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Sample records for sangramiento digestivo primer

  1. Caracterización clínico-terapéutica del sangramiento digestivo alto: Hospital "Dr. Salvador Allende". Primer semestre 2006 Clinicotherapeutical characterization of upper digestive bleeding: "Dr. Salvador Allende" Hospital. First semester 2006

    Directory of Open Access Journals (Sweden)

    José de Jesús Rego Hernández

    2007-12-01

    Full Text Available La hemorragia digestiva constituye una de las principales causas de ingreso hospitalario por enfermedades del tracto gastrointestinal, En la mayoría de casos se presenta de forma aguda y con importantes repercusiones sistémicas, por lo que obliga a adoptar medidas urgentes para estabilizar a los pacientes y permitir efectuar un tratamiento específico adecuado, Esta entidad sigue ocasionando una mortalidad elevada, que se acumula en determinados grupos de riesgo como son los pacientes con edad avanzada y enfermedades graves asociadas, por lo que se decide realizar la caracterización clínico-terapéutica del sangramiento digestivo alto en el Hospital "Dr, Salvador Allende" durante el primer semestre del 2006 mediante un estudio descriptivo que tomó como fuente la revisión de las 161 historias clínicas de los pacientes egresados con este diagnóstico en ese período, El 73,3 % de los pacientes con sangramiento digestivo alto fueron mayores de 60 años de edad; no existieron diferencias en cuanto al sexo; el café y el tabaquismo fueron los hábitos tóxicos más reportados; los antiinflamatorios no esteroides, el grupo farmacológico más relacionado con esta entidad y dentro de ellos, el ácido acetilsalicílico, y la melena, la manifestación clínica más frecuente, En el 91,9 % la pauta de tratamiento fue adecuada, así como el tratamiento en general; hubo solo la asociación irracional de un inhibidor de la bomba de protones con un anti-H2Digestive haemorrhage is one of the main cause of hospital admission due to gastrointestinal tract diseases. In most of the cases, it appears in an acute form, and with important systemic repercussions that lead to the adoption of emergency measures to stabilize the patients and to apply an adequate specific treatment. This entity is still causing a high mortality that is accumulated in certain risk groups as the elderly patients with severe associated diseases. That's why, it was decided to make the

  2. Esclerodermia como causa de sangramiento digestivo alto: A propósito de un caso

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    Armando Leal Mursulí

    2000-04-01

    Full Text Available La esclerosis sistémica o esclerodermia es una enfermedad crónica que afecta la piel y el resto de los sistemas de órganos, entre éstos uno de los más comúnmente dañados es el esófago, donde se manifiesta una esofagitis péptica crónica que raramente produce complicaciones letales como el sangramiento masivo ocurrido en el caso clínico que se presentó en nuestro centro, donde se hizo necesaria la intervención quirúrgica de urgencia, y en la cual se realizó una esofagectomía subtotal con sustitución gástrica (técnica de Ivor-Lewis. La literatura médica revisada indica la infrecuencia de estos casos complicados, pero sí la alta incidencia de los daños ocasionados por esta enfermedadSystemic sclerosis or scleroderma is a chronic disease affecting the skin and the rest of the systems of organs. One of the most commonly damaged is the esophagus, where a chronic peptic esophagitis occurs that rarely produces lethal complicated as the massive bleeding observed in the clinical case that received attention in our center. An urgent operation was necessary and subtotal esophagectomy with gastric substitution (Ivor-Lewis technique was performed. A review of the medical literature showed that these complicated cases are unusual, but that the incidence of damages caused by this disease is high

  3. Caracterización de pacientes con sangramiento digestivo alto Characterization of patients presenting with high digestive bleeding

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    Jean Le'Clerc Nicolás

    2010-06-01

    Full Text Available INTRODUCCIÓN. El sangramiento digestivo alto continúa siendo un problema de salud, y junto al abdomen agudo, las heridas y los traumatismos es prácticamente la razón de ser de una guardia de cirugía. MÉTODOS. Se realizó un estudio observacional, descriptivo y de corte transversal, cuyo universo estuvo constituido por todos los pacientes con este diagnóstico ingresados en el Hospital Docente Clinicoquirúrgico «Joaquín Albarrán», entre enero del 2006 y diciembre del 2007 (2 años. RESULTADOS. Las edades más frecuentes estuvieron entre los 70 y 79 años, y fue más frecuente el sexo masculino y el antecedente de enfermedad cardiovascular. La melena fue la principal manifestación clínica. La endoscopia solo se realizó en el 25,16 % de los casos, y en ella se observó principalmente duodenitis y gastritis. Como medidas terapéuticas más comunes se practicaron la hidratación y el uso sondas de Levine. Solo el 20,48 % de los pacientes recibieron tratamiento contra Helicobacter pylori. La estadía hospitalaria promedio fue de 6 días o más. CONCLUSIONES. Las medidas generales de apoyo hemodinámico y la estrecha vigilancia de los pacientes pueden lograr salvaguardar sus vidas aunque no se disponga de un diagnóstico certero. La infección por Helicobacter pylori y su asociación a lesiones erosivas o ulcerosas de la mucosa gastroduodenal no ha sido totalmente asimilada en el pensamiento médico de los cirujanos. La función de la cirugía es cada vez menor en la terapéutica del sangramiento digestivo alto, a pesar de ser uno de los pilares fundamentales para enfrentarlo.INTRODUCTION. High digestive bleeding remains as health problem and together with acute abdomen, wounds and traumatisms is practically the main responsibility of a surgery rounds. METHODS. A cross-sectional, descriptive and observational study was conducted in a sample including all patients with this diagnosis admitted in "Joaquín Albarrán" Clinical Surgical

  4. Sangramiento gingival y flora bacteriana en la gingivitis y la periodontitis

    OpenAIRE

    Iriam Baldemira Rodríguez; Zaida T Iliasastigui Ortueta²; María E Acosta Navarro³

    1996-01-01

    Se estudiaron 30 sitios o áreas periodontales que presentaban gingivitis y 30 con periodontitis, con el objetivo de determinar la relación existente entre el sangramiento gingival y la flora microbiana presente en la gingivitis y la periodontitis. Los pacientes seleccionados no presentaban antecedentes de enfermedad general y no habían recibido medicación antimicrobiana ni tratamiento periodontal en los útimos 6 meses; en el caso de las mujeres, no podían estar embarazadas. En los dientes sel...

  5. Sangramiento gingival y flora bacteriana en la gingivitis y la periodontitis

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    Iriam Baldemira Rodríguez

    1996-08-01

    Full Text Available Se estudiaron 30 sitios o áreas periodontales que presentaban gingivitis y 30 con periodontitis, con el objetivo de determinar la relación existente entre el sangramiento gingival y la flora microbiana presente en la gingivitis y la periodontitis. Los pacientes seleccionados no presentaban antecedentes de enfermedad general y no habían recibido medicación antimicrobiana ni tratamiento periodontal en los útimos 6 meses; en el caso de las mujeres, no podían estar embarazadas. En los dientes seleccionados se procedió a tomar la muestra cumpliendo con los requisitos establecidos; luego se examinó inmediatamente en el microscopio de campo oscuro. Los resultados obtenidos indican que no hubo relación entre los morfotipos microbianos y los diferentes valores del índice de sangramiento gingival.Thirty periodontal sites presenting with gingivitis and 30 with periodontitis were studied with the aim of determining the relation between gingival bleeding and microflora present in gingivitis and periodontitis. Patients selected for the study did not present with a history of systemic diseases and received neither antimicrobial medication nor periodontal treatment during the last 6 months, in the case of women it was required that they were not pregnant. The sample was taken in the teeth chosen in compliance with the requirements established; then the sample was immediately examined in the dark field microscope. Results obtained suggest that there was no relationship between microbial morphological types and the different values of the gingival bleeding index.

  6. Viviendo con un estoma digestivo: la importancia del apoyo familiar

    OpenAIRE

    Candela Bonill de las Nieves; César Hueso Montoro; Miriam Celdrán Mañas; Concepción Rivas Marín; Inmaculada Sánchez Crisol; José Miguel Morales Asencio

    2013-01-01

    Objetivo principal: Describir la relación y participación de la familia percibida por personas con estomas digestivos. Metodología: Estudio cualitativo descriptivo con 21 personas con estomas digestivos de las provincias de Málaga y Granada (España). La selección se hizo siguiendo los criterios de adecuación y diversidad mediante un muestreo intencional. La recogida de datos se realizó a través de entrevistas semiestructuradas. Se realizó un análisis del contenido, obteniéndose como categoría...

  7. Histologia y morfometria del sistema digestivo del silurido bagre tigrito

    National Research Council Canada - National Science Library

    Olaya C.M; Ovalle C.H; Gomez, E; Rodriguez D; Caldas, M.L; Hurtado H

    2007-01-01

    ... de espesor y se colorearon con H&E. El sistema digestivo presento cuatro capas: mucosa, submucosa, muscular y serosa. En el esofago la mucosa estaba compuesta por epitelio plano estratificado con gran numero de celulas caliciformes, y una submucosa de tejido conectivo laxo, seguida por musculo estriado esqueletico con dos orientaciones (circular y long...

  8. Mortalidad por sangrado digestivo alto en el Hospital “Enrique Cabrera” (2003 a 2007).

    OpenAIRE

    Cruz Alonso, Juan Ramón; Anaya González, Jorge Luís; Pampín Camejo, Luís Enrique; Pérez Blanco, Dora; Lopategui Cabezas, Ileana

    2008-01-01

    Enlaces originales: http://scielo.sld.cu/scielo.php?script=sci_arttext&pid=S0034-74932008000400006 https://www.researchgate.net/publication/262510937_Mortalidad_por_sangrado_digestivo_alto_en_el_Hospital_Enrique_Cabrera INTRODUCCIÓN. El sangrado digestivo alto continúa siendo un problema de salud que conlleva una significativa morbilidad y mortalidad y un elevado consumo de recursos sanitarios. El presente estudio buscó caracterizar la mortalidad por sangrado digestivo alto en el perío...

  9. Cuerpos extraños en el aparato digestivo

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    Trini Fragoso Arbelo

    2002-08-01

    Full Text Available Se expone una revisión sobre ingestión de cuerpos extraños en el aparato digestivo, su epidemiología, etiopatogenia y manifestaciones clínicas, según el tipo y localización del cuerpo extraño en el tracto gastrointestinal, el diagnóstico, así como las posibles complicaciones y el tratamiento. Se hace énfasis en la frecuencia de estos accidentes.A review is made on the finding of foreign bodies in the digestive system, its epidemiology, etiopathogeny and clinical manifestations, according to the type and localization of the foreign body in the gastrointestinal tract, the diagnosis and the possible complications and treatment. Emphasis is made on the frequency of these accidents.

  10. Viviendo con un estoma digestivo: la importancia del apoyo familiar

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    Candela Bonill de las Nieves

    2013-12-01

    Full Text Available Objetivo principal: Describir la relación y participación de la familia percibida por personas con estomas digestivos. Metodología: Estudio cualitativo descriptivo con 21 personas con estomas digestivos de las provincias de Málaga y Granada (España. La selección se hizo siguiendo los criterios de adecuación y diversidad mediante un muestreo intencional. La recogida de datos se realizó a través de entrevistas semiestructuradas. Se realizó un análisis del contenido, obteniéndose como categoría central el apoyo familiar. Resultados principales: Para las personas ostomizadas la familia se convierte en un recurso terapéutico esencial a lo largo de todo el proceso. Que el entorno familiar acepte esta nueva situación es fundamental para favorecer el reencuentro de la persona con su nueva realidad corporal. La implicación familiar en el proceso de aprendizaje de los cuidados desde el inicio es fundamental para la consecución de la autonomía. Contar con la aceptación y el apoyo de la pareja influye positivamente en el restablecimiento de las relaciones sexuales. Conclusión principal: La familia se convierte en un recurso terapéutico esencial a lo largo de todo el proceso, desde la toma de decisión acerca de la realización de la ostomía y durante el proceso de aceptación y adaptación del estoma.

  11. Sangrado digestivo alto en el Servicio de Urgencias del Hospital San Rafael de Alajuela

    OpenAIRE

    Salas-Segura, Donato A.

    1999-01-01

    Justificación: El sangrado digestivo alto se presume como una causa relativamente frecuente de consulta en los servicios de emergencia. Es necesario saber cual es su verdadero impacto en nuestro hospital. El objetivo del presente trabajo fue determinar las características de la población que sufre sangrado digestivo alto, las principales causas etiológicas y evaluar el tratamiento con derivados sanguíneos de que son objetos. Métodos: se realizó un estudio de tipo prospectivo descriptivo de...

  12. Aspectos histológicos del aparato digestivo de la alpaca

    OpenAIRE

    De la Vega D., Elmo; Departamento de Patología, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima, Perú

    2014-01-01

    Se ha realizado el estudio de la anatomía macroscópica y microscópica normal, del aparato digestivo de la Alpaca en 11 animales, clínicamente normales. El aspecto microscópico ha revelado variación estructural en los proventrículos de estos animales, con respecto a los demás rumiantes por nosotros conocidos. The present article deals with the anatomical study of the digestive system in 11 Alpacas ("Lama glama pacos"). The author has made the microscopical studies on the digestive system an...

  13. Tumor gástrico estromal como causa de sangrado digestivo.

    OpenAIRE

    Laura Arroyo-Martínez; Humberto Álvarez-Pertuz; Jorge Acuña-Calvo

    2006-01-01

    Los tumores gastrointestinales de la mesénquima (llamado tumores del músculo liso) se han clasificado como benignos (leiomiomas) o malignos (leiomiosarcomas). Más recientemente se les ha denominado Tumores Gástricos Estromales o GIST (Gastrointestinal Stromal Tumors). En estos tumores pueden abarcar desde la faringe hasta el canal anal, ya que comparten su origen embriológico. Los GIST muestran una gran variedad de manifestaciones clínicas, como lo son: sangrado digestivo, obstrucción o perfo...

  14. Morbimortalidad por Sangrado Digestivo Alto. Hospital Clínico Quirúrgico. Banes. Enero 2007_Diciembre 2008

    OpenAIRE

    Jorge Luís Pérez Jara; Lizandra Naranjo García; Antonio Ricardo García

    2011-01-01

    Se realizó un estudio descriptivo de corte transversal y retrospectivo para analizar la morbimortalidad por sangrado digestivo alto, de los casos atendidos en el servicio de cirugía del Hospital Clínico Quirúrgico de Banes, Holguín, motivados por la alta incidencia en nuestro territorio. La muestra estuvo conformada por los pacientes entre 15 a 65 años y más, se identificaron como principales causas de sangrado digestivo alto a la úlcera péptica crónica, las gastritis hemorrágicas por AINES y...

  15. Conceções dos alunos do 1.º Ciclo do Ensino Básico sobre o sistema digestivo

    OpenAIRE

    Moreira, Dalila; Almeida, Liliana; Lopes, Mónica; Veiga, Vânia; Cavadas, Bento

    2012-01-01

    Este estudo exploratório teve como objetivo determinar os conhecimentos dos alunos do 1º Ciclo do Ensino Básico (1.º CEB) sobre o sistema digestivo. Usou-se uma adaptação do método seguido por Dantas (2006). O instrumento de recolha de dados utilizado foi o desenho. Solicitou-se a 69 alunos (37 raparigas e 32 rapazes) do 4.º ano, de quatro escolas do distrito de Santarém, que elaborassem um desenho sobre a constituição do aparelho digestivo humano. Os alunos fizeram os desenhos em sala de aul...

  16. Metamorfosis del aparato digestivo de larvas carnívoras de Ceratophrys cranwelli (Anura: Leptodactylidae

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    Ulloa Kreisel, Zandra E.

    2000-12-01

    Full Text Available Las larvas carnívoras de Ceratophrys cranwelli presentan un tubo digestivo más corto que la mayoría de las larvas de anuros, tiene 6 veces la longitud del cuerpo del renacuajo y se caracteriza también por tener un estómago larval. El presente trabajo tiene como objetivo el determinar el grado de transformaciones en la cavidad bucofaríngea y tubo digestivo en larvas de esta especie durante la metamorfosis y comparar las estructuras digestivas estudiadas en otras especies de Leptodactylidae de la subfamilia Ceratophryinae y especies con otros hábitos alimenticios. Carnivorous larvae from Ceratophrys cranwelli present a digestive tube shorter than most of the anuran larvae, have 6 times a tadpole’s body length and they are also characterized by the presence of a larval stomach. The aim of this work is determine the grade of transformations in the buccopharyngeal cavity and digestive tube during the metamorphosis in larvae of this species and compare the digestive structures studied in other species of Leptodactylidae of the subfamily Ceratophryinae and another species with different diets.

  17. Organogénesis del sistema digestivo del pez Pterophylum scalare (Perciformes: Cichlidae

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    Mireya Ávila Botello

    2008-12-01

    Full Text Available Debido a la poca información sobre el desarrollo de sistemas orgánicos en el pez Pterophylum scalare (Liechtenstein 1823 estudiamos yiempo neto de desarrollo de cada estadio de la organogénesis, tiempo acumulado y diferenciación de estructuras características de cada estadio. Se obtuvo un total de 8 estadios en la organogénesis del sistema digestivo, comprendidos entre la gástrula y la reabsorción total del saco vitelino. La duración de la organogénesis del sistema digestivo fue de 119 horas 44 minutos.Organogenesis of the digestive system of the fish Pterophylum scalare (Perciformes: Cichlidae. There is little knowledge on the development of the angelfish Pterophyllum scalare (Liechtenstein 1823, a species of economical and biological value for inland water ecosystems. We recorded net development time of each organogenetic stage, cumulative time and characteristic structure differentiation for each stage. We found eight organogenetic stages for the digestive system, between the gastrula and the total re-adsorption of the vitelin sack. The total time for the organogenetic development of the digestive system was 119 hours and 44 minutes. Rev. Biol. Trop. 56 (4: 1857-1870. Epub 2008 December 12.

  18. Estudio histológico e histoquímico de la organogénesis del tubo digestivo de Rhamdia quelen en condiciones de larvicultura intensiva

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    David R Hernández

    2014-11-01

    Full Text Available El desarrollo del tracto digestivo en larvas de Rhamdia quelen y su cronología de diferenciación fue estudiado histológicamente desde el nacimiento hasta los 20 días posteriores a la eclosión (dpe con 530 unidades térmicas acumuladas (UTA. Las larvas se mantuvieron en condiciones de larvicultura intensiva, alimentadas con nauplios de Artemia. La diferenciación anatómica e histológica del tracto digestivo fue un proceso asíncrono, con un tubo recto e indiferenciado a 1 dpe (4,87 mm, mientras que al inicio de la alimentación exógena, se organizó en cuatro zonas histológicamente diferenciadas: cavidad bucofaríngea, esófago, estómago incipiente e intestino. A los 15 dpe (397,5 UTA, la organización fue semejante a la de los adultos. Al nacimiento, se observaron corpúsculos gustativos en los barbillones y cavidad bucofaríngea, distribuidos entre un epitelio estratificado con células mucosas. En el esófago, al inicio de la alimentación exógena, se observó epitelio estratificado con células mucosas de secreción neutra y ácida. En el estómago, las glándulas gástricas comenzaron a hacerse visibles entre 8 y 10 dpe (212 a 265 UTA, siendo completamente activas a 20 dpe. El primer día de vida, el intestino presentó el epitelio cilíndrico simple sin características de actividad absortiva evidente, mientras que a 4 dpe (106 UTA se observaron microvellosidades en la región apical y una importante acumulación de lípidos y proteínas intra-citoplásmicas en el intestino anterior y posterior, respectivamente. En este órgano, las células mucosas fueron ácidas y neutras, siendo ambos tipos los más abundantes en la región distal. Los resultados histológicos indican que las larvas de R. quelen son capaces de digerir y absorber eficientemente el alimento desde los primeros días de vida.

  19. Instrumento quirúrgico de sutura para anastomosis automática del tubo digestivo

    OpenAIRE

    Tornero García, José Antonio; Suárez Feijóo, Raúl; Cano Casas, Francesc; Montaño Sarria, Andrés Felipe; López Cano, Manuel

    2012-01-01

    En la cirugía digestiva, una anastomosis del intestino consiste en la reconstrucción del tubo digestivo por unión de dos cabos tras la resección de una porción del mismo. Este procedimiento, de común aplicación en diversos tipos de intervención quirúrgica se realiza actualmente mediante la aplicación de grapas metálicas debido a la complejidad inherente de la realización de una sutura manual. La automatización del proceso de sutura mediante un dispositivo diseñado a tal efecto supondría una n...

  20. Primer3Plus, an enhanced web interface to Primer3

    NARCIS (Netherlands)

    Untergasser, A.; Nijveen, H.; Rao, X.; Bisseling, T.; Geurts, R.; Leunissen, J.A.M.

    2007-01-01

    Here we present Primer3Plus, a new web interface to the popular Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. Primer3 consists of a command line program and a web interface. The web interface is one large form showing all of the possible

  1. Asset management primer

    Science.gov (United States)

    1999-12-01

    According to this primer, asset management is a systematic process of maintaining, upgrading, and operating physical assets cost-effectively. It combines engineering principles with sound business practices and economic theory, and it provides tools ...

  2. DESCRIPCIÓN MORFOLÓGICA DEL TUBO DIGESTIVO DE JUVENILES DE RUBIO Salminus affinis (PISCES: CHARACIDAE

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    VJ ATENCIO GARCÍA

    2008-01-01

    Full Text Available El objetivo del estudio fue la descripción del tubo digestivo de juveniles de Rubio Salminus affinis. Se analizaron cinco juveniles con 23,6±2,6 cm de longitud total y 142,8±62,5 g de peso. Se realizó descripción topográfica y morfológica de los órganos y cortes histológicos con tinción H-E. El esófago es un órgano tubular corto de pared gruesa que representa el 7,8% de la longitud total del tubo digestivo, presenta pliegues internos que ofrecen gran capacidad de distensión permitiendo el paso de presas de gran tamaño. El estómago es una bolsa asimétrica en forma de “Y”, grande y musculosa, amplio en la porción anterior y estrecho hacia el fondo; el número de ciegos pilóricos varió entre 13 y 23 pudiendo ser monotubulares y ramificados. El intestino, con tres asas, se extiende desde el esfínter pilórico hasta el ano. Histológicamente el tubo digestivo está formado por cuatro capas: mucosa, submucosa, muscular y serosa; el epitelio de revestimiento del esófago es estratificado plano no queratinizado con células caliciformes, cambiando a simple cilíndrico mucosecretor llegando al estómago; en el estómago se encuentra epitelio simple cilíndrico mucosecretor y los ciegos pilóricos e intestino son revestidos por epitelio simple cilíndrico con células caliciformes. Tanto el valor promedio del coeficiente intestinal (0,58, como la pared distensible del estómago sugieren que el Rubio tiene un tubo digestivo propio de carnívoro y sus características histológicas presentan similitud con la mayoría de vertebrados superiores.

  3. DESCRIPCIÓN MORFOLÓGICA DEL TUBO DIGESTIVO DE JUVENILES DE RUBIO Salminus affinis (PISCES: CHARACIDAE

    Directory of Open Access Journals (Sweden)

    VJ Atencio

    2008-09-01

    Full Text Available El objetivo del estudio fue la descripción del tubo digestivo de juveniles de Rubio Salminus affinis. Se analizaron cinco juveniles con 23,6±2,6 cm de longitud total y 142,8±62,5 g de peso. Se realizó descripción topográfica y morfológica de los órganos y cortes histológicos con tinción H-E. El esófago es un órgano tubular corto de pared gruesa que representa el 7,8% de la longitud total del tubo digestivo, presenta pliegues internos que ofrecen gran capacidad de distensión permitiendo el paso de presas de gran tamaño. El estómago es una bolsa asimétrica en forma de “Y”, grande y musculosa, amplio en la porción anterior y estrecho hacia el fondo; el número de ciegos pilóricos varió entre 13 y 23 pudiendo ser monotubulares y ramificados. El intestino, con tres asas, se extiende desde el esfínter pilórico hasta el ano. Histológicamente el tubo digestivo está formado por cuatro capas: mucosa, submucosa, muscular y serosa; el epitelio de revestimiento del esófago es estratificado plano no queratinizado con células caliciformes, cambiando a simple cilíndrico mucosecretor llegando al estómago; en el estómago se encuentra epitelio simple cilíndrico mucosecretor y los ciegos pilóricos e intestino son revestidos por epitelio simple cilíndrico con células caliciformes. Tanto el valor promedio del coeficiente intestinal (0,58, como la pared distensible del estómago sugieren que el Rubio tiene un tubo digestivo propio de carnívoro y sus características histológicas presentan similitud con la mayoría de vertebrados superiores.

  4. MORFOLOGIA DO TUBO DIGESTIVO DA PESCADA AMARELA Cynoscion acoupa (LACEPÈDE, 1801 (PERCIFORMES: SCIAENIDAE NO LITORAL PIAUIENSE, BRASIL

    Directory of Open Access Journals (Sweden)

    Francisca Edna Andrade Cunha

    2016-12-01

    Full Text Available Os objetivos deste trabalho foi descrever a estrutura anatômica do tubo digestivo, relacionando-o ao hábito alimentar da Pescada amarela, Cynoscion acoupa (Lacepède, 1801, capturadas no litoral do Piauí, no período de julho de 2013 a janeiro de 2014. Foram analisados 68 exemplares, com comprimento total variando entre 25 a 70 cm e média de 44,66, enquanto o peso corporal variou entre 2,5 a 11,7 kg e média de 6,4. Os tubos digestivos mostraram adaptações anatômicas ao hábito alimentar carnívoro. Os estômagos apresentaram forma cecal, em Y, com as regiões gástricas (cárdica, fúndica e pilórica bem definida; mucosa interna revestida por pregas distensíveis separadas por profundos sulcos. O esôfago é curto. A região cárdica é a maior do estômago. As pregas da mucosa apresentam-se consideravelmente distensíveis para recepção e condução do alimento pelo esôfago e armazenamento pelo estômago. O intestino é relativamente curto, com coeficiente intestinal de 0,99 dividindo-se em intestino médio e reto, com a presença de valva ileorretal entre eles. O esfíncter pilórico regula o fluxo do alimento para o intestino médio. Os cecos pilóricos, formados por quatro apêndices com função de ampliação da área de absorção intestinal. A morfologia do tubo digestivo de C. acoupa condiz com o seu hábito alimentar carnívoro, ictiófago. Palavras-chave: Aspectos morfológicos, Tubo digestivo, Anatomia, hábito alimentar carnívoro.

  5. DESCRIPCIÓN MORFOLÓGICA DEL TUBO DIGESTIVO DE JUVENILES DE RUBIO Salminus affinis (PISCES: CHARACIDAE

    Directory of Open Access Journals (Sweden)

    Hernandez J

    2008-12-01

    Full Text Available El objetivo del estudio fue la descripción del tubo digestivo de juveniles de Rubio Salminus affinis. Se analizaron cinco juveniles con 23,6±2,6 cm de longitud total y 142,8±62,5 g de peso. Se realizó descripción topográfica y morfológica de los órganos y cortes histológicos con tinción H-E. El esófago es un órgano tubular corto de pared gruesa que representa el 7,8% de la longitud total del tubo digestivo, presenta pliegues internos que ofrecen gran capacidad de distensión permitiendo el paso de presas de gran tamaño. El estómago es una bolsa asimétrica en forma de “Y”, grande y musculosa, amplio en la porción anterior y estrecho hacia el fondo; el número de ciegos pilóricos varió entre 13 y 23 pudiendo ser monotubulares y ramificados. El intestino, con tres asas, se extiende desde el esfínter pilórico hasta el ano. Histológicamente el tubo digestivo está formado por cuatro capas: mucosa, submucosa, muscular y serosa; el epitelio de revestimiento del esófago es estratificado plano no queratinizado con células caliciformes, cambiando a simple cilíndrico mucosecretor llegando al estómago; en el estómago se encuentra epitelio simple cilíndrico mucosecretor y los ciegos pilóricos e intestino son revestidos por epitelio simple cilíndrico con células caliciformes. Tanto el valor promedio del coeficiente intestinal (0,58, como la pared distensible del estómago sugieren que el Rubio tiene un tubo digestivo propio de carnívoro y sus características histológicas presentan similitud con la mayoría de vertebrados superiores.

  6. China Energy Primer

    Energy Technology Data Exchange (ETDEWEB)

    Ni, Chun Chun

    2009-11-16

    Based on extensive analysis of the 'China Energy Databook Version 7' (October 2008) this Primer for China's Energy Industry draws a broad picture of China's energy industry with the two goals of helping users read and interpret the data presented in the 'China Energy Databook' and understand the historical evolution of China's energy inustry. Primer provides comprehensive historical reviews of China's energy industry including its supply and demand, exports and imports, investments, environment, and most importantly, its complicated pricing system, a key element in the analysis of China's energy sector.

  7. Mortalidad por sangrado digestivo alto en el Hospital «Enrique Cabrera» Mortality from upper digestive bleeding in «Enrique Cabrera» Hospital

    OpenAIRE

    Juan Ramón Cruz Alonso; Jorge Luís Anaya González; Luís Enrique Pampín Camejo; Dora Pérez Blanco; Ileana Lopategui Cabezas

    2008-01-01

    INTRODUCCIÓN. El sangrado digestivo alto continúa siendo un problema de salud que conlleva una significativa morbilidad y mortalidad y un elevado consumo de recursos sanitarios. El presente estudio buscó caracterizar la mortalidad por sangrado digestivo alto en el período comprendido entre enero del 2003 y julio del 2007, en el Hospital «Enrique Cabrera» (La Habana). MÉTODO: Se realizó un estudio descriptivo, retrospectivo de corte transversal, donde se revisaron las fichas clínicas de los pa...

  8. Semantic Web Primer

    NARCIS (Netherlands)

    Antoniou, Grigoris; Harmelen, Frank van

    2004-01-01

    The development of the Semantic Web, with machine-readable content, has the potential to revolutionize the World Wide Web and its use. A Semantic Web Primer provides an introduction and guide to this still emerging field, describing its key ideas, languages, and technologies. Suitable for use as a

  9. Identification of ISSR Primers

    African Journals Online (AJOL)

    leaf preferred by consumers. These genotypes ... plants, primers that work for one may not work for another. Hence .... Naidoo, Madhupa and Dr Bayo Shittu for access to laboratory facilities, training in different techniques and editing of manuscript. This work was made possible by a fellowship for Female. Academic Staff ...

  10. An SAT® Validity Primer

    Science.gov (United States)

    Shaw, Emily J.

    2015-01-01

    This primer should provide the reader with a deeper understanding of the concept of test validity and will present the recent available validity evidence on the relationship between SAT® scores and important college outcomes. In addition, the content examined on the SAT will be discussed as well as the fundamental attention paid to the fairness of…

  11. HISTOLOGÍA DEL SISTEMA DIGESTIVO DE Didelphis albiventris (LUND, 1840

    Directory of Open Access Journals (Sweden)

    C. Moreno-Durán1

    2007-06-01

    Full Text Available Didelphis albiventris es un marsupial que se encuentra en Colombia en la región Andina desde los 1800 hasta 4000 m.s.n.m (Cuartas - Calle 2003. Su importancia ecológica radica en que es una especie quecontrola poblaciones de roedores, e insectos y contribuye a la dispersión de las semillas.Se llevó a cabo un estudio histológico del sistema digestivo de marsupiales de Didelphis albiventris, provenientes del municipio de Sotaquirá (Boyacá, Colombia. Los órganos se fijaron en formol buferizado al 10%, y se tiñeron con Hematoxilina - Eosina de acuerdo a la técnica de Propath 1992.Se realizaron descripciones histológicas, desde la cavidad oral hasta el intestino grueso. En la lengua se observaron papilas filiformes y tres papilas circunvaladas dispuestas en forma de triángulo en la parte posterior de la lengua, con botones gustativos. El estómago del marsupial se dividió en varias zonas: cardial, fúndica, del cuerpo y pilórica las cuales presentan características similares a la mayoría de mamíferos. En la primera porción del intestino delgado, se observó el duodeno con ausencia de glándulas de Brunner, la disposición de las fibras musculares lisas presentó variación a nivel de duodeno y cloaca, caracterizándose por poseer una muscular circular externa y una muscular longitudinal interna. No se observaron diferenciassignificativas con respecto a otros mamíferos, como roedores y el hombre en hígado, páncreas, vesícula biliar y glándulas salivares por lo cual no se incluyen en el presente trabajo. Se encontraron diferencias con respecto a los mamíferos en la ubicación de las glándulas de Brunner en el íleon y no en el duodeno y la distribución de nódulos linfoides dentro de la lámina propia de la mucosa de todo el tracto gastrointestinal.

  12. Primer on molecular genetics

    Energy Technology Data Exchange (ETDEWEB)

    1992-04-01

    This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

  13. Coal Bed Methane Primer

    Energy Technology Data Exchange (ETDEWEB)

    Dan Arthur; Bruce Langhus; Jon Seekins

    2005-05-25

    During the second half of the 1990's Coal Bed Methane (CBM) production increased dramatically nationwide to represent a significant new source of income and natural gas for many independent and established producers. Matching these soaring production rates during this period was a heightened public awareness of environmental concerns. These concerns left unexplained and under-addressed have created a significant growth in public involvement generating literally thousands of unfocused project comments for various regional NEPA efforts resulting in the delayed development of public and fee lands. The accelerating interest in CBM development coupled to the growth in public involvement has prompted the conceptualization of this project for the development of a CBM Primer. The Primer is designed to serve as a summary document, which introduces and encapsulates information pertinent to the development of Coal Bed Methane (CBM), including focused discussions of coal deposits, methane as a natural formed gas, split mineral estates, development techniques, operational issues, producing methods, applicable regulatory frameworks, land and resource management, mitigation measures, preparation of project plans, data availability, Indian Trust issues and relevant environmental technologies. An important aspect of gaining access to federal, state, tribal, or fee lands involves education of a broad array of stakeholders, including land and mineral owners, regulators, conservationists, tribal governments, special interest groups, and numerous others that could be impacted by the development of coal bed methane. Perhaps the most crucial aspect of successfully developing CBM resources is stakeholder education. Currently, an inconsistent picture of CBM exists. There is a significant lack of understanding on the parts of nearly all stakeholders, including industry, government, special interest groups, and land owners. It is envisioned the Primer would being used by a variety of

  14. Hipoalbuminemia en el desenlace clínico de pacientes con sangrado de tubo digestivo alto no variceal

    OpenAIRE

    J.A. González-González; G. Vázquez-Elizondo; Monreal-Robles, R.; D. García-Compean; O.D. Borjas-Almaguer; Hernández-Velázquez, B.; Maldonado-Garza, H.J.

    2016-01-01

    Introducción y objetivo: El papel de los niveles séricos de albúmina en pacientes con sangrado de tubo digestivo alto no variceal (SDA-NV) no ha sido estudiado ampliamente. Nuestro objetivo fue evaluar el papel de los niveles de albúmina en la mortalidad de pacientes con SDA-NV. Material y métodos: Se incluyó a pacientes con SDA-NV de forma prospectiva durante un periodo de 4 años. Se recolectaron datos demográficos, clínicos y de laboratorio. Se usó análisis ROC para determinar el mejor p...

  15. HISTOLOGÍA Y MORFOMETRÍA DEL SISTEMA DIGESTIVO DEL SILÚRIDO BAGRE TIGRITO (Pimelodus pictus)

    OpenAIRE

    CM Olaya; CH Ovalle; Gómez, E; Rodríguez, D.; ML Caldas; H Hurtado

    2007-01-01

    El bagre tigrito Pimelodus pictus es un pez ornamental con gran aceptación en el mercado acuarista internacional, sin embargo, se desconocen muchos aspectos de la biología básica de esta especie. Por tal motivo, se realizó un estudio histológico y morfométrico del sistema digestivo a Àn de contribuir al diseño de futuras dietas. Se sacriÀcaron 7 individuos adultos de P. pictus de 10 ± 0,5 cm de longitud total con una sobredosis de MS-222 (0,5 g/l). Los especímenes se Àjaron en formaldehído al...

  16. Math primer for engineers

    CERN Document Server

    Cryer, CW

    2014-01-01

    Mathematics and engineering are inevitably interrelated, and this interaction will steadily increase as the use of mathematical modelling grows. Although mathematicians and engineers often misunderstand one another, their basic approach is quite similar, as is the historical development of their respective disciplines. The purpose of this Math Primer is to provide a brief introduction to those parts of mathematics which are, or could be, useful in engineering, especially bioengineering. The aim is to summarize the ideas covered in each subject area without going into exhaustive detail. Formula

  17. Primer on Health Surveys

    Directory of Open Access Journals (Sweden)

    David L Nordstrom

    2012-06-01

    Full Text Available The aim of this paper is to introduce novice researchers to surveys as a method of data collection. It starts with the definition of a survey, its major purposes and types as well as changes in the goals surveys have helped to achieve over time. Advantages and disadvantages of surveys over population censuses and medical examinations are discussed. Approaches to questionnaire construction are introduced along with properties that questionnaires are evaluated for. Modes of administration, sample size issues, and data analysis approaches are also introduced. The primer is illustrated with examples of surveys conducted in different countries with various public health purposes.

  18. El primer virreinato americano

    Directory of Open Access Journals (Sweden)

    Cassá, Roberto

    2006-12-01

    Full Text Available This article explores the government of viceroy Christopher Columbus in the American territories. We return to the first Spanish settlement in Santo Domingo and the contradictions inherent to this expansionist proyect. The contradictions were part of the logic of the absolutist state and Columbus’ reaction against the controls imposed by the monarchs. Secondly, we look into the dificulties that the Admiral encountered to develop a mercantilist model. In this context, we examine the rationale behind the first government of the Indies and the features that defined the new West Indian society.

    El artículo trata sobre el gobierno de Cristóbal Colón en tierras americanas. Retomamos el tema del primer emplazamiento español en Santo Domingo y las contradicciones que tuvo aquel proyecto debido a la lógica del estado absolutista, a la ambición desmedida del descubridor y a su reacción ante los controles que desde un principio impusieron los monarcas. En un segundo momento analizamos las dificultades que encontró el Almirante para desarrollar un modelo mercantilista acorde a sus ideas y a los acuerdos a que llegó con la Corona. En ese contexto analizamos la lógica del primer gobierno colombinista en las Indias y los rasgos que definieron la nueva sociedad antillana.

