An Objective Scatter Index Based on Double-Pass Retinal Images of a Point Source to Classify Cataracts

PURPOSE: To propose a new objective scatter index (OSI) based in the analysis of double-pass images of a point source to rank and classify cataract patients. This classification scheme is compared with a current subjective system. METHODS: We selected a population including a group of normal young eyes as control and patients diagnosed with cataract (grades NO2, NO3 and NO4) according to the Lens Opacities Classification System (LOCS III). For each eye, we recorded double-pass retinal images of a point source. In each patient, we determined an objective scatter index (OSI) as the ratio of the intensity at an eccentric location in the image and the central part. This index provides information on the relevant forward scatter affecting vision. Since the double-pass retinal images are affected by both ocular aberrations and intraocular scattering, an analysis was performed to show the ranges of contributions of aberrations to the OSI. RESULTS: We used the OSI values to classify each eye according to the degree of scatter. The young normal eyes of the control group had OSI values below 1, while the OSI for subjects in LOCS grade II were around 1 to 2. The use of the objective index showed some of the weakness of subjective classification schemes. In particular, several subjects initially classified independently as grade NO2 or NO3 had similar OSI values, and in some cases even higher than subjects classified as grade NO4. A new classification scheme based in OSI is proposed. CONCLUSIONS: We introduced an objective index based in the analysis of double-pass retinal images to classify cataract patients. The method is robust and fully based in objective measurements; i.e., not depending on subjective decisions. This procedure could be used in combination with standard current methods to improve cataract patient surgery scheduling

Evaluation of Cellular Phenotypes Implicated in Immunopathogenesis and Monitoring Immune Reconstitution Inflammatory Syndrome in HIV/Leprosy Cases

BACKGROUND: It is now evident that HAART-associated immunological improvement often leads to a variety of new clinical manifestations, collectively termed immune reconstitution inflammatory syndrome, or IRIS. This phenomenon has already been described in cases of HIV coinfection with Mycobacterium leprae, most of them belonging to the tuberculoid spectrum of leprosy disease, as observed in leprosy reversal reaction (RR). However, the events related to the pathogenesis of this association need to be clarified. This study investigated the immunological profile of HIV/leprosy patients, with special attention to the cellular activation status, to better understand the mechanisms related to IRIS/RR immunopathogenesis, identifying any potential biomarkers for IRIS/RR intercurrence. METHODS/PRINCIPAL FINDINGS: Eighty-five individuals were assessed in this study: HIV/leprosy and HIV-monoinfected patients, grouped according to HIV-viral load levels, leprosy patients without HIV coinfection, and healthy controls. Phenotypes were evaluated by flow cytometry for T cell subsets and immune differentiation/activation markers. As expected, absolute counts of the CD4+ and CD8+ T cells from the HIV-infected individuals changed in relation to those of the leprosy patients and controls. However, there were no significant differences among the groups, whether in the expression of cellular differentiation phenotypes or cellular activation, as reflected by the expression of CD38 and HLA-DR. Six HIV/leprosy patients identified as IRIS/RR were analyzed during IRIS/RR episodes and after prednisone treatment. These patients presented high cellular activation levels regarding the expression of CD38 in CD8+ cells T during IRIS/RR (median: 77,15%), dropping significantly (p<0,05) during post-IRIS/RR moments (median: 29,7%). Furthermore, an increase of cellular activation seems to occur prior to IRIS/RR. CONCLUSION/SIGNIFICANCE: These data suggest CD38 expression in CD8+ T cells interesting tool identifying HIV/leprosy individuals at risk for IRIS/RR. So, a comparative investigation to leprosy patients at RR should be conducted

