Role of mitochondrial raft-like microdomains in the regulation of cell apoptosis

Lipid rafts are envisaged as lateral assemblies of specific lipids and proteins that dissociate and associate rapidly and form functional clusters in cell membranes. These structural platforms are not confined to the plasma membrane; indeed lipid microdomains are similarly formed at subcellular organelles, which include endoplasmic reticulum, Golgi and mitochondria, named raft-like microdomains. In addition, some components of raft-like microdomains are present within ER-mitochondria associated membranes. This review is focused on the role of mitochondrial raft-like microdomains in the regulation of cell apoptosis, since these microdomains may represent preferential sites where key reactions take place, regulating mitochondria hyperpolarization, fission-associated changes, megapore formation and release of apoptogenic factors. These structural platforms appear to modulate cytoplasmic pathways switching cell fate towards cell survival or death. Main insights on this issue derive from some pathological conditions in which alterations of microdomains structure or function can lead to severe alterations of cell activity and life span. In the light of the role played by raft-like microdomains to integrate apoptotic signals and in regulating mitochondrial dynamics, it is conceivable that these membrane structures may play a role in the mitochondrial alterations observed in some of the most common human neurodegenerative diseases, such as Amyotrophic lateral sclerosis, Huntington's chorea and prion-related diseases. These findings introduce an additional task for identifying new molecular target(s) of pharmacological agents in these pathologies

Electronic health records in outpatient clinics: Perspectives of third year medical students

Abstract Background United States academic medical centers are increasingly incorporating electronic health records (EHR) into teaching settings. We report third year medical students' attitudes towards clinical learning using the electronic health record in ambulatory primary care clinics. Methods In academic year 2005–06, 60 third year students were invited to complete a questionnaire after finishing the required Ambulatory Medicine/Family Medicine clerkship. The authors elicited themes for the questionnaire by asking a focus group of third year students how using the EHR had impacted their learning. Five themes emerged: organization of information, access to online resources, prompts from the EHR, personal performance (charting and presenting), and communication with patients and preceptors. The authors added a sixth theme: impact on student and patient follow-up. The authors created a 21-item questionnaire, based on these themes that used a 5-point Likert scale from "Strongly Agree" to "Strongly Disagree". The authors emailed an electronic survey link to each consenting student immediately following their clerkship experience in Ambulatory Medicine/Family Medicine. Results 33 of 53 consenting students (62%) returned completed questionnaires. Most students liked the EHR's ability to organize information, with 70% of students responding that essential information was easier to find electronically. Only 36% and 33% of students reported accessing online patient information or clinical guidelines more often when using the EHR than when using paper charts. Most students (72%) reported asking more history questions due to EHR prompts, and 39% ordered more clinical preventive services. Most students (69%) reported that the EHR improved their documentation. 39% of students responded that they received more feedback on their EHR notes compared to paper chart notes. Only 64% of students were satisfied with the doctor-patient communication with the EHR, and 48% stated they spent less time looking at the patient. Conclusion Third year medical students reported generally positive attitudes towards using the EHR in the ambulatory setting. They reported receiving more feedback on their electronic charts than on paper charts. However, students reported significant concerns about the potential impact of the EHR on their ability to conduct the doctor-patient encounter.Peer Reviewe

Accelerated large-scale multiple sequence alignment

<p>Abstract</p> <p>Background</p> <p>Multiple sequence alignment (MSA) is a fundamental analysis method used in bioinformatics and many comparative genomic applications. Prior MSA acceleration attempts with reconfigurable computing have only addressed the first stage of progressive alignment and consequently exhibit performance limitations according to Amdahl's Law. This work is the first known to accelerate the third stage of progressive alignment on reconfigurable hardware.</p> <p>Results</p> <p>We reduce subgroups of aligned sequences into discrete profiles before they are pairwise aligned on the accelerator. Using an FPGA accelerator, an overall speedup of up to 150 has been demonstrated on a large data set when compared to a 2.4 GHz Core2 processor.</p> <p>Conclusions</p> <p>Our parallel algorithm and architecture accelerates large-scale MSA with reconfigurable computing and allows researchers to solve the larger problems that confront biologists today. Program source is available from <url>http://dna.cs.byu.edu/msa/</url>.</p