  19. A primer on water

    Science.gov (United States)

    Leopold, Luna Bergere; Langbein, Walter Basil

    1960-01-01

    When you open the faucet you expect water to flow. And you expect it to flow night or day, summer or winter, whether you want to fill a glass or water the lawn. It should be clean and pure, without any odor.You have seen or read about places where the water doesn't have these qualities. You may have lived in a city where you were allowed to water the lawn only during a few hours of certain days. We know a large town where the water turns brown after every big rainstorm.Beginning shortly after World War II, large areas in the Southwestern United States had a 10-year drought, and newspapers published a lot of information about its effects. Some people say that the growing demand for water will cause serious shortages over much of the country in the next 10 to 40 years. But it has always been true that while water wells and springs dry up in some places, floods may be occurring in other places at the same time.Nearly every month news stories are published describing floods somewhere in the country. In fact, every year, on the average, 75,000 persons are forced from their homes by floods. In some years, as in 1951 when the lower Kansas River experienced a great flood, half a million people are affected. To understand the reasons for such recurring distress, it is necessary to know something about rivers and about the flat land or flood plain that borders the river.Interest in water and related problems is growing as our population increases and as the use of water becomes steadily greater. To help meet this heightened interest in general information about water and its use and control is the reason this primer was written. The primer is in two parts. The first part tells about hydrology, or the science that concerns the relation of water to our earth, and the second part describes the development of water supplies and the use of water. The Geological Survey is publishing this primer in nontechnical language in the hope that it will enable the general reader to

  20. Metabolomics: A Primer.

    Science.gov (United States)

    Liu, Xiaojing; Locasale, Jason W

    2017-04-01

    Metabolomics generates a profile of small molecules that are derived from cellular metabolism and can directly reflect the outcome of complex networks of biochemical reactions, thus providing insights into multiple aspects of cellular physiology. Technological advances have enabled rapid and increasingly expansive data acquisition with samples as small as single cells; however, substantial challenges in the field remain. In this primer we provide an overview of metabolomics, especially mass spectrometry (MS)-based metabolomics, which uses liquid chromatography (LC) for separation, and discuss its utilities and limitations. We identify and discuss several areas at the frontier of metabolomics. Our goal is to give the reader a sense of what might be accomplished when conducting a metabolomics experiment, now and in the near future. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. HISTOLOGÍA Y MORFOMETRÍA DEL SISTEMA DIGESTIVO DEL SILÚRIDO BAGRE TIGRITO (Pimelodus pictus

    Directory of Open Access Journals (Sweden)

    CM Olaya

    2007-01-01

    Full Text Available El bagre tigrito Pimelodus pictus es un pez ornamental con gran aceptación en el mercado acuarista internacional, sin embargo, se desconocen muchos aspectos de la biología básica de esta especie. Por tal motivo, se realizó un estudio histológico y morfométrico del sistema digestivo a Àn de contribuir al diseño de futuras dietas. Se sacriÀcaron 7 individuos adultos de P. pictus de 10 ± 0,5 cm de longitud total con una sobredosis de MS-222 (0,5 g/l. Los especímenes se Àjaron en formaldehído al 4%, durante cinco días a 4 °C. Luego se siguió el procedimiento para técnica en paraÀna. Se realizaron cortes de 5 μm de espesor y se colo-rearon con H&E. El sistema digestivo presentó cuatro capas: mucosa, submucosa, muscular y serosa. En el esófago la mucosa estaba compuesta por epitelio plano estratiÀcado con gran número de células caliciformes, y una submucosa de tejido conectivo laxo, seguida por músculo estriado esquelético con dos orientaciones (circular y longitudinal. En todos los órganos evaluados la capa serosa fue muy delgada. En el estómago se identiÀcaron dos regiones, la pilórica y la cardíaca, encontrándose glándulas gástricas en esta última, ambas regiones presentaban una mucosa con epitelio cilíndrico simple, una submucosa de tejido conectivo laxo, y una capa de músculo liso con dos orientaciones (circular y longitudinal así mismo, este órgano fue el que exhibió el mayor espesor en la capa mucosa y muscular. La histología de la mucosa, la submucosa y la capa muscular del intestino fue similar a lo presentado por el estómago, aunque morfométricamente esta región fue la que exhibió los menores valores en todas las capas evaluadas. El estómago bien deÀnido y el intestino con pocos ciegos pilóricos hace suponer que P. pictus es de hábitos omnívoros con preferencia de los alimentos de origen animal.

  2. Estudio histológico del sistema digestivo en diferentes estadios de desarrollo de la cachama blanca (Piaractus brachypomus

    Directory of Open Access Journals (Sweden)

    Miguel Ángel Mendoza R.

    2013-06-01

    Full Text Available La cachama blanca (Piaractus brachypomus es la segunda fuente de producción piscícola en Colombia, después de la tilapia roja (Oreochomi ssp. y antes de la trucha arcoíris (Oncorhynchus mykiss. Se destaca, además, como una de las especies con mayor potencial productivo en el país. Se realizó el estudio histológico del sistema digestivo de la Piaractus brachypomus a fin determinar la morfología normal en diferentes estadios de desarrollo. Para ello se clasificaron los animales según la edad, el tamaño y el peso en ovas embrionadas, larvas con saco vitelino, alevinos después de reabsorción de saco vitelino, juveniles (3-5 cm, 5-7 cm, 10 cm, 15 cm y adultos (300 g. La fijación de los tejidos se realizó en formaldehído al 3,7 % y se describió microscópicamente cavidad bucal, faringe, esófago, estómago, ciegos pilóricos, intestinos y las glándulas anexas, hígado y páncreas. Por último, se describió macroscópicamente la organización anatómica de este sistema.

  3. DISTRIBUCIÓN Y ABUNDANCIA DE LOS HUEVOS DE ESTRÓNGILOS DIGESTIVOS EN BOVINOS INFECTADOS NATURALMENTE

    Directory of Open Access Journals (Sweden)

    Jessica Quijada P

    2008-08-01

    Full Text Available Objetivo. Determinar la prevalencia, cargas parasitarias y distribución de las infecciones naturales con estróngilos digestivos dentro de rebaños bovinos de una zona ganadera del Estado Falcón en Venezuela Materiales y métodos. Se evaluaron cuatro fincas de bovinos doble propósito. Los animales son tipo “Carora” (mestizaje de razas: Holstein, Pardo Suizo, Cebuínos. Durante siete meses se analizaron (Técnica de Mc Master un total de 1140 muestras. La muestra de cada finca se estratificó en cuatro grupo etarios (1: Becerros 0-6 meses; 2: Mautes 7-12; 3: Novillas 13-24 y 4: Adultos >25 meses. Resultados. Los valores de prevalencia promedio fueron: 31.06-50.36%. Se halló diferencia estadística (p<0,05 entre los niveles de prevalencia entre fincas y entre grupos etarios. Las infecciones se distribuyeron de forma sobredispersada en cada rebaño, evidenciado por los bajos valores de K (0.001-0.01. Conclusiones. Los valores de abundancia se afectaron más por el número de animales con altas cargas que por la prevalencia. La mayoría de las infecciones no revistió importancia clínica, las altas cargas parasitarias representaron 1.75-28.56% de todas las infecciones.

  4. Relación de la función masticatoria con los trastornos digestivos Relation of the masticatory function to the digestive disorders

    Directory of Open Access Journals (Sweden)

    Martha Concepción Ibáñez Castillo

    2007-12-01

    Full Text Available Se realizó una investigación en la que se relaciona la función masticatoria con los trastornos digestivos en pacientes que acudieron al chequeo médico en el Hospital Militar Docente "Dr. Joaquín Castillo Duany", en Santiago de Cuba, de enero de 2004 al 2005, mediante un estudio descriptivo y transversal con 199 pacientes de uno y otro sexo y diversos grupos de edades. Se confeccionó un formulario, se agruparon las tablas y se realizó el análisis estadístico. Se observó un predominio de trastornos digestivos en el grupo de 60 años y más, con presencia de desdentamiento y función masticatoria deficiente, por lo que se concluyó que existe una significativa relación entre la función masticatoria y los trastornos digestivos. Se recomienda extender el estudio a todas las áreas de salud, con el fin de utilizar nuestros conocimientos en beneficio de los pacientes.An investigation was carried out to connect the masticatory function with the digestive disorders in patients that had the medical check-up at "Dr. Joaquín Castillo Duany" Military Teaching Hospital, in Santiago de Cuba, from January 2004 to January 2005, by a descriptive cross-sectional study of 199 patients of both sexes and different ages. A questionnaire was designed, tables were grouped and a statistical analysis was made. It was observed a predominance of digestive disorders in the age group 60 and over, with lack of teeth and deficient masticatory function. It was concluded that there was a significant relation between the masticatory function and the digestive disorders. It was recommended to extend the study to all the health areas so as to use our knowledge for the benefit of the patients.

  5. Actividades enzimáticas en aislamientos bacterianos de tractos digestivos de larvas y del contenido de pupas de Automeris zugana y Rothschildia lebeau (Lepidoptera: Saturniidae)

    OpenAIRE

    Adrián Pinto-Tomás; Lorena Uribe-Lorío; John Blanco; Gustavo Fontecha; César Rodríguez; Marielos Mora; Daniel Janzen; Felipe Chavarría; Joel Díaz; Ana Sittenfeld

    2007-01-01

    El tracto digestivo de orugas constituye un microambiente extremo, debido a su elevado pH y presencia de sustancias antimicrobianas secretadas por el insecto o derivadas del tejido vegetal ingerido. Al mismo tiempo, el intestino alberga gran cantidad de alimento, por el cual los microorganismos presentes podrían competir entre sí y con su hospedero. Existe poca información sobre la microbiota asociada con el intestino de orugas tropicales, aunque se ha demostrado la presencia de bacterias de ...

  6. Mortalidad por sangrado digestivo alto en el Hospital «Enrique Cabrera» Mortality from upper digestive bleeding in «Enrique Cabrera» Hospital

    Directory of Open Access Journals (Sweden)

    Juan Ramón Cruz Alonso

    2008-12-01

    Full Text Available INTRODUCCIÓN. El sangrado digestivo alto continúa siendo un problema de salud que conlleva una significativa morbilidad y mortalidad y un elevado consumo de recursos sanitarios. El presente estudio buscó caracterizar la mortalidad por sangrado digestivo alto en el período comprendido entre enero del 2003 y julio del 2007, en el Hospital «Enrique Cabrera» (La Habana. MÉTODO: Se realizó un estudio descriptivo, retrospectivo de corte transversal, donde se revisaron las fichas clínicas de los pacientes fallecidos por sangrado digestivo alto en el período señalado. RESULTADOS: Fallecieron 49 pacientes de un total de 320 ingresados por sangrado digestivo alto (15 %. El 80,6 % de los fallecidos eran mayores de 55 años. Es destacable el antecedente personal de elevado consumo de antiinflamatorios no esteroideos, de forma mantenida, presente en el 54,8 % de los casos, y le siguió la cirrosis hepática. La mitad de los diagnósticos clínicos iniciales fueron errados. El 64 % de los fallecidos se encontraban hemodinámicamente inestables en el momento del ingreso. Solo se intervino quirúrgicamente el 32,2 % de estos fallecidos. Todos los pacientes que no se operaron fallecieron en un cuadro de shock hipovolémico. CONCLUSIONES. Una actitud quirúrgica a tiempo podría salvar a estos enfermos.INTRODUCTION. Upper digestive bleeding is still a health problem leading to a significant morbidity and mortality and to an elevated consumption of health resources. The present study was aimed at characterizing mortality from upper digestive bleeding in «Enrique Cabrera» Hospital (Havana City from January 2003 to July 2007. METHODS: A descriptive, retrospective and cross-sectional study was conducted to review the clinical cards of the dead patients due to upper digestive bleeding in this period. RESULTS: 49 patients died of a total of 320 admitted as a result of upper digestive bleeding (15 %. 80.6 % of the dead were over 55. It was stressed the

  7. Desarrollo de una propuesta de aula para lograr un aprendizaje significativo del sistema digestivo por medio de las analogías

    OpenAIRE

    Ramírez Rincón, Rubén Arnulfo

    2011-01-01

    En este trabajo se desarrolló una estrategia de aula basada en el uso de las analogías. El tema seleccionado es el sistema digestivo, en el cual se utilizan cuatro clases de seres vivos para hacer las comparaciones correspondientes y alcanzar un aprendizaje significativo en los estudiantes de grado séptimo del Instituto Comercial Ruperto Aguilera León del municipio de Nemocón, Cundinamarca. Las especies son: Ameba, Esponja de Mar, Humano y Bovino. Las diversas actividades planteadas se diseña...

  8. Vygotsky on Education Primer. Peter Lang Primer. Volume 30

    Science.gov (United States)

    Lake, Robert

    2012-01-01

    The "Vygotsky on Education Primer" serves as an introduction to the life and work of the Russian psychologist Lev Vygotsky. Even though he died almost eighty years ago, his life's work remains both relevant and significant to the field of education today. This book examines Vygotsky's emphasis on the role of cultural and historical context in…

  9. DNA Extraction and Primer Selection

    DEFF Research Database (Denmark)

    Karst, Søren Michael; Nielsen, Per Halkjær; Albertsen, Mads

    Talk regarding pitfalls in DNA extraction and 16S amplicon primer choice when performing community analysis of complex microbial communities. The talk was a part of Workshop 2 "Principles, Potential, and Limitations of Novel Molecular Methods in Water Engineering; from Amplicon Sequencing to -omics...

  10. A Hearing Aid Primer 1

    Science.gov (United States)

    Yetter, Carol J.

    2009-01-01

    This hearing aid primer is designed to define the differences among the three levels of hearing instrument technology: conventional analog circuit technology (most basic), digitally programmable/analog circuit technology (moderately advanced), and fully digital technology (most advanced). Both moderate and advanced technologies mean that hearing…

  11. Freshwater Wetlands: A Citizen's Primer.

    Science.gov (United States)

    Catskill Center for Conservation and Development, Inc., Hobart, NY.

    The purpose of this "primer" for the general public is to describe the general characteristics of wetlands and how wetland alteration adversely affects the well-being of humans. Particular emphasis is placed on wetlands in New York State and the northeast. Topics discussed include wetland values, destruction of wetlands, the costs of…

  12. Composição corporal na desnutrição causada por câncer e doenças benignas do aparelho digestivo

    Directory of Open Access Journals (Sweden)

    Shirley Ferreira Pereira

    Full Text Available A perda de peso é comum em uma grande variedade de doenças, particularmente entre as neoplasias. O objetivo deste estudo foi o de comparar a composição corporal de pacientes desnutridos portadores de câncer ou doenças benignas do aparelho digestivo, através da impedância bioelétrica. Foram avaliados 35 pacientes desnutridos (Indice de massa corporal < 18,5, de 22 a 70 anos, 26 (74,3% do sexo masculino e nove (25,7% do sexo feminino, sendo 17 (48,6% portadores de neoplasias e 18 (51,4% com doenças benignas. O grupo com neoplasia apresentou idade superior ao de doenças benignas (55,5±10,4 vs 39,8±9,9; p<0,05. O percentual de perda de peso e os valores de albumina sérica não foram diferentes entre os grupos. O percentual de gordura corporal, de massa magra e de água corporal também não diferiu significantemente. Conclui-se que a variação da composição corporal não é diferente em pacientes desnutridos portadores de doença neoplásica ou benigna do aparelho digestivo, quando eliminada a interferência causada por diferentes graus de perda ponderal.

  13. Freqüência de sintomas digestivos em pacientes brasileiros com Diabetes Mellitus Digestive symptoms in Brazilian patients with Diabetes Mellitus

    Directory of Open Access Journals (Sweden)

    L.E. DE A. TRONCON

    2001-06-01

    Full Text Available Sintomas sugestivos do comprometimento do tubo digestivo são comuns em pacientes diabéticos, mas estudos comparando as freqüências destes sintomas com as da população geral são escassos e não existem trabalhos dessa natureza com diabéticos brasileiros. OBJETIVO: Determinar as freqüências de diferentes sintomas digestivos em amostra não selecionada de pacientes diabéticos, em comparação às encontradas em pessoas da comunidade. MÉTODOS: A ocorrência de 13 diferentes sintomas digestivos foi investigada por meio da aplicação de um questionário padronizado, especificamente estruturado, em 153 diabéticos dos tipos 1 e 2 e em 50 pessoas aparentemente sadias, tomadas como controles. RESULTADOS: A freqüência de diabéticos com pelo menos um sintoma digestivo foi significativamente superior à verificada no grupo controle (70% vs 36%, p = 0,01. Freqüências elevadas de plenitude gástrica (30% vs 36%, pirose (30% vs 34% e de constipação (17% vs 12%, foram observadas tanto entre os diabéticos como nos controles. No entanto, somente a freqüência de um único sintoma, a disfagia, foi significativamente maior entre os diabéticos, em relação ao grupo controle (13% vs 2%, p = 0,02. CONCLUSÃO: Estes resultados indicam que a freqüência de sintomas digestivos em diabéticos, apesar de elevada, não difere da verificada na população geral, exceto para a disfagia. As freqüências dos diferentes sintomas estiveram próximas das faixas relatadas em estudos do hemisfério Norte, o que não apóia a hipótese de que fatores inerentes ao meio afetam a ocorrência de queixas digestivas em diabéticos.PURPOSE: To determine the frequencies of digestive symptoms in an unselected sample of Brazilian diabetics, in comparison to those verified in the general population. METHODS: The frequencies of 13 digestive symptoms were determined in 153 type 1 and type 2 diabetics and in 50 apparently healthy controls, utilizing a structured

  14. Flora bacteriana aeróbica del tracto digestivo del vampiro común, Desmodus rotundus (Chiroptera: Phyllostomidae

    Directory of Open Access Journals (Sweden)

    Gloriana Chaverri

    2006-09-01

    Full Text Available El objetivo de esta investigación fue determinar la flora bacteriana del vampiro común (Desmodus rotundus primordialmente debido a que los datos al respecto están desactualizados, y además por la gran importancia económica de esta especie de murciélago. Veintiún murciélagos fueron recolectados y su flora bacteriana identificada separadamente a nivel de estómago e intestino. Las bacterias fueron identificadas con el Analytical Profile Index (API, y los resultados analizados con el paquete APILAB. Un total de treinta especies fueron aisladas en 16 hembras y cinco machos. Las especies más comunes fueron Escherichia coli y Staphylococcus aureus, aunque otras especies, como Acinetobacter johnsonii, Enterobacter sakazakii, Staphylococcus chromogenes, S. hyicus y S. xylosus también se aislaron con frecuencia. El número de especies identificadas en el estómago y el intestino fue significativamente diferente, siendo el intestino más diverso. Esto ha sido encontrado anteriormente en otros mamíferos, y se atribuye probablemente a la reducción en acidez. Asimismo, la mayoría de las especies identificadas en este estudio forman parte de la flora bacteriana normal del tracto digestivo de mamíferos, aunque también se encontraron otras bacterias comunes en la piel de mamíferos y en ambientes acuáticos Las bacterias de la piel podrían estar colonizando el estómago y/o intestino del vampiro cuando éste tiene contacto con sus presas, lo que sugiere que el hábito alimentario de esta especie facilita su colonización por microorganismos que no se encontrarían comúnmente en su tracto digestivo. Ya que también se identificaron bacterias comunes en ambientes acuáticos, es probable que D. rotundus consuma agua cuando esté disponible, lo que respalda los resultados de otros investigadores, y sugiere que esta podría ser una fuente adicional de invasión microbiana.Aerobic bacterial flora from the digestive tract of the common vampire bat

  15. Bioinformatic tools for PCR Primer design

    African Journals Online (AJOL)

    ES

    choosing the most efficient way to design a new specific-primer by applying current publicly available links and Web services. Also, the purpose here is to provide general recommendations for the design and use of PCR primers. Key words: Bio-computing, primer design, web-based resources. INTRODUCTION. In the last ...

  16. Prevalência da microbiota no trato digestivo de fêmeas de Lutzomyia longipalpis (Lutz & Neiva, 1912 (Diptera: Psychodidae provenientes do campo

    Directory of Open Access Journals (Sweden)

    Oliveira Sandra Maria Pereira de

    2000-01-01

    Full Text Available No presente trabalho foram dissecados o trato digestivo de 245 fêmeas de Lutzomyia longipalpis originários da Gruta da Lapinha, Município de Lagoa Santa, MG, formando 7 grupos de 35 flebotomíneos. Das 8 espécies de bactérias isoladas houve uma predominância de bactérias Gram negativas (BGN pertencentes ao grupo de não fermentadoras de açúcar das seguintes espécies: Acinetobacter lowffii, Stenotrophomonas maltophhilia, Pseudomonas putida e Flavimonas orizihabitans. No grupo das fermentadoras tivemos: Enterobacter cloacae e Klebsiella ozaenae. No grupo dos Gram positivos foram identificados Bacillus thuringiensis e Staphylococcus spp.

  17. DESCRIPCIÓN MORFOLÓGICA DEL TUBO DIGESTIVO DE JUVENILES DE RUBIO Salminus affinis (PISCES: CHARACIDAE Alimentary tract of juvenile Rubio Salminus affinis (Pisces: Characidae morphological description

    Directory of Open Access Journals (Sweden)

    VJ ATENCIO GARCÍA

    Full Text Available El objetivo del estudio fue la descripción del tubo digestivo de juveniles de Rubio Salminus affinis. Se analizaron cinco juveniles con 23,6±2,6 cm de longitud total y 142,8±62,5 g de peso. Se realizó descripción topográfica y morfológica de los órganos y cortes histológicos con tinción H-E. El esófago es un órgano tubular corto de pared gruesa que representa el 7,8% de la longitud total del tubo digestivo, presenta pliegues internos que ofrecen gran capacidad de distensión permitiendo el paso de presas de gran tamaño. El estómago es una bolsa asimétrica en forma de "Y", grande y musculosa, amplio en la porción anterior y estrecho hacia el fondo; el número de ciegos pilóricos varió entre 13 y 23 pudiendo ser monotubulares y ramificados. El intestino, con tres asas, se extiende desde el esfínter pilórico hasta el ano. Histológicamente el tubo digestivo está formado por cuatro capas: mucosa, submucosa, muscular y serosa; el epitelio de revestimiento del esófago es estratificado plano no queratinizado con células caliciformes, cambiando a simple cilíndrico mucosecretor llegando al estómago; en el estómago se encuentra epitelio simple cilíndrico mucosecretor y los ciegos pilóricos e intestino son revestidos por epitelio simple cilíndrico con células caliciformes. Tanto el valor promedio del coeficiente intestinal (0,58, como la pared distensible del estómago sugieren que el Rubio tiene un tubo digestivo propio de carnívoro y sus características histológicas presentan similitud con la mayoría de vertebrados superiores.The aim of work was giving biological information about Salminus affinis,a morphological description of the alimentary tract was carried out. Five juvenile Rubio were analyzed (23.6±2.6 cm of total length and 142.8±62.5 g of weight. Topographical and morphological description organs and histology with H-E stain were carried out. The esophagus is a short tubular thick-walled organ that represents 7

  18. A primer of special relativity

    CERN Document Server

    Sardesai, PL

    2004-01-01

    A Primer of Special Relativity1 is an unusually lucid introduction to the subject specifically written for Indian students. It is intended to give the beginner a firm grounding for a more advanced course in relativity. An entire chapter is devoted to applications of the theory to elucidate a large number of topics the students (B.Sc. Physics) come across in Modern Physics. Detailed and well-selected examples are used to illuminate aspects of the theory as well as to show techniques of application. A large number of Illustrative Examples enables the students to gain confidence to solve any problem in relativity normally expected of B.Sc. students.

  19. A primer of multivariate statistics

    CERN Document Server

    Harris, Richard J

    2014-01-01

    Drawing upon more than 30 years of experience in working with statistics, Dr. Richard J. Harris has updated A Primer of Multivariate Statistics to provide a model of balance between how-to and why. This classic text covers multivariate techniques with a taste of latent variable approaches. Throughout the book there is a focus on the importance of describing and testing one's interpretations of the emergent variables that are produced by multivariate analysis. This edition retains its conversational writing style while focusing on classical techniques. The book gives the reader a feel for why

  20. Sample Return Primer and Handbook

    Science.gov (United States)

    Barrow, Kirk; Cheuvront, Allan; Faris, Grant; Hirst, Edward; Mainland, Nora; McGee, Michael; Szalai, Christine; Vellinga, Joseph; Wahl, Thomas; Williams, Kenneth; hide

    2007-01-01

    This three-part Sample Return Primer and Handbook provides a road map for conducting the terminal phase of a sample return mission. The main chapters describe element-by-element analyses and trade studies, as well as required operations plans, procedures, contingencies, interfaces, and corresponding documentation. Based on the experiences of the lead Stardust engineers, the topics include systems engineering (in particular range safety compliance), mission design and navigation, spacecraft hardware and entry, descent, and landing certification, flight and recovery operations, mission assurance and system safety, test and training, and the very important interactions with external support organizations (non-NASA tracking assets, landing site support, and science curation).

  1. A primer of Lebesgue integration

    CERN Document Server

    Bear, H S

    2001-01-01

    The Lebesgue integral is now standard for both applications and advanced mathematics. This books starts with a review of the familiar calculus integral and then constructs the Lebesgue integral from the ground up using the same ideas. A Primer of Lebesgue Integration has been used successfully both in the classroom and for individual study.Bear presents a clear and simple introduction for those intent on further study in higher mathematics. Additionally, this book serves as a refresher providing new insight for those in the field. The author writes with an engaging, commonsense style that appeals to readers at all levels.

  2. UniPrimer: A Web-Based Primer Design Tool for Comparative Analyses of Primate Genomes

    Directory of Open Access Journals (Sweden)

    Nomin Batnyam

    2012-01-01

    Full Text Available Whole genome sequences of various primates have been released due to advanced DNA-sequencing technology. A combination of computational data mining and the polymerase chain reaction (PCR assay to validate the data is an excellent method for conducting comparative genomics. Thus, designing primers for PCR is an essential procedure for a comparative analysis of primate genomes. Here, we developed and introduced UniPrimer for use in those studies. UniPrimer is a web-based tool that designs PCR- and DNA-sequencing primers. It compares the sequences from six different primates (human, chimpanzee, gorilla, orangutan, gibbon, and rhesus macaque and designs primers on the conserved region across species. UniPrimer is linked to RepeatMasker, Primer3Plus, and OligoCalc softwares to produce primers with high accuracy and UCSC In-Silico PCR to confirm whether the designed primers work. To test the performance of UniPrimer, we designed primers on sample sequences using UniPrimer and manually designed primers for the same sequences. The comparison of the two processes showed that UniPrimer was more effective than manual work in terms of saving time and reducing errors.

  3. A primer on quantum fluids

    CERN Document Server

    Barenghi, Carlo

    2016-01-01

    The aim of this primer is to cover the essential theoretical information, quickly and concisely, in order to enable senior undergraduate and beginning graduate students to tackle projects in topical research areas of quantum fluids, for example, solitons, vortices and collective modes. The selection of the material, both regarding the content and level of presentation, draws on the authors analysis of the success of relevant research projects with newcomers to the field, as well as of the students feedback from many taught and self-study courses on the subject matter. Starting with a brief historical overview, this text covers particle statistics, weakly interacting condensates and their dynamics and finally superfluid helium and quantum turbulence. At the end of each chapter (apart from the first) there will be some exercises. Detailed solutions can be made available to instructors upon request to the authors. .

  4. URPD: a specific product primer design tool.

    Science.gov (United States)

    Chuang, Li-Yeh; Cheng, Yu-Huei; Yang, Cheng-Hong

    2012-06-19

    Polymerase chain reaction (PCR) plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users. URPD (yoUR Primer Design), a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq), UCSC In-Silico PCR, memetic algorithm (MA) and genetic algorithm (GA) primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers. URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/.

  5. URPD: a specific product primer design tool

    Directory of Open Access Journals (Sweden)

    Chuang Li-Yeh

    2012-06-01

    Full Text Available Abstract Background Polymerase chain reaction (PCR plays an important role in molecular biology. Primer design fundamentally determines its results. Here, we present a currently available software that is not located in analyzing large sequence but used for a rather straight-forward way of visualizing the primer design process for infrequent users. Findings URPD (yoUR Primer Design, a web-based specific product primer design tool, combines the NCBI Reference Sequences (RefSeq, UCSC In-Silico PCR, memetic algorithm (MA and genetic algorithm (GA primer design methods to obtain specific primer sets. A friendly user interface is accomplished by built-in parameter settings. The incorporated smooth pipeline operations effectively guide both occasional and advanced users. URPD contains an automated process, which produces feasible primer pairs that satisfy the specific needs of the experimental design with practical PCR amplifications. Visual virtual gel electrophoresis and in silico PCR provide a simulated PCR environment. The comparison of Practical gel electrophoresis comparison to virtual gel electrophoresis facilitates and verifies the PCR experiment. Wet-laboratory validation proved that the system provides feasible primers. Conclusions URPD is a user-friendly tool that provides specific primer design results. The pipeline design path makes it easy to operate for beginners. URPD also provides a high throughput primer design function. Moreover, the advanced parameter settings assist sophisticated researchers in performing experiential PCR. Several novel functions, such as a nucleotide accession number template sequence input, local and global specificity estimation, primer pair redesign, user-interactive sequence scale selection, and virtual and practical PCR gel electrophoresis discrepancies have been developed and integrated into URPD. The URPD program is implemented in JAVA and freely available at http://bio.kuas.edu.tw/urpd/.

  6. Prevenção do tromboembolismo na cirurgia do câncer do aparelho digestivo Thromboembolism prevention in surgery of digestive cancer

    Directory of Open Access Journals (Sweden)

    Osvaldo Malafaia

    2012-12-01

    Full Text Available RACIONAL: Tromboembolismo venoso é complicação frequente após tratamento cirúrgico em geral e, de um modo especial, na condução terapêutica do câncer. A cirurgia do aparelho digestivo tem sido referida como potencialmente indutora desta complicação. Os pacientes com câncer digestivo, têm risco substancialmente aumentado de iniciarem ou de terem recorrência de processo tromboembólico. OBJETIVO: Oferecer aos cirurgiões que atuam na cirurgia digestiva e geral orientação segura sobre como efetuar a tromboprofilaxia dos pacientes que necessitam de operações no tratamento de doenças malignas digestivas. MÉTODOS: A Diretriz foi baseada a partir da elaboração de 15 questões clínicas relevantes e relacionadas ao risco, tratamento e prognóstico do paciente submetido ao tratamento cirúrgico do câncer do aparelho digestivo. Elas focaram tanto os eventos tromboembólicos associados às operações quanto os aspectos relacionados à sua profilaxia. As questões foram estruturadas por meio do P.I.C.O. (Paciente, Intervenção ou Indicador, Comparação e Outcome, permitindo gerar estratégias de busca da evidência nas principais bases primárias de informação científica (Medline/Pubmed, Embase, Lilacs/Scielo, Cochrane Library, Premedline via OVID. Também foi realizada busca manual da evidência e de teses (BDTD e IBICT. A evidência recuperada foi selecionada a partir da avaliação crítica utilizando instrumentos (escores discriminatórios de acordo com a categoria da questão: risco, terapêutica e prognóstico (JADAD para Ensaios Clínicos Randomizados e New Castle Otawa Scale para estudos não randômicos. Após definir os estudos potenciais para sustento das recomendações, eles foram selecionados pela força da evidência e grau de recomendação segundo a classificação de Oxford, incluindo a evidência disponível de maior força. RESULTADOS: Foram avaliados 53.555 trabalhos pelo título e/ou resumo. Deste total

  7. Are "universal" DNA primers really universal?

    Science.gov (United States)

    Sharma, Pranay; Kobayashi, Tsuyoshi

    2014-11-01

    "Universal" DNA primers LCO 1490 and HCO 2198 were originally designed from three coding and six anticoding strands by comparing highly conserved regions of mitochondrial cytochrome c oxidase subunit I (COI) genes across 15 taxa. These primers have been successful in amplifying a 710-bp fragment of highly conserved regions of the COI gene for more than 80 invertebrate species from 11 phyla. In the present study, 130,843 variations were reviewed in the primer region of mitochondrial molecular markers by comparing 725 COI sequences from the kingdom Animalia. It was found that, for 177 invertebrate species, the forward primer (LCO 1490) showed only four conserved regions, compared to 12 in the original study. For ascidians, fungi and vertebrates, it showed approximately 50 % conserved regions, dropping to one conserved region for echinoderms. However, the reverse primer (HCO 2198) was highly conserved across 725 COI primer sequences. A similar pattern was observed in amino acid distributions. There was a significant difference in the means of base pair differences from the level of family, genus and species for LCO 1490 [analysis of variance (ANOVA), F 6,188 = 8.193, P primers from reference sequences belonging to the level of order (maximum 5 bp differences), family (maximum 6 bp differences) or genus (maximum 1 bp difference). Reverse primers can be designed from the level of family (maximum 5 bp differences) or genus (maximum 2 bp differences).

  8. Electrostatic Discharge testing of propellants and primers

    Energy Technology Data Exchange (ETDEWEB)

    Berry, R.B.

    1994-02-01

    This report presents the results of testing of selected propellants and primers to Electrostatic Discharge (ESD) characteristic of the human body. It describes the tests and the fixturing built to accommodate loose material (propellants) and the packed energetic material of the primer. The results indicate that all powders passed and some primers, especially the electric primers, failed to pass established requirements which delineate insensitive energetic components. This report details the testing of components and materials to four ESD environments (Standard ESD, Severe ESD, Modified Standard ESD, and Modified Severe ESD). The purpose of this study was to collect data based on the customer requirements as defined in the Sandia Environmental Safety & Health (ES&H) Manual, Chapter 9, and to define static sensitive and insensitive propellants and primers.

  9. [DNA amplification using PCR with abutting primers].

    Science.gov (United States)

    Garafutdinov, R R; Galimova, A A; Sakhabutdinova, A R; Vakhitov, V A; Chemeris, A V

    2015-01-01

    DNA analysis of ñîmplex biological objects (wastewater, soil, archaeological and forensic samples, etc.) is currently of great interest. DNA of these objects is characterized by low suitability for research due to the violation of its integrity and chemical structure; thus, the detection of specific nucleic acid fragments can be achieved by PCR with contiguous primers. In this paper, we present the results that clarify the specific characteristics of PCR with abutting primers. The 3'-ends of these primers are annealed at adjacent nucleotides of complementary chains of DNA target. It has been shown that the proximity of primers enables the formation of specific reaction products with a higher sensitivity and less reaction time. Using artificially damaged DNA and DNA from the soil we demonstrated that the abutting primers provide assured detection of specific DNA fragments. The results of this work may be taken into account in PCR with degraded (fragmented) DNA.

  10. SBE primer : multiplexing minisequencing-based genotyping

    Energy Technology Data Exchange (ETDEWEB)

    Kaderali, L. (Lars); Deshpande, A. (Alina); Uribe-Romeo, F. J. (Francisco J.); Schliep, A.; Torney, D. C. (David C.)

    2002-01-01

    Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and diagnosing disease-related alleles. Most of the known genetic diseases are caused by point mutations, and a growing number of SNPs will be routinely analyzed to diagnose genetic disorders. Mutation analysis by polymerase mediated single-base primer extension (minisequencing) can be massively parallelized using for example DNA microchips or flow cytometry with microspheres as solid support. By adding a unique oligonucleotide tag to the 5-inch end of the minisequencing primer and attaching the complementary anti-tag to the array or bead surface, the assay can be 'demultiplexed'. However, such high-throughput scoring of SNPs requires a high level of primer multiplexing in order to analyze multiple loci in one assay, thus enabling inexpensive and fast polymorphism scoring. Primers can be chosen from either the plus or the minus strand, and primers used in the same experiment must not bind to one another. To genotype a given number of polymorphic sites, the question is which primer to use for each SNP, and which primers to group into the same experiment. Furthermore, a crosshybridization-free tag/anti-tag code is required in order to sort the extended primers to the corresponding microspheres or chip spots. These problems pose challenging algorithmic questions. We present a computer program lo automate the design process for the assay. Oligonucleotide primers for the reaction are automatically selected by the software, a unique DNA tag/anti-tag system is generated, and the pairing of primers and DNA-Tags is automatically done in a way to avoid any crossreactivity. We report first results on a 45-plex genotyping assay, indicating that minisequencing can be adapted to be a powerful tool for high-throughput, massively parallel genotyping.

  11. Primer3_masker: integrating masking of template sequence with primer design software.

    Science.gov (United States)

    Kõressaar, Triinu; Lepamets, Maarja; Kaplinski, Lauris; Raime, Kairi; Andreson, Reidar; Remm, Maido

    2018-01-19

    Designing PCR primers for amplifying regions of eukaryotic genomes is a complicated task because the genomes contain a large number of repeat sequences and other regions unsuitable for amplification by PCR. We have developed a novel k-mer based masking method that uses a statistical model to detect and mask failure-prone regions on the DNA template prior to primer design. We implemented the software as a standalone software primer3_masker and integrated it into the primer design program Primer3. The standalone version of primer3_masker is implemented in C. The source code is freely available at https://github.com/bioinfo-ut/primer3_masker/ (standalone version for Linux and macOS) and at https://github.com/primer3-org/primer3/(integrated version). Primer3 web application that allows masking sequences of 196 animal and plant genomes is available at http://primer3.ut.ee/. maido.remm@ut.ee. Supplementary data are available at Bioinformatics online.

  12. PHUSER (Primer Help for USER): a novel tool for USER fusion primer design

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Hansen, Niels Bjørn; Bonde, Mads

    2011-01-01

    Uracil-Specific Exision Reagent (USER) fusion is a recently developed technique that allows for assembly of multiple DNA fragments in a few simple steps. However, designing primers for USER fusion is both tedious and time consuming. Here, we present the Primer Help for USER (PHUSER) software......, a novel tool for designing primers specifically for USER fusion and USER cloning applications. We also present proof-of-concept experimental validation of its functionality. PHUSER offers quick and easy design of PCR optimized primers ensuring directionally correct fusion of fragments into a plasmid...... containing a customizable USER cassette. Designing primers using PHUSER ensures that the primers have similar annealing temperature (Tm), which is essential for efficient PCR. PHUSER also avoids identical overhangs, thereby ensuring correct order of assembly of DNA fragments. All possible primers...

  13. Primer on spontaneous heating and pyrophoricity

    Energy Technology Data Exchange (ETDEWEB)

    1994-12-01

    This primer was prepared as an information resource for personnel responsible for operation of DOE nuclear facilities. It has sections on combustion principles, spontaneous heating/ignition of hydrocarbons and organics, pyrophoric gases and liquids, pyrophoric nonmetallic solids, pyrophoric metals (including Pu and U), and accident case studies. Although the information in this primer is not all-encompassing, it should provide the reader with a fundamental knowledge level sufficient to recognize most spontaneous combustion hazards and how to prevent ignition and widespread fires. This primer is provided as an information resource only, and is not intended to replace any fire protection or hazardous material training.

  14. Primers-4-Yeast: a comprehensive web tool for planning primers for Saccharomyces cerevisiae.

    Science.gov (United States)

    Yofe, Ido; Schuldiner, Maya

    2014-02-01

    The budding yeast Saccharomyces cerevisiae is a key model organism of functional genomics, due to its ease and speed of genetic manipulations. In fact, in this yeast, the requirement for homologous sequences for recombination purposes is so small that 40 base pairs (bp) are sufficient. Hence, an enormous variety of genetic manipulations can be performed by simply planning primers with the correct homology, using a defined set of transformation plasmids. Although designing primers for yeast transformations and for the verification of their correct insertion is a common task in all yeast laboratories, primer planning is usually done manually and a tool that would enable easy, automated primer planning for the yeast research community is still lacking. Here we introduce Primers-4-Yeast, a web tool that allows primers to be designed in batches for S. cerevisiae gene-targeting transformations, and for the validation of correct insertions. This novel tool enables fast, automated, accurate primer planning for large sets of genes, introduces consistency in primer planning and is therefore suggested to serve as a standard in yeast research. Primers-4-Yeast is available at: http://www.weizmann.ac.il/Primers-4-Yeast Copyright © 2013 John Wiley & Sons, Ltd.

  15. MFEprimer: multiple factor evaluation of the specificity of PCR primers.

    Science.gov (United States)

    Qu, Wubin; Shen, Zhiyong; Zhao, Dongsheng; Yang, Yi; Zhang, Chenggang

    2009-01-15

    We developed a program named MFEprimer for evaluating the specificity of PCR primers based on multiple factors, including sequence similarity, stability at the 3'-end of the primer, melting temperature, GC content and number of binding sites between the primer and DNA templates. MFEprimer can help the user to select more suitable primers before running either standard or multiplex PCR reactions. The cDNA and genomic DNA databases of 10 widely used species, as well as user custom databases, were used as DNA templates for analyzing primers specificity. Furthermore, we maintained a Primer3Plus server with a modified Primer3Manager for one-stop primer design and specificity checking.

  16. Estudio inmunohistoquímico de dos co-transportadores de la familia SLC5 en el sistema digestivo de ratón

    Directory of Open Access Journals (Sweden)

    Matilde Spinel Clara

    2006-12-01

    Full Text Available Los transportadores (Simporter de Sodio/Yoduro, NIS y Transportador Apical de Yoduro, AIT pertenecen a
    la familia de proteínas de membrana, SLC5 las cuales pueden encontrase también en tejidos extratiroideos.
    Para el estudio de la localización celular de los co-transportadores se usaron anticuerpos policlonales que
    detectarían la proteína por el proceso de inmunohistoquímica. El transportador AIT fue inespecífico mientras NIS fue estandarizado en tejido de tiroides. En el sistema digestivo, NIS fue detectado en glándulas salivales, mucosa gástrica, dependiendo de la sección del tracto, y en páncreas, mostrando en este último, un comportamiento atípico de este co-transportador. Este trabajo retoma la teoría de la recirculación, el papel antimicrobiano y el rol antioxidante dado por el yoduro a lo largo del sistema. Además, de mostrar los beneficios
    de usar este tipo de proteínas como una herramienta para el conocimiento del metabolismo, las enfermedades
    autoinmunes y el cáncer.

  17. A practical primer on geostatistics

    Science.gov (United States)

    Olea, Ricardo A.