FI on-line chemiluminescence reaction for determination of MCPA in water samples

This paper reports an economic, simple, and rapid FI-CL method for the determination of MCPA. This method requires simple instrumentation and it is fast enough to be used in routine analyses. A chemiluminescence signal is generated by reaction between photodegraded MCPA and ferricyanide solution in alkaline medium. All physical and chemical parameters in the flow injection chemiluminescence system were optimized in the experimental setting. To eliminate interference, a solid-phase extraction stage with SDB-1 cartridges and ethanol elution is applied. The signal-MCPA concentration relation is linear in concentration intervals between 0.0015 and 0.6 ¿g¿mL -1. The calibration lines are statistically similar in different working conditions: standards with ethanol without extraction and standards with ethanol and extraction, allowing standards to be excluded from the extraction step, which simplifies the process. The detection limit (DL) is 0.5 ng¿mL -1, which is the same order as the maximum limit established in legislation regarding pesticide limits in water destined for human consumption. A DL of 0.13 ng¿mL -1 can be reached if a sample of 100 mL is preconcentrated. The interday variance coefficient is 3% and the sample throughput is 90 h -1. The water analysis method is efficient with relative error percentages lower than 5% with respect to the added concentration. © 2011 Springer-Verlag.Authors acknowledge to the "Ministerio de Educacion y Ciencia" of Spain and FEDER funds for financial support (Project CTM2006-11991)Torres Cartas, S.; Gómez Benito, C.; Meseguer-Lloret, S. (2012). FI on-line chemiluminescence reaction for determination of MCPA in water samples. Analytical and Bioanalytical Chemistry. 402:1289-1296. https://doi.org/10.1007/s00216-011-5567-1S12891296402Navarro JS (2008) Utilización de plaguicidas en las asociaciones de tratamientos integrados en agricultura en la región de Murcia. Consejería de Sanidad Región de MurciaBarceló D, Hennion MC (1997) Trace determination of pesticide and their degradation products in water. Elsevier, AmsterdamKöck M, Farré M, Martínez E, Gajda-Schrantz K, Ginebreda A, Navarro A, López de Alda M, Barceló D (2010) J Hydrol 383(1–2):73–82Woudneh MB, Sekela M, Tuominen T, Gledhill M (2007) J Chromatogr A 1139(1):121–129Laganà A, Bacaloni A, De-Leva I, Faberi A, Fago G, Marino A (2002) Anal Chim Acta 462:187–198Comoretto L, Arfib B, Chiron S (2007) Sci Total Environ 380(1–3):124–132Kuster M, de Alda MJL, Barata C, Raldá D, Barceló D (2008) Talanta 75(2):390–401Kuster M, de Alda MJL, Hernando MD, Petrovic M, Martín-Alonso J, Barceló D (2008) J Hydrol 358(1–2):112–123Gervais G, Brosillon S, Laplanche A, Helen C (2008) J Chromatogr A 1202(2):163–172Housari F, Höhener P, Chiron S (2011) Sci Total Environ 409(3):582–587Delhomme O, Raeppel C, Briand O, Millet M (2011) Anal Bioanal Chem 399:1325–1334Royal decree 140/2003, 7th of February that establishes the health criteria for the water quality for human consumption. (BOE 21 February 2003)von-der-Ohe PC, Dulio V, Slobodnik J, de-Deckere E, Köhne R, Ebert RU, Ginebreda A, de-Cooman de-Cooman W, Schüürmann G, Brack W (2011) Sci Total Environ 409(11):2064–2077Horwitz W (ed) (2000) Official methods of analysis of AOAC International, 17th edn. AOAC International, GaithersburgMoret S, Sánchez JM, Salvadó V, Hidalgo M (2005) J Chromatogr A 1099(1–2):55–63Tran ATK, Hyne RV, Doble P (2007) Chemosphere 67(5):944–953Long F, Shi HC, He M, Zhu AN (2008) Biosens Bioelectron 23:1361–1366Meulenberg EP, Stoks PG (1995) Anal Chim Acta 311:407–413Chuang JC, Van Emon JM, Durnford J, Thomas K (2005) Talanta 67:658–666Boro RC, Kaushal J, Nangia Y, Wangoo N, Bhashi A, Suri CR (2011) Analyst 136(10):2125–2130Eremin SA, Laassis P, Aaron JJ (1996) Talanta 43:295–301Almansa-López EM, García-Campaña AM, Aaron JJ, Cuadros-Rodriguez L (2003) Talanta 60:355–367García LF, Eremin S, Aaron JJ (1996) Anal Lett 29(8):1447–1461García-Campaña AM, Aaron JJ, Bosque-Sendra JM (2002) Luminescence 17:285–287Lara FJ, García-Campaña AM, Aaron JJ (2010) Anal Chim Acta 679:17–30López-Paz J, Catalá-Icardo M (2011) Anal Lett 44(1–3):146–175Mbaye M, Gaye-Seye M, Aaron JJ, Coly A, Tine A (2011) Anal Bioanal Chem 400(2):403–410López-Paz JL, Catalá-Icardo M, Antón-Garrido B (2009) Anal Bioanal Chem 394:1073–1079López-Paz J, Catalá-Icardo M (2008) Anal Chim Acta 625(2):173–179Chen X, Lin Z, Cai Z, Chen X, Wang X (2008) Talanta 76(5):1083–1087Meseguer-Lloret S, Torres-Cartas S, Gómez-Benito M (2010) Anal Bioanal Chem 398:3175–3182Catalá-Icardo M, Martínez-Calatayud J (2008) Crit Rev Anal Chem 38(2):118–13