Characterization of Mycosphaerellaceae species associated with citrus greasy spot in Panama and Spain

[EN] Greasy spot of citrus, caused by Zasmidium citri-griseum (= Mycosphaerella citri), is widely distributed in the Caribbean Basin, inducing leaf spots, premature defoliation, and yield loss. Greasy spot-like symptoms were frequently observed in humid citrus-growing regions in Panama as well as in semi-arid areas in Spain, but disease aetiology was unknown. Citrus-growing areas in Panama and Spain were surveyed and isolates of Mycosphaerellaceae were obtained from citrus greasy spot lesions. A selection of isolates from Panama (n = 22) and Spain (n = 16) was assembled based on their geographical origin, citrus species, and affected tissue. The isolates were characterized based on multi-locus DNA (ITS and EF-1 alpha) sequence analyses, morphology, growth at different temperatures, and independent pathogenicity tests on the citrus species most affected in each country. Reference isolates and sequences were also included in the analysis. Isolates from Panama were identified as Z. citri-griseum complex, and others from Spain attributed to Amycosphaerella africana. Isolates of the Z. citri-griseum complex had a significantly higher optimal growth temperature (26.8 degrees C) than those of A. africana (19.3 degrees C), which corresponded well with their actual biogeographical range. The isolates of the Z. citri-griseum complex from Panama induced typical greasy spot symptoms in 'Valencia' sweet orange plants and the inoculated fungi were reisolated. No symptoms were observed in plants of the 'Ortanique' tangor inoculated with A. africana. These results demonstrate the presence of citrus greasy spot, caused by Z. citri-griseum complex, in Panama whereas A. africana was associated with greasy spot-like symptoms in Spain.Research was partially funded by 'Programa de Formacion de los INIA Iberoamerica' and INIA RTA2010-00105-00-00-FEDER to Vidal Aguilera Cogley.. We thank J. Martinez-Minaya (UV) for assistance with INLAAguilera-Cogley, VA.; Berbegal Martinez, M.; Català, S.; Collison Brentu, F.; Armengol Fortí, J.; Vicent Civera, A. (2017). Characterization of Mycosphaerellaceae species associated with citrus greasy spot in Panama and Spain. PLoS ONE. 12(12):1-19. https://doi.org/10.1371/journal.pone.0189585S1191212Crous, P. W., Summerell, B. A., Carnegie, A. J., Wingfield, M. J., Hunter, G. C., Burgess, T. I., … Groenewald, J. Z. (2009). Unravelling Mycosphaerella: do you believe in genera? Persoonia - Molecular Phylogeny and Evolution of Fungi, 23(1), 99-118. doi:10.3767/003158509x479487Mondal, S. N., & Timmer, L. W. (2006). Greasy Spot, a Serious Endemic Problem for Citrus Production in the Caribbean Basin. Plant Disease, 90(5), 532-538. doi:10.1094/pd-90-0532Whiteside, J. O. (1970). Etiology and Epidemiology of Citrus Greasy Spot. Phytopathology, 60(10), 1409. doi:10.1094/phyto-60-1409Huang, F., Groenewald, J. Z., Zhu, L., Crous, P. W., & Li, H. (2015). Cercosporoid diseases of Citrus. Mycologia, 107(6), 1151-1171. doi:10.3852/15-059Wellings, C. R. (1981). Pathogenicity of fungi associated with citrus greasy spot in New South Wales. Transactions of the British Mycological Society, 76(3), 495-499. doi:10.1016/s0007-1536(81)80080-0Marco, G. M. (1986). A Disease Similar to Greasy Spot but of Unknown Etiology on Citrus Leaves in Argentina. Plant Disease, 70(11), 1074a. doi:10.1094/pd-70-1074aVidal Aguilera-Cogley, & Antonio Vicent. (2015). FUNGAL DISEASES OF CITRUS IN PANAMA. Acta Horticulturae, (1065), 947-952. doi:10.17660/actahortic.2015.1065.118Honger J. Aetiology and importance of foliage diseases affecting citrus in the nursery at the Agricultural Research Station (ARS). PhD Thesis. Accra: University of Ghana; 2004.Vicent A, Álvarez A, León M, García-Jiménez J. Mycosphaerella sp. asociada a manchas foliares de cítricos en España. 