    2009-01-01

    has significant methodological implications.Historical Remarks—As a discipline, geostatistics was firmly established in the 1960s by the French engineer Georges Matheron, who was interested in the appraisal of ore reserves in mining. Geostatistics did not develop overnight. Like other disciplines, it has built on previous results, many of which were formulated with different objectives in various fields.Pioneers—Seminal ideas conceptually related to what today we call geostatistics or spatial statistics are found in the work of several pioneers, including: 1940s: A.N. Kolmogorov in turbulent flow and N. Wiener in stochastic processing; 1950s: D. Krige in mining; 1960s: B. Mathern in forestry and L.S. Gandin in meteorologyCalculations—Serious applications of geostatistics require the use of digital computers. Although for most geostatistical techniques rudimentary implementation from scratch is fairly straightforward, coding programs from scratch is recommended only as part of a practice that may help users to gain a better grasp of the formulations.Software—For professional work, the reader should employ software packages that have been thoroughly tested to handle any sampling scheme, that run as efficiently as possible, and that offer graphic capabilities for the analysis and display of results. This primer employs primarily the package Stanford Geomodeling Software (SGeMS) - recently developed at the Energy Resources Engineering Department at Stanford University - as a way to show how to obtain results practically. This applied side of the primer should not be interpreted as the notes being a manual for the use of SGeMS. The main objective of the primer is to help the reader gain an understanding of the fundamental concepts and tools in geostatistics.Organization of the Primer—The chapters of greatest importance are those covering kriging and simulation. All other materials are peripheral and are included for better comprehension of these main

  18. Multiplexing Short Primers for Viral Family PCR

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, S N; Hiddessen, A L; Hara, C A; Williams, P L; Wagner, M; Colston, B W

    2008-06-26

    We describe a Multiplex Primer Prediction (MPP) algorithm to build multiplex compatible primer sets for large, diverse, and unalignable sets of target sequences. The MPP algorithm is scalable to larger target sets than other available software, and it does not require a multiple sequence alignment. We applied it to questions in viral detection, and demonstrated that there are no universally conserved priming sequences among viruses and that it could require an unfeasibly large number of primers ({approx}3700 18-mers or {approx}2000 10-mers) to generate amplicons from all sequenced viruses. We then designed primer sets separately for each viral family, and for several diverse species such as foot-and-mouth disease virus, hemagglutinin and neuraminidase segments of influenza A virus, Norwalk virus, and HIV-1.

  19. Hexavalent Chromium IV-Free Primer Development

    Science.gov (United States)

    Alldredge, Michael J.; Buck, Amy L.

    2015-01-01

    Primer materials provide corrosion protection for metal parts as well as an increased adhesion between metallic substrates and thermal protection systems (TPSs). Current primers for use in cryogenic applications contain hexavalent chromium. This hexavalent chromium provides excellent corrosion protection even in a cryogenic environment, but it is a carcinogen that requires special equipment and waste control procedures to use. The hazardous nature of hexavalent chromium makes it an obsolescence risk in the future. This study included two phases of evaluation. Thirteen primers were initially identified as candidates and twelve of those primers were tested in phase 1. Four of the best performing candidates from phase 1 continued into phase 2 testing. Phase 1 testing consisted mostly of liquid constituent and physical property testing. Cryoflex and salt fog testing were included in phase 1 because of their importance to the overall success of a candidate material. Phase 2 consisted of physical, thermal, and mechanical properties for nominally processed and fabricated specimens.

  20. Primer on transportation and climate change

    Science.gov (United States)

    2008-04-01

    This primer is an introduction to the issue of climate change and its implications for transportation policy in the United States. Its purpose is to outline the current thinking of governmental agencies, researchers, and advocacy groups on the issue ...

  1. ANL supplement to the UNICOS primer

    Energy Technology Data Exchange (ETDEWEB)

    Wiley, M.S. (ed.); Karlovsky, S.R.

    1991-06-01

    The ANL Supplement to the UNICOS Primer (ANL/TM 460) introduces the Cray X-MP interactive and batch services available at Argonne National Laboratory. It serves as a companion to the UNICOS Primer (Cray publication SG-2010 6.0). Whereas the UNICOS Primer discusses standard Unix issues of Cray computing, this manual discusses those issues specific to Cray computing at ANL. If this is your first experience on a Unix-based system, we assume that you have read at least Chapters 1 through 3 of the UNICOS Primer. The Glossary at the back of the UNICOS Primer will also be useful to you. If you are already familiar with a Unix system, it should suffice to keep the UNICOS Primer handy as you use this document. To learn about Unix programming in greater detail, we recommend A Practical Guide to the Unix System, by Mark G. Sobell. This manual and all other sources referred to in this document are available for purchase at the Document Distribution Counter in Building 221, Room A-134. We assume that you have already read the Guide to Computing at ANL (ANL/TM 336) to get an overview of all the computing facilities and services available at Argonne National Laboratory. You should also refer to Recommended Documentation for Computer Users at ANL (ANL/TM 379) for additional guidance in selecting available documentation that will best fill your particular computing needs.

  2. PHUSER (Primer Help for USER): a novel tool for USER fusion primer design.

    Science.gov (United States)

    Olsen, Lars Rønn; Hansen, Niels Bjørn; Bonde, Mads Tvillinggaard; Genee, Hans Jasper; Holm, Dorte Koefoed; Carlsen, Simon; Hansen, Bjarne Gram; Patil, Kiran Raosaheb; Mortensen, Uffe Hasbro; Wernersson, Rasmus

    2011-07-01

    Uracil-Specific Exision Reagent (USER) fusion is a recently developed technique that allows for assembly of multiple DNA fragments in a few simple steps. However, designing primers for USER fusion is both tedious and time consuming. Here, we present the Primer Help for USER (PHUSER) software, a novel tool for designing primers specifically for USER fusion and USER cloning applications. We also present proof-of-concept experimental validation of its functionality. PHUSER offers quick and easy design of PCR optimized primers ensuring directionally correct fusion of fragments into a plasmid containing a customizable USER cassette. Designing primers using PHUSER ensures that the primers have similar annealing temperature (T(m)), which is essential for efficient PCR. PHUSER also avoids identical overhangs, thereby ensuring correct order of assembly of DNA fragments. All possible primers are individually analysed in terms of GC content, presence of GC clamp at 3'-end, the risk of primer dimer formation, the risk of intra-primer complementarity (secondary structures) and the presence of polyN stretches. Furthermore, PHUSER offers the option to insert linkers between DNA fragments, as well as highly flexible cassette options. PHUSER is publicly available at http://www.cbs.dtu.dk/services/phuser/.

  3. VizPrimer: a web server for visualized PCR primer design based on known gene structure.

    Science.gov (United States)

    Zhou, Yang; Qu, Wubin; Lu, Yiming; Zhang, Yanchun; Wang, Xiaolei; Zhao, Dongsheng; Yang, Yi; Zhang, Chenggang

    2011-12-15

    The visualization of gene structure plays an important role in polymerase chain reaction (PCR) primer design, especially for eukaryotic genes with a number of splice variants that users need to distinguish between via PCR. Here, we describe a visualized web server for primer design named VizPrimer. It utilizes the new information technology (IT) tools, HTML5 to display gene structure and JavaScript to interact with the users. In VizPrimer, the users can focus their attention on the gene structure and primer design strategy, without wasting time calculating the exon positions of splice variants or manually configuring complicated parameters. In addition, VizPrimer is also suitable for the design of PCR primers for amplifying open reading frames and detecting single nucleotide polymorphisms (SNPs). VizPrimer is freely available at http://biocompute.bmi.ac.cn/CZlab/VizPrimer/. The web server supported browsers: Chrome (≥5.0), Firefox (≥3.0), Safari (≥4.0) and Opera (≥10.0). zhangcg@bmi.ac.cn; yangyi528@vip.sina.com.

  4. RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation

    Directory of Open Access Journals (Sweden)

    Suwannasri Payiarat

    2009-12-01

    Full Text Available Abstract Background Polymerase chain reaction (PCR is very useful in many areas of molecular biology research. It is commonly observed that PCR success is critically dependent on design of an effective primer pair. Current tools for primer design do not adequately address the problem of PCR failure due to mis-priming on target-related sequences and structural variations in the genome. Methods We have developed an integrated graphical web-based application for primer design, called RExPrimer, which was written in Python language. The software uses Primer3 as the primer designing core algorithm. Locally stored sequence information and genomic variant information were hosted on MySQLv5.0 and were incorporated into RExPrimer. Results RExPrimer provides many functionalities for improved PCR primer design. Several databases, namely annotated human SNP databases, insertion/deletion (indel polymorphisms database, pseudogene database, and structural genomic variation databases were integrated into RExPrimer, enabling an effective without-leaving-the-website validation of the resulting primers. By incorporating these databases, the primers reported by RExPrimer avoid mis-priming to related sequences (e.g. pseudogene, segmental duplication as well as possible PCR failure because of structural polymorphisms (SNP, indel, and copy number variation (CNV. To prevent mismatching caused by unexpected SNPs in the designed primers, in particular the 3' end (SNP-in-Primer, several SNP databases covering the broad range of population-specific SNP information are utilized to report SNPs present in the primer sequences. Population-specific SNP information also helps customize primer design for a specific population. Furthermore, RExPrimer offers a graphical user-friendly interface through the use of scalable vector graphic image that intuitively presents resulting primers along with the corresponding gene structure. In this study, we demonstrated the program

  5. RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.

    Science.gov (United States)

    Piriyapongsa, Jittima; Ngamphiw, Chumpol; Assawamakin, Anunchai; Wangkumhang, Pongsakorn; Suwannasri, Payiarat; Ruangrit, Uttapong; Agavatpanitch, Gallissara; Tongsima, Sissades

    2009-12-03

    Polymerase chain reaction (PCR) is very useful in many areas of molecular biology research. It is commonly observed that PCR success is critically dependent on design of an effective primer pair. Current tools for primer design do not adequately address the problem of PCR failure due to mis-priming on target-related sequences and structural variations in the genome. We have developed an integrated graphical web-based application for primer design, called RExPrimer, which was written in Python language. The software uses Primer3 as the primer designing core algorithm. Locally stored sequence information and genomic variant information were hosted on MySQLv5.0 and were incorporated into RExPrimer. RExPrimer provides many functionalities for improved PCR primer design. Several databases, namely annotated human SNP databases, insertion/deletion (indel) polymorphisms database, pseudogene database, and structural genomic variation databases were integrated into RExPrimer, enabling an effective without-leaving-the-website validation of the resulting primers. By incorporating these databases, the primers reported by RExPrimer avoid mis-priming to related sequences (e.g. pseudogene, segmental duplication) as well as possible PCR failure because of structural polymorphisms (SNP, indel, and copy number variation (CNV)). To prevent mismatching caused by unexpected SNPs in the designed primers, in particular the 3' end (SNP-in-Primer), several SNP databases covering the broad range of population-specific SNP information are utilized to report SNPs present in the primer sequences. Population-specific SNP information also helps customize primer design for a specific population. Furthermore, RExPrimer offers a graphical user-friendly interface through the use of scalable vector graphic image that intuitively presents resulting primers along with the corresponding gene structure. In this study, we demonstrated the program effectiveness in successfully generating primers for strong

  6. Beam shaping for laser initiated optical primers

    Science.gov (United States)

    Lizotte, Todd E.

    2008-08-01

    Remington was one of the first firearm manufacturing companies to file a patent for laser initiated firearms, in 1969. Nearly 40 years later, the development of laser initiated firearms has not become a mainstream technology in the civilian market. Requiring a battery is definitely a short coming, so it is easy to see how such a concept would be problematic. Having a firearm operate reliably and the delivery of laser energy in an efficient manner to ignite the shock-sensitive explosive primer mixtures is a tall task indeed. There has been considerable research on optical element based methods of transferring or compressing laser energy to ignite primer charges, including windows, laser chip primers and various lens shaped windows to focus the laser energy. The focusing of laser light needs to achieve igniting temperatures upwards of >400°C. Many of the patent filings covering this type of technology discuss simple approaches where a single point of light might be sufficient to perform this task. Alternatively a multi-point method might provide better performance, especially for mission critical applications, such as precision military firearms. This paper covers initial design and performance test of the laser beam shaping optics to create simultaneous multiple point ignition locations and a circumferential intense ring for igniting primer charge compounds. A simple initial test of the ring beam shaping technique was evaluated on a standard large caliber primer to determine its effectiveness on igniting the primer material. Several tests were conducted to gauge the feasibility of laser beam shaping, including optic fabrication and mounting on a cartridge, optic durability and functional ignition performance. Initial data will be presented, including testing of optically elements and empirical primer ignition / burn analysis.

  7. Modelagem aplicada aos processos digestivos e metabólicos do suíno Applied modeling to the digestive and metabolic processes of the pig

    Directory of Open Access Journals (Sweden)

    Paulo Alberto Lovatto

    2001-08-01

    Full Text Available Esse estudo bibliográfico descreve os princípios mais importantes da modelagem aplicada aos processos digestivos e metabólicos do suíno. Essa forma de modelagem se apóia, sobretudo, em dois princípios matemáticos: a linearidade e a não-linearidade, sendo representada essencialmente pelas leis de ação de massa e de Michaelis-Menten, respectivamente. Os modelos foram classificados em explicativos, temporais e paramétricos. Os explicativos descrevem a forma de integração do conhecimento, podendo ser empíricos ou mecânicos. Os temporais definem a forma de integração do conhecimento em função do tempo, podendo ser estáticos ou dinâmicos. Os paramétricos associam os parâmetros temporais e explicativos, podendo ser deterministas ou estocásticos. Os modelos de crescimento foram integrados em níveis mais subjacentes que os de digestão. Os princípios metabólicos que envolvem o anabolismo e o catabolismo tissulares, bem como as vias de utilização dos nutrientes foram melhor estudados nos tecidos proteicos. A presente revisão mostra que os modelos de digestão e de metabolismo já desenvolvidos são dinâmicos, deterministas e empíricos. Na maioria dos casos, esses modelos representam parcialmente os fenômenos digestivos e metabólicos do suíno. Os novos modelos devem integrar as formas paramétricas estocásticas, o que os aproxima mais d realidade da cinética celular nos seres vivos, considerando os nutrientes desde a ingestão até sua utilização em nível molecular.This paper reviews the main principles and characterizes the evolution of modeling applied to the swine digestive and metabolic processes. Such modeling is largely based on two mathematical principles: linearity and non-linearity, which were represented essentially by action mass and Michaelis-Menten laws. The digestive and metabolic models were classified in explanatory, temporal and parametric. Explanatory ones describe the knowledge integration, and

  8. Descripción histológica comparativa del desarrollo del sistema digestivo y visual de larvas de chame Dormitator latifrons (Pisces: Eleotridae

    Directory of Open Access Journals (Sweden)

    Vanesa V López-López

    2015-07-01

    Full Text Available Se realizó la descripción del desarrollo de larvas de uno a seis días post-eclosión (dpe, para generar información que ayude a comprender la capacidad alimenticia en etapas tempranas. Las larvas se obtuvieron mediante la inducción hormonal de reproductores, utilizando implantes de análogos sintéticos de GnRH durante la temporada de septiembre-noviembre de 2010. Las muestras fueron incluídas en historesina y teñidas con hematoxilina-eosina. Una vez eclosionada, la larva presenta gran cantidad de vitelo que absorbe gradualmente (1° a 3° dpe. Al 4° dpe, existe una cavidad bucal abierta con estructuras dentales, en este estadio se ha completado el desarrollo ocular, que presenta pigmentación. Se observa la formación de las hendiduras branquiales y se diferencia el intestino en anterior y posterior y se distingue la presencia de vacuolas digestivas en el intestino anterior. En el 5° dpe, se observaron los paquetes de fibras musculares y se distinguió una estructura estomacal. En el 6° dpe, el páncreas, pliegues intestinales y membrana de borde de cepillo son visibles y se observaron partículas de alimento y bacterias dentro del intestino. En base a lo anterior, se concluye que las larvas de D. latifrons han desarrollado completamente el tracto digestivo y órganos asociados que le ayudarán a la búsqueda de alimento, entonces a partir del 4° dpe son capaces de iniciar la alimentación exógena.

  9. Fungal flora of the digestive tract of Triatoma infestans (Hemiptera: Reduviidae from Argentina Flora fúngica de tractos digestivos en Triatoma infestans (Hemiptera: Reduviidae en Argentina

    Directory of Open Access Journals (Sweden)

    G. A. Marti

    Full Text Available A survey of the fungal microbiota of the digestive tract of Triatoma infestans (Klug (Hemiptera: Reduviidae adults was carried out. Insects captured in the field from different provinces in Argentina, as well as individuals reared in artificial colonies, were used for dissection. Axenic cultures of the fungal species were identified and were deposited with mycological collections at La Plata , Argentina. A total of 33 fungal species, with the exception of three that were mycelia sterilia, belonging to 11 genera were identified. Thirty two species belonged to Ascomycota (Eurotiomycetes and Sordariomycetes and one to Zygomycota (Zygomycetes. The genera with the greatest number of species were Penicillium (15, Aspergillus (5, and Cladosporium (2. Among the isolated fungi, some of the species were entomopathogenic or pathogens of humans and other animals.En el presente estudio se realizó un relevamiento de la flora fúngica microbiana en tractos digestivos de adultos de Triatoma infestans (Klug (Hemiptera: Reduviidae. Se disecaron insectos capturados del campo en diferentes provincias Argentinas, así como también se utilizaron individuos de una colonia artificial. Fueron realizados cultivos axénicos de las especies fúngicas aisladas, los que fueron identificados y luego depositados en las colecciones de hongos entomopatógenos del CEPAVE La Plata , Argentina. Fueron identificadas 33 especies fúngicas perteneciente a 11 géneros. Treinta y dos especies pertenecen a Ascomycota (Eurotiomycetes y Sordariomycetes y una a Zygomycota (Zygomycetes. Los géneros con mayor número de especies fueron Penicillium (15, Aspergillus (5, y Cladosporium (2. Entre los aislamientos fúngicos, algunas de las especies encontradas son entomopatogénicas o patógenas de humanos y otros animales.

  10. Actividades enzimáticas en aislamientos bacterianos de tractos digestivos de larvas y del contenido de pupas de Automeris zugana y Rothschildia lebeau (Lepidoptera: Saturniidae

    Directory of Open Access Journals (Sweden)

    Adrián Pinto-Tomás

    2007-06-01

    Full Text Available El tracto digestivo de orugas constituye un microambiente extremo, debido a su elevado pH y presencia de sustancias antimicrobianas secretadas por el insecto o derivadas del tejido vegetal ingerido. Al mismo tiempo, el intestino alberga gran cantidad de alimento, por el cual los microorganismos presentes podrían competir entre sí y con su hospedero. Existe poca información sobre la microbiota asociada con el intestino de orugas tropicales, aunque se ha demostrado la presencia de bacterias de diversos géneros tanto en el intestino como en el interior de pupas. El estudio de las actividades enzimáticas de estos microorganismos constituye un punto de partida en la comprensión de la posible relación metabólica y fisiológica que establecen con sus hospederos, a la vez que permite investigar enzimas con potenciales aplicaciones biotecnológicas. En este trabajo se evaluó la presencia de actividades gelatinolítica, caseinolítica, esterásica, lipolítica, quitinolítica, amilásica, celulolítica y xilanolítica en dos colecciones de aislamientos bacterianos provenientes de tractos digestivos de orugas y de pupas de los lepidópteros Automeris zugana y Rothschildia lebeau. Se utilizaron ensayos bioquímicos tradicionales para detectar enzimas secretadas en condiciones aerobias, en las que ambas colecciones exhibieron un comportamiento enzimático similar. Ningún aislamiento produjo un resultado positivo en todas las pruebas, pero como conjunto ambas colecciones fueron capaces de utilizar todos los sustratos evaluados. Los aislamientos obtenidos de pupas presentaron prácticamente las mismas actividades que sus homólogos provenientes de intestinos. En ambas colecciones fue posible agrupar los aislamientos de acuerdo con su patrón de producción de enzimas. Además de un conjunto heterogéneo de aislamientos poco activos (dos o menos actividades, se destacan dos grupos muy activos (al menos cinco actividades, que manifiestan una aparente

  11. Ultramorphology of digestive tract of Anticarsia gemmatalis (Hübner, 1818 (Lepidoptera: Noctuidae at final larval development/ Ultramorfologia do trato digestivo de Anticarsia gemmatalis (Hübner, 1818 (Lepidoptera: Noctuidae no final do desenvolvimento larval

    Directory of Open Access Journals (Sweden)

    Luis Antônio Toledo

    2008-08-01

    Full Text Available The digestive tract of insects is an important natural, physical, and chemical defense barrier against pathogen invasion. Certain lepidopteran caterpillars are serious pests of agricultural crops and their biology has received much attention, but little is known about the larval noctuid gut. The morphological analysis of the digestive tract in Anticarsia gemmatalis under scanning electron microscopy (SEM is a good model for studies about its defense mechanism. The material was fixed (2,5% glutaraldehyde solution; 0.1M-phosphate buffer, pH 7.3, post-fixed (1% osmium tetroxide in the same buffer, dried at critical point, gold coated and analyzed in a SEM 515-Philips. A. gemmatalis digestive tract consists of a straight duct of varying length and diameter, subdivided in three main regions: the foregut formed by the oral cavity, pharynx, esophagus, and crop; the midgut that is the largest portion of the digestive tract without noticeable morphological differentiation along its length; and the hindgut that is morphologically differentiated in pylorus, ileum, colon, and rectum. Although the general morphology of the A. gemmatalis digestive tract is quite similar to the other Lepidoptera species, the anatomical array of the crop muscular layers is quite different comparing with the description for other larval insect.O trato digestivo dos insetos constitui uma importante barreira físico-química natural contra invasão de patógenos. Algumas larvas de lepidópteros são consideradas pragas agrícolas potenciais e sua biologia tem recebido muita atenção; no entanto, pouco se sabe sobre a morfologia do sistema digestivo. A análise morfológica do trato digestivo de Anticarsia gemmatalis em nível ultraestrutural é um método bastante eficaz para o estudo dos seus mecanismos de defesa. Os materiais foram fixados (solução de glutaraldeído 2,5%; 0.1M tampão fosfato, pH 7.3, pós-fixados (tetróxido de ósmio 1% no mesmo tampão, desidratados em

  12. Ayuda del Campus Virtual en la creación por los alumnos de un juego-simulación sobre la fisiología del aparato digestivo

    OpenAIRE

    Fernández Galaz, María del Carmen; Colino Matilla, Asunción; Prada Elena, Carmen; Mora Novaro, Orlando Ángel; Comas Rengifo, María Dolores; García Seoane, Jorge

    2007-01-01

    El objetivo docente fue: • Motivar a los alumnos para facilitar el aprendizaje de una parte de la fisiología. • Ayudar a integrar las funciones y mecanismos de control del aparato digestivo. • Facilitar la comunicación entre alumnos y el trabajo en grupo. • Realizar una práctica de simulación de la digestión con las normas generadas. El juego consistiría en mover, digerir (cortar) y absorber un trozo de comida artificial que iría pasando sucesivamente desde la...

  13. Microsatellite Primers for Fungus-Growing Ants

    DEFF Research Database (Denmark)

    Villesen Fredsted, Palle; Gertsch, Pia J.; Boomsma, Jacobus Jan (Koos)

    2002-01-01

    We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...... developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants....

  14. Microsatellite primers for fungus-growing ants

    DEFF Research Database (Denmark)

    Villesen, Palle; Gertsch, P J; Boomsma, JJ

    2002-01-01

    We isolated five polymorphic microsatellite loci from a library of two thousand recombinant clones of two fungus-growing ant species, Cyphomyrmex longiscapus and Trachymyrmex cf. zeteki. Amplification and heterozygosity were tested in five species of higher attine ants using both the newly...... developed primers and earlier published primers that were developed for fungus-growing ants. A total of 20 variable microsatellite loci, developed for six different species of fungus-growing ants, are now available for studying the population genetics and colony kin-structure of these ants....

  15. Issues Primer. EEE708 Negotiated Study Program.

    Science.gov (United States)

    Jennings, Leonie

    This issues primer is structured around a series of 20 contemporary concerns in the changing world of work and training in Australia in the early 1990s. It is part of the study materials for the one-semester distance education unit, Negotiated Study Program, in the Open Campus Program at Deakin University (Australia). Information on each issue is…

  16. Scrimer: designing primers from transcriptome data

    Czech Academy of Sciences Publication Activity Database

    Mořkovský, Libor; Pačes, Jan; Rídl, Jakub; Reifová, R.

    2015-01-01

    Roč. 15, č. 6 (2015), s. 1415-1420 ISSN 1755-098X R&D Projects: GA MŠk EE2.3.20.0303 Institutional support: RVO:68081766 ; RVO:68378050 Keywords : next-generation sequencing * primer design * SNaPshot * SNP genotyping * transcriptome Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 5.298, year: 2015

  17. A Primer on the Functional Equation

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 22; Issue 10. A Primer on the Functional Equation: f(x+y) = f(x) + f(y). Kaushal Verma. General Article Volume 22 Issue 10 October 2017 pp 935-941. Fulltext. Click here to view fulltext PDF. Permanent link:

  18. A Primer on Policies for Jobs

    OpenAIRE

    Bhattacharya, Rwitwika; Griffith, Breda; Chen, Derek H. C.; Nallari, Raj; Andriamananjara, Soamiely; Wang, Yidan

    2012-01-01

    A primer on policies for jobs is based on materials and input provided during the labor market courses conducted during the past 10 years. Its objective is to provide government policy makers, researchers, and labor market practitioners and other specialists with a practical guide on how to strengthen labor market institutions, especially in light of the global financial crisis. This prime...

  19. Reforming Science Instruction in California: A Primer

    Science.gov (United States)

    EdSource, 2017

    2017-01-01

    As schools across the state implement the Next Generation Science Standards, this EdSource primer provides an easy-to-read guide for parents and other community members to understand the rationale for the standards and their potential to affect science instruction in California schools. California adopted the Next Generation Science Standards, or…

  20. Universal primers for rapid detection of hytrosaviruses.

    Science.gov (United States)

    Abd-Alla, Adly M M; Salem, Tamer Z; Parker, Andrew G; Wang, Yongjie; Jehle, Johannes A; Vreysen, Marc J B; Boucias, Drion

    2011-01-01

    Hytrosaviridae is a proposed virus family encompassing viruses that cause salivary gland hypertrophy (SGH) syndrome in infected insects and reduce the fertility in their dipteran insect hosts. They contain a large, double stranded DNA genome of 120-190 kbp. To date, these viruses have been detected only in adult Diptera. These include hytrosaviruses detected in various tsetse fly species (Glossina spp.), the narcissus bulb fly Merodon equestris and the house fly Musca domestica. The limited number of hytrosaviruses reported to date may be a reflection of the frequent absence of external symptoms in infected adult flies and the fact that the virus does not cause rapid mortality. Based on the complete genome sequence of Glossinia pallidipes (GpSGHV) and Musca domestica (MdSGHV) salivary gland hypertrophy viruses, a PCR based methodology was developed to detect the viruses in these species. To be able to detect hytrosaviruses in other Diptera, five degenerate primer pairs were designed and tested on GpSGHV and MdSGHV DNA using gradient PCR with annealing temperatures from 37 to 61°C. Two pairs of primers were selected from p74, two pairs from PIF-1 and one pair from ODV-e66 homologous proteins. Four primer pairs generated a virus specific PCR product on both MdSGHV and GpSGHV at all tested annealing temperatures, while the ODV-e66 based primers did not generate a virus specific product with annealing temperatures higher that 47°C. No non-specific PCR product was found when using genomic DNA of infected flies as template DNA. These results offer new sets of primers that could be used to detect hytrosaviruses in other insects. Copyright © 2010 Elsevier B.V. All rights reserved.

  1. Aluminum Rich Epoxy Primer for Ground and Air Vehicles

    Science.gov (United States)

    2017-03-01

    UNCLASSIFIED DOCUMENT Aluminum Rich Epoxy Primer for Ground and Air Vehicles Monthly Technical Report for the Period: January 20, 2017...Objective: To further develop the Aluminum Rich Epoxy Primer systems for Air and Ground Vehicles while addressing the objective requirements

  2. New primers for adhesive bonding of aluminum alloys

    Science.gov (United States)

    Burrell, B. W.; Port, W. S.

    1971-01-01

    Synthetic polypeptide adhesive primers are effective, with high temperature epoxy resins, at temperatures from 100 deg to 300 deg C. Lap-shear failure loads and lap-shear strength of both primers are discussed.

  3. Economics : pricing, demand, and economic efficiency : a primer.

    Science.gov (United States)

    2008-11-01

    The Congestion Pricing Primer Series is part of : FHWAs outreach efforts to introduce the various : aspects of congestion pricing to decision-makers and : transportation professionals in the United States. The : primers are intended to lay out the...

  4. Primer on consumer marketing research : procedures, methods, and tools

    Science.gov (United States)

    1994-03-01

    The Volpe Center developed a marketing research primer which provides a guide to the approach, procedures, and research tools used by private industry in predicting consumer response. The final two chapters of the primer focus on the challenges of do...

  5. Pesquisaje activo de sospechas de reacciones adversas a medicamentos en el Hospital "Dr. Salvador Allende: Primer semestre 2006 Active screening of suspicions of adverse reactions to drugs in "Dr. Salvador Allende" Hospital: First semester 2006

    Directory of Open Access Journals (Sweden)

    José de Jesús Rego Hernández

    2007-12-01

    Full Text Available Se realizó un estudio descriptivo mediante la revisión diaria del movimiento hospitalario, obtenido en el Departamento de Registros Médicos del Hospital "Dr. Salvador Allende" desde enero hasta junio de 2006 a fin de poder identificar los ingresos susceptibles de ser reacciones adversas a medicamentos, con el objetivo de detectar la frecuencia de ingresos por sospechas de reacciones adversas a medicamentos, así como de caracterizar a estos pacientes. Se llenó una planilla de notificación para cada sospecha de reacción adversa y se analizaron los datos contenidos en las historias clínicas respectivas. Se utilizó una base de Excel diseñada al efecto por el Centro para el Desarrollo de la Farmacoepidemiología. Ingresaron 6 201 pacientes, de los cuales 384 eran susceptibles de tener una reacción adversa a medicamentos (6,2 % y finalmente, se consideraron 57 pacientes cuyo motivo de ingreso se relacionó con algún medicamento (0,9 %. El 66,7 % de los casos eran mayores de 60 años de edad, sin diferencias en cuanto al sexo. Los grupos farmacológicos con mayores afectaciones fueron los analgésicos no opiodes (59,7 % y los antibacterianos (19,4 %. El sangramiento digestivo alto resultó la reacción adversa que más se encontró (57,9 %, con predominio en mayores de 60 años de edad (72,7 %; el ácido acetilsalicílico estuvo presente en el 66,7 % de los casos con este diagnóstico. En el75,5 % de los casos la reacción se consideró como graveA descriptive study was conducted by the daily revision of hospital movement obtained in the Department of Medical Registries of "Dr. Salvador Allende" Hospital from January to June, 2006, aimed at identifying the admissions susceptible to adverse reactions to drugs to detect the frequency of admissions due to suspicions of adverse reactions to drugs, as well as to characterize these patients. A notification form was filled in per each suspicion of adverse reaction, and the data contained in the

  6. Universal COI primers for DNA barcoding amphibians.

    Science.gov (United States)

    Che, Jing; Chen, Hong-Man; Yang, Jun-Xiao; Jin, Jie-Qiong; Jiang, Ke; Yuan, Zhi-Yong; Murphy, Robert W; Zhang, Ya-Ping

    2012-03-01

    DNA barcoding is a proven tool for the rapid and unambiguous identification of species, which is essential for many activities including the vouchering tissue samples in the genome 10K initiative, genealogical reconstructions, forensics and biodiversity surveys, among many other applications. A large-scale effort is underway to barcode all amphibian species using the universally sequenced DNA region, a partial fragment of mitochondrial cytochrome oxidase subunit I COI. This fragment is desirable because it appears to be superior to 16S for barcoding, at least for some groups of salamanders. The barcoding of amphibians is essential in part because many species are now endangered. Unfortunately, existing primers for COI often fail to achieve this goal. Herein, we report two new pairs of primers (➀, ➁) that in combination serve to universally amplify and sequence all three orders of Chinese amphibians as represented by 36 genera. This taxonomic diversity, which includes caecilians, salamanders and frogs, suggests that the new primer pairs will universally amplify COI for the vast majority species of amphibians. © 2011 Blackwell Publishing Ltd.

  7. Parâmetros digestivos, produção e qualidade do leite de cabras Saanen recebendo rações com casca do grão de soja em substituição ao milho = Digestive parameters, production and quality of milk from Saanen goats fed rations with soybean hulls as a replacement for ground corn

    National Research Council Canada - National Science Library

    Maximiliane Alavarse Zambom; Claudete Regina Alcalde; Juliano Hideo Hashimoto; Francisco de Assis Fonseca de Macedo; Gabriella de Oliveira Passianoto; Luciano Soares de Lima

    2007-01-01

    O experimento objetivou avaliar os parâmetros digestivos, produção e qualidade do leite de cabras Saanen, recebendo rações com casca do grão de soja (CGS), em três níveis de substituição ao milho moído (0% CGS, 50% CGS e 100% CGS...

  8. Paracoccidioidomicose duodenal com sangramento digestivo

    Directory of Open Access Journals (Sweden)

    Roberto Martinez

    1984-06-01

    Full Text Available Apresenta-se um caso de hematêmese fatal por úlcera duodenal paracoccidioidomicótica. Tanto esta localização da paracoccidioidomicose, como sua manifestação clínica são incomuns, resultando provavelmente do grande comprometimento da cavidade abdominal.

  9. MPprimer: a program for reliable multiplex PCR primer design

    Directory of Open Access Journals (Sweden)

    Wang Xiaolei

    2010-03-01

    Full Text Available Abstract Background Multiplex PCR, defined as the simultaneous amplification of multiple regions of a DNA template or multiple DNA templates using more than one primer set (comprising a forward primer and a reverse primer in one tube, has been widely used in diagnostic applications of clinical and environmental microbiology studies. However, primer design for multiplex PCR is still a challenging problem and several factors need to be considered. These problems include mis-priming due to nonspecific binding to non-target DNA templates, primer dimerization, and the inability to separate and purify DNA amplicons with similar electrophoretic mobility. Results A program named MPprimer was developed to help users for reliable multiplex PCR primer design. It employs the widely used primer design program Primer3 and the primer specificity evaluation program MFEprimer to design and evaluate the candidate primers based on genomic or transcript DNA database, followed by careful examination to avoid primer dimerization. The graph-expanding algorithm derived from the greedy algorithm was used to determine the optimal primer set combinations (PSCs for multiplex PCR assay. In addition, MPprimer provides a virtual electrophotogram to help users choose the best PSC. The experimental validation from 2× to 5× plex PCR demonstrates the reliability of MPprimer. As another example, MPprimer is able to design the multiplex PCR primers for DMD (dystrophin gene which caused Duchenne Muscular Dystrophy, which has 79 exons, for 20×, 20×, 20×, 14×, and 5× plex PCR reactions in five tubes to detect underlying exon deletions. Conclusions MPprimer is a valuable tool for designing specific, non-dimerizing primer set combinations with constrained amplicons size for multiplex PCR assays.

  10. Ontogenia del sistema digestivo y caracterización de la actividad enzimática de las larvas de chita Anisotremus scapularis (Tschudi, 1846)

    OpenAIRE

    Cota Mamani, Noemí Jackelith

    2016-01-01

    La chita Anisotremus scapularis es un pez marino que habita las costas de Perú, es muy valorado para el consumo humano directo, y, es considerada una especie con potencial acuícola. El cultivo larval en muchas especies de peces marinos se considera como uno de los cuellos de botella para el desarrollo de la tecnología de cultivo a escala comercial, este es el caso de la chita. Como primer alimento y durante los primeros días de vida de las larvas se les suministra presas vivas,...

  11. Primer Concilio Provincial del Nuevo Reino

    Directory of Open Access Journals (Sweden)

    Manuel Lucena Salmoral

    1963-01-01

    Full Text Available El acontecimiento más sobresaliente del patriarcado de don Fernando Arias de Ugarte, en el que hubo muchos notables, fue el Primer Concilio Provincial del Nuevo Reino de Granada, celebrado en el año 1623. Cumplió así una vieja aspiración de los arzobispos santafereños y la obligación impuesta en el Concilio de Trento, por lo que resulta incomprensible lo historiado por don José Antonio Plaza quien, al referirse a este hecho, dice lo siguiente...

  12. Signals and systems primer with Matlab

    CERN Document Server

    Poularikas, Alexander D

    2006-01-01

    Signals and Systems Primer with MATLAB® equally emphasizes the fundamentals of both analog and digital signals and systems. To ensure insight into the basic concepts and methods, the text presents a variety of examples that illustrate a wide range of applications, from microelectromechanical to worldwide communication systems. It also provides MATLAB functions and procedures for practice and verification of these concepts.Taking a pedagogical approach, the author builds a solid foundation in signal processing as well as analog and digital systems. The book first introduces orthogonal signals,

  13. Bayesian models a statistical primer for ecologists

    CERN Document Server

    Hobbs, N Thompson

    2015-01-01

    Bayesian modeling has become an indispensable tool for ecological research because it is uniquely suited to deal with complexity in a statistically coherent way. This textbook provides a comprehensive and accessible introduction to the latest Bayesian methods-in language ecologists can understand. Unlike other books on the subject, this one emphasizes the principles behind the computations, giving ecologists a big-picture understanding of how to implement this powerful statistical approach. Bayesian Models is an essential primer for non-statisticians. It begins with a definition of probabili

  14. Emulsion primers, their contribution to bonding

    OpenAIRE

    González Sburlati, Rubén Osmar; Sapei, José

    2014-01-01

    Asphalt irrigation in its various types, performs specific functions in the structure of a road during the construction phase or their service life. In particular, the so-called "Irrigation Primer " is used in underlying layers, in order to generate a transition surface with the new asphalt layer; thus the tack or prime coat will be placed on a surface to ensure a good bond with the overlying layer. For a long time Diluted Asphalts (Cut Back mediums) where used, but have been discontinued for...

  15. Dominant culturable bacterial microbiota in the digestive tract of the American black vulture (Coragyps atratus Bechstein 1793 and search for antagonistic substances Microbiota bacteriana dominante cultivável no trato digestivo do urubu (Coragyps atratus Bechstein 1793

    Directory of Open Access Journals (Sweden)

    Lydston Rodrigues de Carvalho

    2003-07-01

    Full Text Available Strict and facultative culturable anaerobic bacteria from the digestive tract of six American black vultures (Coragyps atratus Bechstein 1793 were isolated and identified. After capture, the birds received a non-contaminated diet for one week to eliminate possible allochthonous microorganisms. Then, specimens collected from tongue, stomach and intestines were weighed, submitted to decimal dilution in an anaerobic chamber, inoculated into culture media and incubated aerobically and anaerobically at 37ºC for enumeration, isolation and identification. Isolated bacteria were submitted to tests to detect possible antagonisms between them. The total bacterial population along the digestive tract ranged from 3.46 ± 0.39 log CFU/g in the stomach to 10.75 ± 0.37 log CFU/g in the distal intestine. Some bacteria were isolated for the first time from the digestive tract of C. atratus: Actinomyces bovis, Lactobacillus cellobiosus, Micrococcus luteus, Neisseria sicca, Clostridium bifermentans, Enterobacter agglomerans, Peptostreptococcus sp., Sarcina sp., Serratia odorifera, and Shigella flexneri. Associations between microorganisms were observed during isolation on two occasions, one involving A. bovis and N. sicca, and the other involving A. bovis and a Gram-negative rod. Hetero-, iso- and autoantagonisms were observed, suggesting the ecological role of these indigenous microorganisms in terms of population auto-control and environmental barrier in the digestive tract of carrion-feeding birds.As bactérias anaeróbias estritas e facultativas cultiváveis do trato digestivo de seis urubus (Coragyps atratus Bechstein 1793 foram isoladas e identificadas. Após a captura, as aves receberam uma alimentação de baixa contaminação durante uma semana para eliminar possíveis microorganismos alóctonos. A seguir, amostras colhidas na língua, estomago e intestinos foram pesadas, submetidas a diluições decimais numa câmara anaeróbia, inoculadas em meios de

  16. Primer on CDM programme of activities

    Energy Technology Data Exchange (ETDEWEB)

    Hinostroza, M. (UNEP Risoe Centre, Roskilde (Denmark)); Lescano, A.D. (A2G Carbon Partners (Peru)); Alvarez, J.M. (Ministerio del Ambiente del Peru (Peru)); Avendano, F.M. (EEA Fund Management Ltd. (United Kingdom)

    2009-07-01

    As an advanced modality introduced in 2005, the Programmatic CDM (POA) is expected to address asymmetries of participation, especially of very small-scale project activities in certain areas, key sectors and many countries with considerable potential for greenhouse gas emission reductions, not reached by the traditional single-project-based CDM. Latest experiences with POAs and the recently finalized official guidance governing the Programmatic CDM are the grassroots of this Primer, which has the purpose of supporting the fully understanding of rules and procedures of POAs by interpreting them and analyzing real POA cases. Professional and experts from the public and private entities have contributed to the development of this Primer, produced by the UNEP Risoe Centre, as part of knowledge support activities for the Capacity Development for the CDM (CD4CDM) project. The overall objective of the CD4CDM is to develop the capacities of host countries to identify, design, approve, finance, implement CDM projects and commercialize CERs in participating countries. The CDM4CDM is funded by the Netherlands Ministry of Foreign Affairs. (author)

  17. An iterative method for selecting degenerate multiplex PCR primers.

    Science.gov (United States)

    Souvenir, Richard; Buhler, Jeremy; Stormo, Gary; Zhang, Weixiong

    2007-01-01

    Single-nucleotide polymorphism (SNP) genotyping is an important molecular genetics process, which can produce results that will be useful in the medical field. Because of inherent complexities in DNA manipulation and analysis, many different methods have been proposed for a standard assay. One of the proposed techniques for performing SNP genotyping requires amplifying regions of DNA surrounding a large number of SNP loci. To automate a portion of this particular method, it is necessary to select a set of primers for the experiment. Selecting these primers can be formulated as the Multiple Degenerate Primer Design (MDPD) problem. The Multiple, Iterative Primer Selector (MIPS) is an iterative beam-search algorithm for MDPD. Theoretical and experimental analyses show that this algorithm performs well compared with the limits of degenerate primer design. Furthermore, MIPS outperforms an existing algorithm that was designed for a related degenerate primer selection problem.

