Leading order analysis of neutrino induced dimuon events in the CHORUS experiment

We present a leading order QCD analysis of a sample of neutrino induced charged-current events with two muons in the final state originating in the lead-scintillating fibre calorimeter of the CHORUS detector. The results are based on a sample of 8910 neutrino and 430 antineutrino induced opposite-sign dimuon events collected during the exposure of the detector to the CERN Wide Band Neutrino Beam between 1995 and 1998. % with $E_{\mu 1},E_{\mu 2} > 5$ GeV and $Q^2 > 3$ GeV$^2$ collected %between 1995 and 1998. The analysis yields a value of the charm quark mass of \mc = (1.26\pm 0.16 \pm 0.09) \GeVcc and a value of the ratio of the strange to non-strange sea in the nucleon of $\kappa = 0.33 \pm 0.05 \pm 0.05$, improving the results obtained in similar analyses by previous experiments.Comment: Submitted to Nuclear Physics

The data acquisition system of the CHORUS experiment

In the years 1994--1998 the CHORUS Collaboration has recorded data in the CERN WA95 experiment. Here we describe the data acquisition system that has been used, featuring concurrent hierarchical state machines, a remote operating system, a buffer manager, a dispatcher, a control panel and a supervisor

Presence of intestinal Mycobacterium avium subspecies paratuberculosis (MAP) DNA is not associated with altered MMP expression in ulcerative colitis

<p>Abstract</p> <p>Background</p> <p><it>Mycobacterium avium </it>subspecies <it>paratuberculosis </it>(MAP) is suspected to be a causative agent in human Crohn's disease (CD). Recent evidence suggests that pathogenic mycobacteria and MAP can induce the expression of Matrix Metalloproteinases (MMP), which are the main proteases in the pathogenesis of mucosal ulcerations in inflammatory bowel disease (IBD). Within this study we assessed the prevalence of intestinal MAP specific DNA in patients with Crohn's disease, ulcerative colitis (UC), and healthy controls. We further analysed regulation patterns of MMPs in mucosal tissues of UC patients with and without intestinal MAP DNA detection.</p> <p>Methods</p> <p>Colonic biopsy samples were obtained from 63 Norwegian and German IBD patients and 21 healthy controls. RNA was quantified by quantitative real-time polymerase chain reaction (PCR) to study MMP gene expression in both pathological and healthy mucosal specimens. The presence of MAP DNA in colonic mucosa was examined using MAP specific PCR.</p> <p>Results</p> <p>MAP DNA was detected in 20% of UC patients and 33% of healthy controls but only in 7% of patients with CD. UC patients treated with corticosteroids exhibited a significantly increased frequency of intestinal MAP DNA compared to those not receiving corticosteroids. Expression of MMP-1, -2, -7, -9, -13, -19, -28 and TNF-α did not differ between UC patients with presence of intestinal MAP DNA compared to those without. MMP-2, MMP-9 and MMP-13 were significantly decreased in UC patients receiving corticosteroids.</p> <p>Conclusions</p> <p>The presence of intestinal MAP specific DNA is not associated with altered MMP expression in UC <it>in vivo</it>. Corticosteroids are associated with increased detection of intestinal MAP DNA and decreased expression of certain MMPs. Frequent detection of MAP DNA in healthy controls might be attributable to the wide environmental distribution of MAP and its presence in the food-chain.</p

Observation of weak neutral current neutrino production of J/ψJ/\psi

Observation of \jpsi production by neutrinos in the calorimeter of the CHORUS detector exposed to the CERN SPS wide-band \numu beam is reported. A spectrum-averaged cross-section $\sigma^{\mathrm{J/\psi}}$ = (6.3 $\pm$ 3.0) $\times \mathrm{10^{-41}~cm^{2}}$ is obtained for 20 GeV $\leq E_{\nu} \leq$ 200 GeV. The data are compared with the theoretical model based on the QCD Z-gluon fusion mechanism

New Triplex Real-Time PCR Assay for Detection of Mycobacterium avium subsp. paratuberculosis in Bovine Feces▿

In the present study, a robust TaqMan real-time PCR amplifying the F57 and the ISMav2 sequences of Mycobacterium avium subsp. paratuberculosis from bovine fecal samples was developed and validated. The validation was based on the recommendations of International Organization for Standardization protocols for PCR and real-time PCR methods. For specificity testing, 205 bacterial strains were selected, including 105 M. avium subsp. paratuberculosis strains of bovine, ovine, and human origin and 100 non-M. avium subsp. paratuberculosis strains. Diagnostic quality assurance was obtained by use of an internal amplification control. By investigating six TaqMan reagents from different suppliers, the 100% detection probability was assessed to be 0.1 picogram M. avium subsp. paratuberculosis DNA per PCR. The amplification efficiency was 98.2% for the single-copy gene F57 and 97.8% for the three-copy insertion sequence ISMav2. The analytical method was not limited due to instrument specificity. The triplex real-time PCR allowed the reliable detection of M. avium subsp. paratuberculosis DNA using the ABI Prism 7000 sequence detection system, and the LightCycler 1.0. TaqManmgb and locked nucleic acid fluorogenic probes were suitable for fluorescent signal detection. To improve the detection of M. avium subsp. paratuberculosis from bovine fecal samples, a more efficient DNA extraction method was developed, which offers the potential for automated sample processing. The 70% limit of detection was assessed to be 102 CFU per gram of spiked bovine feces. Comparative analysis of 108 naturally contaminated samples of unknown M. avium subsp. paratuberculosis status resulted in a relative accuracy of 98.9% and a sensitivity of 94.4% for fecal samples containing <10 CFU/g feces compared to the traditional culture method