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Nature Methods, 9(8), 772-772. doi:10.1038/nmeth.2109Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., … Huelsenbeck, J. P. (2012). MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space. Systematic Biology, 61(3), 539-542. doi:10.1093/sysbio/sys029Rambaut A. FigTree v1. 4.0, a graphical viewer of phylogenetic trees. Edinburgh, Scotland: University of Edinburgh; 2016.Spiegelhalter, D. J., Best, N. G., Carlin, B. P., & van der Linde, A. (2002). Bayesian measures of model complexity and fit. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 64(4), 583-639. doi:10.1111/1467-9868.00353Rue, H., Martino, S., & Chopin, N. (2009). Approximate Bayesian inference for latent Gaussian models by using integrated nested Laplace approximations. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 71(2), 319-392. doi:10.1111/j.1467-9868.2008.00700.xChristensen RH. Ordinal—regression models for ordinal data. R package version 2015.1–21. 2015. http://www.cran.r-project.org/package=ordinal/ Accessed 8 May 2017.Hunter, G. C., Wingfield, B. D., Crous, P. W., & Wingfield, M. J. (2006). A multi-gene phylogeny for species of Mycosphaerella occurring on Eucalyptus leaves. Studies in Mycology, 55, 147-161. doi:10.3114/sim.55.1.147Braun, U., & Urtiaga, R. (2013). New species and new records of cercosporoid hyphomycetes from Cuba and Venezuela (Part 2). Mycosphere, 4(2), 172-214. doi:10.5943/mycosphere/4/2/3Braun, U., Crous, P. W., & Nakashima, C. (2014). Cercosporoid fungi (Mycosphaerellaceae) 2. Species on monocots (Acoraceae to Xyridaceae, excluding Poaceae). IMA Fungus, 5(2), 203-390. doi:10.5598/imafungus.2014.05.02.04Aptroot A. Mycosphaerella and its anamorphs: conspectus of Mycosphaerella CBS Biodiversity Series 5. Utrecht: CBS-KNAW Fungal Biodiversity Centre; 2006.Crous, P. W., & Wingfield, M. J. (1996). Species of Mycosphaerella and Their Anamorphs Associated with Leaf Blotch Disease of Eucalyptus in South Africa. Mycologia, 88(3), 441. doi:10.2307/3760885Aguín, O., Sainz, M. J., Ares, A., Otero, L., & Pedro Mansilla, J. (2013). Incidence, severity and causal fungal species of Mycosphaerella and Teratosphaeria diseases in Eucalyptus stands in Galicia (NW Spain). Forest Ecology and Management, 302, 379-389. doi:10.1016/j.foreco.2013.03.021Maxwell, A., Dell, B., Neumeister-Kemp, H. G., & Hardy, G. E. S. J. (2003). Mycosphaerella species associated with Eucalyptus in south-western Australia: new species, new records and a key. Mycological Research, 107(3), 351-359. doi:10.1017/s0953756203007354Otero L, Aguín O, Mansilla J, Hunter G, Wingfield M. Identificación de especies de Mycosphaerella en Eucalyptus globulus y E. nitens en Galicia. In: Proceedings of the 13th Congress of the Spanish Phytopathological Society; 2006; Murcia, Spain.ZHAN, J., & McDONALD, B. A. (2011). 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Protein-Binding Microarray Analysis of Tumor Suppressor AP2α Target Gene Specificity