  18. Screening of rapd primer for teak (Tectona grandis

    Directory of Open Access Journals (Sweden)

    Imas Cintamulya

    2016-04-01

    Full Text Available Identification of DNA polymorphisms in teak is important. It is a first step to determine the presence of genetic varia-tion in teak. The information of genetic variation is needed for teak breeding development. RAPD is one of method which can be used for identification of DNA polymorphism. This study aim to get the RAPD primer which can detect the DNA polymorphism in teak. Benefits of this study are provide information about primer which can detect the DNA polymorphism in teak, DNA polymorphism data can be used for genetic variation analysis which needed for teak breeding development. The primers which used in this study shown the DNA polymorphism in teak. The primer are OPF6 (5'-GGGAATTCGG-3 ', OPF8 (5'-GGGATATCGC-3', and OPF11 (5'-TTGGTACCCC-3 '. The highest DNA poly-morphism is shown in DNA which amplified with OPF-8 primer. Keywords: RAPD, Primer, Polymorphism, DNA, Tectona grandis

  19. Specific PCR product primer design using memetic algorithm.

    Science.gov (United States)

    Yang, Cheng-Hong; Cheng, Yu-Huei; Chuang, Li-Yeh; Chang, Hsueh-Wei

    2009-01-01

    To provide feasible primer sets for performing a polymerase chain reaction (PCR) experiment, many primer design methods have been proposed. However, the majority of these methods require a relatively long time to obtain an optimal solution since large quantities of template DNA need to be analyzed. Furthermore, the designed primer sets usually do not provide a specific PCR product size. In recent years, evolutionary computation has been applied to PCR primer design and yielded promising results. In this article, a memetic algorithm (MA) is proposed to solve primer design problems associated with providing a specific product size for PCR experiments. The MA is compared with a genetic algorithm (GA) using an accuracy formula to estimate the quality of the primer design and test the running time. Overall, 50 accession nucleotide sequences were sampled for the comparison of the accuracy of the GA and MA for primer design. Five hundred runs of the GA and MA primer design were performed with PCR product lengths of 150-300 bps and 500-800 bps, and two different methods of calculating T(m) for each accession nucleotide sequence were tested. A comparison of the accuracy results for the GA and MA primer design showed that the MA primer design yielded better results than the GA primer design. The results further indicate that the proposed method finds optimal or near-optimal primer sets and effective PCR products in a dry dock experiment. Related materials are available online at http://bio.kuas.edu.tw/ma-pd/. 2009 American Institute of Chemical Engineers

  20. GENOMEMASKER package for designing unique genomic PCR primers

    Directory of Open Access Journals (Sweden)

    Kaplinski Lauris

    2006-03-01

    Full Text Available Abstract Background The design of oligonucleotides and PCR primers for studying large genomes is complicated by the redundancy of sequences. The eukaryotic genomes are particularly difficult to study due to abundant repeats. The speed of most existing primer evaluation programs is not sufficient for large-scale experiments. Results In order to improve the efficiency and success rate of automatic primer/oligo design, we created a novel method which allows rapid masking of repeats in large sequence files, for example in eukaryotic genomes. It also allows the detection of all alternative binding sites of PCR primers and the prediction of PCR products. The new method was implemented in a collection of efficient programs, the GENOMEMASKER package. The performance of the programs was compared to other similar programs. We also modified the PRIMER3 program, to be able to design primers from lowercase-masked sequences. Conclusion The GENOMEMASKER package is able to mask the entire human genome for non-unique primers within 6 hours and find locations of all binding sites for 10 000 designed primer pairs within 10 minutes. Additionally, it predicts all alternative PCR products from large genomes for given primer pairs.

  1. Characteristics of Primer of High Performance Bismaleimide Resin

    Directory of Open Access Journals (Sweden)

    LI Hong-feng

    2016-06-01

    Full Text Available A primer of the bismaleimide resin toughened with block copolymer was prepared. The properties of the primer, such as adhesion, pencil hardness, impact resistance, environment resistant, ageing resistant performance and etc. meet the requirements of the technical specifications of GJB1388. The thermal property of the primer was characterized by differential scanning calorimeter (DSC, thermal gravity analysis (TG, and dynamic mechanical analysis (DMA. The results show that the primer possesses good heat resistance, the glass transition temperature of the primer reach 238℃, 5% mass heat lost temperature is 384℃ after 200℃ cured, and the glass transition temperature of the primer reach 268℃, 5% mass heat lost temperature is 407℃ after 230℃ heat treatment respectively. Bonding strength will increase when the bismaleimide primer doubled with bismaleimide film adhesive, when the primer doubled with J-188 bismaleimide film adhesive, peel strength increases to 107%, the room temperature shear strength and high temperature shear strength increase by 10%.The primer can also be used with other bismaleimide film structural adhesives, which are suitable for the bonding between metals or bismaleimide composites with metals.

  2. Complex and adaptive dynamical systems a primer

    CERN Document Server

    Gros, Claudius

    2015-01-01

    This primer offers readers an introduction to the central concepts that form our modern understanding of complex and emergent behavior, together with detailed coverage of accompanying mathematical methods. All calculations are presented step by step and are easy to follow. This new fourth edition has been fully reorganized and includes new chapters, figures and exercises. The core aspects of modern complex system sciences are presented in the first chapters, covering network theory, dynamical systems, bifurcation and catastrophe theory, chaos and adaptive processes, together with the principle of self-organization in reaction-diffusion systems and social animals. Modern information theoretical principles are treated in further chapters, together with the concept of self-organized criticality, gene regulation networks, hypercycles and coevolutionary avalanches, synchronization phenomena, absorbing phase transitions and the cognitive system approach to the brain. Technical course prerequisites are the standard ...

  3. Complex and adaptive dynamical systems a primer

    CERN Document Server

    Gros, Claudius

    2007-01-01

    We are living in an ever more complex world, an epoch where human actions can accordingly acquire far-reaching potentialities. Complex and adaptive dynamical systems are ubiquitous in the world surrounding us and require us to adapt to new realities and the way of dealing with them. This primer has been developed with the aim of conveying a wide range of "commons-sense" knowledge in the field of quantitative complex system science at an introductory level, providing an entry point to this both fascinating and vitally important subject. The approach is modular and phenomenology driven. Examples of emerging phenomena of generic importance treated in this book are: -- The small world phenomenon in social and scale-free networks. -- Phase transitions and self-organized criticality in adaptive systems. -- Life at the edge of chaos and coevolutionary avalanches resulting from the unfolding of all living. -- The concept of living dynamical systems and emotional diffusive control within cognitive system theory. Techn...

  4. Complex and Adaptive Dynamical Systems A Primer

    CERN Document Server

    Gros, Claudius

    2011-01-01

    We are living in an ever more complex world, an epoch where human actions can accordingly acquire far-reaching potentialities. Complex and adaptive dynamical systems are ubiquitous in the world surrounding us and require us to adapt to new realities and the way of dealing with them. This primer has been developed with the aim of conveying a wide range of "commons-sense" knowledge in the field of quantitative complex system science at an introductory level, providing an entry point to this both fascinating and vitally important subject. The approach is modular and phenomenology driven. Examples of emerging phenomena of generic importance treated in this book are: -- The small world phenomenon in social and scale-free networks. -- Phase transitions and self-organized criticality in adaptive systems. -- Life at the edge of chaos and coevolutionary avalanches resulting from the unfolding of all living. -- The concept of living dynamical systems and emotional diffusive control within cognitive system theory. Techn...

  5. Complex and adaptive dynamical systems a primer

    CERN Document Server

    Gros, Claudius

    2013-01-01

    Complex system theory is rapidly developing and gaining importance, providing tools and concepts central to our modern understanding of emergent phenomena. This primer offers an introduction to this area together with detailed coverage of the mathematics involved. All calculations are presented step by step and are straightforward to follow. This new third edition comes with new material, figures and exercises. Network theory, dynamical systems and information theory, the core of modern complex system sciences, are developed in the first three chapters, covering basic concepts and phenomena like small-world networks, bifurcation theory and information entropy. Further chapters use a modular approach to address the most important concepts in complex system sciences, with the emergence and self-organization playing a central role. Prominent examples are self-organized criticality in adaptive systems, life at the edge of chaos, hypercycles and coevolutionary avalanches, synchronization phenomena, absorbing phase...

  6. Formaldehyde as hypothetical primer of biohomochirality

    Energy Technology Data Exchange (ETDEWEB)

    Goldanskii, V.I. [N. N. Semenov Institute of Chemical Physics of the Russian Academy of Sciences, Kosygin Street 4, Moscow, 117334 (Russia)

    1996-07-01

    One of the most intriguing and crucial problems of the prebiotic evolution and the origin of life is the explanation of the origin of biohomochirality. A scheme of conversions originated by formaldehyde (FA) as hypothetical primer of biohomochirality is proposed. The merit of FA as executor of this function is based -inter alia - on the distinguished role of FA as one of the earliest and simplest molecules in both warm, terrestrial and cold, extraterrestrial scenarios of the origin of life. The confirmation of the role of FA as primer of biohomochirality would support the option of an RNA world as an alternative to the protein world. The suggested hypothesis puts forward for the first time a concrete sequence of chemical reactions which can lead to biohomochirality. The spontaneous breaking of the mirror symmetry is secured by the application of the well-known Frank scheme (combination of autocatalysis and {open_quote}{open_quote}annihilation{close_quote}{close_quote} of L and D enantiomers) to the series of interactions of FA {open_quote}{open_quote}trimers{close_quote}{close_quote} (i.e. C{sub 3}H{sub 6}O{sub 3} compounds) of (aaa), (apa) and (app) types, where the monomeric groups (a) means {open_quote}{open_quote}achirons{close_quote}{close_quote} (a=CH{sub n}, n{ge}2 and C=M, M=C,O) and (p) mean {open_quote}{open_quote}prochirons{close_quote}{close_quote} (p=HC{asterisk}OM, M=H,C). {copyright} {ital 1996 American Institute of Physics.}

  7. Adhesive primers for bonding cobalt-chromium alloy to resin.

    Science.gov (United States)

    Yoshida, K; Kamada, K; Atsuta, M

    1999-06-01

    This study evaluated the effect of five adhesive primers on the shear bond strength of a self-curing resin to cobalt-chromium (Co-Cr) alloy. The adhesive primers Acryl Bond (AB, Shofu), Cesead Opaque Primer (COP, Kuraray), Metacolor Opaque Bonding Liner (MOBL, Sun-Medical), Metal PrimerII (MPII, GC) and MR. Bond (MRB, Tokuyama) were used. A brass ring which was placed over the casting alloy disk surface non-primed or primed with each primer was filled with the self-curing MMA-PMMA resin. The specimens were stored in water at 37 degrees C for 24 h and then immersed alternately in water baths at 4 C and 60 degrees C for 1 min each for up to 50000 thermal cycles before shear mode testing at a crosshead speed of 0.5 mm/min. All of the primers examined, except MOBL, improved the shear bond strength between the resin and Co-Cr alloy compared with nonprimed specimens prior to thermal cycling. Regardless of which primer was used, the shear bond strength significantly differed between thermal cycles 0 and 50000. However, after 50000 thermal cycles, the bond strengths of resin to Co-Cr alloy primed with COP or MPII were significantly greater than those of specimens primed with AB, MOBL or MRB and non-primed controls. This study indicated that COP and MPII are effective primers to obtain higher bond strength between resin and Co-Cr alloy.

  8. Marketing Information Products and Services: A Primer for Librarians ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    ... and Services: A Primer for Librarians and Information Professionals. Book cover Marketing Information Products and Services: A Primer for Librarians and Information Professionals. Directeur(s) : Abhinandan K. Jain, Ashok Jambhekar, T.P.Rama Rao, and S. Sreenivas Rao. Maison(s) d'édition : Tata McGraw-Hill, IDRC.

  9. Marketing Information Products and Services : A Primer for ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    ... and Services : A Primer for Librarians and Information Professionals. Couverture du livre Marketing Information Products and Services : A Primer for Librarians and Information Professionals. Editor(s):. Abhinandan K. Jain, Ashok Jambhekar, T.P.Rama Rao et S. Sreenivas Rao. Publisher(s):. Tata McGraw-Hill, CRDI.

  10. Mapping of randomly amplified polymorphic DNA primer (RAPD) on ...

    African Journals Online (AJOL)

    Genet & Botany only

    2012-08-14

    Aug 14, 2012 ... RAPD primers GLC-07 and GLB-11. PCR amplification using primer GLC-07 produced single band of ... PCR amplification profile of the two genetic stocks of common wheat,. NT2A2B and NT1D1B using .... Isolation of recombinants involving barley arms 3HL and 6HL. Theor. Appl. Genet. 83:489-494.

  11. Bioinformatic tools and guideline for PCR primer design | Abd ...

    African Journals Online (AJOL)

    This review intends to provide a guide to choosing the most efficient way to design a new specific-primer by applying current publicly available links and Web services. Also, the purpose here is to provide general recommendations for the design and use of PCR primers. (African Journal of Biotechnology: 2003 2(5): 91-95) ...

  12. High-speed measurement of firearm primer blast waves

    CERN Document Server

    Courtney, Michael; Eng, Jonathan; Courtney, Amy

    2012-01-01

    This article describes a method and results for direct high-speed measurements of firearm primer blast waves employing a high-speed pressure transducer located at the muzzle to record the blast pressure wave produced by primer ignition. Key findings are: 1) Most of the lead styphnate based primer models tested show 5.2-11.3% standard deviation in the magnitudes of their peak pressure. 2) In contrast, lead-free diazodinitrophenol (DDNP) based primers had standard deviations of the peak blast pressure of 8.2-25.0%. 3) Combined with smaller blast waves, these large variations in peak blast pressure of DDNP-based primers led to delayed ignition and failure to fire in brief field tests.

  13. Analysis of digestive tract content of the larvae of Polybia scutellaris (White (Hymenoptera, Vespidae Análise do conteúdo do trato digestivo das larvas de Polybia scutellaris (White (Hymenoptera, Vespidae

    Directory of Open Access Journals (Sweden)

    Victoria Lilian Fernández Corujo

    2011-06-01

    Full Text Available Polybia scutellaris (White, 1841 is a social wasp of biological interest for its role as pollinator and maybe as biological control agent of sanitary and agricultural pests. This study examines the digestive tract contents of the larvae of P. scutellaris from four nests in Magdalena (Buenos Aires province, Argentina. Contents included both animal (arthropod parts and plant (pollen, leaf and fruit epidermis parts. The pollen content analysis showed that the wasps visited 19 different taxa of plants during the last active period of the colony before the nests had been collected. The range of sources used by P. scutellaris allows us characterizing the species as a generalist flower visitor. Wasps visited both native and exotic plants located nearby the nest. Most of the epidermal plant remains found in the larval digestive tract belonged to Malvaceae, a family not exploited by the studied colonies as pollen source.Polybia scutellaris (White, 1841 é uma vespa social de interesse biológico devido ao seu papel como polinizador e possível agente de controle biológico de pragas sanitárias e agrícolas. O presente estudo analisou o conteúdo do trato digestivo de larvas de P. scutellaris de quatros ninhos em Magdalena (província de Buenos Aires, Argentina. O conteúdo inclui restos animais (partes de artrópodos e vegetais (pólen, epiderme de folhas e frutos. A análise do conteúdo polínico mostrou que as vespas visitaram 19 táxons durante o último período ativo da colônia antes dos ninhos serem coletados. A diversidade de recursos utilizados por P. scutellaris permite caracterizá-la como um visitante generalista de flores. As vespas visitaram plantas nativas e exóticas localizados nas proximidades do ninho. A maioria dos restos de epiderme encontradas no trato digestivo das larvas pertence às Malvaceae, uma família não explorada pelas colônias estudadas como fonte de pólen.

  14. Anatomía comparada del sistema digestivo de las rayas Urotrygon chilensis y Dasyatis sabina (Myliobatiformes Comparative anatomy of the digestive system of the skates, Urotrygon chilensis and Dasyatis sabina (Myliobatiformes

    Directory of Open Access Journals (Sweden)

    ABRAHAM KOBELKOWSKY

    2010-01-01

    Full Text Available La organización general del sistema digestivo de la raya pinta Urotrygon chilensis y la raya de espina Dasyatis sabina corresponde al patrón morfológico general de los Myliobatiformes. La dentición de estas especies muestra un dimorfismo sexual, consistente en dientes planos en las hembras y dientes puntiagudos en los machos. Entre los músculos mandibulares, el adductor mandibulae es el más complejo. Las cavidades bucofaríngea y visceral son aplanadas dorsoventralmente. El esófago es relativamente largo, el estómago tiene forma de U, el intestino está regionalizado en duodeno, intestino valvular y recto. El mesenterio dorsal está restringido al recto y la glándula rectal. Los caracteres morfológicos más notables que diferencian el sistema digestivo de las dos especies son: la presencia de esfínter cardiaco y la forma en S del recto en U. chilensis, la presencia de escotaduras en las mandíbulas y el mayor número de vueltas de la válvula espiral en D. sabina.The general organization of the digestive system of the rays Urotrygon chilensis and Dasyatis sabina fits with the general morphological pattern of the Myliobatiformes. Dentition of both species shows sexual dimorphism, having the females flattened teeth whereas pointed teeth the males. Among the mandibular muscles, the adductor mandibulae is the most complex. Both the buccopharyngeal and the visceral cavities are dorsoventrally flattened. The esophagus is long, the stomach is U shaped, and the intestine is formed by the duodene, valvular intestine and rectum. The dorsal mesentery is restricted to the rectum and rectal gland. The main morphological characters differentiating both species are: the presence in U. chilensis of the cardiac sphincter and the S shape of the rectum, and the presence in D. sabina of mandibular notches and a higher number of coils of the valvular fold of the intestine.

  15. Primers on molecular pathways--caspase pathway.

    Science.gov (United States)

    Lomberk, Gwen; Urrutia, Raul

    2009-01-01

    Apoptosis, or programmed cell death, is a physiological process of cellular autodestruction, or cell suicide. This process is strictly controlled in response to integrity of pro-death signaling and plays critical roles in development, maintenance of homeostasis and host defense in multicellular organisms. As pancreatologists, apoptosis plays a central role in the pancreas and its disease states, from diabetes to pancreatitis to pancreatic cancer. In pancreatic beta-cells, apoptotic cell death is involved in the pathogenesis of diabetes, as signals from death receptors and DNA damage have been widely accepted as being triggers of apoptosis in beta-cells. During acute pancreatitis, this common clinical condition is of variable severity in which some patients experience mild, self-limited attacks while others manifest a severe, highly morbid, and frequently lethal attack. However, recent research in this area has demonstrated the importance of acinar cell death in the form of apoptosis and necrosis as a determinant of pancreatitis severity. In pancreatic cancer, various survival mechanisms have been shown to act in the prevention of cell death to result in promotion of tumor growth and metastasis. Thus, resistance of pancreatic cancer to apoptosis is the key factor preventing responses to therapies. Thus, it is for these reasons that in the current 'Primers on Molecular Pathways,' we take a closer look at the pathway cascade that is triggered during apoptosis. Copyright 2008 S. Karger AG, Basel and IAP.

  16. Primer on electricity futures and other derivatives

    Energy Technology Data Exchange (ETDEWEB)

    Stoft, S.; Belden, T.; Goldman, C.; Pickle, S.

    1998-01-01

    Increased competition in bulk power and retail electricity markets is likely to lower electricity prices, but will also result in greater price volatility as the industry moves away from administratively determined, cost-based rates and encourages market-driven prices. Price volatility introduces new risks for generators, consumers, and marketers. Electricity futures and other derivatives can help each of these market participants manage, or hedge, price risks in a competitive electricity market. Futures contracts are legally binding and negotiable contracts that call for the future delivery of a commodity. In most cases, physical delivery does not take place, and the futures contract is closed by buying or selling a futures contract on or near the delivery date. Other electric rate derivatives include options, price swaps, basis swaps, and forward contracts. This report is intended as a primer for public utility commissioners and their staff on futures and other financial instruments used to manage price risks. The report also explores some of the difficult choices facing regulators as they attempt to develop policies in this area.

  17. Transforming practices: a primer on action research.

    Science.gov (United States)

    Acosta, Sandra; Goltz, Heather Honoré

    2014-07-01

    Action research (AR) is a powerful tool for health education and promotion practitioners who want to focus on improving the quality of their programs and services. In this Tool, we describe the characteristics and controversial aspects of AR, differentiate between traditional and action research, present the benefits of applying AR methods/techniques for investigating problems related to professional practice, and offer a four-phase methodological framework for conducting AR studies. Unlike traditional research, AR is a methodology that links theory, research, and practice; advances new knowledge and understandings via iterative action cycles; employs frontline health practitioners as researchers; and promotes collaborative practitioner-community partnerships. Egalitarian in its approach, AR offers an "insider's perspective" centered on context-specific problems and issues related to health promotion. AR falls into two categories: large-scale community-based research and small-scale practice-based research. Each cycle of the AR framework includes four phases: (a) preplanning/needs assessment, (b) planning/study organization, (c) action and observation/study implementation, and (d) reflection and planning/data analysis and interpretation. Using the AR primer in this Tool has the potential to empower health education/promotion practitioners, encourage collaborative partnerships, enhance practitioners' knowledge base, and promote social change. © 2014 Society for Public Health Education.

  18. Value for money assessment for public-private partnerships : a primer.

    Science.gov (United States)

    2015-01-01

    This primer addresses Value for Money Assessment for public-private partnerships (P3s). Companion : primers on Financial Assessment and Risk Assessment for P3s are also available as part of this series of : primers.

  19. Complementation of a primer binding site-impaired murine leukemia virus-derived retroviral vector by a genetically engineered tRNA-like primer

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M; Lovmand, J

    1997-01-01

    , but not with a noncomplementary tRNA-like molecule. The engineered primer was shown to be involved in both the initiation of first-strand synthesis and second-strand transfer. These results provide an in vivo demonstration that the retroviral replication machinery may recognize sequence complementarity rather than actual primer...... binding site and 3' primer sequences. Use of mutated primer binding site vectors replicating via engineered primers may add additional control features to retroviral gene transfer technology....

  20. cutPrimers: A New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing.

    Science.gov (United States)

    Kechin, Andrey; Boyarskikh, Uljana; Kel, Alexander; Filipenko, Maxim

    2017-11-01

    Cutting of primers from reads is an important step of processing targeted amplicon-based next generation sequencing data. Existing tools are adapted for cutting of one or several primer/adapter sequences from reads and removing all of their occurrences. Also most of the existing tools use kmers and may cut only part of primers or primers with studied sequence of gene. Because of this, use of such programs leads to incorrect trimming, reduction of coverage, and increase in the number of false-positive and/or false-negative results. We have developed a new tool named cutPrimers for accurate cutting of any number of primers from reads. Using sequencing reads that were obtained during study of BRCA1/2 genes, we compared it with cutadapt, AlienTrimmer, and BBDuk. All of them trimmed reads in such a way that coverage of at least two amplicons decreased to unacceptable level (cut all occurrences of primer sequences, so the length of the remaining reads was less than prospective.

  1. A Psicologia Latinoamericana: El Primer Medio Siglo

    Directory of Open Access Journals (Sweden)

    Rubén Ardila

    2004-01-01

    Full Text Available Se presentan los principales desarrollos de la psicología en América Latina, desde el contexto de la psicología interamericana. La Sociedad Interamericana de Psicología (SIP fue fundada el 17 de diciembre de 1951 en Ciudad de México. El primer Congreso Interamericano de Psicología se llevó a cabo en Santo Domingo (República Dominicana entre el 10 y el 20 de diciembre de 1953. Este medio siglo ha marcado un acelerado proceso de desarrollo en la psicología en América Latina, en todo el continente americano, y en el mundo en general. Se han creado programas de formación profesional a lo largo y ancho del continente, y podemos afirmar que hoy existen psicólogos profesionales en todos los países de las Américas El papel del psicólogo en la sociedad ha logrado tener importancia y relevancia habiendo partido de comienzos muy modestos. Se está llevando a cabo investigación científica de alto nivel, especialmente en algunos países líderes, como son México y Brasil, pero también en Perú, Venezuela, Argentina, Cuba, Chile, Colombia, y en general en América Latina. La falta de originalidad que señalaba Alarcón en su libro Orientaciones Teóricas de la Psicología en América Latina, en 1997, ha comenzado a dar paso a trabajos originales y a investigaciones pioneras. Los siguientes 50 años de la psicología en este contexto cultural probablemente van a continuar con estos desarrollos, y seguramente llevarán a integrar la psicología latinoamericana al contexto internacional

  2. propósito del primer centenario

    Directory of Open Access Journals (Sweden)

    René Martínez Lemoine

    2007-01-01

    Full Text Available Este trabajo, trata de las apreciaciones públicas y urbanas que se dieron en la ciudad de Santiago a instancias de la celebración del primer Centenario de la República, en el año 1910. Es una rememoranza de aquellas visiones que la ciudad sustrajo a los medios periodísticos, personajes y liderazgos de una sociedad autosatisfecha por el progreso notable alcanzado por el país en las últimas décadas del siglo XIX y los primeros años del siglo XX, pero que ignoró los movimientos obreros y expresiones de disconformidad social que ya comenzaban a ebullir en esos años. La ciudad, como una vasta, compleja y heterogénea construcción en el espacio, erigida a través de las edades por innumerables y, la más de las veces, anónimos constructores, representa la mayor suma de obra humana acumulada en el tiempo, en la que cada generación va dejando una muestra de su aporte en vivienda, espacios, instalaciones y monumentos, vale decir, de su particular cultura y modo de vida en su propio tiempo. Ciertamente, cada ciudad es historia y memoria de sí misma, testimonio permanente de la continuidad del hombre y de la sociedad humana con su propio pasado. En ese sentido, como somos herederos de nuestra historia y de los hombres y mujeres que construyeron y legaron las ciudades en las que vivimos, es importante rescatar esos valores culturales, sociales, arquitectónicos y urbanísticos de modo de visualizar el paso del tiempo, que se materializa, se hace objeto y se torna visible en la ciudad, en la medida que nos “cuenta” algo.

  3. Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs

    Directory of Open Access Journals (Sweden)

    Beckett Stephanie E

    2006-10-01

    Full Text Available Abstract Background Cross-species primers have been used with moderate success to address a variety of questions concerning genome structure, evolution, and gene function. However, the factors affecting their success have never been adequately addressed, particularly with respect to producing a consistent method to achieve high throughput. Using 1,147 mammalian cross-species primer pairs (1089 not previously reported, we tested several factors to determine their influence on the probability that a given target will amplify in a given species under a single amplification condition. These factors included: number of mismatches between the two species (the index species used to identify conserved regions to which the primers were designed, GC-content of the gene and amplified region, CpG dinucleotides in the primer region, degree of encoded protein conservation, length of the primers, and the degree of evolutionary distance between the target species and the two index species. Results The amplification success rate for the cross-species primers was significantly influenced by the number of mismatches between the two index species (6–8% decrease per mismatch in a primer pair, the GC-content within the amplified region (for the dog, GC ≥ 50%, 56.9% amplified; GC2 = 0.14 and the relatedness of the target species to the index species. For the dog, 598 products of 930 primer pairs (64.3% (excluding primers in which dog was an index species were sequenced and shown to be the expected product, with an additional three percent producing the incorrect sequence. When hamster DNA was used with the single amplification condition in a microtiter plate-based format, 510 of 1087 primer pairs (46.9% produced amplified products. The primer pairs are spaced at an average distance of 2.3 Mb in the human genome and may be used to produce up to several hundred thousand bp of species-specific sequence. Conclusion The most important factors influencing the proportion

  4. New primers for DNA barcoding of digeneans and cestodes (Platyhelminthes).

    Science.gov (United States)

    Van Steenkiste, Niels; Locke, Sean A; Castelin, Magalie; Marcogliese, David J; Abbott, Cathryn L

    2015-07-01

    Digeneans and cestodes are species-rich taxa and can seriously impact human health, fisheries, aqua- and agriculture, and wildlife conservation and management. DNA barcoding using the COI Folmer region could be applied for species detection and identification, but both 'universal' and taxon-specific COI primers fail to amplify in many flatworm taxa. We found that high levels of nucleotide variation at priming sites made it unrealistic to design primers targeting all flatworms. We developed new degenerate primers that enabled acquisition of the COI barcode region from 100% of specimens tested (n = 46), representing 23 families of digeneans and 6 orders of cestodes. This high success rate represents an improvement over existing methods. Primers and methods provided here are critical pieces towards redressing the current paucity of COI barcodes for these taxa in public databases. © 2014 Her Majesty the Queen in Right of Canada Molecular Ecology Resources © 2014 John Wiley & Sons Ltd.

  5. Preparation and Characterization of Acrylic Primer for Concrete Substrate Application

    Directory of Open Access Journals (Sweden)

    El-Sayed Negim

    2016-01-01

    Full Text Available This study dealt with the properties of acrylic primer for concrete substrate using acrylic syrup, made from a methyl methacrylate monomer solution of terpolymers. Terpolymer systems consisting of methyl methacrylate (MMA, 2-ethylhexyl acrylate (2-EHA, and methacrylic acid (MAA with different chemical composition ratios of MMA and 2-EHA were synthesized through bulk polymerization using azobisisobutyronitrile (AIBN as initiator. The terpolymer composition is characterized by FTIR, 1H NMR, DSC, TGA, and SEM. The glass transition temperature and the thermal stability increased with increasing amounts of MMA in the terpolymer backbone. The effect of chemical composition of terpolymers on physicomechanical properties of primer films was investigated. However, increasing the amount of MMA in terpolymer backbone increased tensile and contact angle of primer films while elongation at break, water absorption, and bond strength are decreased. In particular, the primer syrup containing 65% 2-EHA has good bonding strength with concrete substrate around 1.1 MPa.

  6. USER-derived cloning methods and their primer design.

    Science.gov (United States)

    Salomonsen, Bo; Mortensen, Uffe H; Halkier, Barbara A

    2014-01-01

    Uracil excision-based cloning through USER™ (Uracil-Specific Excision Reagent) is an efficient ligase-free cloning technique that comprises USER cloning, USER fusion, and USER cassette-free (UCF) USER fusion. These USER-derived cloning techniques enable seamless assembly of multiple DNA fragments in one construct. Though governed by a few simple rules primer design for USER-based fusion of PCR fragments can prove time-consuming for inexperienced users. The Primer Help for USER (PHUSER) software is an easy-to-use primer design tool for USER-based methods. In this chapter, we present a PHUSER software protocol for designing primers for USER-derived cloning techniques.

  7. Best Development Practices: A Primer for Smart Growth

    Science.gov (United States)

    Best Development Practices: A Primer for Smart Growth lists specific practices to achieve development principles that mix land uses, support transportation options, protect natural systems, and provide housing choices.

  8. PrecisePrimer: an easy-to-use web server for designing PCR primers for DNA library cloning and DNA shuffling

    Science.gov (United States)

    Pauthenier, Cyrille; Faulon, Jean-Loup

    2014-01-01

    PrecisePrimer is a web-based primer design software made to assist experimentalists in any repetitive primer design task such as preparing, cloning and shuffling DNA libraries. Unlike other popular primer design tools, it is conceived to generate primer libraries with popular PCR polymerase buffers proposed as pre-set options. PrecisePrimer is also meant to design primers in batches, such as for DNA libraries creation of DNA shuffling experiments and to have the simplest interface possible. It integrates the most up-to-date melting temperature algorithms validated with experimental data, and cross validated with other computational tools. We generated a library of primers for the extraction and cloning of 61 genes from yeast DNA genomic extract using default parameters. All primer pairs efficiently amplified their target without any optimization of the PCR conditions. PMID:24829457

  9. Development and characterization of microsatellite primers in Pogostemon cablin (Lamiaceae).

    Science.gov (United States)

    Sandes, S S; Pinheiro, J B; Zucchi, M I; Monteiro, M; Arrigoni-Blank, M F; Blank, A F

    2013-08-08

    Microsatellite primers were developed and optimized for patchouli (Pogostemon cablin) to characterize the patchouli Active Germplasm Bank of Universidade Federal de Sergipe. Creation of a genomic library for patchouli enabled the design of 12 microsatellite primers. Six of these microsatellites were polymorphic, revealing two well-defined groups of individuals that possess exclusive alleles. The data allowed us to characterize the patchouli active Germplasm Bank, identify its genetic diversity, and provide new information for researching this species.

  10. Karakterisasi Unjuk Kerja Pompa Sistem Pendingin Primer Reaktor Triga 2000

    OpenAIRE

    Soekodijat, B

    2002-01-01

    KARAKTERISASI UNJUK KERJA POMPA SISTEM PENDINGIN PRIMER REAKTOR TRIGA 2000. Pompa sistem pendingin primer adalah salah satu komponen utama pada sistem pendingin Reaktor TRIGA 2000. Karakteristik unjuk kerja pompa sangat penting diketahui agar pompa dapat dioperasikan dengan baik dan aman. Penelitian dilakukan dengan cara memverifikasi kurva kinerja pompa yang diberikan oleh pabrik. Proses verifikasi dilakukan dengan mengubah-ubah laju alir pompa (dengan cara mengatur besar kecilnya pembukaan ...

  11. Universal PCR primers for ribosomal protein gene introns of fish

    Directory of Open Access Journals (Sweden)

    Seinen Chow

    2016-01-01

    Full Text Available Abstract Human ribosomal protein (RP gene sequences with respect to intron/exon structures and corresponding cDNA or genomic data of fish species were obtained from the GenBank database. Based on conserved exon sequences, 128 primer pairs for 41 genes were designed for exon-primed intron-crossing (EPIC polymerase chain reaction (PCR. In reference to the draft genome sequences of the Pacific bluefin tuna (Thunnus orientalis, 12 primer pairs expected to amplify introns of the bluefin tuna with lengths of 500–1000 bp were selected and applied to six distantly related fish species belonging to the Orders Clupeiformes, Tetraodontiformes, Pleuronectiformes, Perciformes, Scorpaeniformes, and Anguilliformes. PCR amplification was observed for at least four species in each primer pair, and all fragments were larger than those expected for intronless amplification. Single fragment amplification was observed for at least seven primer pairs per species. Fragment sizes of the bluefin tuna for nine primer pairs corresponded to those expected from the genomic data. Thus, our primer pairs are potentially applicable to a wide variety of fish species and serve as an initial step for isolating single-copy nuclear DNA sequences.

  12. TSUNAMI Primer: A Primer for Sensitivity/Uncertainty Calculations with SCALE

    Energy Technology Data Exchange (ETDEWEB)

    Rearden, Bradley T [ORNL; Mueller, Don [ORNL; Bowman, Stephen M [ORNL; Busch, Robert D. [University of New Mexico, Albuquerque; Emerson, Scott [University of New Mexico, Albuquerque

    2009-01-01

    This primer presents examples in the application of the SCALE/TSUNAMI tools to generate k{sub eff} sensitivity data for one- and three-dimensional models using TSUNAMI-1D and -3D and to examine uncertainties in the computed k{sub eff} values due to uncertainties in the cross-section data used in their calculation. The proper use of unit cell data and need for confirming the appropriate selection of input parameters through direct perturbations are described. The uses of sensitivity and uncertainty data to identify and rank potential sources of computational bias in an application system and TSUNAMI tools for assessment of system similarity using sensitivity and uncertainty criteria are demonstrated. Uses of these criteria in trending analyses to assess computational biases, bias uncertainties, and gap analyses are also described. Additionally, an application of the data adjustment tool TSURFER is provided, including identification of specific details of sources of computational bias.

  13. Evaluation of a new universal primer for ceramics and alloys.

    Science.gov (United States)

    Azimian, Farhad; Klosa, Karsten; Kern, Matthias

    2012-06-01

    To evaluate in vitro the effect of using a universal primer on the resin bond strength to ceramics (silicate and zirconia) and two noble alloys for metal-ceramic restorations. Disk-like specimens made of four dental restoration materials (silicate ceramic, zirconia ceramic, gold-based alloy and palladium-based alloy) were ground with abrasive paper, prepared for bonding (silicate ceramic: etching with 5% hydrofluoric acid for 60 s; the other materials: air abrasion with 50-µm Al2O3 at 2.5 bar) and ultrasonically cleaned in 96% isopropanol. Eight specimens of each material were primed with a universal primer, 8 specimens were primed with a well-established material-specific method (silicate ceramic: silanization; zirconia ceramic: phosphate monomer-containing primer; alloys: sulfuric monomer-containing primer). Plexiglas tubes filled with a composite resin were bonded to the specimens using an alignment apparatus and a composite luting resin. After storage in 37°C tap water for three days, or 167 days with additional thermocycling, tensile bond strength (TBS) was measured in a universal testing machine at a crosshead speed of 2 mm/min. After 167 days of storage, median TBS values for each material were (well-established method/universal primer) 40 MPa/37 MPa (silicate ceramic), 41 MPa/41 MPa (zirconia ceramic), 20 MPa/17 MPa (gold-based alloy), and 20 MPa/19 MPa (palladium-based alloy). Statistical analysis revealed no statistically significant differences among control groups and test groups. The universal primer seems to be a promising alternative compared to using three different primers for alloys, silicate and zirconia ceramics.

  14. Mutated primer binding sites interacting with different tRNAs allow efficient murine leukemia virus replication

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M; Lovmand, J

    1993-01-01

    Two Akv murine leukemia virus-based retroviral vectors with primer binding sites matching tRNA(Gln-1) and tRNA(Lys-3) were constructed. The transduction efficiency of these mutated vectors was found to be comparable to that of a vector carrying the wild-type primer binding site matching t......RNA(Pro). Polymerase chain reaction amplification and sequence analysis of transduced proviruses confirmed the transfer of vectors with mutated primer binding sites and further showed that tRNA(Gln-2) may act efficiently in conjunction with the tRNA(Gln-1) primer binding site. We conclude that murine leukemia virus...... can replicate by using various tRNA molecules as primers and propose primer binding site-tRNA primer interactions to be of major importance for tRNA primer selection. However, efficient primer selection does not require perfect Watson-Crick base pairing at all 18 positions of the primer binding site....

