibit the innate immune response were identified in some Gram-negative bacteria. Here we report the presence of two proteins, S. aureus TIR-like Protein 1 (SaTlp1) and S. aureus TIR-like Protein 2 (SaTlp2), expressed by ST398 which contain domain of unknown function 1863 (DUF1863), similar to the Toll/IL-1 receptor (TIR) domain. In contrast to the Tcps in Gram-negative bacteria, our data suggest that SaTlp1 and SaTlp2 increase activation of the transcription factor NF-κB as well as downstream pro-inflammatory cytokines and immune effectors. To assess the role of both proteins as potential virulence factors knock-out mutants were created. These showed a slightly enhanced survival rate in a murine infectious model compared to the wild-type strain at one dose. Our data suggest that both proteins may act as factors contributing to the enhanced ability of ST398 to cross species-barriers.
doi:10.3389/fmicb.2014.00662
PMCID: PMC4260764  PMID: 25538689
TLR signaling; Staphylococcus aureus; bacterial proteins; TCP; innate immune response; mouse model
20.  The histone demethylase enzyme KDM3A is a key estrogen receptor regulator in breast cancer 
Nucleic Acids Research  2014;43(1):196-207.
Endocrine therapy has successfully been used to treat estrogen receptor (ER)-positive breast cancer, but this invariably fails with cancers becoming refractory to treatment. Emerging evidence has suggested that fluctuations in ER co-regulatory protein expression may facilitate resistance to therapy and be involved in breast cancer progression. To date, a small number of enzymes that control methylation status of histones have been identified as co-regulators of ER signalling. We have identified the histone H3 lysine 9 mono- and di-methyl demethylase enzyme KDM3A as a positive regulator of ER activity. Here, we demonstrate that depletion of KDM3A by RNAi abrogates the recruitment of the ER to cis-regulatory elements within target gene promoters, thereby inhibiting estrogen-induced gene expression changes. Global gene expression analysis of KDM3A-depleted cells identified gene clusters associated with cell growth. Consistent with this, we show that knockdown of KDM3A reduces ER-positive cell proliferation and demonstrate that KDM3A is required for growth in a model of endocrine therapy-resistant disease. Crucially, we show that KDM3A catalytic activity is required for both ER-target gene expression and cell growth, demonstrating that developing compounds which target demethylase enzymatic activity may be efficacious in treating both ER-positive and endocrine therapy-resistant disease.
doi:10.1093/nar/gku1298
PMCID: PMC4288188  PMID: 25488809
21.  Low-field MRI can be more sensitive than high-field MRI 
MRI signal-to-noise ratio (SNR) is the key factor for image quality. Conventionally, SNR is proportional to nuclear spin polarization, which scales linearly with magnetic field strength. Yet ever-stronger magnets present numerous technical and financial limitations. Low-field MRI can mitigate these constraints with equivalent SNR from non-equilibrium ‘hyperpolarization’ schemes, which increase polarization by orders of magnitude independently of the magnetic field. Here, theory and experimental validation demonstrate that combination of field independent polarization (e.g. hyperpolarization) with frequency optimized MRI detection coils (i.e. multi-turn coils using the maximum allowed conductor length) results in low-field MRI sensitivity approaching and even rivaling that of high-field MRI. Four read-out frequencies were tested using samples with identical numbers of 1H and 13C spins. Experimental SNRs at 0.0475 T were ∼40% of those obtained at 4.7 T. Conservatively, theoretical SNRs at 0.0475 T 1.13-fold higher than 4.7 T were possible despite an ∼100-fold lower detection frequency, indicating feasibility of high-sensitivity MRI without technically challenging, expensive high-field magnets. The data at 4.7 T and 0.0475 T was obtained from different spectrometers with different RF probes. The SNR comparison between the two field strengths accounted for many differences in parameters such as system noise figures and variations in the probe detection coils including Q factors and coil diameters.