An integration of complementary strategies for gene-expression analysis to reveal novel therapeutic opportunities for breast cancer

INTRODUCTION. Perhaps the major challenge in developing more effective therapeutic strategies for the treatment of breast cancer patients is confronting the heterogeneity of the disease, recognizing that breast cancer is not one disease but multiple disorders with distinct underlying mechanisms. Gene-expression profiling studies have been used to dissect this complexity, and our previous studies identified a series of intrinsic subtypes of breast cancer that define distinct populations of patients with respect to survival. Additional work has also used signatures of oncogenic pathway deregulation to dissect breast cancer heterogeneity as well as to suggest therapeutic opportunities linked to pathway activation. METHODS. We used genomic analyses to identify relations between breast cancer subtypes, pathway deregulation, and drug sensitivity. For these studies, we use three independent breast cancer gene-expression data sets to measure an individual tumor phenotype. Correlation between pathway status and subtype are examined and linked to predictions for response to conventional chemotherapies. RESULTS. We reveal patterns of pathway activation characteristic of each molecular breast cancer subtype, including within the more aggressive subtypes in which novel therapeutic opportunities are critically needed. Whereas some oncogenic pathways have high correlations to breast cancer subtype (RAS, CTNNB1, p53, HER1), others have high variability of activity within a specific subtype (MYC, E2F3, SRC), reflecting biology independent of common clinical factors. Additionally, we combined these analyses with predictions of sensitivity to commonly used cytotoxic chemotherapies to provide additional opportunities for therapeutics specific to the intrinsic subtype that might be better aligned with the characteristics of the individual patient. CONCLUSIONS. Genomic analyses can be used to dissect the heterogeneity of breast cancer. We use an integrated analysis of breast cancer that combines independent methods of genomic analyses to highlight the complexity of signaling pathways underlying different breast cancer phenotypes and to identify optimal therapeutic opportunities.V Foundation for Cancer Research (Partners in Excellence grant

The construction of a Solanum habrochaites LYC4 introgression line population and the identification of QTLs for resistance to Botrytis cinerea

Tomato (Solanum lycopersicum) is susceptible to grey mold (Botrytis cinerea). Partial resistance to this fungus has been identified in accessions of wild relatives of tomato such as Solanum habrochaites LYC4. In a previous F2 mapping study, three QTLs conferring resistance to B. cinerea (Rbcq1, Rbcq2 and Rbcq4a) were identified. As it was probable that this study had not identified all QTLs involved in resistance we developed an introgression line (IL) population (n = 30), each containing a S. habrochaites introgression in the S. lycopersicum cv. Moneymaker genetic background. On average each IL contained 5.2% of the S. habrochaites genome and together the lines provide an estimated coverage of 95%. The level of susceptibility to B. cinerea for each of the ILs was assessed in a greenhouse trial and compared to the susceptible parent S. lycopersicum cv. Moneymaker. The effect of the three previously identified loci could be confirmed and seven additional loci were detected. Some ILs contains multiple QTLs and the increased resistance to B. cinerea in these ILs is in line with a completely additive model. We conclude that this set of QTLs offers good perspectives for breeding of B. cinerea resistant cultivars and that screening an IL population is more sensitive for detection of QTLs conferring resistance to B. cinerea than the analysis in an F2 population

Atrial arrhythmogenicity in aged Scn5a+/∆KPQ mice modeling long QT type 3 syndrome and its relationship to Na+ channel expression and cardiac conduction