  15. Upper gastrointestinal findings detected by capsule endoscopy in obscure gastrointestinal bleeding Hallazgos digestivos altos de la cápsula endoscópica en la hemorragia digestiva de origen oscuro

    Directory of Open Access Journals (Sweden)

    B. Velayos

    2009-01-01

    Full Text Available Objective: we analyzed our experience with the use of capsule endoscopy in areas that can be explored with gastroscopy to justify obscure bleeding, as well as the outcome after a new recommended gastroscopy in order to determine if a second gastroscopy before the capsule study can provide any benefit in the management of this disease. Methods: we retrospectively studied 82 patients who were explored with capsule endoscopy for obscure gastrointestinal bleeding who had undergone previously only one gastroscopy. Findings in the zones which were accessible by gastroscopy were normal, mild/known and severe/unknown. In the latter cases we recommended a second gastroscopy, and their treatment and outcome were subjected to further study. Results: capsule endoscopy did not find any unknown esophageal findings. In 63% of cases, no gastric or duodenal lesions were shown; in 20%, lesions were mild or had been previously diagnosed, and in 17%, a new gastroscopy was recommended due to the discovery of an unknown condition which could be the cause of the obscure bleeding. This new information brought about a change in treatment for 78% of patients in this group, all of whom improved from their illness. Capsule endoscopy found significant intercurrent alterations in the small intestine in only 14% of cases. Conclusions: the performance of a second gastroscopy, previous to capsule endoscopy, in the study of obscure gastrointestinal bleeding can offer benefits in diagnostic terms and may introduce therapeutic changes. A detailed analysis of the upper tract frames in intestinal capsule endoscopy studies is mandatory since it may provide relevant information with clinical impact on the management of these patients.Objetivo: hemos analizado los hallazgos que la cápsula endoscópica aportó de las zonas accesibles a una gastroscopia que podrían justificar un sangrado digestivo oscuro, así como la evolución de estos enfermos tras la nueva gastroscopia recomendada

  16. Reconstituição do trato digestivo após falha de esofagogastro ou esofagocolo anastomose Digestive tract reconstitution after failed esophago-gastro or esophago-coloanastomosis

    Directory of Open Access Journals (Sweden)

    Italo Braghetto

    2013-03-01

    Full Text Available RACIONAL: Disfagia grave ou mesmo afagia pode ocorrer após esofagectomia secundária à necrose do órgão ascendido com estenose severa ou separação completa dos cotos. Ruptura catastrófica esofágica ou gástrica impulsiona a decisão de "desconectar" o esôfago, a fim de evitar graves complicações sépticas. As operações utilizadas para restabelecer a descontinuidade do esôfago não são padronizadas e reoperações para restabelecimento do trânsito digestivo superior são um verdadeiro desafio. MÉTODOS: Este é estudo retrospectivo da experiência dos autores durante 17 anos incluindo 18 pacientes, 14 previamente submetidos à esofagectomia e quatro esofagogastrectomia. Eles foram operados com o fim de restabelecer o trato digestivo superior. RESULTADOS: Refazer esofagogastro anastomose foi possível em 12 pacientes, 10 por meio da abordagem cervical e combinando esternotomia em quatro, a fim de realizar a nova anastomose. Em cinco pacientes esofagocolo anastomose foi novamente realizada. Interposição de enxerto livre de jejuno foi realizada em um paciente. As complicações ocorreram em 10 pacientes (55,5%: deiscência anastomótica em três, estenose em quatro, condrite esternal em dois e abscesso cervical em um. Não se observou mortalidade. CONCLUSÃO: Existem diferentes opções cirúrgicas para o tratamento desta situação clínica difícil e arriscada; deve ser tratada com procedimentos adaptados de acordo com o segmento anatômico disponível para ser usado, escolhendo o procedimento mais conservador.BACKGROUND: Severe dysphagia or even aphagia can occur after esophagectomy secondary to necrosis of the ascended organ with severe stricture or complete separation of the stumps. Catastrophic esophageal or gastric disruption drives the decision to "disconnect" the esophagus in order to prevent severe septic complications. The operations employed to re-establish esophageal discontinuity are not standardized and reoperations

  17. Utilización del Tisuacryl® en la anastomosis del esófago con otros segmentos del tubo digestivo Use of Tisuacryl® in esophagus anastomosis with other segments of the digestive tube

    Directory of Open Access Journals (Sweden)

    Rosalba Roque González

    2006-06-01

    Full Text Available Las dehiscencias y fístulas de las anastomosis del esófago con segmentos pediculados del tubo digestivo son complicaciones frecuentes en la cirugía del esófago. En diversas estadísticas recientes, nacionales y extranjeras, se ha registrado una incidencia de hasta el 40 %. Este hecho, unido a las ventajas reportadas en la utilización de los adhesivos sintéticos del tipo del Tisuacryl®, hace interesante realizar un estudio clínico para extender el uso del producto al reforzamiento de las suturas en la anastomosis del esófago con otros segmentos del tubo digestivo, con el fin de prevenir las dehiscencias. Se realizó un ensayo clínico de fase II, prospectivo, controlado, aleatorizado, multicéntrico, a simple ciegas, que se extendió desde enero de 1998 hasta febrero de 2005. En él se incluyeron pacientes que ingresaron en los hospitales «Calixto García» y «Miguel Enríquez» con el diagnóstico de enfermedades esofágicas. Se logró la introducción en el país de una nueva aplicación para el adhesivo tisular Tisuacryl® y se demostró que la utilización del producto es una opción significativamente más ventajosa que el procedimiento convencional sólo con sutura, ya que se obtuvo una eficacia del 93 % en el grupo experimental respecto al 64 % en el grupo control. Uno y otro grupo eran homogéneos respecto a las variables de control. El tratamiento con Tisuacryl® disminuyó la frecuencia de aparición de fístulas esofágicas y no se reportaron eventos adversos en relación con la aplicación del producto.The dehiscences and fistulae of esophagus anastomosis with pedicular segments of the digestive tube are frequent complications in esophagus surgery. In various recent national and foreign statistics, an incidence of even 40 % has been registered. This fact, together with the advantages reported on the use of synthetic adhesives like Tisuacryl® made us to take an interest in conducting a clinical study to extend the use of

  18. PCR primers for metazoan mitochondrial 12S ribosomal DNA sequences.

    Directory of Open Access Journals (Sweden)

    Ryuji J Machida

    Full Text Available BACKGROUND: Assessment of the biodiversity of communities of small organisms is most readily done using PCR-based analysis of environmental samples consisting of mixtures of individuals. Known as metagenetics, this approach has transformed understanding of microbial communities and is beginning to be applied to metazoans as well. Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics is less clear. In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete mitochondrial genomes and then tested their efficacy. METHODOLOGY/PRINCIPAL FINDINGS: A total of the 64 complete mitochondrial genome sequences representing all metazoan classes available in GenBank were downloaded using the NCBI Taxonomy Browser. Alignment of sequences was performed for the excised mitochondrial 12S ribosomal DNA sequences, and conserved regions were identified for all 64 mitochondrial genomes. These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete metazoan mitochondrial genomes available in NCBI's Organelle Genome Resources database were used to determine the percentage of taxa that would likely be amplified using these primers. Results suggest that these primers will amplify target sequences for many metazoans. CONCLUSIONS/SIGNIFICANCE: Newly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis because of their ability to amplify sequences from many metazoans.

  19. Antagonistic and protective effects against Salmonella enterica serovar typhimurium by Lactobacillus murinus in the digestive tract of gnotobiotic mice Efeitos antagonista e protetor contra Salmonella enterica sorovar Typhimurium por Lactobacillus murinus no trato digestivo de camundongos gnotobióticos

    Directory of Open Access Journals (Sweden)

    Ana Luiza Sampaio Vasconcelos

    2003-11-01

    Full Text Available In the present study, production of antagonistic substances by Lactobacillus murinus against enteropathogenic bacteria was evaluated in vivo as well as a possible protective effect against an oral challenge with Salmonella Typhimurium using a gnotobiotic animal model. A higher mean survival time (P No presente estudo, a produção de substâncias antagonistas por Lactobacillus murinus contra bactérias enteropatogênicas foi avaliada in vivo assim como um possível efeito protetor contra um desafio oral com Salmonella Typhimurium utilizando um modelo animal gnotobiótico. Um maior tempo médio de sobrevida (P < 0,05 foi observado nos animais associados com L. murinus (7,89 ± 3,83 dias quando comparado com os controles (4,44 ± 0,73 dias. Lactobacillus murinus exerceu um potente efeito antagonista in vivo contra S. sonnei e com menos intensidade contra S. Typhimurium como revelado pelos halos de inibição ao redor das fezes dos animais associados com L. murinus. Os diâmetros dos halos de inibição ao redor dos conteúdos intestinais aumentaram ao longo do trato digestivo, seguindo proporcionalmente os níveis populacionais de L. murinus nas respectivas porções intestinais. Concluindo, o presente estudo mostra que a associação com L. murinus em camundongos gnotobióticos retarda a morte após um desafio oral com S. Typhimurium e que compostos inibitórios difusíveis obtidos em ensaios in vitro foram também produzidos in vivo e podem ser responsáveis por este efeito.

  20. Fungal flora of the digestive tract of Rhodnius prolixus, Rhodnius neglectus, Diptelanogaster maximus and Panstrongylus megistus, vectors of Trypanosoma cruzi, Chagas, 1909 Flora fúngica do trato digestivo de Rhodnius prolixus, Rhodnius neglectus, Diptelanogaster maximus e Panstrongylus megistus vetores de Trypanosoma cruzi, Chagas 1909

    Directory of Open Access Journals (Sweden)

    Aurea Maria Lage de Moraes

    2004-12-01

    Full Text Available This paper reports a study on the mycobiota in the digestive tract of four important species of triatomines: Rhodnius prolixus, R. neglectus, Diptelanogaster maximus and Panstrongylus megistus. The digestive tracts of 90 adults and 425 nymphs of these four triatomine species were studied and 365 fungal strains were isolated. The genera with the greatest number of species were Aspergillus, Penicillium (14 species in each genus, Acremonium and Cladosporium (three species in each genus, and the most frequent species, in decreasing order, were Aspergillus awamori, Penicillium corylophilum, Cladosporium herbarum and Aspergillus niger. It was concluded that, among the isolated fungi, Aspergillus niger and Penicillium corylophilum might be part of the natural flora of the digestive tract of triatomines.Um estudo da micobiota do trato digestivo de quatro importantes espécies de triatomíneos, Rhodnius prolixus, R. neglectus, Diptelanogaster maximus e Panstrongylus megistus, foi realizado. Foram examinados os tratos digestivos de 90 adultos e 425 ninfas destas espécies de triatomíneos e 365 cepas fúngicas foram isoladas. Os gêneros com o maior número de espécies encontradas foram Aspergillus, Penicillium (14 espécies cada, Acremonium e Cladosporium (3 espécies cada e as espécies mais freqüentes, em ordem decrescente, foram Aspergillus awamori, Penicillium corylophilum, Cladosporium herbarum e Aspergillus niger. Dentre os fungos isolados, concluímos que Aspergillus niger e Penicillium corylophilum possam fazer parte da flora natural do trato digestivo destes triatomíneos.

  1. New cyt b gene universal primer set for forensic analysis.

    Science.gov (United States)

    Lopez-Oceja, A; Gamarra, D; Borragan, S; Jiménez-Moreno, S; de Pancorbo, M M

    2016-07-01

    Analysis of mitochondrial DNA, and in particular the cytochrome b gene (cyt b), has become an essential tool for species identification in routine forensic practice. In cases of degraded samples, where the DNA is fractionated, universal primers that are highly efficient for the amplification of the target region are necessary. Therefore, in the present study a new universal cyt b primer set with high species identification capabilities, even in samples with highly degraded DNA, has been developed. In order to achieve this objective, the primers were designed following the alignment of complete sequences of the cyt b from 751 species from the Class of Mammalia listed in GenBank. A highly variable region of 148bp flanked by highly conserved sequences was chosen for placing the primers. The effectiveness of the new pair of primers was examined in 63 animal species belonging to 38 Families from 14 Orders and 5 Classes (Mammalia, Aves, Reptilia, Actinopterygii, and Malacostraca). Species determination was possible in all cases, which shows that the fragment analyzed provided a high capability for species identification. Furthermore, to ensure the efficiency of the 148bp fragment, the intraspecific variability was analyzed by calculating the concordance between individuals with the BLAST tool from the NCBI (National Center for Biotechnological Information). The intraspecific concordance levels were superior to 97% in all species. Likewise, the phylogenetic information from the selected fragment was confirmed by obtaining the phylogenetic tree from the sequences of the species analyzed. Evidence of the high power of phylogenetic discrimination of the analyzed fragment of the cyt b was obtained, as 93.75% of the species were grouped within their corresponding Orders. Finally, the analysis of 40 degraded samples with small-size DNA fragments showed that the new pair of primers permits identifying the species, even when the DNA is highly degraded as it is very common in

  2. RUCS: rapid identification of PCR primers for unique core sequences.

    Science.gov (United States)

    Thomsen, Martin Christen Frølund; Hasman, Henrik; Westh, Henrik; Kaya, Hülya; Lund, Ole

    2017-12-15

    Designing PCR primers to target a specific selection of whole genome sequenced strains can be a long, arduous and sometimes impractical task. Such tasks would benefit greatly from an automated tool to both identify unique targets, and to validate the vast number of potential primer pairs for the targets in silico. Here we present RUCS, a program that will find PCR primer pairs and probes for the unique core sequences of a positive genome dataset complement to a negative genome dataset. The resulting primer pairs and probes are in addition to simple selection also validated through a complex in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin resistance gene. Three of the predicted pairs were chosen for experimental validation using PCR and gel electrophoresis. All three pairs successfully produced an amplicon with the target length for the samples containing mcr-1 and no amplification products were produced for the negative samples. The novel methods presented in this manuscript can reduce the time needed to identify target sequences, and provide a quick virtual PCR validation to eliminate time wasted on ambiguously binding primers. Source code is freely available on https://bitbucket.org/genomicepidemiology/rucs. Web service is freely available on https://cge.cbs.dtu.dk/services/RUCS. mcft@cbs.dtu.dk. Supplementary data are available at Bioinformatics online.

  3. Depth profiles and free volume in aircraft primer films

    Science.gov (United States)

    Van Horn, J. D.; Chen, H.; Jean, Y. C.; Zhang, W.; Jaworowski, M. R.

    2015-06-01

    Positron annihilation lifetime spectroscopy (PALS) and associated techniques provide non-destructive methods to study the free volume inside polymeric materials, and to study material characteristics over a depth profile. Cast free films of organic- or aqueous-based, non-chromated aerospace primers, when cured for about one week, had very different water vapour transport (through-plane) behaviour. In addition, both types of primer films showed strong anisotropic behaviour in in-plane versus through-plane water vapour transport rates. We report the differences between the organic- and aqueous-based aircraft primer films samples and their surface depth profiles. In bulk PALS measurements, an aged, organic-based film exhibited typical lifetimes and intensities for a particulate-containing polymer film on both faces. In contrast, aqueous-based films exhibited face oriented-dependent differences. In all aqueous- based samples, the I3 value of the back of the sample was smaller. The primer film samples were also evaluated with mono-energetic positron beam techniques to generate depth profile information. The heterogeneity in the samples was verified by Doppler broadening of energy spectroscopy (DBES). A model for the differences in the faces of the films, and their layered structure is discussed.

  4. Improved primer for bonding polyurethane adhesives to metals

    Science.gov (United States)

    Constanza, L. J.

    1969-01-01

    Primer ensures effective bonding integrity of polyurethane adhesives on metal surfaces at temperatures ranging from minus 423 degrees to plus 120 degrees F. It provides greater metal surface protection and bond strengths over this temperature range than could be attained with other adhesive systems.

  5. Barcoded primers used in multiplex amplicon pyrosequencing bias amplification.

    Science.gov (United States)

    Berry, David; Ben Mahfoudh, Karim; Wagner, Michael; Loy, Alexander

    2011-11-01

    "Barcode-tagged" PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.

  6. RUCS: Rapid identification of PCR primers for unique core sequences

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Hasman, Henrik; Westh, Henrik

    2017-01-01

    in silico PCR simulation. We compared our method, which identifies the unique core sequences, against an existing tool called ssGeneFinder, and found that our method was 6.5-20 times more sensitive. We used RUCS to design primer pairs that would target a set of genomes known to contain the mcr-1 colistin...

  7. Sights, Sounds, Senses in Step with Reading. Primer.

    Science.gov (United States)

    Norris, Mildred W.; Messerli, John H.

    This Title III bibliography presents books, films, filmstrips, and records that correlate with stories from primers. The list of books is prepared from the suggested lists of the Ginn, Houghton Mifflin, Lippincott, and Scott, Foresman reading series. The bibliography includes sections about animals, birthdays, cowboys, fantasy, helpers, holidays,…

  8. Children on Medication: A Primer for School Personnel.

    Science.gov (United States)

    Gadow, Kenneth D.

    Intended as a primer for school personnel, the book discusses children whose various disorders require them to be on medication, and describes the behavioral effects of these drugs along with their major side effects. Fundamental concepts in pharmacotherapy are reviewed, including dosage adjustment and side effects, and a brief introduction to the…

  9. A Primer on Ways To Explore Item Bias.

    Science.gov (United States)

    Cromwell, Susan

    This paper provides an introductory primer on methods for exploring item bias. The purposes of item bias analysis are to investigate whether test scores are affected by different sources of variance in the various subpopulations, and if different sources of variance are found, to determine if an unfair advantage exists. The review discusses three…

  10. Onchocercal DNA amplification using beta actin gene primers ...

    African Journals Online (AJOL)

    Detecting any parts of the parasite stages such as antigens, enzymes and nucleic acids (DNA and RNA) is a definitive diagnosis and highly sensitive. This study was to evaluate the diagnostic reliability of the beta actin gene primer pair to confirm its suitability for validating presence or absence of skin microfilaria at ...

  11. STITCHER 2.0: primer design for overlapping PCR applications.

    Science.gov (United States)

    O'Halloran, Damien M; Uriagereka-Herburger, Isabel; Bode, Katrin

    2017-03-30

    Overlapping polymerase chain reaction (PCR) is a common technique used by researchers in very diverse fields that enables the user to 'stitch' individual pieces of DNA together. Previously, we have reported a web based tool called STITCHER that provides a platform for researchers to automate the design of primers for overlapping PCR applications. Here we present STITCHER 2.0, which represents a substantial update to STITCHER. STITCHER 2.0 is a newly designed web tool that automates the design of primers for overlapping PCR. Unlike STITCHER, STITCHER 2.0 considers diverse algorithmic parameters, and returns multiple result files that include a facility for the user to draw their own primers as well as comprehensive visual guides to the user's input, output, and designed primers. These result files provide greater control and insight during experimental design and troubleshooting. STITCHER 2.0 is freely available to all users without signup or login requirements and can be accessed at the following webpage: www.ohalloranlab.net/STITCHER2.html.

  12. Characteristics of the population employed in primer sector in Turkey

    Directory of Open Access Journals (Sweden)

    Bayar Rüya

    2006-01-01

    Full Text Available Activities related to the production of raw material like agriculture husbandry, forestry, fishery are called as primer activities. Especially people living in rural areas earn their livings on primer activities, mainly agriculture. Rural planning is inevitable for providing rural development which has an important place in all development of a country. And achievement of this planning depends on putting forth the characteristics of the population living in rural areas with its different aspects. Therefore, the requirements will be introduced more clearly and the increase in the welfare levels of the people living in rural areas will have been achieved. To achieve the rural development and progress, in addition to the features like the size of agricultural products, products that are cultivated, activities like husbandry, forestry, hunting, etc. and the qualities of the enterprises in which these activities are carried out, policies applied, capital, market and technology, the characteristics of the population employed in this sector is also of importance. Considering these points, what is aimed in this study is to put forth the characteristics of the population employed in primer sector in Turkey. According to the census results of the year 2000 in Turkey 38% of the population is employed, and 48% of this work is in primer sector.

  13. A Primer on Concepts and Applications of Proteomics in Neuroscience

    DEFF Research Database (Denmark)

    Hosp, Fabian; Mann, Matthias

    2017-01-01

    The enormous complexity of the central nervous system has impeded its systemic exploration for decades but powerful "omic" technologies are now pushing forward the frontiers of neuroscience research at an increasing pace. This Primer reviews the most recent progress in mass spectrometry (MS...

  14. Development of a microsatellite primer set to investigate the genetic ...

    Indian Academy of Sciences (India)

    Development of a microsatellite primer set to investigate the genetic population structure of Armadillidium nasatum (Crustacea, Oniscidea). Séverine Masson, Cédric Faivre, Isabelle Giraud, Catherine Souty-Grosset, Richard Cordaux, Carine Delaunay,. Didier Bouchon and Nicolas Bech. J. Genet. 93, 545–549. Table 1.

  15. Bioinformatic tools and guideline for PCR primer design | Abd ...

    African Journals Online (AJOL)

    A poorly designed primer can result in little or no product due to non-specific ... There are several online tools devoted to serving molecular biologist design effective ... This review intends to provide a guide to choosing the most efficient way to ...

  16. Diversity of internal structures in inhibited epoxy primers

    Directory of Open Access Journals (Sweden)

    Anthony E. Hughes

    2015-10-01

    Full Text Available Computed tomography is making a significant impact in the field of materials science in recent years. In this paper the authors report on advances made in three areas of characterization and also identified where further research needs to be focused. First we report on a new approach to data analysis called “Data Constrained Modelling (DCM” in which compositional tomography can be undertaken rather than adsorption or phase contrast tomography. This is achieved by collecting X-ray CT data at different energies and then combining the datasets to reconstruct 3D compositional tomography. Second, on the application of this approach to inhibited primers typical of those used in the aerospace industry. Aerospace primers are effectively composite materials containing inorganic phases which are bound together with a polymer. Understanding the materials science of these systems requires information over several orders of magnitude in length-scale. In this paper we report on how DCM can be used to extend our understanding at the smaller length scales at the limits of resolution of the technique. The third and final advance is in extending the approach to include 4-dimensional studies. In this case we examine the primer before and after leaching. This process causes changes in the primer which can be both detected and quantified using the above approach.

  17. Racial Microaggressions: A Primer with Implications for Counseling Practice

    Science.gov (United States)

    Houshmand, Sara; Spanierman, Lisa B.; De Stefano, Jack

    2017-01-01

    Given their societal toll and ubiquitous nature, counselors and other mental health professionals inevitably will encounter clients who have experienced racial microaggressions in their practice. In this primer, we examine key issues relative to racial microaggressions and their impact on the lives of members of racial and ethnic minority groups.…

  18. Editorial primer Numero Revista Chilena de Relaciones Internacionales

    OpenAIRE

    Hugo Castro Valdebenito

    2017-01-01

    Con inmenso agrado y entusiasmo presentamos el primer número de la Revista Chilena de Relaciones Internacionales. Confiamos que el producto de las investigaciones presentadas servirá como un aporte a la aún naciente, disciplina de las Relaciones Internacionales.

  19. Criticality calculations with MCNP{trademark}: A primer

    Energy Technology Data Exchange (ETDEWEB)

    Harmon, C.D. II; Busch, R.D.; Briesmeister, J.F.; Forster, R.A. [New Mexico Univ., Albuquerque, NM (United States)

    1994-06-06

    With the closure of many experimental facilities, the nuclear criticality safety analyst increasingly is required to rely on computer calculations to identify safe limits for the handling and storage of fissile materials. However, in many cases, the analyst has little experience with the specific codes available at his/her facility. This primer will help you, the analyst, understand and use the MCNP Monte Carlo code for nuclear criticality safety analyses. It assumes that you have a college education in a technical field. There is no assumption of familiarity with Monte Carlo codes in general or with MCNP in particular. Appendix A gives an introduction to Monte Carlo techniques. The primer is designed to teach by example, with each example illustrating two or three features of MCNP that are useful in criticality analyses. Beginning with a Quickstart chapter, the primer gives an overview of the basic requirements for MCNP input and allows you to run a simple criticality problem with MCNP. This chapter is not designed to explain either the input or the MCNP options in detail; but rather it introduces basic concepts that are further explained in following chapters. Each chapter begins with a list of basic objectives that identify the goal of the chapter, and a list of the individual MCNP features that are covered in detail in the unique chapter example problems. It is expected that on completion of the primer you will be comfortable using MCNP in criticality calculations and will be capable of handling 80 to 90 percent of the situations that normally arise in a facility. The primer provides a set of basic input files that you can selectively modify to fit the particular problem at hand.

  20. Técnica de Rosanov modificada na reconstrução do trato digestivo após gastrectomia total The modified Rosanov technique in the reconstruction of digestive tract after total gastrectomy

    Directory of Open Access Journals (Sweden)

    Luiz Roberto Lopes

    2011-06-01

    Full Text Available RACIONAL: A gastrectomia total nas neoplasias gástricas é um procedimento não isento de complicações precoces e tardias e o tipo de reconstrução do trato digestivo a ser utilizado é ainda questão controversa na literatura. OBJETIVO: Descrever a técnica de Rosanov modificada, após a gastrectomia total, empregada com o objetivo de minimizar a má absorção intestinal e outras complicações após este tipo de procedimento. MÉTODOS: A modificação técnica consiste de não realizar a ligadura distal à anastomose jejuno-duodenal, fazendo assim com que o trânsito alimentar tenha duas vias de passagens, pelo duodeno e pelo jejuno. RESULTADOS: Não foram registradas complicações e a casuística inicial mostrou vantagens sob os aspectos nutricionais após seis meses de seguimento pós-operatório. CONCLUSÃO: É técnica de fácil execução e os resultados preliminares com o seu emprego foram muito satisfatórios, no entanto outros estudos clínicos devem ser realizados para demonstrar as vantagens da técnica a longo prazo.BACKGROUND: Total gastrectomy in gastric cancer is a procedure not without early and late complications and type of reconstruction of the digestive tract to be used is still a controversial issue in literature. AIM: To describe a modified Rosanov technique after total gastrectomy, employed with the aim of minimizing the intestinal malabsorption and other complications following this procedure. METHOD: Technical modification is not to hold distal ligature on jejuno-duodenal anastomosis, thereby offering to the food transit two routes by the duodenum and by the jejunum. RESULTS: There were no complications and the initial series showed a benefit in the nutritional aspects after six months of postoperative follow-up. CONCLUSION: It is a simple technique and preliminary results with its use were very satisfactory, although other clinical studies must be conducted to demonstrate the advantages of the technique in the

  1. Técnicas de sutura do tubo digestivo em plano único com nós atados no lume, em cães: pontos simples totais versus pontos extramucosos

    Directory of Open Access Journals (Sweden)

    Azevedo João Luiz Moreira Coutinho

    2005-01-01

    Full Text Available OBJETIVO: Comparar a anastomose do tubo digestivo em plano único com nós atados no lume por sutura com pontos totais versus pontos extramucosos. MÉTODOS: Foram operados seis cães, com realização de duas secções transversas do jejuno a 30 cm e a 70 cm da flexura duodenojejunal e sutura, na face posterior com pontos extramucosos atados sobre a submucosa, e na face anterior com pontos totais atados sobre a mucosa. No 7º PO foram avaliadas, na face posterior, as aderências na linha de sutura e feitos exames macroscópico e microscópico. RESULTADOS: As aderências peritoneais foram mais profusas nas suturas extramucosas com tecido aderencial sobre a linha de sutura, sem reconstituição da serosa, ou com a deformidade cicatricial das serosas dos cotos angulando a anastomose. A serosa teve boa reconstituição nas suturas totais. O epitélio mucoso reconstituiu-se perfeitamente nas extramucosas, mas não nas totais. Nas suturas totais houve focos residuais de inflamação aguda.O realinhamento, a reestruturação e a regeneração das camadas (exceto a serosa, cuja regeneração foi prejudicada por aderências foi melhor na sutura extramucosa que na total. A muscular da mucosa não se regenerou em nenhuma anastomose. Os polimorfonucleares, os macrófagos, os fibroblastos e as fibras colágenas foram mais numerosos (significância estatística na sutura total. CONCLUSÃO: As suturas totais da parede posterior da anastomose com nós atados no lume, sobre a mucosa, são seguras, apesar da inflamação maior. A sutura extramucosa da parede posterior, com nós atados no lume, sobre a submucosa, propicia a formação de aderências peritoneais, devendo ser evitada.

  2. Primer Output and Initial Projectile Motion for 5.56- and 7.62-mm Ammunition

    Science.gov (United States)

    2015-09-01

    10 The impulse from the primer firing was calculated from the integration of the first primer pressure pulse over the time for which it is...ARL-TR-7479 ● SEP 2015 US Army Research Laboratory Primer Output and Initial Projectile Motion for 5.56- and 7.62-mm Ammunition...report when it is no longer needed. Do not return it to the originator. ARL-TR-7479 ● SEP 2015 US Army Research Laboratory Primer

  3. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis

    OpenAIRE

    Riaz, Tiayyba; Shehzad, Wasim; Viari, Alain; Pompanon, Fran?ois; Taberlet, Pierre; Coissac, Eric

    2011-01-01

    Using non-conventional markers, DNA metabarcoding allows biodiversity assessment from complex substrates. In this article, we present ecoPrimers, a software for identifying new barcode markers and their associated PCR primers. ecoPrimers scans whole genomes to find such markers without a priori knowledge. ecoPrimers optimizes two quality indices measuring taxonomical range and discrimination to select the most efficient markers from a set of reference sequences, according to specific experime...

  4. Quantitative Experimental Determination of Primer-Dimer Formation Risk by Free-Solution Conjugate Electrophoresis

    OpenAIRE

    Desmarais, Samantha M.; Leitner, Thomas; Barron, Annelise E.

    2012-01-01

    DNA barcodes are short, unique ssDNA primers that “mark” individual biomolecules. To gain better understanding of biophysical parameters constraining primer-dimer formation between primers that incorporate barcode sequences, we have developed a capillary electrophoresis method that utilizes drag-tag-DNA conjugates to quantify dimerization risk between primer-barcode pairs. Results obtained with this unique free-solution conjugate electrophoresis (FSCE) approach are useful as quantitatively pr...

  5. Usefulness of endoscopic ultrasonography in the preoperative diagnosis of submucosal digestive tumours Utilidad de la encoendoscopia en el diagnóstico preoperatorio de malignidad de los tumores submucosos digestivos

    Directory of Open Access Journals (Sweden)

    D. Martínez-Ares

    2005-06-01

    last three factors were considered independent predictive factors for malignancy. Conclusions: endoscopic ultrasonography has a great sensitivity and specificity in the diagnosis of malignancy regarding submucosal lesions. The irregularity of lesion borders, a heterogeneous ultrasonographic pattern, and the presence of cystic areas above 2 mm in size were considered independent predictive factors for malignancy.Introducción: el diagnóstico preoperatorio de las lesiones submucosas del tubo digestivo puede ser complicado. La endoscopia convencional no permite establecer claramente un diagnóstico y no valora adecuadamente el tamaño de las lesiones. Además, la biopsia endoscópica no suele ser diagnóstica. La citología obtenida por medio de la punción con aguja fina tampoco presenta la suficiente sensibilidad y especificidad como para ser considerada como el patrón oro en el diagnóstico de estas lesiones. Evaluamos a continuación la utilidad de la ultrasonografía endoscópica en el estudio de los tumores submucosos digestivos. Material y métodos: hemos recogido de forma prospectiva los estudios ultrasonográficos de todos los pacientes con tumores submucosos tratados quirúrgicamente en nuestro centro. Se ha evaluado la sensibilidad y especificidad de esta técnica en el diagnóstico de malignidad de estas lesiones, así como los factores que con mayor fiabilidad predicen el comportamiento maligno. También se valoró la fiabilidad de la ecoendoscopia en la valoración del tamaño y en identificar la capa de la pared en que se localizan las lesiones. Los resultados del estudio anatomopatológico fueron considerados el patrón oro en el diagnóstico. Resultados: el tamaño medio de las lesiones medido por ecoendoscopia no presenta diferencias significativas con el de la pieza quirúrgica. Sin embargo, la endoscopia convencional infravalora el tamaño de las lesiones. La ultrasonografía endoscópica estableció adecuadamente la capa de origen de las lesiones en

  6. Endoscopic ultrasound-assisted endoscopic resection of carcinoid tumors of the gastrointestinal tract Resección endoscópica asistida por ecoendoscopia de tumores carcinoides del aparato digestivo

    Directory of Open Access Journals (Sweden)

    D. Martínez-Ares

    2004-12-01

    in 2 cases (8.3% after ligating the lesion with elastic bands. In all cases the resection was complete, with no recurrence during the follow-up period, and no major complications, except for a single case in which a post-polypectomy hemorrhage occurred that was endoscopically solved. Conclusions: in properly selected patients, the endoscopic resection of carcinoid tumors is a safe and effective technique that permits a complete resection in all cases with few complications. Endoscopic ultrasonography is the technique of choice for selecting the patients who are candidates for endoscopic resection.Introducción: los carcinoides son los tumores neuroendocrinos más frecuentes, representado el tracto digestivo una de sus localizaciones más habituales. La mayoría de las lesiones se localizan en áreas poco accesibles para la endoscopia convencional (intestino delgado y apéndice; los carcinoides localizados en el tracto gastroduodenal y en el intestino grueso pueden ser estudiados endoscópicamente; en estos casos, si se confirma una enfermedad localizada, el tratamiento local mediante resección endoscópica puede ser el tratamiento de elección. Dado que la ecoendoscopia se ha mostrado como la técnica de elección en el estudio de los tumores de crecimiento submucoso, la selección de los pacientes candidatos a una resección local segura y efectiva ha de basarse en esta técnica. Pacientes y método: se han seleccionado los pacientes con tumores carcinoides digestivos tratados endoscópicamente entre 1997 y 2002. Se consideraron subsidiarios de resección endoscópica aquellos pacientes con tumores menores de 10 mm, que respetan la muscular propia y con un estudio de extensión negativo. Los objetivos finales del estudio fueron la evaluación de la eficacia (resección completa y seguridad (complicaciones de la técnica. El seguimiento consistió en biopsias de la escara al mes y los 12 meses de la resección. Resultados: en el periodo referido hemos resecado

  7. Chemical and mechanical aspects of HMR primer in relationship to wood bonding

    Science.gov (United States)

    Alfred W. Christiansen

    2005-01-01

    The mechanism by which hydroxymethylated resorcinol (HMR) primer improves the durability of various adhesives to wood has been hypothesized as covalent chemical links between the adhesive and primer and possibly between the primer and wood. The present work presents experiments to test this hypothesis. In the first test, some resorcinol was displaced by 2- methylres-...

  8. Guidelines - A Primer for Communicating Effectively with NABIR Stakeholders

    Energy Technology Data Exchange (ETDEWEB)

    A Harding; B Metting; C Word; G Bilyard; G Hund; J Amaya; J Weber; S Gajewski; S Underriner; T Peterson

    1998-12-10

    This primer is a tool to help prepare scientists for meetings with stakeholders. It was prepared for staff involved with the Natural and Accelerated Bioremediation Research (NABIR) program, sponsored by the U.S. Department of Energy. It discusses why some efforts in science communication may succeed while others fail, provides methods of approaching group interactions about science that may better orient expert participants, and summarizes experience drawn from observations of @oups interacting about topics in bioremediation or the NABIR program. The primer also provides briez usefid models for interacting with either expert or non-expert groups. Finally, it identifies topical areas that may help scientists prepare for public meetings, based on the developers' ongoing research in science communication in public forums.

  9. Microsatellite Primers for the Pacific Northwest Conifer Callitropsis nootkatensis (Cupressaceae

    Directory of Open Access Journals (Sweden)

    Tara N. Jennings

    2013-09-01

    Full Text Available Premise of the study: Microsatellite primers were developed for Nootka cypress (Callitropsis nootkatensis to provide quantitative measures for gene conservation that can assist in guiding management decisions for a species experiencing climate-induced decline. Methods and Results: Using multiplexed massively parallel sequencing, we identified 136,785 microsatellite-containing sequences from 489,625 Illumina paired-end 80-bp reads. After stringent filtering, we selected 144 primer pairs and screened variation at these loci in five populations of C. nootkatensis. Loci show between three and 36 dinucleotide repeats per locus, with an average of 13. Screening of these markers in the Pacific Northwest relative Chamaecyparis lawsoniana demonstrated no marker transferability. This finding highlights the narrow taxonomic utility of microsatellite markers in Callitropsis. Conclusions: These microsatellites show high polymorphism and can be used for routine screening of natural variation in Callitropsis nootkatensis, and will be particularly helpful in identifying clones and inbred relatives at the stand-level.

  10. Primer and interviews: molecular mechanisms of morphological evolution.

    Science.gov (United States)

    Kiefer, Julie C

    2010-12-01

    The beauty of the developing embryo, and the awe that it inspires, lure many scientists into the field of developmental biology. What compels cells to divide, migrate, and morph into a being with a complex body plan? Evolutionary developmental biologists hold similar fascinations, with dynamics that take place on a grander timescale. How do phenotypic traits diverge over evolutionary time? This primer illustrates how a deep understanding of the basic principles that underlie developmental biology have changed how scientists think about the evolution of body form. The primer culminates in a conversation with David Stern, PhD, and Michael Shapiro, PhD, who discuss current topics in morphological evolution, why the field should be of interest to classic developmental biologists, and what lies ahead. © 2010 Wiley-Liss, Inc.

  11. Guidelines - A Primer for Communicating Effectively with NABIR Stakeholders

    Energy Technology Data Exchange (ETDEWEB)

    Bilyard, Gordon R.; Word, Charlotte J.; Weber, James R.; Harding, Anna K.

    2000-09-27

    This primer is a tool to help prepare scientists for meetings with stakeholders. It was prepared for staff involved with the Natural and Accelerated Bioremediation Research (NABIR) program, sponsored by the U.S. Department of Energy. It discusses why some efforts in science communication may succeed while others fail, provides methods of approaching group interactions about science that may better orient expert participants, and summarizes experience drawn from observations of groups interacting about topics in bioremediation or the NABIR program. The primer also provides brief, useful models for interacting with either expert or non-expert groups. Finally, it identifies topical areas that may help scientists prepare for public meetings, based on the developers' ongoing research in science communication in public forums.

  12. Primer on molecular genetics. DOE Human Genome Program

    Energy Technology Data Exchange (ETDEWEB)

    1992-04-01

    This report is taken from the April 1992 draft of the DOE Human Genome 1991--1992 Program Report, which is expected to be published in May 1992. The primer is intended to be an introduction to basic principles of molecular genetics pertaining to the genome project. The material contained herein is not final and may be incomplete. Techniques of genetic mapping and DNA sequencing are described.

  13. Transient Heat Transfer Model for Car Body Primer Curing

    OpenAIRE

    D. Zabala; N. Sánchez; J. Pinto

    2010-01-01

    A transient heat transfer mathematical model for the prediction of temperature distribution in the car body during primer baking has been developed by considering the thermal radiation and convection in the furnace chamber and transient heat conduction governing equations in the car framework. The car cockpit is considered like a structure with six flat plates, four vertical plates representing the car doors and the rear and front panels. The other two flat plates are the...

  14. PRIMER REGISTRO DE SLOANEA (ELAEOCARPACEAE PARA LA ARGENTINA

    Directory of Open Access Journals (Sweden)

    Héctor A. Keller

    2012-01-01

    Full Text Available Sloanea lasiocoma (Elaeocarpaceae se cita por primera vez para la flora argentina en la provincia de Misiones y es el primer registro de Eleocarpaceae en el nordeste argentino. Se describe e ilustra la especie y se brindan observaciones ecológicas. Se incluye una clave para distinguir a Sloanea de los otros tres géneros de la familia Elaeocarpaceae presentes en la Argentina.

  15. Small Commercial Building Re-tuning: A Primer

    Energy Technology Data Exchange (ETDEWEB)

    Cort, Katherine A.; Hostick, Donna J.; Underhill, Ronald M.; Fernandez, Nicholas; Katipamula, Srinivas

    2013-09-30

    To help building owners and managers address issues related to energy-efficient operation of small buildings, DOE has developed a Small Building Re-tuning training curriculum. This "primer" provides additional background information to understand some of the concepts presented in the Small Building Re-tuning training. The intent is that those who are less familiar with the buidling energy concepts will review this material before taking the building re-tuning training class.

  16. Long-distance translocation of photosynthates: a primer.

    Science.gov (United States)

    Knoblauch, Michael; Peters, Winfried S

    2013-11-01

    The storage of light energy in chemical form through photosynthesis is the key process underlying life as we know it. To utilize photosynthates efficiently as structural materials or as fuel to drive endergonic processes, they have to be transported from where they are produced to where they are needed. In this primer, we provide an overview of basic biophysical concepts underlying our current understanding of the mechanisms of photosynthate long-distance transport, and briefly discuss current developments in the field.