Toward an international standard for PCR-based detection of Escherichia coli O157 - Part 1. Assay development and multi-center validation

ilustracionesEscherichia coli del serogrupo O157 pertenece al patotipo de las enterohemorrágicas, la más virulenta de E. coli, porque además de producir endotoxinas, libera dos exotoxinas conocidas como toxinas Shiga, Stx1 y Stx2 (Stx, Shiga toxin), causantes de graves patologías que pueden ser letales, como Colitis Hemorrágica (CH) y Síndrome Urémico Hemolítico (SUH), para personas con un sistema inmune deficiente o poco desarrollado (niños menores de cinco años y personas de la tercera edad). Esta STEC O157 (Shiga-Toxin producing E. coli) puede contaminar alimentos como productos cárnicos, derivados lácteos y vegetales, encontrándose también en aguas de consumo no tratadas. En la actualidad, la detección y la cuantificación de microrganismos patógenos en diferentes matrices alimenticias representan un gran reto para la industria. La técnica molecular qPCR-SYBR Green, entre otras, es sensible, rápida y específica, permitiendo detectar ADN de STEC del serogrupo O157, en un proceso automatizado que reduce ampliamente los tiempos de los procedimientos, con obtención de resultados en cuestión de horas, con un mínimo de contaminaciones y falsos positivos. En esta investigación se validaron cuatro protocolos de qPCR-SYBR Green para la detección específica de los genes rfbE (dos secuencias de oligonucleótidos), stx1 y sxt2 expresados por E. coli del serogrupo O157 (ATCC 43895), en muestras de carne molida bovina contaminada de forma artificial. Los parámetros de validación desarrollados fueron la selectividad, la sensibilidad y la robustez. Además, se hizo una comparación entre la qPCR-SYBR Green y otros métodos tradicionales como los gold standar, para determinar la confiabilidad de los protocolos. Las qPCR desarrolladas presentaron eficiencias entre 77 % y 97 % y una elevada linealidad (R2 0,99). Los límites de corte para cada secuencia de primers fueron: 3,1667 x 10-2 ng µL-1 para rfbE (primers rfbE y O157); 1,7228 x 10-3 ng µL-1 para stx1 y 3,5185 x 10-3 ng µL-1 para stx2. Tanto la inclusividad y la exclusividad fueron del 100 %, así como la precisión analítica, valor predictivo positivo y negativo. Además, fueron procesos bastante robustos. En la matriz contaminada se logró detectar hasta 4 UFC mL-1. Por los resultados obtenidos, los protocolos de qPCR-SYBR Green podrían implementarse para rastrear la presencia de E. coli O157 en el análisis rutinario de carne molida bovina, o como una prueba diagnóstica sencilla, rápida, altamente sensible y específica. (Tomado de la fuente)Escherichia coli from serogroup O157 belongs to the enterohemorrhagic pathotype, the most virulent of E. coli, because in addition to producing endotoxins, it releases two exotoxins known as Shiga toxins, Stx1 and Stx2 (Stx, Shiga toxin), causing serious pathologies that can be lethal, such as Hemorrhagic Colitis (CH) and Hemolytic Uremic Syndrome (HUS), for people with a poor or poorly developed immune system (children under five and the elderly). This STEC (Shiga-Toxin producing E. coli) O157 can contaminate foods such as meat products, dairy products, vegetables, and is also found in untreated drinking water. Currently, the detection and quantification of pathogenic microorganisms in different food matrices represents a great challenge for the industry; the qPCR-SYBR Green molecular technique, among others, is sensitive, fast and specific, allowing the detection of STEC DNA from serogroup O157, in an automated process that greatly reduces procedure times, obtaining results in a matter of hours, with a minimum of contaminations and false positives. In this investigation, four qPCR-SYBR Green protocols were validated for the specific detection of the rfbE (two oligonucleotide sequences), stx1 and sxt2 genes expressed by E. coli from serogroup O157 (ATCC 43895), in samples of contaminated ground beef artificially. The validation parameters developed were selectivity, sensitivity and robustness. Also, a comparison was made between the qPCR-SYBR Green and other traditional methods such as the gold standard, to determine the reliability of the protocols. The developed qPCRs presented efficiencies between 77% and 97% and high linearity (R2 0.99). The cutoff limits for each sequence of primers were: 3.1667 x 10-2 ng µL-1 for rfbE (primers rfbE and O157); 1.7228 x 10-3 ng µL-1 for stx1 and 3.5185 x 10-3 ng µL-1 for stx2. Both inclusivity and exclusivity were 100%, as well as analytical precision, positive and negative predictive value. They were also quite robust processes. Up to 4 CFU mL-1 were detected in the contaminated matrix. Based on the results obtained, the qPCR-SYBR Green protocols could be implemented to track the presence of E. coli O157 in the routine analysis of bovine ground beef, or as a simple, rapid, highly sensitive and specific diagnostic test. (Tomado de la fuente)MaestríaMagister en Ciencias - QuímicaBioquímica, Biología Molecula