doi:10.1016/j.jmr.2013.10.013
PMCID: PMC3897717  PMID: 24239701
hyperpolarization; MRI; NMR; low-field MRI; Litz wire; 13C
22.  Disparities in Rates of Inpatient Mortality and Adverse Events: Race/Ethnicity and Language as Independent Contributors 
Patients with limited English proficiency have known limitations accessing health care, but differences in hospital outcomes once access is obtained are unknown. We investigate inpatient mortality rates and obstetric trauma for self-reported speakers of English, Spanish, and languages of Asia and the Pacific Islands (API) and compare quality of care by language with patterns by race/ethnicity. Data were from the United States Agency for Healthcare Research and Quality, Healthcare Cost and Utilization Project, 2009 State Inpatient Databases for California. There were 3,757,218 records. Speaking a non-English principal language and having a non-White race/ethnicity did not place patients at higher risk for inpatient mortality; the exception was significantly higher stroke mortality for Japanese-speaking patients. Patients who spoke API languages or had API race/ethnicity had higher risk for obstetric trauma than English-speaking White patients. Spanish-speaking Hispanic patients had more obstetric trauma than English-speaking Hispanic patients. The influence of language on obstetric trauma and the potential effects of interpretation services on inpatient care are discussed. The broader context of policy implications for collection and reporting of language data is also presented. Results from other countries with and without English as a primary language are needed for the broadest interpretation and generalization of outcomes.
doi:10.3390/ijerph111213017
PMCID: PMC4276659  PMID: 25514153
health status disparities; language; inpatients; quality indicators; Whites; Blacks; Asians; Hispanics
23.  DIPA-family coiled-coils bind conserved isoform-specific head domain of p120-catenin family: potential roles in hydrocephalus and heterotopia 
Molecular Biology of the Cell  2014;25(17):2592-2603.
Isoform-specific expression of p120 affects cell motility and migration during development and tumor progression. The DIPA coiled-coil protein is a novel binding partner to the conserved isoform 1–specific head domain of p120 family members. Zebrafish data suggest that DIPA is mechanistically linked to p120 isoform–specific function in development.
p120-catenin (p120) modulates adherens junction (AJ) dynamics by controlling the stability of classical cadherins. Among all p120 isoforms, p120-3A and p120-1A are the most prevalent. Both stabilize cadherins, but p120-3A is preferred in epithelia, whereas p120-1A takes precedence in neurons, fibroblasts, and macrophages. During epithelial-to-mesenchymal transition, E- to N-cadherin switching coincides with p120-3A to -1A alternative splicing. These isoforms differ by a 101–amino acid “head domain” comprising the p120-1A N-terminus. Although its exact role is unknown, the head domain likely mediates developmental and cancer-associated events linked to p120-1A expression (e.g., motility, invasion, metastasis). Here we identified delta-interacting protein A (DIPA) as the first head domain–specific binding partner and candidate mediator of isoform 1A activity. DIPA colocalizes with AJs in a p120-1A- but not 3A-dependent manner. Moreover, all DIPA family members (Ccdc85a, Ccdc85b/DIPA, and Ccdc85c) interact reciprocally with p120 family members (p120, δ-catenin, p0071, and ARVCF), suggesting significant functional overlap. During zebrafish neural tube development, both knockdown and overexpression of DIPA phenocopy N-cadherin mutations, an effect bearing functional ties to a reported mouse hydrocephalus phenotype associated with Ccdc85c. These studies identify a novel, highly conserved interaction between two protein families that may participate either individually or collectively in N-cadherin–mediated development.