  17. The Use of Degenerate Primers in qPCR Analysis of Functional Genes Can Cause Dramatic Quantification Bias as Revealed by Investigation of nifH Primer Performance.

    Science.gov (United States)

    Gaby, John Christian; Buckley, Daniel H

    2017-10-01

    The measurement of functional gene abundance in diverse microbial communities often employs quantitative PCR (qPCR) with highly degenerate oligonucleotide primers. While degenerate PCR primers have been demonstrated to cause template-specific bias in PCR applications, the effect of such bias on qPCR has been less well explored. We used a set of diverse, full-length nifH gene standards to test the performance of several universal nifH primer sets in qPCR. We found significant template-specific bias in all but the PolF/PolR primer set. Template-specific bias caused more than 1000-fold mis-estimation of nifH gene copy number for three of the primer sets and one primer set resulted in more than 10,000-fold mis-estimation. Furthermore, such template-specific bias will cause qPCR estimates to vary in response to beta-diversity, thereby causing mis-estimation of changes in gene copy number. A reduction in bias was achieved by increasing the primer concentration. We conclude that degenerate primers should be evaluated across a range of templates, annealing temperatures, and primer concentrations to evaluate the potential for template-specific bias prior to their use in qPCR.

  18. Heterologous microsatellite primer pairs informative for the whole genus Arachis

    Directory of Open Access Journals (Sweden)

    Andrea Akemi Hoshino

    2006-01-01

    Full Text Available The genus Arachis currently comprises 69 described species, some of which have potential and real value as human and animal foods. These Arachis species have been collected and maintained in germplasm banks to provide material that can be used as sources of genes in breeding programs and for the selection of new cultivars. One of the principal objectives of germplasm conservation is the evaluation of genetic variability, which is best conducted using molecular markers. We investigated the use of heterologous primers to amplify microsatellite loci that could be used to evaluate genetic variability in Arachis germplasm. Fifteen microsatellite primer pairs were tested in 76 accessions of 34 species from the nine Arachis sections. The data indicated that heterologous primers were very useful in Arachis since they had high transferability among the species (91% and allowed the amplification of very polymorphic putative loci, which allowed both the characterization of most accessions and to make inferences about the mating systems of some species analyzed. Our data also revealed that the germplasm analyzed showed high variability, even when represented by few accessions.

  19. Sensory reception of the primer pheromone ethyl oleate

    Science.gov (United States)

    Muenz, Thomas S.; Maisonnasse, Alban; Plettner, Erika; Le Conte, Yves; Rössler, Wolfgang

    2012-05-01

    Social work force distribution in honeybee colonies critically depends on subtle adjustments of an age-related polyethism. Pheromones play a crucial role in adjusting physiological and behavioral maturation of nurse bees to foragers. In addition to primer effects of brood pheromone and queen mandibular pheromone—both were shown to influence onset of foraging—direct worker-worker interactions influence adult behavioral maturation. These interactions were narrowed down to the primer pheromone ethyl oleate, which is present at high concentrations in foragers, almost absent in young bees and was shown to delay the onset of foraging. Based on chemical analyses, physiological recordings from the antenna (electroantennograms) and the antennal lobe (calcium imaging), and behavioral assays (associative conditioning of the proboscis extension response), we present evidence that ethyl oleate is most abundant on the cuticle, received by olfactory receptors on the antenna, processed in glomeruli of the antennal lobe, and learned in olfactory centers of the brain. The results are highly suggestive that the primer pheromone ethyl oleate is transmitted and perceived between individuals via olfaction at close range.

  20. Perbedaan Kadar Superokside Dismutase pada Remaja dengan Dismenore Primer dan Tanpa Dismenore Primer

    Directory of Open Access Journals (Sweden)

    Yanti .

    2016-01-01

    Full Text Available Abstrak             Dismenore didefinisikan sebagai rasa kram saat menstruasi yang menyakitkan tanpa patologi yang jelas. Kram berlangsung selama satu hari atau lebih dan disertai rasa mual, diare, sakit kepala. Masalah yang ditimbulkan oleh dismenore adalah  peningkatan ketidakhadiran di sekolah pada remaja sehingga menyebabkan rendahnya nilai akademik pada pelajar. Superokside dismutase (SOD adalah bahan bioaktif yang diketahui bersifat antioksidan. SOD melindungi sel terhadap gangguan oksidan (radikal bebas. SOD mengubah anion superoksida menjadi hidrogen peroksida dan oksigen, sering disebut juga sebagai pertahanan primer terhadap stress oksidatif. Tujuan penelitian ini adalah mengetahui  perbedaan kadar superokside dismutase pada remaja dengan dismenore dan tanpa dismenore. Penelitian ini adalah observasional desain cross sectional comparative. Data dianalisis menggunakan uji Mann-Withney  dengan nilai p<0.05 dianggap bermakna secara statistik. Rerata kadar SOD pada remaja yang mengalami dismenore yaitu 36,76 u/ml dan rerata kadar SOD pada remaja tanpa dismenore yaitu 32,24 u/ml. Dengan nilai p>0,005 (0,345. Hasil penelitian ini menyimpulkan bahwa tidak terdapat perbedaan yang bermakna  kadar SOD pada remaja dengan dismenore dan tanpa dismenore. Kata kunci: remaja, dismenore, antioksidan, superokside dismutase AbstractPrimary dysmenorrhoe is  a painful menstrual cramps without obvious pathology. Cramps is lasting for one day or more, accaompanied by nausea, diarrhea and headache. Problems cause by dysmenorrhea are an increase in school attendance in adolescents resulting in low academic grades of students. Superokside Dismeutase (SOD is a bioactive ingredient that is known as antioxidants, protecting cells against harmful SOD oxidants (free radicals SOD convert superoxide anion into hydrogen perokxide and oxygen, often call  as primary defense agains oxidative stress. Primary dysmenorrhoe increased uterine activity or

  1. Adhesive bonding of resin cements to cast titanium with adhesive primers

    OpenAIRE

    Di Francescantonio,Marina; Oliveira,Marcelo Tavares de; Daroz,Luiz Gustavo Dias; Henriques, Guilherme Elias Pessanha; Giannini,Marcelo

    2012-01-01

    The purpose of this study was to evaluate the effects of adhesive primer applications on the bond strength of resin cements to cast titanium. Four adhesive primers - Metaltite, Metal Primer II, Alloy Primer and Ceramic Primer - and their respective resin cements - Bistite II DC, Link Max, Panavia F 2.0, RelyX Unicem and RelyX ARC - were tested. Cast plates were prepared from titanium ingots (n=6 specimens/cement) and had their surfaces airborne-particle abraded with Al2O3 (50 μ m). Three...

  2. FACTORES AMBIENTALES QUE AFECTAN LA EDAD AL PRIMER PARTO Y PRIMER INTERVALO DE PARTOS EN VACAS DEL SISTEMA DOBLE PROPOSITO

    Directory of Open Access Journals (Sweden)

    Caty Martínez B

    2009-04-01

    Full Text Available Objetivo. Determinar los factores que influyen en la edad al primer parto (AFC y primer intervalo de parto (PIDP en hembras bovinas bajo el sistema de doble propósito, en la finca “El Rodeo”, municipio de Magangué, Bolívar - Colombia. Materiales y métodos. Se analizaron 379 datos provenientes de los registros productivos entre los años 1993 hasta 2002, usando el programa estadístico GLM del Statistical Analysis System, donde se obtuvieron la media y el error estándar de cada fuente de variación. En el análisis se consideraron los efectos de año de parto, época de parto, edad al primer parto (no se consideró para EPP, sexo de la cría, grupo racial y peso a los 24 meses. Resultados. La media para la EPP y PIDP fue de 38.9 ± 3.9 meses y 469.2 ± 9 días, respectivamente, donde el efecto época de parto, fue significativo para la duración del PIDP. Los efectos sexo de la cría, peso a los 24 meses y época, no fueron significativos sobre la EPP. Los efectos año de parto, edad al primer parto, sexo de la cría, peso a los 24 meses no fueron significativos sobre el PIDP. Conclusiones. La EPP y PIDP fueron afectados por el año y la época de parto, respectivamente.

  3. Recovery of the mitochondrial COI barcode region in diverse Hexapoda through tRNA-based primers.

    Science.gov (United States)

    Park, Doo-Sang; Suh, Soo-Jung; Oh, Hyun-Woo; Hebert, Paul D N

    2010-07-09

    DNA barcoding uses a 650 bp segment of the mitochondrial cytochrome c oxidase I (COI) gene as the basis for an identification system for members of the animal kingdom and some other groups of eukaryotes. PCR amplification of the barcode region is a key step in the analytical chain, but it sometimes fails because of a lack of homology between the standard primer sets and target DNA. Two forward PCR primers were developed following analysis of all known arthropod mitochondrial genome arrangements and sequence alignment of the tRNA-W gene which was usually located within 200 bp upstream of the COI gene. These two primers were combined with a standard reverse primer (LepR1) to produce a cocktail which generated a barcode amplicon from 125 of 141 species that included representatives of 121 different families of Hexapoda. High quality sequences were recovered from 79% of the species including groups, such as scale insects, that invariably fail to amplify with standard primers. A cocktail of two tRNA-W forward primers coupled with a standard reverse primer amplifies COI for most hexapods, allowing characterization of the standard barcode primer binding region in COI 5' as well as the barcode segment. The current results show that primers designed to bind to highly conserved gene regions upstream of COI will aid the amplification of this gene region in species where standard primers fail and provide valuable information to design a primer for problem groups.

  4. Recovery of the mitochondrial COI barcode region in diverse Hexapoda through tRNA-based primers

    Directory of Open Access Journals (Sweden)

    Oh Hyun-Woo

    2010-07-01

    Full Text Available Abstract Background DNA barcoding uses a 650 bp segment of the mitochondrial cytochrome c oxidase I (COI gene as the basis for an identification system for members of the animal kingdom and some other groups of eukaryotes. PCR amplification of the barcode region is a key step in the analytical chain, but it sometimes fails because of a lack of homology between the standard primer sets and target DNA. Results Two forward PCR primers were developed following analysis of all known arthropod mitochondrial genome arrangements and sequence alignment of the tRNA-W gene which was usually located within 200 bp upstream of the COI gene. These two primers were combined with a standard reverse primer (LepR1 to produce a cocktail which generated a barcode amplicon from 125 of 141 species that included representatives of 121 different families of Hexapoda. High quality sequences were recovered from 79% of the species including groups, such as scale insects, that invariably fail to amplify with standard primers. Conclusions A cocktail of two tRNA-W forward primers coupled with a standard reverse primer amplifies COI for most hexapods, allowing characterization of the standard barcode primer binding region in COI 5' as well as the barcode segment. The current results show that primers designed to bind to highly conserved gene regions upstream of COI will aid the amplification of this gene region in species where standard primers fail and provide valuable information to design a primer for problem groups.

  5. Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies.

    Directory of Open Access Journals (Sweden)

    Michiel Op De Beeck

    Full Text Available Current metabarcoding studies aiming to characterize microbial communities generally rely on the amplification and sequencing of relatively short DNA regions. For fungi, the internal transcribed spacer (ITS region in the ribosomal RNA (rRNA operon has been accepted as the formal fungal barcode. Despite an increasing number of fungal metabarcoding studies, the amplification efficiency of primers is generally not tested prior to their application in metabarcoding studies. Some of the challenges that metabarcoding primers should overcome efficiently are the amplification of target DNA strands in samples rich in non-target DNA and environmental pollutants, such as humic acids, that may have been co-extracted with DNA. In the current study, three selected primer pairs were tested for their suitability as fungal metabarcoding primers. The selected primer pairs include two primer pairs that have been frequently used in fungal metabarcoding studies (ITS1F/ITS2 and ITS3/ITS4 and a primer pair (ITS86F/ITS4 that has been shown to efficiently amplify the ITS2 region of a broad range of fungal taxa in environmental soil samples. The selected primer pairs were evaluated in a 454 amplicon pyrosequencing experiment, real-time PCR (qPCR experiments and in silico analyses. Results indicate that experimental evaluation of primers provides valuable information that could aid in the selection of suitable primers for fungal metabarcoding studies. Furthermore, we show that the ITS86F/ITS4 primer pair outperforms other primer pairs tested in terms of in silico primer efficiency, PCR efficiency, coverage, number of reads and number of species-level operational taxonomic units (OTUs obtained. These traits push the ITS86F/ITS4 primer pair forward as highly suitable for studying fungal diversity and community structures using DNA metabarcoding.

  6. Predictors of in-hospital mortality in patients with non-variceal upper gastrointestinal bleeding Factores predictivos de mortalidad intrahospitalaria en pacientes con sangrado de tubo digestivo alto no variceal

    Directory of Open Access Journals (Sweden)

    José Alberto González-González

    2011-04-01

    Full Text Available Objective: to determine the independent predictors of in-hospital death of Hispanic patients with nonvariceal upper gastrointestinal bleeding (NVUGB. Experimental design: prospective and observational trial. Patients: in a period between 2000 and 2009, all patients with NVUGB admitted to our hospital were studied. Demographical and clinical characteristics, endoscopic findings and laboratory tests were evaluated χ² and Mann-Whitney U analyses were performed for comparisons, and binary logistic regression was employed to identify independent predictors of in-hospital mortality. Results: 1,067 patients were included, 65% male with a mean age of 58.8 years. Mean number of comorbidities per patient was 1.6 ± 0.76. The most frequent cause of bleeding were gastric and duodenal ulcers (55.4%; 278 patients (25.8% received endoscopic treatment of which 69.1% had combined therapy. Rebleeding occurred in 36 patients (3.4% of which 50% died. In-hospital mortality was 10.2%, of which only 3.1% was associated to bleeding. When comparing causes of death among patients with and without comorbidities, only hypovolemic shock was found significative (48.3 vs. 25%; p = 0.020. Binary logistic regression found that the number of comorbidities, Rockall scale score; serum albumin Objetivo: determinar los factores de riesgo para mortalidad intrahospitalaria en pacientes hispanos con sangrado de tubo digestivo alto no variceal (STDANV. Diseño experimental: estudio prospectivo y observacional. Pacientes: del año 2000 al 2009 se estudiaron pacientes con STDANV. Se evaluaron variables demográficas y clínicas así como resultados de laboratorio y hallazgos endoscópicos. Se utilizaron análisis de χ² y U de Mann-Whitney para las comparaciones y de regresión logística binaria para la identificación de factores predictores de mortalidad. Resultados: se estudiaron 1.067 pacientes (65% hombres con promedio de edad de 58,8 años. La media de comorbilidades por

  7. Environmental DNA sequencing primers for eutardigrades and bdelloid rotifers.

    Science.gov (United States)

    Robeson, Michael S; Costello, Elizabeth K; Freeman, Kristen R; Whiting, Jeremy; Adams, Byron; Martin, Andrew P; Schmidt, Steve K

    2009-12-11

    The time it takes to isolate individuals from environmental samples and then extract DNA from each individual is one of the problems with generating molecular data from meiofauna such as eutardigrades and bdelloid rotifers. The lack of consistent morphological information and the extreme abundance of these classes makes morphological identification of rare, or even common cryptic taxa a large and unwieldy task. This limits the ability to perform large-scale surveys of the diversity of these organisms.Here we demonstrate a culture-independent molecular survey approach that enables the generation of large amounts of eutardigrade and bdelloid rotifer sequence data directly from soil. Our PCR primers, specific to the 18s small-subunit rRNA gene, were developed for both eutardigrades and bdelloid rotifers. The developed primers successfully amplified DNA of their target organism from various soil DNA extracts. This was confirmed by both the BLAST similarity searches and phylogenetic analyses. Tardigrades showed much better phylogenetic resolution than bdelloids. Both groups of organisms exhibited varying levels of endemism. The development of clade-specific primers for characterizing eutardigrades and bdelloid rotifers from environmental samples should greatly increase our ability to characterize the composition of these taxa in environmental samples. Environmental sequencing as shown here differs from other molecular survey methods in that there is no need to pre-isolate the organisms of interest from soil in order to amplify their DNA. The DNA sequences obtained from methods that do not require culturing can be identified post-hoc and placed phylogenetically as additional closely related sequences are obtained from morphologically identified conspecifics. Our non-cultured environmental sequence based approach will be able to provide a rapid and large-scale screening of the presence, absence and diversity of Bdelloidea and Eutardigrada in a variety of soils.

  8. A plastome primer set for comprehensive quantitative real time RT-PCR analysis of Zea mays: a starter primer set for other Poaceae species

    Directory of Open Access Journals (Sweden)

    Dunn Sade N

    2008-06-01

    Full Text Available Abstract Background Quantitative Real Time RT-PCR (q2(RTPCR is a maturing technique which gives researchers the ability to quantify and compare very small amounts of nucleic acids. Primer design and optimization is an essential yet time consuming aspect of using q2(RTPCR. In this paper we describe the design and empirical optimization of primers to amplify and quantify plastid RNAs from Zea mays that are robust enough to use with other closely related species. Results Primers were designed and successfully optimized for 57 of the 104 reported genes in the maize plastome plus two nuclear genes. All 59 primer pairs produced single amplicons after end-point reverse transcriptase polymerase chain reactions (RT-PCR as visualized on agarose gels and subsequently verified by q2(RTPCR. Primer pairs were divided into several categories based on the optimization requirements or the uniqueness of the target gene. An in silico test suggested the majority of the primer sets should work with other members of the Poaceae family. An in vitro test of the primer set on two unsequenced species (Panicum virgatum and Miscanthus sinensis supported this assumption by successfully producing single amplicons for each primer pair. Conclusion Due to the highly conserved chloroplast genome in plant families it is possible to utilize primer pairs designed against one genomic sequence to detect the presence and abundance of plastid genes or transcripts from genomes that have yet to be sequenced. Analysis of steady state transcription of vital system genes is a necessary requirement to comprehensively elucidate gene expression in any organism. The primer pairs reported in this paper were designed for q2(RTPCR of maize chloroplast genes but should be useful for other members of the Poaceae family. Both in silico and in vitro data are presented to support this assumption.

  9. Accelerating MATLAB with GPU computing a primer with examples

    CERN Document Server

    Suh, Jung W

    2013-01-01

    Beyond simulation and algorithm development, many developers increasingly use MATLAB even for product deployment in computationally heavy fields. This often demands that MATLAB codes run faster by leveraging the distributed parallelism of Graphics Processing Units (GPUs). While MATLAB successfully provides high-level functions as a simulation tool for rapid prototyping, the underlying details and knowledge needed for utilizing GPUs make MATLAB users hesitate to step into it. Accelerating MATLAB with GPUs offers a primer on bridging this gap. Starting with the basics, setting up MATLAB for

  10. Comentarios 2015 de G. Brousseau sobre su primer libro

    OpenAIRE

    Brousseau, Guy; Aguilar, Mabel (trad.); Fregona, Dilma (trad.)

    2015-01-01

    Comunicación presentada en el “Congreso Internacional de Didáctica de la Matemática. Una mirada epistemológica y empírica" (Santa Marta, Colombia 2015) Reflexiones de G. Brousseau, en 2015 sobre su primer libro de 1964, un cuaderno de ejercicios, destinado a alumnos de 6 años para los primeros meses de estudio. Los visitantes de esta propuesta podrán, desde el tercer milenio en el que se encuentran, exhumar las huellas arqueológicas del nacimiento de algunos de los principales temas de ...

  11. A primer on physical-layer network coding

    CERN Document Server

    Liew, Soung Chang; Zhang, Shengli

    2015-01-01

    The concept of physical-layer network coding (PNC) was proposed in 2006 for application in wireless networks. Since then it has developed into a subfield of communications and networking with a wide following. This book is a primer on PNC. It is the outcome of a set of lecture notes for a course for beginning graduate students at The Chinese University of Hong Kong. The target audience is expected to have some prior background knowledge in communication theory and wireless communications, but not working knowledge at the research level. Indeed, a goal of this book/course is to allow the reader

  12. Guidelines - A Primer for Communicating Effectively with NABIR Stakeholders

    Energy Technology Data Exchange (ETDEWEB)

    Weber, James R.; Schell, Charlotte J.; Marino, T; Bilyard, Gordon R.

    2004-02-10

    This version of the communication primer comprises two interlocking parts: Pat 1, a practical section, intended to prepare you for public interactions, and Part 2, a theoretical section that provides social and technical bases for the practices recommended in Part 1. The mutual support of practice and theory is very familiar in science and clearly requires a willingness to observe and revise our prior assumptions--in this document, we invoke both. We hope that is offering will represent a step both towards improving practice and maturing the theory of practical science communication.

  13. Automated guided vehicle systems a primer with practical applications

    CERN Document Server

    Ullrich, Günter

    2015-01-01

    This primer is directed at experts and practitioners in intralogistics who are concerned with optimizing material flows. The presentation is comprehensive covering both, practical and theoretical aspects with a moderate degree of specialization, using clear and concise language. Areas of operation as well as technical standards of all relevant components and functions are described. Recent developments in technology and in the markets are taken into account. The goal of this book is to further stronger use of automated guided transport systems and the enhancement of their future performance.

  14. A finite element primer for beginners the basics

    CERN Document Server

    Zohdi, Tarek I

    2014-01-01

    The purpose of this primer is to provide the basics of the Finite Element Method, primarily illustrated through a classical model problem, linearized elasticity. The topics covered are:(1) Weighted residual methods and Galerkin approximations,(2) A model problem for one-dimensional?linear elastostatics,(3) Weak formulations in one dimension,(4) Minimum principles in one dimension,(5) Error estimation in one dimension,(5) Construction of Finite Element basis functions in one dimension,(6) Gaussian Quadrature,(7) Iterative solvers and element by element data structures,(8) A model problem for th

  15. Transport phenomena in Newtonian fluids a concise primer

    CERN Document Server

    Olsson, Per

    2013-01-01

    This short primer provides a concise and tutorial-style introduction to transport phenomena in Newtonian fluids , in particular the transport of mass, energy and momentum.  The reader will find detailed derivations of the transport equations for these phenomena, as well as selected analytical solutions to the transport equations in some simple geometries. After a brief introduction to the basic mathematics used in the text, Chapter 2, which deals with momentum transport, presents a derivation of the Navier-Stokes-Duhem equation describing the basic flow in a Newtonian fluid.  Also provided at

  16. Steel Primer Chamber Assemblies for Dual Initiated Pyrovalves

    Science.gov (United States)

    Guemsey, Carl S.; Mizukami, Masashi; Zenz, Zac; Pender, Adam A.

    2009-01-01

    A solution was developed to mitigate the potential risk of ignition failures and burn-through in aluminum primer chamber assemblies on pyrovalves. This was accomplished by changing the assembly material from aluminum to steel, and reconfiguration of flame channels to provide more direct paths from initiators to boosters. With the geometric configuration of the channels changed, energy is more efficiently transferred from the initiators to the boosters. With the alloy change to steel, the initiator flame channels do not erode upon firing, eliminating the possibility of burn-through. Flight qualification tests have been successfully passed.

  17. Discrete random signal processing and filtering primer with Matlab

    CERN Document Server

    Poularikas, Alexander D

    2013-01-01

    Engineers in all fields will appreciate a practical guide that combines several new effective MATLAB® problem-solving approaches and the very latest in discrete random signal processing and filtering.Numerous Useful Examples, Problems, and Solutions - An Extensive and Powerful ReviewWritten for practicing engineers seeking to strengthen their practical grasp of random signal processing, Discrete Random Signal Processing and Filtering Primer with MATLAB provides the opportunity to doubly enhance their skills. The author, a leading expert in the field of electrical and computer engineering, offe

  18. Primer reporte de la familia Cheiridiidae (Arachnida: Pseudoscorpionida en Colombia

    Directory of Open Access Journals (Sweden)

    Jorge Alexander Quirós-Rodríguez

    2015-09-01

    Full Text Available Durante un estudio de la fauna de artrópodos asociada a montículos de detritos de hormigas de la especie Atta colombica Guérin-Méneville, 1844 (Hymenoptera: Formicidae en la hacienda Santa Isabel, corregimiento de Patio Bonito en el departamento de Córdoba, se encontraron representantes de la familia Cheiridiidae. Por tanto, estos pseudoescorpiones se convierten en el primer reporte de la familia para Colombia y por primera vez se registra su presencia en detritus de hormigas. Así mismo, este reporte, amplía su distribución conocida para Suramérica.

  19. Shining On: A primer on solar radiation data

    Energy Technology Data Exchange (ETDEWEB)

    Dunlap, M.A.; Cook, G. [eds.; Marion, B.; Riordan, C.; Renne, D.

    1992-05-01

    This document is a primer on solar radiation data. General uses of solar energy are presented. The manner in which solar radiation data is used to aid engineers in optimizing the use of solar thermal conversion and photovoltaic conversion is discussed. Methods for acquiring and assimilating the solar radiation data are illustrated. This would include the design and use of pyranometers and pyrheliometers. Seasonal and geographical variations in solar flux reaching the earth are evaluated. Other uses of compiled data include the determination of meteorological impacts of atmospheric disturbances such as volcano eruptions.

  20. Atmel AVR Microcontroller Primer Programming and Interfacing, Second Edition

    CERN Document Server

    Barrett, Steven F

    2012-01-01

    This textbook provides practicing scientists and engineers a primer on the Atmel AVR microcontroller. In this second edition we highlight the popular ATmega164 microcontroller and other pin-for-pin controllers in the family with a complement of flash memory up to 128 kbytes. The second edition also adds a chapter on embedded system design fundamentals and provides extended examples on two different autonomous robots. Our approach is to provide the fundamental skills to quickly get up and operating with this internationally popular microcontroller. We cover the main subsystems aboard the ATmega

  1. New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA.

    Directory of Open Access Journals (Sweden)

    Asma Asemaninejad

    Full Text Available Metabarcoding has become an important tool in the discovery of biodiversity, including fungi, which are the second most speciose group of eukaryotes, with diverse and important ecological roles in terrestrial ecosystems. We have designed and tested new PCR primers that target the D1 variable region of nuclear large subunit (LSU ribosomal DNA; one set that targets the phylum Ascomycota and another that recovers all other fungal phyla. The primers yield amplicons compatible with the Illumina MiSeq platform, which is cost-effective and has a lower error rate than other high throughput sequencing platforms. The new primer set LSU200A-F/LSU476A-R (Ascomycota yielded 95-98% of reads of target taxa from environmental samples, and primers LSU200-F/LSU481-R (all other fungi yielded 72-80% of target reads. Both primer sets have fairly low rates of data loss, and together they cover a wide variety of fungal taxa. We compared our results with these primers by amplifying and sequencing a subset of samples using the previously described ITS3_KYO2/ITS4_KYO3 primers, which amplify the internal transcribed spacer 2 (ITS2 of Ascomycota and Basidiomycota. With approximately equivalent read depth, our LSU primers recovered a greater number and phylogenetic diversity of sequences than the ITS2 primers. For instance, ITS3_KYO2/ITS4_KYO3 primers failed to pick up any members of Eurotiales, Mytilinidiales, Pezizales, Saccharomycetales, or Venturiales within Ascomycota, or members of Exobasidiomycetes, Microbotryomycetes, Pucciniomycetes, or Tremellomycetes within Basidiomycota, which were retrieved in good numbers from the same samples by our LSU primers. Among the OTUs recovered using the LSU primers were 127 genera and 28 species that were not obtained using the ITS2 primers, although the ITS2 primers recovered 10 unique genera and 16 species that were not obtained using either of the LSU primers These features identify the new primer sets developed in this study as

  2. New Primers for Discovering Fungal Diversity Using Nuclear Large Ribosomal DNA.

    Science.gov (United States)

    Asemaninejad, Asma; Weerasuriya, Nimalka; Gloor, Gregory B; Lindo, Zoë; Thorn, R Greg

    2016-01-01

    Metabarcoding has become an important tool in the discovery of biodiversity, including fungi, which are the second most speciose group of eukaryotes, with diverse and important ecological roles in terrestrial ecosystems. We have designed and tested new PCR primers that target the D1 variable region of nuclear large subunit (LSU) ribosomal DNA; one set that targets the phylum Ascomycota and another that recovers all other fungal phyla. The primers yield amplicons compatible with the Illumina MiSeq platform, which is cost-effective and has a lower error rate than other high throughput sequencing platforms. The new primer set LSU200A-F/LSU476A-R (Ascomycota) yielded 95-98% of reads of target taxa from environmental samples, and primers LSU200-F/LSU481-R (all other fungi) yielded 72-80% of target reads. Both primer sets have fairly low rates of data loss, and together they cover a wide variety of fungal taxa. We compared our results with these primers by amplifying and sequencing a subset of samples using the previously described ITS3_KYO2/ITS4_KYO3 primers, which amplify the internal transcribed spacer 2 (ITS2) of Ascomycota and Basidiomycota. With approximately equivalent read depth, our LSU primers recovered a greater number and phylogenetic diversity of sequences than the ITS2 primers. For instance, ITS3_KYO2/ITS4_KYO3 primers failed to pick up any members of Eurotiales, Mytilinidiales, Pezizales, Saccharomycetales, or Venturiales within Ascomycota, or members of Exobasidiomycetes, Microbotryomycetes, Pucciniomycetes, or Tremellomycetes within Basidiomycota, which were retrieved in good numbers from the same samples by our LSU primers. Among the OTUs recovered using the LSU primers were 127 genera and 28 species that were not obtained using the ITS2 primers, although the ITS2 primers recovered 10 unique genera and 16 species that were not obtained using either of the LSU primers These features identify the new primer sets developed in this study as useful

  3. Microsatellite Primer Development for Post Oak, Quercus stellata (Fagaceae

    Directory of Open Access Journals (Sweden)

    Warren B. Chatwin

    2014-10-01

    Full Text Available Premise of the study: The American Cross Timbers forest ecosystem runs from southeastern Kansas to Central Texas and is primarily composed of post oak (Quercus stellata. This old-growth forest currently occupies only about 2% of its ancestral range. To facilitate genetic research on this species, we developed microsatellite primers specific to post oak from reduced genomic libraries. Methods and Results: Two Q. stellata individuals, sampled from the northern and southern range of the post oak forest, were subject to genomic reduction and 454 pyrosequencing. Bioinformatic analysis identified putative microsatellites from which 12 polymorphic primer sets were screened on three populations. The number of alleles observed ranged from five to 20 across all populations, while observed and expected heterozygosity values ranged from 0.05 to 0.833 and 0.236 to 0.893, respectively, within individual populations. Conclusions: We report the development of microsatellite markers, specific to post oak, to aid the study of genetic diversity and population structure of extant forest remnants.

  4. De neurocirujano a primer ministro de Salud de la Argentina

    Directory of Open Access Journals (Sweden)

    Karina Inés Ramacciotti

    2008-01-01

    Full Text Available La trayectoria y los vínculos que entabló Ramón Carrillo con anterioridad a ejercer el cargo de primer secretario de Salud Pública en la Argentina (1946 no han sido objeto de estudio pormenorizado. Así pues en este artículo se analizarán en primer lugar, una serie de cartas de lectores publicadas en La Semana Médica en los primeros años de la década del '40 del siglo XX. Estas notas permiten comprender las disputas internas que se produjeron en la Facultad de Ciencias Médicas al producirse el concurso de Titular de Neurocirugía de la Universidad de Buenos Aires. En segundo lugar, se revisará cómo Carrillo pasa de ocupar este prestigioso cargo académico a convertirse en decano interi- no de la Facultad de Ciencias Médicas. Son las relaciones que anuda durante estos años las que lo posicionan en un escenario político privilegiado para alcanzar un relevante puesto en la administración pública.

  5. FullSSR: Microsatellite Finder and Primer Designer

    Directory of Open Access Journals (Sweden)

    Sebastián Metz

    2016-01-01

    Full Text Available Microsatellites are genomic sequences comprised of tandem repeats of short nucleotide motifs widely used as molecular markers in population genetics. FullSSR is a new bioinformatic tool for microsatellite (SSR loci detection and primer design using genomic data from NGS assay. The software was tested with 2000 sequences of Oryza sativa shotgun sequencing project from the National Center of Biotechnology Information Trace Archive and with partial genome sequencing with ROCHE 454® from Caiman latirostris, Salvator merianae, Aegla platensis, and Zilchiopsis collastinensis. FullSSR performance was compared against other similar SSR search programs. The results of the use of this kind of approach depend on the parameters set by the user. In addition, results can be affected by the analyzed sequences because of differences among the genomes. FullSSR simplifies the detection of SSRs and primer design on a big data set. The command line interface of FullSSR was intended to be used as part of genomic analysis tools pipeline; however, it can be used as a stand-alone program because the results are easily interpreted for a nonexpert user.

  6. Universal multiplexable matK primers for DNA barcoding of angiosperms.

    Science.gov (United States)

    Heckenhauer, Jacqueline; Barfuss, Michael H J; Samuel, Rosabelle

    2016-06-01

    PCR amplification of the matK barcoding region is often difficult when dealing with multiple angiosperm families. We developed a primer cocktail to amplify this region efficiently across angiosperm diversity. We developed 14 matK primers (seven forward, seven reverse) for multiplex PCR, using sequences available in GenBank for 178 taxa belonging to 123 genera in 41 families and 18 orders. Universality of these new multiplexed primers was tested with 53 specimens from 44 representative angiosperm families in 23 different orders. Our primers showed high PCR amplification and sequencing success. These results show that our newly developed primers are highly effective for multiplex PCR and can be employed in future barcode projects involving taxonomically diverse samples across angiosperms. Using multiplex primers for barcoding will reduce the cost and time needed for PCR amplification.

  7. Rapid single nucleotide polymorphism analysis by primer extension and capillary electrophoresis using polyvinyl pyrrolidone matrix.

    Science.gov (United States)

    Barta, C; Ronai, Z; Sasvari-Szekely, M; Guttman, A

    2001-01-01

    Rapid molecular diagnosis of 21-hydroxylase deficiency by detecting the most common mutation in the 21-hydroxylase gene is presented using primer extension and capillary electrophoresis with a polyvinyl pyrrolidone matrix. DNA samples were subjected to polymerase chain reaction (PCR) in order to amplify a 422 bp fragment of the CYP21 gene containing the single nucleotide polymorphism (SNP) site. This product served as a template in the primer extension reaction using a fluorescently labeled primer in close proximity to the SNP. ddGTP was used to block the extension if the mutation was present and the other three dNTPs to enable elongation of the primer. Fast analysis of the resulting fragments was performed by capillary electrophoresis using 10% polyvinylpyrrolidone as sieving and wall coating matrix. The Cy5-labeled primer and the two possible primer extension products (mutant and wild type) were completely separated in 90 s.

  8. Selection of functional tRNA primers and primer binding site sequences from a retroviral combinatorial library: identification of new functional tRNA primers in murine leukemia virus replication

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Duch, M; Pedersen, F S

    2000-01-01

    retro-viruses have revealed evidence of molecular adapt-ation towards the specific tRNA isoacceptor used as replication primer. In this study, murine leukemia virus tRNA utilisation is investigated by in vivo screening of a retroviral vector combinatorial library with randomised primer binding sites....... While most of the selected primer binding sites are complementary to the 3'-end of tRNA((Pro)), we also retrieved PBS sequences matching four other tRNA molecules and demonstrate that Akv murine leukemia virus vectors may efficiently replicate using tRNA(Arg(CCU)), tRNA(Phe(GAA))and a hitherto unknown......Retroviral reverse transcription is initiated from a cellular tRNA molecule and all known exogenous isolates of murine leukemia virus utilise a tRNA(Pro)molecule. While several studies suggest flexibility in murine leukemia virus primer utilisation, studies on human immunodeficiency virus and avian...

  9. Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans

    OpenAIRE

    Lobo, Jorge; Costa, Pedro M; Teixeira, Marcos AL; Ferreira, Maria SG; Costa, Maria H; Costa, Filipe O

    2013-01-01

    Background Building reference libraries of DNA barcodes is relatively straightforward when specifically designed primers are available to amplify the COI-5P region from a relatively narrow taxonomic group (e.g. single class or single order). DNA barcoding marine communities have been comparatively harder to accomplish due to the broad taxonomic diversity and lack of consistently efficient primers. Although some of the so-called ?universal? primers have been relatively successful, they still f...

  10. Pengujian Dua Pasang Primer Universal Untuk Amplifikasi Gen Cytochrome Oxidase I Copepoda

    OpenAIRE

    Sumampow, Thalita C. P

    2015-01-01

    Copepoda merupakan zooplankton kaya manfaat dengan diversitas yang sangat tinggi dan terdiri dari banyak spesies kriptik. Identifikasi cepat, akurat, dan hemat dapat dilakukan dengan menggunakan teknik DNA Barcoding. Kesuksesan teknik tersebut sangat dipengaruhi oleh penggunaan primer yang tepat. Tujuan penelitian ini adalah untuk menguji kemampuan dua pasang primer universal, yakni LCO1490-HCO2198 dan FF2d-FR1d, mengamplifikasi gen COI Copepoda. Dalam penelitian ini, pasangan primer LCO1490-...

  11. Chrome-Free Paint Primer for Zn/Ni Plated High-Strength Steel (Briefing Charts)

    Science.gov (United States)

    2014-11-19

    Chrome -Free Paint Primer for Zn/Ni Plated High- Strength Steel 11-19-14 Presentation at ASETSDefense 2014 George Zafiris Team: Mark Jaworowski, Mike...AND SUBTITLE Chrome -Free Paint Primer for Zn/Ni Plated High-Strength Steel 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6... Chrome -free Primer TCP LHE= Low Hydrogen Embrittlement CCC= Chromate (Cr6+) Conversion Coating TCP= Trivalent (Cr3+) Chromium Process  Regulatory EHS

  12. Studi Operasi Resin Penukar Ion Dalam Sistem Purifikasi Air Primer Pwr

    OpenAIRE

    Biyantoro, Dwi; Basuki, Kris Tri; Subagiono, Subagiono

    2006-01-01

    STUDI OPERASI RESIN PENUKAR ION DALAM SISTEM PURIFIKASI AIR PRIMER PWR. Telah dilakukan studioperasi resin penukar ion dalam sistem purifikasi air primer PWR. Air pendingin reaktor yang pada awalnya sesuaidengan persyaratan setelah pengoperasian reaktor sering kualitasnya berubah, sehingga harus dimurnikan. Unsurunsurpengotor dalam air primer PWR diidentifikasi sebagai penyebab pengotor seperti korosi, pelepasan produk fisi(Cs137, Sr90, Co60,C14, Tc99), dan pelepasan kembali unsur oleh resin ...

  13. A method for predicting service life of zinc rich primers on carbon steel

    Science.gov (United States)

    Hoppesch, C. W.

    1986-01-01

    The service life of zinc rich primers on carbon steel can be estimated by immersing a primer coated glass slide into an aqueous copper sulfate solution and measuring the amount of zinc that reacts with the copper in 15 minutes. This zinc availability test was used to evaluate eleven primers currently available for which marine beach exposure data was available from previous programs. Results were evaluated and a correlation between zinc availability and ASTM rust grade was shown.