Cheap and massively parallel methods to assess the DNA-binding specificity of transcription factors are actively sought, given their prominent regulatory role in cellular processes and diseases. Here we evaluated the use of protein-binding microarrays (PBM) to probe the association of the tumor suppressor AP2α with 6000 human genomic DNA regulatory sequences. We show that the PBM provides accurate relative binding affinities when compared to quantitative surface plasmon resonance assays. A PBM-based study of human healthy and breast tumor tissue extracts allowed the identification of previously unknown AP2α target genes and it revealed genes whose direct or indirect interactions with AP2α are affected in the diseased tissues. AP2α binding and regulation was confirmed experimentally in human carcinoma cells for novel target genes involved in tumor progression and resistance to chemotherapeutics, providing a molecular interpretation of AP2α role in cancer chemoresistance. Overall, we conclude that this approach provides quantitative and accurate assays of the specificity and activity of tumor suppressor and oncogenic proteins in clinical samples, interfacing genomic and proteomic assays

Gaps in clinical research in frontotemporal dementia: A call for diversity and disparities–focused research

Frontotemporal dementia (FTD) is one of the leading causes of dementia before age 65 and often manifests as abnormal behavior (in behavioral variant FTD) or language impairment (in primary progressive aphasia). FTD's exact clinical presentation varies by culture, language, education, social norms, and other socioeconomic factors; current research and clinical practice, however, is mainly based on studies conducted in North America and Western Europe. Changes in diagnostic criteria and procedures as well as new or adapted cognitive tests are likely needed to take into consideration global diversity. This perspective paper by two professional interest areas of the Alzheimer's Association International Society to Advance Alzheimer's Research and Treatment examines how increasing global diversity impacts the clinical presentation, screening, assessment, and diagnosis of FTD and its treatment and care. It subsequently provides recommendations to address immediate needs to advance global FTD research and clinical practice

Mid-infrared passively switched pulsed dual wavelength Ho3+ -doped fluoride fiber laser at 3 μm and 2 μm

Cascade transitions of rare earth ions involved in infrared host fiber provide the potential to generate dual or multiple wavelength lasing at mid-infrared region. In addition, the fast development of saturable absorber (SA) towards the long wavelengths motivates the realization of passively switched mid-infrared pulsed lasers. In this work, by combing the above two techniques, a new phenomenon of passively Q-switched ~3 μm and gain-switched ~2 μm pulses in a shared cavity was demonstrated with a Ho3+-doped fluoride fiber and a specifically designed semiconductor saturable absorber (SESAM) as the SA. The repetition rate of ~2 μm pulses can be tuned between half and same as that of ~3 μm pulses by changing the pump power. The proposed method here will add new capabilities and more flexibility for generating mid-infrared multiple wavelength pulses simultaneously that has important potential applications for laser surgery, material processing, laser radar, and free-space communications, and other areas

Human Pathogen Shown to Cause Disease in the Threatened Eklhorn Coral Acropora palmata

Coral reefs are in severe decline. Infections by the human pathogen Serratia marcescens have contributed to precipitous losses in the common Caribbean elkhorn coral, Acropora palmata, culminating in its listing under the United States Endangered Species Act. During a 2003 outbreak of this coral disease, called acroporid serratiosis (APS), a unique strain of the pathogen, Serratia marcescens strain PDR60, was identified from diseased A. palmata, human wastewater, the non-host coral Siderastrea siderea and the corallivorous snail Coralliophila abbreviata. In order to examine humans as a source and other marine invertebrates as vectors and/or reservoirs of the APS pathogen, challenge experiments were conducted with A. palmata maintained in closed aquaria to determine infectivity of strain PDR60 from reef and wastewater sources. Strain PDR60 from wastewater and diseased A. palmata caused disease signs in elkhorn coral in as little as four and five days, respectively, demonstrating that wastewater is a definitive source of APS and identifying human strain PDR60 as a coral pathogen through fulfillment of Koch's postulates. A. palmata inoculated with strain PDR60 from C. abbreviata showed limited virulence, with one of three inoculated fragments developing APS signs within 13 days. Strain PDR60 from non-host coral S. siderea showed a delayed pathogenic effect, with disease signs developing within an average of 20 days. These results suggest that C. abbreviata and non-host corals may function as reservoirs or vectors of the APS pathogen. Our results provide the first example of a marine “reverse zoonosis” involving the transmission of a human pathogen (S. marcescens) to a marine invertebrate (A. palmata). These findings underscore the interaction between public health practices and environmental health indices such as coral reef survival