doi:10.1091/mbc.E13-08-0492
PMCID: PMC4148249  PMID: 25009281
24.  CANDLES, an assay for monitoring GPCR induced cAMP generation in cell cultures 
Background
G protein-coupled receptors (GPCRs) represent a physiologically and pharmacologically important family of receptors that upon coupling to GαS stimulate cAMP production catalyzed by adenylyl cyclase. Thus, developing assays to monitor cAMP production is crucial to screen for ligands in studies of GPCR signaling. Primary cell cultures represent a more robust model than cell lines to study GPCR signaling since they physiologically resemble the parent tissue. Current cAMP assays have two fundamental limitations: 1) absence of cAMP kinetics as competition-based assays require cell lysis and measure only a single time-point, and 2) high variation with separate samples needed to measure consecutive time points. The utility of real-time cAMP biosensors is also limited in primary cell cultures due to their poor transfection efficiency, variable expression levels and inability to select stable clones. We therefore, decided to develop an assay that can measure cAMP not only at a single time-point but the entire cAMP kinetics after GPCR activation in untransfected primary cells.
Results
CANDLES (Cyclic AMP iNdirect Detection by Light Emission from Sensor cells) assay for monitoring cAMP kinetics in cell cultures, particularly in primary cultures was developed. The assay requires co-culturing of primary cells with sensor cells that stably express a luminescent cAMP sensor. Upon GPCR activation in primary cells, cAMP is transferred to sensor cells via gap junction channels, thereby evoking a luminescent read-out. GPCR activation using primary cultures of rat cortical neurons and mouse granulosa cells was measured. Kinetic responses of different agonists to adrenergic receptors were also compared using rat cortical neurons. The assay optimization was done by varying sensor-test cell ratio, using phosphodiesterase inhibitors and testing cell-cell contact requirement.
Conclusions
Here we present CANDLES assay based on co-culturing test cells with cAMP-detecting sensor cells. This co-culture setup allows kinetic measurements, eliminates primary cell transfections and reduces variability. A variety of cell types (rat cortical neurons, mouse granulosa cells and established cell lines) and receptors (adrenergic, follicle stimulating hormone and luteinizing hormone/chorionic gonadotropin receptors) were tested for use with CANDLES. The assay is best applied while comparing cAMP generation curves upon different drug treatments to untransfected primary cells.
Electronic supplementary material
The online version of this article (doi:10.1186/s12964-014-0070-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12964-014-0070-x
PMCID: PMC4228090  PMID: 25366423
cAMP; Bioassay; GPCR; Biosensor; Cell-cell interaction; Kinetics; CANDLES; Gap junctions; Connexin; FRET
25.  Affect Regulation Training (ART) for Alcohol Use Disorders: Development of a Novel Intervention for Negative Affect Drinkers 
Although negative affect is a common precipitant of alcohol relapse, there are few interventions for alcohol dependence that specifically target negative affect. In this Stage 1a/1b treatment development study, several affect regulation strategies (e.g., mindfulness, prolonged exposure, distress tolerance) were combined to create a new treatment supplement called Affect Regulation Training (ART), which could be added to enhance Cognitive-Behavioral Therapy (CBT) for alcohol dependence. A draft therapy manual was given to therapists and treatment experts before being administered to several patients who also provided input. After two rounds of manual development (Stage 1a), a pilot randomized clinical trial (N = 77) of alcohol-dependent outpatients who reported drinking often in negative affect situations was conducted (Stage 1b). Participants received 12-weekly, 90-minute sessions of either CBT for alcohol dependence plus ART (CBT + ART) or CBT plus a healthy lifestyles control condition (CBT + HLS). Baseline, end-of-treatment, and 3- and 6-month posttreatment interviews were conducted. For both treatment conditions, participant ratings of treatment satisfaction were high, with CBT + ART rated significantly higher. Drinking outcome results indicated greater reductions in alcohol use for CBT + ART when compared to CBT + HLS, with moderate effect sizes for percent days abstinent, drinks per day, drinks per drinking day, and percent heavy drinking days. Overall, findings support further research on affect regulation interventions for negative affect drinkers.
doi:10.1016/j.jsat.2013.05.012
PMCID: PMC3773302  PMID: 23876455

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