  14. Optimal pcr primers for rapid and accurate detection of Aspergillus flavus isolates.

    Science.gov (United States)

    Al-Shuhaib, Mohammed Baqur S; Albakri, Ali H; Alwan, Sabah H; Almandil, Noor B; AbdulAzeez, Sayed; Borgio, J Francis

    2018-02-07

    Aspergillus flavus is among the most devastating opportunistic pathogens of several food crops including rice, due to its high production of carcinogenic aflatoxins. The presence of these organisms in economically important rice strip farming is a serious food safety concern. Several polymerase chain reaction (PCR) primers have been designed to detect this species; however, a comparative assessment of their accuracy has not been conducted. This study aims to identify the optimal diagnostic PCR primers for the identification of A. flavus, among widely available primers. We isolated 122 A. flavus native isolates from randomly collected rice strips (N = 300). We identified 109 isolates to the genus level using universal fungal PCR primer pairs. Nine pairs of primers were examined for their PCR diagnostic specificity on the 109 isolates. FLA PCR was found to be the optimal PCR primer pair for specific identification of the native isolates, over aflP(1), aflM, aflA, aflD, aflP(3), aflP(2), and aflR. The PEP primer pair was found to be the most unsuitable for A. flavus identification. In conclusion, the present study indicates the powerful specificity of the FLA PCR primer over other commonly available diagnostic primers for accurate, rapid, and large-scale identification of A. flavus native isolates. This study provides the first simple, practical comparative guide to PCR-based screening of A. flavus infection in rice strips. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. A comprehensive collection of experimentally validated primers for Polymerase Chain Reaction quantitation of murine transcript abundance

    Directory of Open Access Journals (Sweden)

    Wang Xiaowei

    2008-12-01

    Full Text Available Abstract Background Quantitative polymerase chain reaction (QPCR is a widely applied analytical method for the accurate determination of transcript abundance. Primers for QPCR have been designed on a genomic scale but non-specific amplification of non-target genes has frequently been a problem. Although several online databases have been created for the storage and retrieval of experimentally validated primers, only a few thousand primer pairs are currently present in existing databases and the primers are not designed for use under a common PCR thermal profile. Results We previously reported the implementation of an algorithm to predict PCR primers for most known human and mouse genes. We now report the use of that resource to identify 17483 pairs of primers that have been experimentally verified to amplify unique sequences corresponding to distinct murine transcripts. The primer pairs have been validated by gel electrophoresis, DNA sequence analysis and thermal denaturation profile. In addition to the validation studies, we have determined the uniformity of amplification using the primers and the technical reproducibility of the QPCR reaction using the popular and inexpensive SYBR Green I detection method. Conclusion We have identified an experimentally validated collection of murine primer pairs for PCR and QPCR which can be used under a common PCR thermal profile, allowing the evaluation of transcript abundance of a large number of genes in parallel. This feature is increasingly attractive for confirming and/or making more precise data trends observed from experiments performed with DNA microarrays.

  16. ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis.

    Science.gov (United States)

    Riaz, Tiayyba; Shehzad, Wasim; Viari, Alain; Pompanon, François; Taberlet, Pierre; Coissac, Eric

    2011-11-01

    Using non-conventional markers, DNA metabarcoding allows biodiversity assessment from complex substrates. In this article, we present ecoPrimers, a software for identifying new barcode markers and their associated PCR primers. ecoPrimers scans whole genomes to find such markers without a priori knowledge. ecoPrimers optimizes two quality indices measuring taxonomical range and discrimination to select the most efficient markers from a set of reference sequences, according to specific experimental constraints such as marker length or specifically targeted taxa. The key step of the algorithm is the identification of conserved regions among reference sequences for anchoring primers. We propose an efficient algorithm based on data mining, that allows the analysis of huge sets of sequences. We evaluate the efficiency of ecoPrimers by running it on three different sequence sets: mitochondrial, chloroplast and bacterial genomes. Identified barcode markers correspond either to barcode regions already in use for plants or animals, or to new potential barcodes. Results from empirical experiments carried out on a promising new barcode for analyzing vertebrate diversity fully agree with expectations based on bioinformatics analysis. These tests demonstrate the efficiency of ecoPrimers for inferring new barcodes fitting with diverse experimental contexts. ecoPrimers is available as an open source project at: http://www.grenoble.prabi.fr/trac/ecoPrimers.

  17. The Corrosion Protection of 2219-T87 Aluminum by Organic and Inorganic Zinc-Rich Primers

    Science.gov (United States)

    Danford, M. D.; Mendrek, M. J.; Walsh, D. W.

    1995-01-01

    The behavior of zinc-rich primer-coated 2219-T87 aluminum in a 3.5-percent Na-Cl was investigated using electrochemical techniques. The alternating current (ac) method of electrochemical impedance spectroscopy (EIS), in the frequency range of 0.001 to 40,000 Hz, and the direct current (dc) method of polarization resistance (PR) were used to evaluate the characteristics of an organic, epoxy zinc-rich primer and an inorganic, ethyl silicate zinc-rich primer. A dc electrochemical galvanic corrosion test was also used to determine the corrosion current of each zinc-rich primer anode coupled to a 2219-T87 aluminum cathode. Duration of the EIS/PR and galvanic testing was 21 days and 24 h, respectively. The galvanic test results demonstrated a very high galvanic current between the aluminum cathode and both zinc-rich primer anodes (37.9 pA/CM2 and 23.7 pA/CM2 for the organic and inorganic primers, respectively). The PR results demonstrated a much higher corrosion rate of the zinc in the inorganic primer than in the organic primer, due primarily to the higher porosity in the former. Based on this investigation, the inorganic zinc-rich primer appears to provide superior galvanic protection and is recommended for additional study for application in the solid rocket booster aft skirt.

  18. Development of genotype-specific primers for differentiation of genotypes A and B of Aichi viruses.

    Science.gov (United States)

    Pham, Ngan Thi Kim; Trinh, Quang Duy; Nguyen, Tuan Anh; Dey, Shuvra Kanti; Phan, Tung Gia; Hoang, Le Phuc; Khamrin, Pattara; Maneekarn, Niwat; Okitsu, Shoko; Mizuguchi, Masashi; Ushijima, Hiroshi

    2009-03-01

    A nested polymerase chain reaction method using genotype-specific primers based on the capsid gene was developed to differentiate between genotypes A and B of Aichi viruses. Results of the study showed that the PCR using newly designed genotype-specific primers could generate appropriate PCR products from all 17 samples tested, the newly developed primers could differentiate genotype A from genotype B, and all matched those obtained by nucleotide sequencing of the capsid regions. The nested PCR method using genotype-specific primers is useful and can be used for genotyping of Aichi viruses isolated from epidemiological studies.

  19. Utilidad de la ecografía en el diagnóstico de los pacientes con sospecha de neoplasias del tubo digestivo Uselfulness of ultrasonography in diagnosing patients suspect for digestive tract neoplasms

    Directory of Open Access Journals (Sweden)

    D. Martínez Ares

    2008-09-01

    Full Text Available Introducción: el valor predictivo positivo de síntomas y signos en el diagnóstico del cáncer de colon y gástrico es bajo. Además, muchos pacientes son remitidos para descartar una neoplasia digestiva, sin síntomas que sugieran su localización, siendo el VPP de la clínica aún menor. En este trabajo evaluamos la utilidad de la ecografía como primera aproximación diagnóstica. Material y método: se han reclutado 79 pacientes (48 varones, edad media 69,3 años. En todos ellos se realiza una ecografía antes de la endoscopia. Se evalúa la precisión en el diagnóstico del cáncer de colon y gástrico, los diagnósticos ecográficos y el número de endoscopias que se evitarían. También se buscan factores predictivos de la localización de la neoplasia. Resultados: se han diagnosticado 5 neoplasias gástricas (6,3% y 12 de colon (19%, 3 cáncer de páncreas (3,8%, 2 neoplasias uterinas (2,5% y 2 hipernefromas (2,5%. Las cifras de sensibilidad, especificidad, VPP, VPN y precisión de la ecografía fueron 80%, 98,6%; 80%; 98,6%; y 97,4% respectivamente en el diagnóstico del cáncer gástrico, y del 100%, 94,5%; 80%; 100% y 95,5% respectivamente en el diagnóstico del cáncer de colon. La ecografía permitió evitar el 10% de las endoscopias. El único dato que orienta la localización de la neoplasia es la presencia de anemia, que se asocia con mayor frecuencia al diagnóstico de cáncer de colon: 30,4 versus 4,3% (p = 0,033. Conclusiones: en los pacientes remitidos para descartar una neoplasia digestiva, con síntomas inespecíficos, se diagnostica con frecuencia de patología neoplásica ajena al tubo digestivo. Si consideramos, además, la elevada precisión diagnóstica de la ecografía, esta podría ser una muy buena primera aproximación diagnóstica.Background: the Positive Predictive Value (PPV of signs and symptoms for the diagnosis of colon and gastric cancer is low. Furthermore, many patients are referred to us to discard a

  20. Prader-Willi syndrome: A primer for clinicians

    Science.gov (United States)

    2011-01-01

    The advent of sensitive genetic testing modalities for the diagnosis of Prader-Willi syndrome has helped to define not only the phenotypic features of the syndrome associated with the various genotypes but also to anticipate clinical and psychological problems that occur at each stage during the life span. With advances in hormone replacement therapy, particularly growth hormone children born in circumstances where therapy is available are expected to have an improved quality of life as compared to those born prior to growth hormone. This manuscript was prepared as a primer for clinicians-to serve as a resource for those of you who care for children and adults with Prader-Willi syndrome on a daily basis in your practices. Appropriate and anticipatory interventions can make a difference. PMID:22008714

  1. A Primer on Performing Systematic Reviews and Meta-analyses.

    Science.gov (United States)

    Umscheid, Craig A

    2013-09-01

    The number of systematic reviews published in the peer-reviewed literature has increased dramatically in the last decade, and for good reason. They have become an essential resource for clinicians who want unbiased and current answers for their clinical questions; researchers and funders who want to identify the most critical evidence gaps for study; payers and administrators who want to make coverage, formulary, and purchasing decisions; and policymakers who want to develop quality measures and clinical guidelines. Targeted to beginners interested in conducting their own systematic reviews and users of systematic reviews looking for a brief introduction, this primer (1) highlights the differences between review types; (2) outlines the major steps in performing a systematic review; and (3) offers a set of resources to help authors perform and report valid and actionable systematic reviews.

  2. El Primer Congreso de la Cultura del Olivo

    Directory of Open Access Journals (Sweden)

    Criado Costa, Joaquín

    2008-06-01

    Full Text Available It is studied the notification, the organization and the development of the First Conference on the Olive Culture as an activity shared by the CECEL, the Institute of Jaen Studies, the Institute of La Mancha Studies and the Royal Academy of Science, Fine Literature and Noble Arts of Cordoba with the support of Jaen Provincial Council.Se estudia la convocatoria, organización y desarrollo del Primer Congreso de la Cultura del Olivo como actividad conjunta de la CECEL, el Instituto de Estudios Jiennenses, el Instituto de Estudios Manchegos y la Real Academia de Ciencias, Bellas Letras y Nobles Artes de Córdoba, con el patrocinio de la Diputación Provincial de Jaén.

  3. Demystifying eResearch a primer for librarians

    CERN Document Server

    Martin, Victoria

    2014-01-01

    Today's librarians need to be technology-savvy information experts who understand how to manage datasets. Demystifying eResearch: A Primer for Librarians prepares librarians for careers that involve eResearch, clearly defining what it is and how it impacts library services and collections, explaining key terms and concepts, and explaining the importance of the field. You will come to understand exactly how the use of networked computing technologies enhances and supports collaboration and innovative methods particularly in scientific research, learn about eResearch library initiatives and best practices, and recognize the professional development opportunities that eResearch offers. This book takes the broad approach to the complex topic of eResearch and how it pertains to the library community, providing an introduction that will be accessible to readers without a background in electronic research. The author presents a conceptual overview of eResearch with real-world examples of electronic research activit...

  4. Soft solids a primer to the theoretical mechanics of materials

    CERN Document Server

    Freed, Alan D

    2014-01-01

    This textbook presents the physical principles pertinent to the mathematical modeling of soft materials used in engineering practice, including both man-made materials and biological tissues. It is intended for seniors and masters-level graduate students in engineering, physics, or applied mathematics. It will also be a valuable resource for researchers working in mechanics, biomechanics, and other fields where the mechanical response of soft solids is relevant.   Soft Solids: A Primer to the Theoretical Mechanics of Materials is divided into two parts. Part I introduces the basic concepts needed to give both Eulerian and Lagrangian descriptions of the mechanical response of soft solids. Part II presents two distinct theories of elasticity and their associated theories of viscoelasticity. Seven boundary-value problems are studied over the course of the book, each pertaining to an experiment used to characterize materials. These problems are discussed at the end of each chapter, giving students the opportunit...

  5. Prader-Willi syndrome: A primer for clinicians

    Directory of Open Access Journals (Sweden)

    Hertz Gila

    2011-10-01

    Full Text Available Abstract The advent of sensitive genetic testing modalities for the diagnosis of Prader-Willi syndrome has helped to define not only the phenotypic features of the syndrome associated with the various genotypes but also to anticipate clinical and psychological problems that occur at each stage during the life span. With advances in hormone replacement therapy, particularly growth hormone children born in circumstances where therapy is available are expected to have an improved quality of life as compared to those born prior to growth hormone. This manuscript was prepared as a primer for clinicians-to serve as a resource for those of you who care for children and adults with Prader-Willi syndrome on a daily basis in your practices. Appropriate and anticipatory interventions can make a difference.

  6. Primer Part 1-The building blocks of epilepsy genetics.

    Science.gov (United States)

    Helbig, Ingo; Heinzen, Erin L; Mefford, Heather C

    2016-06-01

    This is the first of a two-part primer on the genetics of the epilepsies within the Genetic Literacy Series of the Genetics Commission of the International League Against Epilepsy. In Part 1, we cover the foundations of epilepsy genetics including genetic epidemiology and the range of genetic variants that can affect the risk for developing epilepsy. We discuss various epidemiologic study designs that have been applied to the genetics of the epilepsies including population studies, which provide compelling evidence for a strong genetic contribution in many epilepsies. We discuss genetic risk factors varying in size, frequency, inheritance pattern, effect size, and phenotypic specificity, and provide examples of how genetic risk factors within the various categories increase the risk for epilepsy. We end by highlighting trends in epilepsy genetics including the increasing use of massive parallel sequencing technologies. Wiley Periodicals, Inc. © 2016 International League Against Epilepsy.

  7. Microsatellite primers for the gynodioecious grassland perennial Saxifraga granulata (Saxifragaceae).

    Science.gov (United States)

    van der Meer, Sascha; Van Houdt, Jeroen K J; Maes, Gregory E; Hellemans, Bart; Jacquemyn, Hans

    2014-09-01

    Nine polymorphic and 12 monomorphic microsatellite loci (simple sequence repeats [SSRs]) were isolated and characterized for the gynodioecious grassland perennial Saxifraga granulata. • Based on genomic screening of leaf material of four individuals from four populations, a total of 21 microsatellite primer pairs were designed for S. granulata. Nine loci were polymorphic and were optimized into two PCR multiplex reactions and tested on 100 individuals from five riparian populations from central Belgium. The number of alleles of the polymorphic loci ranged from three to 18, and gametic heterozygosity ranged from 0.26 to 0.94. • The markers that are presented here are the first microsatellite markers reported for S. granulata and will be used to assess how river systems shape the spatial genetic structure and diversity of riparian populations of this species.

  8. Microsatellite Primers for the Gynodioecious Grassland Perennial Saxifraga granulata (Saxifragaceae

    Directory of Open Access Journals (Sweden)

    Sascha van der Meer

    2014-08-01

    Full Text Available Premise of the study: Nine polymorphic and 12 monomorphic microsatellite loci (simple sequence repeats [SSRs] were isolated and characterized for the gynodioecious grassland perennial Saxifraga granulata. Methods and Results: Based on genomic screening of leaf material of four individuals from four populations, a total of 21 microsatellite primer pairs were designed for S. granulata. Nine loci were polymorphic and were optimized into two PCR multiplex reactions and tested on 100 individuals from five riparian populations from central Belgium. The number of alleles of the polymorphic loci ranged from three to 18, and gametic heterozygosity ranged from 0.26 to 0.94. Conclusions: The markers that are presented here are the first microsatellite markers reported for S. granulata and will be used to assess how river systems shape the spatial genetic structure and diversity of riparian populations of this species.

  9. Development of polymerase chain reaction primers to detect Mycoplasma hyopneumoniae.

    Science.gov (United States)

    Artiushin, S; Stipkovits, L; Minion, F C

    1993-10-01

    Mycoplasma hyopneumoniae (Mhp) is the etiologic agent of mycoplasma pneumonia in swine. The purpose of this study was to develop a species-specific polymerase chain reaction (PCR)-based diagnostic reagent for the identification of Mhp. Based upon DNA sequence analysis of a cloned fragment of Mhp DNA, PCR primers were constructed and tested against different strains of Mhp, Mycoplasma flocculare, other mycoplasma species, and non-Mollicute micro-organisms which commonly inhabit the respiratory tracts of swine. A total of 40 field isolates from Mhp and four field isolates of M. flocculare have been examined. Positive signals were obtained in PCR with Mhp reference strains and all 40 Mhp field isolates, but not with other Mollicutes micro-organisms.

  10. Streamlining DNA barcoding protocols: automated DNA extraction and a new cox1 primer in arachnid systematics.

    Science.gov (United States)

    Vidergar, Nina; Toplak, Nataša; Kuntner, Matjaž

    2014-01-01

    DNA barcoding is a popular tool in taxonomic and phylogenetic studies, but for most animal lineages protocols for obtaining the barcoding sequences--mitochondrial cytochrome C oxidase subunit I (cox1 AKA CO1)--are not standardized. Our aim was to explore an optimal strategy for arachnids, focusing on the species-richest lineage, spiders by (1) improving an automated DNA extraction protocol, (2) testing the performance of commonly used primer combinations, and (3) developing a new cox1 primer suitable for more efficient alignment and phylogenetic analyses. We used exemplars of 15 species from all major spider clades, processed a range of spider tissues of varying size and quality, optimized genomic DNA extraction using the MagMAX Express magnetic particle processor-an automated high throughput DNA extraction system-and tested cox1 amplification protocols emphasizing the standard barcoding region using ten routinely employed primer pairs. The best results were obtained with the commonly used Folmer primers (LCO1490/HCO2198) that capture the standard barcode region, and with the C1-J-2183/C1-N-2776 primer pair that amplifies its extension. However, C1-J-2183 is designed too close to HCO2198 for well-interpreted, continuous sequence data, and in practice the resulting sequences from the two primer pairs rarely overlap. We therefore designed a new forward primer C1-J-2123 60 base pairs upstream of the C1-J-2183 binding site. The success rate of this new primer (93%) matched that of C1-J-2183. The use of C1-J-2123 allows full, indel-free overlap of sequences obtained with the standard Folmer primers and with C1-J-2123 primer pair. Our preliminary tests suggest that in addition to spiders, C1-J-2123 will also perform in other arachnids and several other invertebrates. We provide optimal PCR protocols for these primer sets, and recommend using them for systematic efforts beyond DNA barcoding.

  11. Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing

    Directory of Open Access Journals (Sweden)

    Li Kelvin

    2012-11-01

    Full Text Available Abstract Background In a high-throughput environment, to PCR amplify and sequence a large set of viral isolates from populations that are potentially heterogeneous and continuously evolving, the use of degenerate PCR primers is an important strategy. Degenerate primers allow for the PCR amplification of a wider range of viral isolates with only one set of pre-mixed primers, thus increasing amplification success rates and minimizing the necessity for genome finishing activities. To successfully select a large set of degenerate PCR primers necessary to tile across an entire viral genome and maximize their success, this process is best performed computationally. Results We have developed a fully automated degenerate PCR primer design system that plays a key role in the J. Craig Venter Institute’s (JCVI high-throughput viral sequencing pipeline. A consensus viral genome, or a set of consensus segment sequences in the case of a segmented virus, is specified using IUPAC ambiguity codes in the consensus template sequence to represent the allelic diversity of the target population. PCR primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the full length of the specified target region. As part of the tiling process, primer pairs are computationally screened to meet the criteria for successful PCR with one of two described amplification protocols. The actual sequencing success rates for designed primers for measles virus, mumps virus, human parainfluenza virus 1 and 3, human respiratory syncytial virus A and B and human metapneumovirus are described, where >90% of designed primer pairs were able to consistently successfully amplify >75% of the isolates. Conclusions Augmenting our previously developed and published JCVI Primer Design Pipeline, we achieved similarly high sequencing success rates with only minor software modifications. The recommended methodology for the construction of the consensus

  12. Comparison of Shear Bond Strength of New Self-etching Primer with Conventional Self-etching Primers: An In-vitro Study.

    Science.gov (United States)

    Sorake, Abhinay; Rai, Rohan; Hegde, Gautham; Suneja, Ridhima; Kumar, Naveena; Skaria, Jibin

    2015-07-01

    In the past few years, there has been a major research drive to increase bond strength between dental materials and dental hard tissue and to reduce the associated demineralization around fixed orthodontic appliances. Thus, a recent approach is to incorporate an antibacterial agent into the primer to reduce the demineralization and enhance bond strength. The objective of this study was: (1) To evaluate the shear bond strength of orthodontic preadjusted edgewise appliance brackets bonded to extracted premolar teeth with antimicrobial self-etch primer (Reliance self-etching primer, Clearfil Protect Bond) and self-etching primer without antimicrobial agent (Clearfil SE bond). (2) To compare the mean shear bond strength values of the tested materials to conventional self-etching primer Transbond Plus. A total of 125 extracted human premolar teeth were randomly divided into five groups of 25 teeth each. Each sample was embedded in an acrylic block of polymethyl meth acrylate resin till coronal portion. Instron testing machine model LR LOYD 50 K was used for testing the shear bond strength of individual samples. The results of the study showed that all five groups had adequate clinically acceptable bond strength. In intergroup comparison, there was statistically significant difference in bond strength of Reliance self-etching primer, Promt L pop, Clearfil Protect Bond, clearfil SE bond and Transbond Plus. Reliance self-etching primer showed highest bond strength, followed by Clearfil Protect Bond, clearfil SE bond, and Transbond Plus. Clearfil Protect Bond primer containing methacryloxy dodecyl pyridium bromide have been demonstrated to kill Streptococcus mutans within a short time of contact and also exhibits an inhibitory effect on the growth of bacteria on its surface.

  13. Gut size flexibility in rodents: what we know, and don't know, after a century of research Flexibilidad en el tamaño del tracto digestivo en roedores: qué sabemos, y qué no sabemos, después de un siglo de investigación

    Directory of Open Access Journals (Sweden)

    DANIEL E NAYA

    2008-12-01

    specific absorption (e.g., during highly demanding periods. (6 The qualities of an energetic demand (e.g., its relative intensity rather than simply its presence or absence can affect the amount of digestive flexibility. (7 Quantitative comparisons of the existing data are difficult due to several factors, such as the disparity of experimental treatments and differences in the types of data collected. At the end of this review, further directions for the study of digestive flexibility in rodents are presented.La plasticidad fenotípica constituye un concepto medular en el entendimiento de cómo los organismos interactúan con su ambiente y, por tanto, un tema central en ecología y evolución. Un caso particular de la plasticidad fenotípica es la flexibilidad fenotípica, la cual refiere a los cambios reversibles en un organismo producto de cambios en las condiciones ambientales. La flexibilidad en los rasgos digestivos ha sido estudiada por más de un siglo en diversas especies y contextos. Para el caso de los roedores, los estudios sobre la flexibilidad en el tamaño del tracto digestivo han sido desarrollados principalmente desde dos áreas de la biología, la fisiología y la ecología. Sin embargo, como ha ocurrido con muchos tópicos relacionados con la fisiología ecológica, ambos tipos de estudios se desarrollaron por vías separadas. En este trabajo se intenta evaluar de forma conjunta la información proveniente de ambas áreas. Las principales conclusiones alcanzadas son: (1 la flexibilidad en el tamaño del tracto digestivo puede ser considerada un mecanismo fisiológico ampliamente distribuido, existiendo un clara congruencia entre los ajustes en la morfología digestiva y los cambios en las condiciones ambientales. (2 Los factores experimentales más investigados han sido la calidad de la dieta, el estatus reproductivo, la temperatura ambiental y el ayuno para las especies de laboratorio y la calidad de la dieta y la temperatura para las especies salvajes

  14. Supplementary table 6. Primers used in real-time PCR for relative ...

    Indian Academy of Sciences (India)

    pushpa

    Supplementary table 6. Primers used in real-time PCR for relative expression analysis of osa-miR399i and osa-miR530 and their predicted target genes. Gene Locus. Primer sequence. TTGTTGGACATGCTCGTGACA. LOC_Os05g48390. TGGTGACAAGCTTCGGCAA. CGTGTGGAGGATTGTATGCATG. LOC_Os01g54480.

  15. A database of PCR primers for the chloroplast genomes of higher plants

    Directory of Open Access Journals (Sweden)

    Heinze Berthold

    2007-02-01

    Full Text Available Abstract Background Chloroplast genomes evolve slowly and many primers for PCR amplification and analysis of chloroplast sequences can be used across a wide array of genera. In some cases 'universal' primers have been designed for the purpose of working across species boundaries. However, the essential information on these primer sequences is scattered throughout the literature. Results A database is presented here which assembles published primer information for chloroplast DNA. Additional primers were designed to fill gaps where little or no primer information could be found. Amplicons are either the genes themselves (typically useful in studies of sequence variation in higher-order phylogeny or they are spacers, introns, and intergenic regions (for studies of phylogeographic patterns within and among species. The current list of 'generic' primers consists of more than 700 sequences. Wherever possible, we give the locations of the primers in the thirteen fully sequenced chloroplast genomes (Nicotiana tabacum, Atropa belladonna, Spinacia oleracea, Arabidopsis thaliana, Populus trichocarpa, Oryza sativa, Pinus thunbergii, Marchantia polymorpha, Zea mays, Oenothera elata, Acorus calamus, Eucalyptus globulus, Medicago trunculata. Conclusion The database described here is designed to serve as a resource for researchers who are venturing into the study of poorly described chloroplast genomes, whether for large- or small-scale DNA sequencing projects, to study molecular variation or to investigate chloroplast evolution.

  16. The use of cross species SSR primers to study genetic diversity of ...

    African Journals Online (AJOL)

    Sixteen pairs of primers designed to amplify SSR regions of Medicago truncatula were used to amplify genomic DNA samples of 20 different okra accessions collected from different regions Burkina Faso. These primers amplified a number of fragments that range from 1-16 with the sizes of 396-506 bp. Each accession was ...

  17. Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch

    Directory of Open Access Journals (Sweden)

    Mitui Marcelo

    2012-08-01

    Full Text Available Abstract Reverse transcription (RT-PCR is now the standard method for typing group A rotaviruses (RVA to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch. We tested two published G-genotype specific primers sets, designed by Gouvea and colleagues (Set A and Iturriza‐Gomara and colleagues (Set B on RVA from Hong Kong and Sri Lanka. Among 52 rotaviruses typed as G3 by set A primers, 36 (69.2% were identified as G9 by nucleotide sequencing and set B primers. Moreover, of 300 rotaviruses tested, 28.3% were untypable by set A primers whereas only 12.3% were untypable by set B primers. Our findings reinforce the need to periodically monitor the primers used for RVA genotyping.

  18. One fungus , which genes ? Development and assessment of universal primers for potential secondary fungal DNA barcodes

    NARCIS (Netherlands)

    Stielow, J B; Lévesque, C A; Seifert, K A; Meyer, W; Irinyi, L; Smits, D; Renfurm, R; Verkley, G J M; Groenewald, M; Chaduli, D; Lomascolo, A; Welti, S; Lesage-Meessen, L; Favel, A; Al-Hatmi, A M S; Damm, U; Yilmaz, N.; Houbraken, J.; Lombard, L.; Quaedvlieg, W.; Binder, M.; Vaas, L.A.I.; Vu, D.; Yurkov, A.; Begerow, D.; Roehl, O.; Guerreiro, M.; Fonseca, A.; Samerpitak, K.; Diepeningen, A.D. van; Dolatabadi, S.; Moreno, L.F.; Casaregola, S.; Mallet, S.; Jacques, N.; Roscini, L.; Egidi, E.; Bizet, C.; Garcia-Hermoso, D.; Martín, M.P.; Deng, S.; Groenewald, J.Z.; Boekhout, T.; Beer, Z.W. de; Barnes, I.; Duong, T.A.; Wingfield, M.J.; Hoog, G.S. de; Crous, P.W.; Lewis, C.T.; Hambleton, S.; Moussa, T.A.A.; Al-Zahrani, H.S.; Almaghrabi, O.A.; Louis-Seize, G.; Assabgui, R.; McCormick, W.; Omer, G.; Dukik, K.; Cardinali, G.; Eberhardt, U.; Vries, M. de; Robert, V.

    2015-01-01

    The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic

  19. One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes

    NARCIS (Netherlands)

    Stielow, J.B.; Lévesque, C.A.; Seifert, K.A.; Meyer, W.; Irinyi, L.; Smits, D.; Renfurm, R.; Verkley, G.J.M.; Groenewald, M.; Chaduli, D.; Lomascolo, A.; Welti, S.; Lesage-Meessen, L.; Favel, A.; Al-Hatmi, A.M.S.; Damm, U.; Yilmaz, N.; Houbraken, J.; Lombard, L.; Quaedvlieg, W.; Binder, M.; Vaas, L.A.I.; Vu, D.; Yurkov, A.; Begerow, D.; Roehl, O.; Guerreiro, M.; Fonseca, A.; Samerpitak, K.; Diepeningen, van A.D.; Dolatabadi, S.; Moreno, L.F.; Casaregola, S.; Mallet, S.; Jacques, N.; Roscini, L.; Egidi, E.; Bizet, C.; Garcia-Hermoso, D.; Martin, M.P.; Deng, S.; Groenewald, J.Z.; Boekhout, T.; Beer, de Z.W.; Barnes, I.; Duong, T.A.; Wingfield, M.J.; Hoog, de G.S.; Crous, P.W.; Lewis, C.T.; Hambleton, S.; Moussa, T.A.A.; Al-Zahrani, H.S.; Almaghrabi, O.A.; Louis-Seize, G.; Assabgui, R.; McCormick, W.; Omer, G.; Dukik, K.; Cardinali, G.; Eberhardt, U.; Vries, de M.; Robert, V.

    2015-01-01

    The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers

  20. Sediment transport primer: estimating bed-material transport in gravel-bed rivers

    Science.gov (United States)

    Peter Wilcock; John Pitlick; Yantao Cui

    2009-01-01

    This primer accompanies the release of BAGS, software developed to calculate sediment transport rate in gravel-bed rivers. BAGS and other programs facilitate calculation and can reduce some errors, but cannot ensure that calculations are accurate or relevant. This primer was written to help the software user define relevant and tractable problems, select appropriate...

  1. Taxon-specific PCR primers to detect two inconspicuous arbuscular mycorrhizal fungi from temperate agricultural grassland

    NARCIS (Netherlands)

    Gamper, H.A.; Leuchtmann, A.

    2007-01-01

    Taxon-specific polymerase chain reaction (PCR) primers enable detection of arbuscular mycorrhizal fungi (AMF, Glomeromycota) in plant roots where the fungi lack discriminative morphological and biochemical characters. We designed and validated pairs of new PCR primers targeted to the flanking

  2. GETPrime: a gene- or transcript-specific primer database for quantitative real-time PCR

    Science.gov (United States)

    Gubelmann, Carine; Gattiker, Alexandre; Massouras, Andreas; Hens, Korneel; David, Fabrice; Decouttere, Frederik; Rougemont, Jacques; Deplancke, Bart

    2011-01-01

    The vast majority of genes in humans and other organisms undergo alternative splicing, yet the biological function of splice variants is still very poorly understood in large part because of the lack of simple tools that can map the expression profiles and patterns of these variants with high sensitivity. High-throughput quantitative real-time polymerase chain reaction (qPCR) is an ideal technique to accurately quantify nucleic acid sequences including splice variants. However, currently available primer design programs do not distinguish between splice variants and also differ substantially in overall quality, functionality or throughput mode. Here, we present GETPrime, a primer database supported by a novel platform that uniquely combines and automates several features critical for optimal qPCR primer design. These include the consideration of all gene splice variants to enable either gene-specific (covering the majority of splice variants) or transcript-specific (covering one splice variant) expression profiling, primer specificity validation, automated best primer pair selection according to strict criteria and graphical visualization of the latter primer pairs within their genomic context. GETPrime primers have been extensively validated experimentally, demonstrating high transcript specificity in complex samples. Thus, the free-access, user-friendly GETPrime database allows fast primer retrieval and visualization for genes or groups of genes of most common model organisms, and is available at http://updepla1srv1.epfl.ch/getprime/. Database URL: http://deplanckelab.epfl.ch. PMID:21917859

  3. Inaccurate identification of rotavirus genotype G9 as genotype G3 strains due to primer mismatch.

    Science.gov (United States)

    Mitui, Marcelo Takahiro; Chandrasena, Tga Nilmini; Chan, Paul Ks; Rajindrajith, Shaman; Nelson, E Anthony S; Leung, Ting Fan; Nishizono, Akira; Ahmed, Kamruddin

    2012-08-03

    Reverse transcription (RT)-PCR is now the standard method for typing group A rotaviruses (RVA) to monitor the circulating genotypes in a population. Selection of primers that can accurately type the circulating genotypes is crucial in the context of vaccine introduction and correctly interpreting the impact of vaccination on strain distribution. To our knowledge this study is the first report from Asia of misidentification of genotype G9 as G3 due to a primer-template mismatch. We tested two published G-genotype specific primers sets, designed by Gouvea and colleagues (Set A) and Iturriza-Gomara and colleagues (Set B) on RVA from Hong Kong and Sri Lanka. Among 52 rotaviruses typed as G3 by set A primers, 36 (69.2%) were identified as G9 by nucleotide sequencing and set B primers. Moreover, of 300 rotaviruses tested, 28.3% were untypable by set A primers whereas only 12.3% were untypable by set B primers. Our findings reinforce the need to periodically monitor the primers used for RVA genotyping.

  4. Development of Species-Specific Primers for Plasmodiophora brassicae, Clubroot Pathogen of Kimchi Cabbage

    Directory of Open Access Journals (Sweden)

    Jin Su Choi

    2014-03-01

    Full Text Available Clubroot caused by the obligate biotrophic protist Plasmodiophora brassicae Woronin is one of the most damaging diseases of Brassicaceae family. In this study, we developed species-specific primer sets for rapid and accurate detection of P. brassicae. The primer sets developed amplified a specific fragment only from P. brassicae DNA while they did not amplify a band from 10 other soilborne pathogens or from Kimchi cabbage. In sensitivity test, the species-specific primer set ITS1-1/ITS1-2 could work for approximately 10 spores/ml of genomic DNA showing more sensitivity and accuracy than previous methods. With quantitative real-time PCR test, the primer set detected less spores of P. brassicae than before, confirming that the species-specific primer set could be useful for rapid and accurate detection of P. brassicae.

  5. Bond Strength of Resin Cements to Zirconia Ceramic Using Adhesive Primers.

    Science.gov (United States)

    Stefani, Ariovaldo; Brito, Rui Barbosa; Kina, Sidney; Andrade, Oswaldo Scopin; Ambrosano, Gláucia Maria Bovi; Carvalho, Andreia Assis; Giannini, Marcelo

    2016-07-01

    To evaluate the influence of adhesive primers on the microshear bond strength of resin cements to zirconia ceramic. Fifty zirconia plates (12 mm × 5 mm × 1.5 mm thick) of a commercially available zirconium oxide ceramic (ZirCad) were sintered, sandblasted with aluminum oxide particles, and cleaned ultrasonically before bonding. The plates were randomly divided into five groups of 10. Three resin cements were selected (RelyX ARC, Multilink Automix, Clearfil SA Cement self-adhesive resin cement), along with two primers (Metal-Zirconia Primer, Alloy Primer) and one control group. The primers and resin cements were used according to manufacturers' recommendations. The control group comprised the conventional resin cement (RelyX ARC) without adhesive primer. Test cylinders (0.75 mm diameter × 1 mm high) were formed on zirconia surfaces by filling cylindrical Tygon tube molds with resin cement. The specimens were stored in distilled water for 24 hours at 37°C, then tested for shear strength on a Shimadzu EZ Test testing machine at 0.5 mm/min. Bond strength data were analyzed statistically by two-way ANOVA and Dunnett's test (5%). The bond strength means in MPa (± s.d.) were: RelyX ARC: 28.1 (6.6); Multilink Automix: 37.6 (4.5); Multilink Automix + Metal-Zirconia Primer: 55.7 (4.0); Clearfil SA Cement: 46.2 (3.3); and Clearfil SA Cement + Alloy Primer: 47.0 (4.1). Metal-Zirconia Primer increased the bond strength of Multilink Automix resin cement to zirconia, but no effect was observed for Alloy Primer using Clearfil SA Cement. RelyX ARC showed the lowest bond strength to zirconia. © 2015 by the American College of Prosthodontists.

  6. Formação do cirurgião em cirurgia laparoscópica do aparelho digestivo. Experiência de 1.818 intervenções sem acidentes e sem mortalidade Digestive tract laparoscopic surgeon formations - experience in 1818 laparoscopic choleystectomies without complications or mortality

    Directory of Open Access Journals (Sweden)

    H. W. Pinotti

    1999-12-01

    Full Text Available Desde a instalação da cirurgia laparoscópica no Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, a Disciplina de Cirurgia do Aparelho Digestivo passou a estruturar um programa para a formação do cirurgião em laparoscopia do aparelho digestivo. OBJETIVO: A estrutura de ensino inclui a informação no ensino médico regular, extensão na Liga de Cirurgia Laparoscópica, formando o médico a partir de residência, principalmente em seu quarto ano, com estágio na Unidade de Cirurgia Laparoscópica de três meses. MÉTODO: Este modelo de formação e preparo do cirurgião do aparelho digestivo assim implantado, com rigor, profundidade e seriedade é, certamente, responsável pelos resultados de nível de excelência obtidos. RESULTADOS: Exemplo disso representam as 1818 colecistectomias laparoscópicas realizadas na Unidade de Cirurgia Laparoscópica no período de outubro 1990 a dezembro de 1998, com índice de conversão de 0,9% e sem mortalidade. A ausência de acidentes operatórios e de complicações verificadas na experiência adquirida nas operações realizadas por nosso grupo cirúrgico, dá consistente suporte à orientação assumida pela Disciplina. CONCLUSÃO: Reforçam-se os princípios que foram adotados dentro da atividade em hospital universitário, que são: necessidade de formação de profissionais dentro de programa bem estruturado, ensejando-lhes preparo educacional humanístico e técnico, em torno de projeto pedagógico longo, mas com grande e sólido embasamento informativo e prático.Since the beginning or laparoscopic surgery on University of Sao Paulo Medical School Clinics Hospital, the Digestive Surgery Division established an educational program for surgeons of the alimentary tract. PURPOSE: The course structure includes the information on medical school, extension in laparoscopic surgery league, and surgical formation during the residence, mainly in the fourth year, with a three

  7. KENO V.a Primer: A Primer for Criticality Calculations with SCALE/KENO V.a Using CSPAN for Input

    Energy Technology Data Exchange (ETDEWEB)

    Busch, R.D.

    2003-01-17

    The SCALE (Standardized Computer Analyses for Licensing Evaluation) computer software system developed at Oak Ridge National Laboratory (ORNL) is widely used and accepted around the world for criticality safety analyses. The well-known KENO V.a three-dimensional Monte Carlo criticality computer code is the primary criticality safety analysis tool in SCALE. The KENO V.a primer is designed to help a new user understand and use the SCALE/KENO V.a Monte Carlo code for nuclear criticality safety analyses. It assumes that the user has a college education in a technical field. There is no assumption of familiarity with Monte Carlo codes in general or with SCALE/KENO V.a in particular. The primer is designed to teach by example, with each example illustrating two or three features of SCALE/KENO V.a that are useful in criticality analyses. The primer is based on SCALE 4.4a, which includes the Criticality Safety Processor for Analysis (CSPAN) input processor for Windows personal computers (PCs). A second edition of the primer, which uses the new KENO Visual Editor, is currently under development at ORNL and is planned for publication in late 2003. Each example in this first edition of the primer uses CSPAN to provide the framework for data input. Starting with a Quickstart section, the primer gives an overview of the basic requirements for SCALE/KENO V.a input and allows the user to quickly run a simple criticality problem with SCALE/KENO V.a. The sections that follow Quickstart include a list of basic objectives at the beginning that identifies the goal of the section and the individual SCALE/KENO V.a features which are covered in detail in the example problems in that section. Upon completion of the primer, a new user should be comfortable using CSPAN to set up criticality problems in SCALE/KENO V.a.