Recent studies have reported that human mutations in Nav1.5 predispose to early age onset atrial arrhythmia. The present experiments accordingly assess atrial arrhythmogenicity in aging Scn5a+/∆KPQ mice modeling long QT3 syndrome in relationship to cardiac Na+ channel, Nav1.5, expression. Atrial electrophysiological properties in isolated Langendorff-perfused hearts from 3- and 12-month-old wild type (WT), and Scn5a+/∆KPQ mice were assessed using programmed electrical stimulation and their Nav1.5 expression assessed by Western blot. Cardiac conduction properties were assessed electrocardiographically in intact anesthetized animals. Monophasic action potential recordings demonstrated increased atrial arrhythmogenicity specifically in aged Scn5a+/ΔKPQ hearts. These showed greater action potential duration/refractory period ratios but lower atrial Nav1.5 expression levels than aged WT mice. Atrial Nav1.5 levels were higher in young Scn5a+/ΔKPQ than young WT. These levels increased with age in WT but not Scn5a+/ΔKPQ. Both young and aged Scn5a+/ΔKPQ mice showed lower heart rates and longer PR intervals than their WT counterparts. Young Scn5a+/ΔKPQ mice showed longer QT and QTc intervals than young WT. Aged Scn5a+/ΔKPQ showed longer QRS durations than aged WT. PR intervals were prolonged and QT intervals were shortened in young relative to aged WT. In contrast, ECG parameters were similar between young and aged Scn5a+/ΔKPQ. Aged murine Scn5a+/ΔKPQ hearts thus exhibit an increased atrial arrhythmogenicity. The differing Nav1.5 expression and electrocardiographic indicators of slowed cardiac conduction between Scn5a+/ΔKPQ and WT, which show further variations associated with aging, may contribute toward atrial arrhythmia in aged Scn5a+/ΔKPQ hearts

Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

This is the final version of the article. Available from the publisher via the DOI in this record.Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.The Sclerotinia sclerotiorum genome project was supported by the USDA Cooperative State Research, Education and Extension Service (USDA-NRI 2004). Sclerotinia sclerotiorum ESTs were funded by a grant to JA Rollins from USDA specific cooperative agreement 58-5442-4-281. The genome sequence of Botrytis cinerea strain T4 was funded by Genoscope, CEA, France. M Viaud was funded by the “Projet INRA Jeune-Equipe”. PM Coutinho and B Henrissat were funded by the ANR to project E-Tricel (grant ANR-07-BIOE-006). The CAZy database is funded in part by GIS-IBiSA. DM Soanes and NJ Talbot were partly funded by the UK Biotechnology and Biological Sciences Research Council. KM Plummer was partially funded by the New Zealand Bio-Protection Research Centre, http://bioprotection.org.nz/. BJ Howlett and A Sexton were partially funded by the Australian Grains Research and Development Corporation, www.grdc.com.au. L Kohn was partially funded by NSERC Discovery Grant (Natural Sciences and Engineering Research Council of Canada) - Grant number 458078. M Dickman was supported by the NSF grant MCB-092391 and BARD grant US-4041-07C. O Yarden was supported by BARD grant US-4041-07C. EG Danchin obtained financial support from the European Commission (STREP FungWall grant, contract: LSHB - CT- 2004 - 511952). A Botrytis Genome Workshop (Kaiserslautern, Germany) was supported by a grant from the German Science Foundation (DFG; HA1486) to M Hahn

Bioinformatic Characterization of P-Type ATPases Encoded Within the Fully Sequenced Genomes of 26 Eukaryotes

P-type ATPases play essential roles in numerous processes, which in humans include nerve impulse propagation, relaxation of muscle fibers, secretion and absorption in the kidney, acidification of the stomach and nutrient absorption in the intestine. Published evidence suggests that uncharacterized families of P-type ATPases with novel specificities exist. In this study, the fully sequenced genomes of 26 eukaryotes, including animals, plants, fungi and unicellular eukaryotes, were analyzed for P-type ATPases. We report the organismal distributions, phylogenetic relationships, probable topologies and conserved motifs of nine functionally characterized families and 13 uncharacterized families of these enzyme transporters. We have classified these proteins according to the conventions of the functional and phylogenetic IUBMB-approved transporter classification system (www.tcdb.org, Saier et al. in Nucleic Acids Res 34:181–186, 2006; Nucleic Acids Res 37:274–278, 2009)