Clinical and epidemiological correlates of antibody response to human papillomaviruses (HPVs) as measured by a novel ELISA based on denatured recombinant HPV16 late (L) and early (E) antigens

<p>Abstract</p> <p>Background</p> <p>At present, seroreactivity is not a valuable parameter for diagnosis of Human Papillomavirus (HPV) infection but, it is potentially valuable as marker of viral exposure in elucidating the natural history of this infection. More data are needed to asses the clinical relevance of serological response to HPV.</p> <p>Objectives</p> <p>The objective was to assess the clinical and epidemiological correlates of HPV-seroreactivity in a cohort of HIV-negative and HIV-positive women.</p> <p>Methods</p> <p>Seroreactivity of 96 women, evaluated in an ELISA test based on denatured HPV16 late (L) and early (E) antigens, was correlated with their clinical and epidemiological data previously collected for a multi-centre Italian study, HPV-PathogenISS study.</p> <p>Results</p> <p>No significant correlation was found between HPV DNA detection and seroreactivity. Women, current smokers showed significantly less seroreactivity to L antigens as compared with the non-smokers. HIV-positive women showed significantly less (66.7%) antibody response as compared with HIV-negative women (89.3%), with particularly impaired response to L antigens. Women, HIV-positive and current smokers, showed by far the lowest seroprevalence (33.3%) as compared to 75.9% among all other women (OR = 0.158; 95%CI 0.036–0.695, p = 0.014; Fisher's exact test). Importantly, this association did not loose its significance when controlled for confounding from age (continuous variable) in multivariate analysis or using Mantel-Haenszel test for age-groups.</p> <p>Conclusion</p> <p>It is tempting to speculate that HIV-positive current smokers comprise a special high-risk group, with highly impaired immunological response that could prevent eradication of persistent HPV infections and thus contribute to development of CIN3/CC.</p

ERG Deregulation Induces PIM1 Over-Expression and Aneuploidy in Prostate Epithelial Cells

The ERG gene belongs to the ETS family of transcription factors and has been found to be involved in atypical chromosomal rearrangements in several cancers. To gain insight into the oncogenic activity of ERG, we compared the gene expression profile of NIH-3T3 cells stably expressing the coding regions of the three main ERG oncogenic fusions: TMPRSS2/ERG (tERG), EWS/ERG and FUS/ERG. We found that all three ERG fusions significantly up-regulate PIM1 expression in the NIH-3T3 cell line. PIM1 is a serine/threonine kinase frequently over-expressed in cancers of haematological and epithelial origin. We show here that tERG expression induces PIM1 in the non-malignant prostate cell line RWPE-1, strengthening the relation between tERG and PIM1 up-regulation in the initial stages of prostate carcinogenesis. Silencing of tERG reversed PIM1 induction. A significant association between ERG and PIM1 expression in clinical prostate carcinoma specimens was found, suggesting that such a mechanism may be relevant in vivo. Chromatin Immunoprecipitation experiments showed that tERG directly binds to PIM1 promoter in the RWPE-1 prostate cell line, suggesting that tERG could be a direct regulator of PIM1 expression. The up-regulation of PIM1 induced by tERG over-expression significantly modified Cyclin B1 levels and increased the percentage of aneuploid cells in the RWPE-1 cell line after taxane-based treatment. Here we provide the first evidence for an ERG-mediated PIM1 up-regulation in prostate cells in vitro and in vivo, suggesting a direct effect of ERG transcriptional activity in the alteration of genetic stability