  8. Acesso ao alimento artificial e enchimento do trato digestivo de juvenis do camarão marinho Litopenaeus vannamei (Boone (Crustacea, Decapoda, Penaeidae durante as fases clara e escura do período de 24 horas Artificial food access and digestive tract filling of juvenil marine shrimp Litopenaeus vannamei (Boone (Crustacea, Decapoda, Penaeidae during light and dark phases in 24-hour period

    Directory of Open Access Journals (Sweden)

    Cibele S. Pontes

    2005-12-01

    Full Text Available A escassez de dados acerca do comportamento alimentar do camarão marinho Litopenaeus vannamei (Boone, 1931 com relação ao alimento artificial ofertado em bandejas poderá induzir a uma alimentação inadequada, resultando no desperdício da ração, no aporte desnecessário de nutrientes, e conseqüente aumento dos custos com a alimentação e da poluição ambiental potencial desta atividade. Objetivando fornecer subsídios para a melhoria do manejo alimentar praticado nas fazendas, foram realizados estudos comportamentais utilizando 64 juvenis de Litopenaeus vannamei (7,57 ± 1,01g, mantidos em densidade populacional de 33 m², submetidos a fotoperíodo artificial, em ciclo invertido, para observação durante as fases clara e escura. A ração foi ofertada em intervalos pré-estabelecidos, registrando-se posteriormente através de método focal contínuo: a latência para chegada à bandeja, b latência para consumo do alimento e c Índice de Enchimento do Trato Digestivo. Os animais foram mais rápidos para chegar à bandeja e também para iniciar o consumo do alimento nos horários da fase clara. O enchimento do trato digestivo mostrou-se superior na meia hora subsequente à oferta do alimento, especialmente nos horários da fase clara.The few data on the marine shrimp Litopenaeus vannamei (Boone, 1931 behavior related to feed offer in trays can result inadequate feeding by the animal, feed wastage and unnecessary nutrient input, increasing feed costs and potential environmental pollution of that culture. In order to provide tools for improved feed management methods in shrimp farms, a behavioral study was conducted, using 64 Litopenaeus vannamei juveniles (7,57 ± 1,01g, one animal per 33 m². They were submitted to artificial photoperiods, half of them in reversed cycle, in order to register behavior during light and dark phases. The following variables were registered (continuous sampling after feed exposition: a latency to access the

  9. Collider physics within the standard model a primer

    CERN Document Server

    Altarelli, Guido

    2017-01-01

    With this graduate-level primer, the principles of the standard model of particle physics receive a particular skillful, personal and enduring exposition by one of the great contributors to the field. In 2013 the late Prof. Altarelli wrote: The discovery of the Higgs boson and the non-observation of new particles or exotic phenomena have made a big step towards completing the experimental confirmation of the standard model of fundamental particle interactions. It is thus a good moment for me to collect, update and improve my graduate lecture notes on quantum chromodynamics and the theory of electroweak interactions, with main focus on collider physics. I hope that these lectures can provide an introduction to the subject for the interested reader, assumed to be already familiar with quantum field theory and some basic facts in elementary particle physics as taught in undergraduate courses. “These lecture notes are a beautiful example of Guido’s unique pedagogical abilities and scientific vision”. From...

  10. An ASIC Low Power Primer Analysis, Techniques and Specification

    CERN Document Server

    Chadha, Rakesh

    2013-01-01

    This book provides an invaluable primer on the techniques utilized in the design of low power digital semiconductor devices.  Readers will benefit from the hands-on approach which starts form the ground-up, explaining with basic examples what power is, how it is measured and how it impacts on the design process of application-specific integrated circuits (ASICs).  The authors use both the Unified Power Format (UPF) and Common Power Format (CPF) to describe in detail the power intent for an ASIC and then guide readers through a variety of architectural and implementation techniques that will help meet the power intent.  From analyzing system power consumption, to techniques that can employed in a low power design, to a detailed description of two alternate standards for capturing the power directives at various phases of the design, this book is filled with information that will give ASIC designers a competitive edge in low-power design. Starts from the ground-up and explains what power is, how it is measur...

  11. Congenital heart disease: A primer for the pediatric neuropsychologist.

    Science.gov (United States)

    Cassidy, Adam R; Ilardi, Dawn; Bowen, Susan R; Hampton, Lyla E; Heinrich, Kimberley P; Loman, Michelle M; Sanz, Jacqueline H; Wolfe, Kelly R

    2017-09-06

    Congenital heart disease (CHD) affects millions of people worldwide, including over one million children in the United States. Approximately 25% of children born with CHD require intensive surgical intervention within the first year of life. Despite improved rates of survival into adulthood - rates that exceed 90% in the modern era - children and adolescents with CHD remain at risk for neurological injury and a range of neurobehavioral and psychosocial challenges that pose a threat to quality of life across the lifespan. Consequently, as experts in both clinical psychology and brain development, neuropsychologists are becoming increasingly involved in cardiac follow-up and monitoring to promote optimal developmental outcomes. The primary objective of this paper is to provide an evidence-based, clinically-oriented primer on CHD for pediatric neuropsychologists working with this growing population of survivors. Following an introduction to current standard-of-care guidelines for managing children and adolescents with CHD, we present an overview of brain development within the context of CHD, review neuropsychological outcomes, examine factors influencing variability in outcomes, and discuss implications and strategies for clinical assessment.

  12. A Transparent Window into Biology: A Primer on Caenorhabditis elegans.

    Science.gov (United States)

    Corsi, Ann K; Wightman, Bruce; Chalfie, Martin

    2015-06-01

    A little over 50 years ago, Sydney Brenner had the foresight to develop the nematode (round worm) Caenorhabditis elegans as a genetic model for understanding questions of developmental biology and neurobiology. Over time, research on C. elegans has expanded to explore a wealth of diverse areas in modern biology including studies of the basic functions and interactions of eukaryotic cells, host-parasite interactions, and evolution. C. elegans has also become an important organism in which to study processes that go awry in human diseases. This primer introduces the organism and the many features that make it an outstanding experimental system, including its small size, rapid life cycle, transparency, and well-annotated genome. We survey the basic anatomical features, common technical approaches, and important discoveries in C. elegans research. Key to studying C. elegans has been the ability to address biological problems genetically, using both forward and reverse genetics, both at the level of the entire organism and at the level of the single, identified cell. These possibilities make C. elegans useful not only in research laboratories, but also in the classroom where it can be used to excite students who actually can see what is happening inside live cells and tissues. Copyright © 2015 Corsi, Wightman, and Chalfie.

  13. Neurociencia y bilingüismo: efecto del primer idioma

    Directory of Open Access Journals (Sweden)

    Germary Díaz-Sánchez

    2013-08-01

    Full Text Available Desde la perspectiva neurobiológica, en este trabajo abordamos los efectos del idioma materno sobre el aprendizaje de una segunda lengua. Aunque existen investigaciones en diferentes países sobre este problema, pocas tratan el enfoque de la neurobiología y, menos aún, cuando se trata del español como idioma materno. Para la investigación se recopiló literatura descriptiva y experimental, con el fin de obtener los datos necesarios para alcanzar los objetivos; se realizó un metaanálisis cualitativo de los datos obtenidos, utilizando tablas de correlación. Los datos reflejaron que la adquisición de un segundo idioma siempre va a estar mediatizada por los esquemas ya establecidos del primer idioma y que existen aspectos neurobiológicos que subyacen a algunos mecanismos de interferencia y a la adquisición de un segundo lenguaje. Además, encontramos que, mientras más similares sean los idiomas, los mecanismos neurales subyacentes facilitan la transferencia del uno al otro.

  14. Primer reporte de alcaptonuria en el Perú

    Directory of Open Access Journals (Sweden)

    Daniel Guillén-Mendoza

    Full Text Available La alcaptonuria es un error innato del metabolismo causado por la deficiencia de la homogentisiato 1,2 dioxidasa (HGD, produciéndose un exceso de ácido homogentísico (HGA. Se presenta el caso de una mujer de 57 años quien, desde que nació, su orina se tornaba de color negro; desde hacía 9 años presentaba una pigmentación verdosa en los lechos ungueales que no mejoró con tratamientos antifúngicos y en los últimos 9 meses presentó artrosis de articulaciones grandes que fue empeorando, forzándola a usar una silla de ruedas por el intenso dolor generado por la artrosis de caderas y columna lumbar. Por la descripción de los síntomas se le solicitó la medición de HGA en orina lo que confirmó el diagnóstico de alcaptonuria. Se sugirieron analgésicos, dieta sin productos que contuvieran tirosina y fue referida para cirugía de reemplazo de cadera. Se trata del primer reporte de caso de alcaptonuria en el Perú.

  15. Genetic analysis of presbycusis by arrayed primer extension.

    Science.gov (United States)

    Rodriguez-Paris, Juan; Ballay, Charles; Inserra, Michelle; Stidham, Katrina; Colen, Tahl; Roberson, Joseph; Gardner, Phyllis; Schrijver, Iris

    2008-01-01

    Using the Hereditary Hearing Loss arrayed primer extension (APEX) array, which contains 198 mutations across 8 hearing loss-associated genes (GJB2, GJB6, GJB3, GJA1, SLC26A4, SLC26A5, 12S-rRNA, and tRNA Ser), we compared the frequency of sequence variants in 94 individuals with early presbycusis to 50 unaffected controls and aimed to identify possible genetic contributors. This cross-sectional study was performed at Stanford University with presbycusis samples from the California Ear Institute. The patients were between ages 20 and 65 yr, with adult-onset sensorineural hearing loss of unknown etiology, and carried a clinical diagnosis of early presbycusis. Exclusion criteria comprised known causes of hearing loss such as significant noise exposure, trauma, ototoxic medication, neoplasm, and congenital infection or syndrome, as well as congenital or pediatric onset. Sequence changes were identified in 11.7% and 10% of presbycusis and control alleles, respectively. Among the presbycusis group, these solely occurred within the GJB2 and SLC26A4 genes. Homozygous and compound heterozygous pathogenic mutations were exclusively seen in affected individuals. We were unable to detect a statistically significant difference between our control and affected populations regarding the frequency of sequence variants detected with the APEX array. Individuals who carry two mild mutations in the GJB2 gene possibly have an increased risk of developing early presbycusis.

  16. A Transparent Window into Biology: A Primer on Caenorhabditis elegans

    Science.gov (United States)

    Corsi, Ann K.; Wightman, Bruce; Chalfie, Martin

    2015-01-01

    A little over 50 years ago, Sydney Brenner had the foresight to develop the nematode (round worm) Caenorhabditis elegans as a genetic model for understanding questions of developmental biology and neurobiology. Over time, research on C. elegans has expanded to explore a wealth of diverse areas in modern biology including studies of the basic functions and interactions of eukaryotic cells, host–parasite interactions, and evolution. C. elegans has also become an important organism in which to study processes that go awry in human diseases. This primer introduces the organism and the many features that make it an outstanding experimental system, including its small size, rapid life cycle, transparency, and well-annotated genome. We survey the basic anatomical features, common technical approaches, and important discoveries in C. elegans research. Key to studying C. elegans has been the ability to address biological problems genetically, using both forward and reverse genetics, both at the level of the entire organism and at the level of the single, identified cell. These possibilities make C. elegans useful not only in research laboratories, but also in the classroom where it can be used to excite students who actually can see what is happening inside live cells and tissues. PMID:26088431

  17. Esteatosis en un burro (Equus asinus. Primer reporte en Colombia

    Directory of Open Access Journals (Sweden)

    José Cardona Á.

    2011-12-01

    Full Text Available Se describe un caso de esteatosis en un burro (Equus asinus, castrado, de 15 años de edad, procedente del municipio de San Antero (Córdoba, Colombia, al cual se le detectó ligamento nucal engrosado, duro y doloroso, dando la impresión de un doble cuello y edemas subcutáneos indurados en pared costal, abdominal y pectoral. Tambiénpresentó masas duras en la unión de músculos semimembranoso y semitendinoso. Por todo lo anterior, mostró dificultad para realizar movimientos coordinados del cuello, nuca y de traslado. Estos hallazgos obedecen principalmente a una deficiencia de selenio y vitamina E, sirviendo como parámetro diagnóstico para la identificación de esta enfermedad en equinos, por lo cual se determinó la actividad eritrocitica de la enzima glutatión peroxidada (GSH-Px, arrojando resultados muy bajos. Este cuadro es también conocido en equinos como enfermedad de la grasa amarilla o esteatitis, que produce degeneración del tejido adiposo, siendo reemplazado por tejido conectivo con depósitos de calcio. Puede estar asociada a miodegeneración nutricional o distrófica (enfermedad del músculo blanco. Es el primer reporte de esta enfermedad en burros(Equus asinus que se hace en Colombia.

  18. PRIMER REPORTE DE LA FAMILIA CHEIRIDIIDAE (ARACHNIDA: PSEUDOSCORPIONIDA EN COLOMBIA

    Directory of Open Access Journals (Sweden)

    Jorge Alexander QUIROZ-RODRÍGUEZ

    2015-07-01

    Full Text Available Durante un estudio de la fauna de artrópodos asociada a montículos de detritos de hormigas de la especie Atta colombica Guérin-Méneville, 1844 (Hymenoptera: Formicidae en la hacienda Santa Isabel, corregimiento de Patio Bonito en el departamento de Córdoba, se encontraron representantes de la familia Cheiridiidae. Por tanto, estos pseudoescorpiones se convierten en el primer reporte de la familia para Colombia y por primera vez se registra su presencia en detritus de hormigas. Así mismo, este reporte, amplía su distribución conocida para Suramérica.First Report of Family Cheiridiidae (Arachnida: Pseudoscorpionida in ColombiaDuring a study of the arthropod fauna associated with mounds of detritus produced by Atta colombica (Hymenoptera: Formicidae in the Santa Isabel estate, locality of Patio Bonito, Department of Córdoba, were found representatives of the family Cheiridiidae. Therefore, these pseudoscorpions becomes in the first report of the family to Colombia and for the first time is recorded its presence in ant detritus. Also, this report extends its known distribution range in South America.   

  19. Complement: A primer for the coming therapeutic revolution.

    Science.gov (United States)

    Barnum, Scott R

    2017-04-01

    The complement system is an important part of the innate and adaptive immune systems. Originally characterized as a single serum component contributing to the killing of bacteria, we now know that there are close to sixty complement proteins, multiple activation pathways and a wide range of effector functions mediated by complement. The system plays a critical role in host defense against bacteria, viruses, fungi and other pathogens. However, inappropriate complement activation contributes to the pathophysiology of autoimmune diseases and many inflammatory syndromes. Over the last several decades, therapeutic approaches to inhibit complement activation at various steps in the pathways have met with initial success, particularly at the level of the terminal pathway. This success, combined with insight from animal model studies, has lead to an unprecedented effort by biotech and pharmaceutical companies to begin developing complement inhibitors. As a result, complement has been brought for the first time to the attention of pharmacologists, toxicologists, project managers and others in the drug development industry, as well as those in the investment world. The purpose of this primer is to provide a broad overview of complement immunobiology to help those new to complement understand the rationale behind the current therapeutic directions and the investment potential of these new therapeutics. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Elektronsko izobraževanje v praksi. Primer programa LOLA

    Directory of Open Access Journals (Sweden)

    Lea Bregar

    2003-12-01

    Full Text Available Slovenija je bila vkljucena v program Phare za studij na da!javo v obdobju od I995 do konca I999 kot ena izmed 11 srednje- in vzhodnoevropskih drzav. Eden od najpomembnejsih cil jev programa Phare je bit razviti človeške vire na podrocju studija na dal javo in odprtega ucenja. v okviru podprojekta Phare Train the Trainers so na Harriot Watt University iz Velike Britanije razvili izobrazevalni program LOLA (ucenje o odprtem ucenju. Leta I999 je bilo organizirano usposab!janje za 400 udeležencev iz 11 drzav Phare. Program LOLAje bit uspdna novost v evropskem izobrazevalnem prostoru ne le zaradi svojih vsebin, temvee tudi zaradi inovativne didaktike, sa} je bit celoten program oblikovan in izvajan kot 'on-line' program. V Clanku je na kratko predstavljen izobrazevalni program LOLA in izkusnje z njegovim izvajanjem kot primer e-izobrazevanja v praksi. Clanek avtorici zakljucujeta s predstavitvijo svojih pogledov na nadaljnje izvajanje programa LOLA in razvoj e-izobrazevanja v Sloveniji ter poudarjata potrebo po kakovostno doloceni in jasni strategiji na podrocju studija na daljavo, odprtega ucenja in e-izobrazevanja v Sloveniji.

  1. New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida).

    Science.gov (United States)

    Liu, Yingkui; Erséus, Christer

    2017-12-01

    Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate-specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.

  2. Influence of Ortho Primer Morelli adhesion booster on orthodontic brackets shear bond strength

    Directory of Open Access Journals (Sweden)

    Sabrina de Mendonça Invernici

    2012-06-01

    Full Text Available OBJECTIVE: This work aimed at assessing the bond strength (AS, the site of the flaw and the relation between them and Ortho Primer Morelli® (OPM adhesion optimizer. METHODS: Sixty test specimens, made out of bovine permanent lower incisors, were divided into three groups: TXT Primer (control, in which a conventional adhesive system was applied (primer and paste; OPM, in which TXT primer was replaced by OPM; and TXT without Primer, in which only TXT paste was used. A shear force was applied at a speed of 0,5 mm/min. Failure site was assessed by the Remaining Adhesion Index (RAI. RESULTS: Kruskal-Wallis demonstrated that OPM (8.54 ± 1.86 MPa presented a statistically higher AS (p 0.05 between TXT with or without Primer (6.42 ± 2.12 MPa. Regarding the RAI, the K test demonstrated that TXT Primer and OPM (prevailing scores 2 and 3 showed higher values (p 0.05. CONCLUSION: OPM increases AS and presents the same bond failure location if compared to a conventional adhesive system; the use of the TXT adhesive system paste only was shown to have the same AS if compared to conventional systems, except it does not allow to predict the adhesive failure site; there is no correlation between AS and bond failure location, regardless of the use of any adhesion optimizer.

  3. Comprehensive primer design for analysis of population genetics in non-sequenced organisms.

    Directory of Open Access Journals (Sweden)

    Ayumi Tezuka

    Full Text Available Nuclear sequence markers are useful tool for the study of the history of populations and adaptation. However, it is not easy to obtain multiple nuclear primers for organisms with poor or no genomic sequence information. Here we used the genomes of organisms that have been fully sequenced to design comprehensive sets of primers to amplify polymorphic genomic fragments of multiple nuclear genes in non-sequenced organisms. First, we identified a large number of candidate polymorphic regions that were flanked on each side by conserved regions in the reference genomes. We then designed primers based on these conserved sequences and examined whether the primers could be used to amplify sequences in target species, montane brown frog (Rana ornativentris, anole lizard (Anolis sagrei, guppy (Poecilia reticulata, and fruit fly (Drosophila melanogaster, for population genetic analysis. We successfully obtained polymorphic markers for all target species studied. In addition, we found that sequence identities of the regions between the primer sites in the reference genomes affected the experimental success of DNA amplification and identification of polymorphic loci in the target genomes, and that exonic primers had a higher success rate than intronic primers in amplifying readable sequences. We conclude that this comparative genomic approach is a time- and cost-effective way to obtain polymorphic markers for non-sequenced organisms, and that it will contribute to the further development of evolutionary ecology and population genetics for non-sequenced organisms, aiding in the understanding of the genetic basis of adaptation.

  4. Primique: automatic design of specific PCR primers for each sequence in a family

    Directory of Open Access Journals (Sweden)

    Lange Mette

    2007-10-01

    Full Text Available Abstract Background In many contexts, researchers need specific primers for all sequences in a family such that each primer set amplifies only its target sequence and none of the others, e.g. to detect which transcription factor out of a family of very similar proteins that is present in a sample, or to design diagnostic assays for the identification of pathogen strains. Results This paper presents primique, a new graphical, user-friendly, fast, web-based tool which solves the problem: It designs specific primers for each sequence in an uploaded set. Further, a secondary set of sequences not to be amplified by any primer pair may be uploaded. Primers with high sequence similarity to non-target sequences are selected against. Lastly, the suggested primers may be checked against the National Center for Biotechnology Information databases for possible mis-priming. Conclusion Results are presented in interactive tables, and various primer properties are listed and displayed graphically. Any close match alignments can be displayed. Given 30 sequences, the running time of primique is about 20 seconds. primique can be reached via this web address: http://cgi-www.daimi.au.dk/cgi-chili/primique/front.py

  5. Construction of Specific Primers for Rapid Detection of South African Exportable Vegetable Macergens

    Directory of Open Access Journals (Sweden)

    Bukola Rhoda Aremu

    2015-09-01

    Full Text Available Macergens are bacteria causing great damages to the parenchymatous tissues of vegetable both on the field and in transit. To effectively and rapidly investigate the diversity and distribution of these macergens, four specific primers were designed by retrieving 16S rDNA sequences of pectolytic bacteria from GenBank through the National Center for Biotechnology Information (NCBI. These were aligned using ClusterW via BioEdit and primers were designed using Primer3Plus platform. The size and primer location of each species and PCR product size were accurately defined. For specificity enhancement, DNA template of known macergens (Pectobacterium chrysanthermi and fresh healthy vegetable were used. These primers yielded expected size of approximately 1100 bp product only when tested with known macergens and no amplicon with fresh healthy vegetable was detected. Rapid detection of macergens in rotten vegetable samples was then carried out using these primers. Nucleotide sequences of macergens identified were deposited into the GenBank and were assigned accession numbers. Hence, with these specific primers, macergens can be identified with minimal quantities of the vegetable tissues using molecular techniques, for future use of the quarantine section of the Agricultural Department of the country for quick and rapid detection of macergens before exportation.

  6. UNIVERSAL PRIMERS FOR THE AMPLIFICATION AND SEQUENCE ANALYSIS OF ACTIN-1 FROM DIVERSE MOSQUITO SPECIES

    Science.gov (United States)

    STALEY, MOLLY; DORMAN, KARIN S.; BARTHOLOMAY, LYRIC C.; FERNÁNDEZ-SALAS, ILDEFONSO; FARFAN-ALE, JOSE A.; LOROÑO-PINO, MARIA A.; GARCIA-REJON, JULIAN E.; IBARRA-JUAREZ, LUIS

    2010-01-01

    We report the development of universal primers for the reverse-transcription polymerase chain reaction (RT-PCR) amplification and nucleotide sequence analysis of actin cDNAs from taxonomically diverse mosquito species. Primers specific to conserved regions of the invertebrate actin-1 gene were designed after actin cDNA sequences of Anopheles gambiae, Bombyx mori, Drosophila melanogaster, and Caenorhabditis elegans. The efficacy of these primers was determined by RT-PCR with the use of total RNA from mosquitoes belonging to 30 species and 8 genera (Aedes, Anopheles, Culex, Deinocerites, Mansonia, Psorophora, Toxorhynchites, and Wyeomyia). The RT-PCR products were sequenced, and sequence data were used to design additional primers. One primer pair, denoted as Act-2F (5′-ATGGTCGGYATGGGNCAGAAGGACTC-3′) and Act-8R (5′-GATTCCATACCCAGGAAG-GADGG-3′), successfully amplified an RT-PCR product of the expected size (683-nt) in all mosquito spp. tested. We propose that this primer pair can be used as an internal control to test the quality of RNA from mosquitoes collected in vector surveillance studies. These primers can also be used in molecular experiments in which the detection, amplification or silencing of a ubiquitously expressed mosquito housekeeping gene is necessary. Sequence and phylogenetic data are also presented in this report. PMID:20649132

  7. Laboratory and gas-fired furnace performance tests of epoxy primers for intumescent coatings

    DEFF Research Database (Denmark)

    Nørgaard, Kristian Petersen; Dam-Johansen, Kim; Catala, Pere

    2014-01-01

    Protection of steel structures, using so-called intumescent coatings, is an efficient and space saving way to prolong the time before a building, with load bearing steel constructions, collapses in the event of a fire. In addition to the intumescent coating, application of a primer may be required......, either to ensure adhesion of the intumescent coating to the steel or to provide corrosion resistance. It is essential to document the performance of the intumescent coating together with the primer to ensure the overall quality of coating system. In the present work, two epoxy primers were used...

  8. THE QUALITY IMPROVEMENT OF PRIMER PACKAGING PROCESS USING SIX SIGMA METHODOLOGY

    Directory of Open Access Journals (Sweden)

    Prima Ditahardiyani

    2008-01-01

    Full Text Available The implementation of Six Sigma has become a common theme in many organizations. This paper presents the Six Sigma methodology and its implementation in a primer packaging process of Cranberry drink. DMAIC (Define, Measure, Analyze, Improve and Control approach is used to analyze and to improve the primer packaging process, which have high variability and defects output. After the improvement, the results showed that there was an increasing sigma level. However, it is not significantly and has not achieved the world standard quality, yet. Therefore, the implementation of Six Sigma in primer packaging process of Cranberry drink still has a room for doing a further research.

  9. Improved COI barcoding primers for Southeast Asian perching birds (Aves: Passeriformes).

    Science.gov (United States)

    Lohman, David J; Prawiradilaga, Dewi M; Meier, Rudolf

    2009-01-01

    The All Birds Barcoding Initiative aims to assemble a DNA barcode database for all bird species, but the 648-bp 'barcoding' region of cytochrome c oxidase subunit I (COI) can be difficult to amplify in Southeast Asian perching birds (Aves: Passeriformes). Using COI sequences from complete mitochondrial genomes, we designed a primer pair that more reliably amplifies and sequences the COI barcoding region of Southeast Asian passerine birds. The 655-bp region amplified with these primers overlaps the COI region amplified with other barcoding primer pairs, enabling direct comparison of sequences with previously published DNA barcodes. © 2008 The Authors. Journal compilation © 2008 Blackwell Publishing Ltd.

  10. A Primer on Electric Utilities, Deregulation, and Restructuring of U.S. Electricity Markets

    Energy Technology Data Exchange (ETDEWEB)

    Warwick, William M.

    2002-06-03

    This primer is offered as an introduction to utility restructuring to better prepare readers for ongoing changes in public utilities and associated energy markets. It is written for use by individuals with responsibility for the management of facilities that use energy, including energy managers, procurement staff, and managers with responsibility for facility operations and budgets. The primer was prepared by the Pacific Northwest National Laboratory under sponsorship from the U.S. Department of Energy?s Federal Energy Management Program. The impetus for this primer originally came from the Government Services Administration who supported its initial development.

  11. Primer-dependent and primer-independent initiation of double stranded RNA synthesis by purified arabidopsis RNA-dependent RNA polymerases RDR2 and RDR6

    DEFF Research Database (Denmark)

    Devert, Anthony; Fabre, Nicolas; Floris, Maina Huguette Joséphine

    2015-01-01

    Cellular RNA-dependent RNA polymerases (RDRs) are fundamental components of RNA silencing in plants and many other eukaryotes. In Arabidopsis thaliana genetic studies have demonstrated that RDR2 and RDR6 are involved in the synthesis of double stranded RNA (dsRNA) from single stranded RNA (ss......RNA) targeted by RNA silencing. The dsRNA is subsequently cleaved by the ribonuclease DICER-like into secondary small interfering RNAs (siRNAs) that reinforce and/or maintain the silenced state of the target RNA. Models of RNA silencing propose that RDRs could use primer-independent and primer......-dependent initiation to generate dsRNA from a transcript targeted by primary siRNA or microRNA (miRNA). However, the biochemical activities of RDR proteins are still partly understood. Here, we obtained active recombinant RDR2 and RDR6 in a purified form. We demonstrate that RDR2 and RDR6 have primer...

  12. El menor infractor que comete su primer delito

    Directory of Open Access Journals (Sweden)

    Antonia Luzón García

    2014-10-01

    Full Text Available Existe un consenso social y la sociedad se posiciona al lado del menor maltratado, la cosa cambia cuando el menor es infractor, entonces es declarado culpable y merecedor de castigo. El menor aun siendo infractor es un ser humano con pleno derechos establecidos en la Declaración de Derechos del Niño y en los textos internacionales sobre Derechos Humanos. Mediante la socialización se estrechan los vínculos entre el individuo y el sistema social en el que vive. Por ello, la socialización y sus implicaciones son de nuestro interés para este estudio y conocer qué lleva a un menor a cometer su primer delito. Una correcta socialización, de asunción de normas y valores sociales, pautas, creencias, ritos, etc., posibilita la adaptación y previene de la exclusión social. La combinación de la influencia que ha ejercido los agentes de socialización en el menor y los factores de riesgo como el clima familiar, la adaptación escolar, los rasgos de personalidad y el grupo de iguales nos va a permitir pronosticar la probabilidad de que el menor lleve a cabo comportamientos infractores. En este estudio se intentará demostrar que la mayoría de menores que realizan infracciones penales carecen de un adecuado proceso de socialización con desestructuración familiar, inadaptación escolar y la influencia negativa del grupo de iguales que faciliten una socialización positiva y sana. Este proceso de socialización es importante si queremos comprender el comportamiento humano, entendido como la interiorización de normas y valores que han ido estructurando la personalidad del niño, su manera de pensar, de actuar, en resumidas cuentas su desarrollo mental y social

  13. Robust SNP genotyping by multiplex PCR and arrayed primer extension

    Directory of Open Access Journals (Sweden)

    Podder Mohua

    2008-01-01

    Full Text Available Abstract Background Arrayed primer extension (APEX is a microarray-based rapid minisequencing methodology that may have utility in 'personalized medicine' applications that involve genetic diagnostics of single nucleotide polymorphisms (SNPs. However, to date there have been few reports that objectively evaluate the assay completion rate, call rate and accuracy of APEX. We have further developed robust assay design, chemistry and analysis methodologies, and have sought to determine how effective APEX is in comparison to leading 'gold-standard' genotyping platforms. Our methods have been tested against industry-leading technologies in two blinded experiments based on Coriell DNA samples and SNP genotype data from the International HapMap Project. Results In the first experiment, we genotyped 50 SNPs across the entire 270 HapMap Coriell DNA sample set. For each Coriell sample, DNA template was amplified in a total of 7 multiplex PCRs prior to genotyping. We obtained good results for 41 of the SNPs, with 99.8% genotype concordance with HapMap data, at an automated call rate of 94.9% (not including the 9 failed SNPs. In the second experiment, involving modifications to the initial DNA amplification so that a single 50-plex PCR could be achieved, genotyping of the same 50 SNPs across each of 49 randomly chosen Coriell DNA samples allowed extremely robust 50-plex genotyping from as little as 5 ng of DNA, with 100% assay completion rate, 100% call rate and >99.9% accuracy. Conclusion We have shown our methods to be effective for robust multiplex SNP genotyping using APEX, with 100% call rate and >99.9% accuracy. We believe that such methodology may be useful in future point-of-care clinical diagnostic applications where accuracy and call rate are both paramount.

  14. Binary electrokinetic separation of target DNA from background DNA primers.

    Energy Technology Data Exchange (ETDEWEB)

    James, Conrad D.; Derzon, Mark Steven

    2005-10-01

    This report contains the summary of LDRD project 91312, titled ''Binary Electrokinetic Separation of Target DNA from Background DNA Primers''. This work is the first product of a collaboration with Columbia University and the Northeast BioDefense Center of Excellence. In conjunction with Ian Lipkin's lab, we are developing a technique to reduce false positive events, due to the detection of unhybridized reporter molecules, in a sensitive and multiplexed detection scheme for nucleic acids developed by the Lipkin lab. This is the most significant problem in the operation of their capability. As they are developing the tools for rapidly detecting the entire panel of hemorrhagic fevers this technology will immediately serve an important national need. The goal of this work was to attempt to separate nucleic acid from a preprocessed sample. We demonstrated the preconcentration of kilobase-pair length double-stranded DNA targets, and observed little preconcentration of 60 base-pair length single-stranded DNA probes. These objectives were accomplished in microdevice formats that are compatible with larger detection systems for sample pre-processing. Combined with Columbia's expertise, this technology would enable a unique, fast, and potentially compact method for detecting/identifying genetically-modified organisms and multiplexed rapid nucleic acid identification. Another competing approach is the DARPA funded IRIS Pharmaceutical TIGER platform which requires many hours for operation, and an 800k$ piece of equipment that fills a room. The Columbia/SNL system could provide a result in 30 minutes, at the cost of a few thousand dollars for the platform, and would be the size of a shoebox or smaller.

  15. Magnetic Helicity and Large Scale Magnetic Fields: A Primer

    Science.gov (United States)

    Blackman, Eric G.

    2015-05-01

    Magnetic fields of laboratory, planetary, stellar, and galactic plasmas commonly exhibit significant order on large temporal or spatial scales compared to the otherwise random motions within the hosting system. Such ordered fields can be measured in the case of planets, stars, and galaxies, or inferred indirectly by the action of their dynamical influence, such as jets. Whether large scale fields are amplified in situ or a remnant from previous stages of an object's history is often debated for objects without a definitive magnetic activity cycle. Magnetic helicity, a measure of twist and linkage of magnetic field lines, is a unifying tool for understanding large scale field evolution for both mechanisms of origin. Its importance stems from its two basic properties: (1) magnetic helicity is typically better conserved than magnetic energy; and (2) the magnetic energy associated with a fixed amount of magnetic helicity is minimized when the system relaxes this helical structure to the largest scale available. Here I discuss how magnetic helicity has come to help us understand the saturation of and sustenance of large scale dynamos, the need for either local or global helicity fluxes to avoid dynamo quenching, and the associated observational consequences. I also discuss how magnetic helicity acts as a hindrance to turbulent diffusion of large scale fields, and thus a helper for fossil remnant large scale field origin models in some contexts. I briefly discuss the connection between large scale fields and accretion disk theory as well. The goal here is to provide a conceptual primer to help the reader efficiently penetrate the literature.

  16. In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River

    OpenAIRE

    Cannon, M.V.; Hester, J; Shalkhauser, A.; Chan, E. R.; Logue, K.; S. T. Small; Serre, D.

    2016-01-01

    Analysis of environmental DNA (eDNA) enables the detection of species of interest from water and soil samples, typically using species-specific PCR. Here, we describe a method to characterize the biodiversity of a given environment by amplifying eDNA using primer pairs targeting a wide range of taxa and high-throughput sequencing for species identification. We tested this approach on 91 water samples of 40?mL collected along the Cuyahoga River (Ohio, USA). We amplified eDNA using 12 primer pa...

  17. Investigation of Small-Caliber Primer Function Using a Multiphase Computational Model

    National Research Council Canada - National Science Library

    Schmidt, John R; Nusca, Michael J

    2008-01-01

    This report describes further development in the formulation of a primer model that is compatible with the ARL-NGEN3 code and small caliber weapons that takes in account multidimensional, multiphase...

  18. Development of Primer Pairs from Molecular Typing of Rabies Virus Variants Present in Mexico

    Directory of Open Access Journals (Sweden)

    Fernando Bastida-González

    2016-01-01

    Full Text Available Nucleoprotein (N gene from rabies virus (RABV is a useful sequence target for variant studies. Several specific RABV variants have been characterized in different mammalian hosts such as skunk, dog, and bats by using anti-nucleocapsid monoclonal antibodies (MAbs via indirect fluorescent antibody (IFA test, a technique not available in many laboratories in Mexico. In the present study, a total of 158 sequences of N gene from RABV were used to design eight pairs of primers (four external and four internal primers, for typing four different RABV variants (dog, skunk, vampire bat, and nonhematophagous bat which are most common in Mexico. The results indicate that the primer and the typing variant from the brain samples, submitted to nested and/or real-time PCR, are in agreement in all four singleplex reactions, and the designed primer pairs are an alternative for use in specific variant RABV typing.

  19. Discrimination of reproductive forms of Thrips tabaci (Thysanoptera: Thripidae) by PCR with sequence specific primers.

    Science.gov (United States)

    Kobayashi, Kazuya; Hasegawa, Eisuke

    2012-04-01

    In agriculture, although it is important to identify species of pest insects, the morphological identification is often difficult. DNA genotyping is useful for the identification of species in morphologically indiscriminable species. Thrips tabaci (Lindeman) can be divided into two reproductive forms (arrhenotoky and thelytoky, each of which different in pesticide resistance) but morphological discrimination is not possible. Here, we establish a simple method to discriminate the strains based on their mitochondrial DNA sequences. Phylogenetic analysis including the T. tabaci and congeneric species provided ancestor sequences of each strain of T tabaci. Based on the ancestor sequences, we developed a primer set that include strain specific primers on sense strand and common primer on anti sense strand. Using this primer set, the strains of 196 individuals of T. tabaci were successfully assigned to each ofgenotypic forms. As the phylogeny and ancestor sequences were based on worldwide samples, this method will work well on most populations around the world.

  20. Sindrome de Smith-Lemli-Opitz e hipotiroidismo: el primer caso venezolano

    National Research Council Canada - National Science Library

    Lima-Martinez, Marcos M; Zerpa, Jose; Gil, Victor

    2014-01-01

    ... de la conversion de 7-dehidrocolesterol a colesterol. La ocurrencia de hipotiroidismo en asociacion con SSLO es muy inusual. Este constituye el primer caso venezolano en el que se asocian ambas patologias.

  1. Microsatellite primers in the foundation tree species Pinus edulis and P. monophylla (Pinaceae)1

    Science.gov (United States)

    Krohn, Andrew L.; Flores-Rentería, Lluvia; Gehring, Catherine A.

    2013-01-01

    • Premise of the study: Microsatellite primers were developed in the foundational tree species Pinus edulis to investigate population differentiation of P. edulis and hybridization among closely related species. • Methods and Results: Using a hybridization protocol, primer sets for 11 microsatellite loci were developed using megagametophyte tissue from P. edulis and scored for polymorphism in three populations of P. edulis and a single P. monophylla population. The primers amplified simple and compound di-, tri-, and pentanucleotide repeats with two to 18 alleles per locus. • Conclusions: These results demonstrate the utility of the described primers for studies of population differentiation within and among P. edulis populations as well as across putative hybrid zones where P. edulis may coexist with sister species. PMID:25202571

  2. Discovery of EST-derived microsatellite primers in the legume Lens culinaris (Fabaceae).

    Science.gov (United States)

    Jain, Neelu; Dikshit, H K; Singh, D; Singh, Akanksha; Kumar, Harish

    2013-07-01

    We developed microsatellite markers in the legume Lens culinaris from publicly available databases to enrich the limited marker resource available for the crop. • Eighty-two primer sets were identified using expressed sequence sets of L. culinaris available in the National Center for Biotechnology Information (NCBI) database and were characterized in six species of Lens. Among them, 20 simple sequence repeat (SSR) primers produced no amplification product, 43 produced monomorphic products, and 19 were polymorphic. The primers amplified mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats with one to four alleles. These SSR loci successfully amplified in five related wild species, with a total of 61 primer pairs in L. nigricans and L. odemensis (98.39%), 59 in L. tomentosus (95.1%), and 60 in L. ervoides and L. orientalis (96.7%), respectively. • The microsatellite markers discovered in this study will be useful in genetic mapping, marker-assisted breeding, and characterization of germplasm.

  3. Replication and pathogenicity of primer binding site mutants of SL3-3 murine leukemia viruses

    DEFF Research Database (Denmark)

    Lund, Anders Henrik; Schmidt, J; Luz, A

    1999-01-01

    Retroviral reverse transcription is primed by a cellular tRNA molecule annealed to an 18-bp primer binding site sequence. The sequence of the primer binding site coincides with that of a negatively acting cis element that mediates transcriptional silencing of murine leukemia virus (MLV) in undiff...... delayed relative to that of the wild-type virus, molecular tumor analysis indicated that all the primer binding site-modified viruses induce T-cell lymphomas similar to those induced by the wild-type virus in terms of frequencies of genomic rearrangements within the T-cell receptor beta......, recombination with endogenous viruses resulting in the generation of recombinant viruses carrying a glutamine primer binding site was detected in the majority of the tumors induced by the SL3-3 Lys3 mutant as well as in two tumors induced by wild-type SL3-3 and the SL3-3 Arg1,2 mutant....

  4. Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans

    National Research Council Canada - National Science Library

    Lobo, Jorge; Costa, Pedro M; Teixeira, Marcos A L; Ferreira, Maria S G; Costa, Maria H; Costa, Filipe O

    2013-01-01

    Building reference libraries of DNA barcodes is relatively straightforward when specifically designed primers are available to amplify the COI-5P region from a relatively narrow taxonomic group (e.g...

  5. One fungus , which genes ? Development and assessment of universal primers for potential secondary fungal DNA barcodes

    National Research Council Canada - National Science Library

    Stielow, J B; Lévesque, C A; Seifert, K A; Meyer, W; Irinyi, L; Smits, D; Renfurm, R; Verkley, G J M; Groenewald, M; Chaduli, D; Lomascolo, A; Welti, S; Lesage-Meessen, L; Favel, A; Al-Hatmi, A M S; Damm, U; Yilmaz, N; Houbraken, J; Lombard, L; Quaedvlieg, W; Binder, M; Vaas, L.A.I; Vu, D; Yurkov, A; Begerow, D; Roehl, O; Guerreiro, M; Fonseca, A; Samerpitak, K; Diepeningen, A.D. van; Dolatabadi, S; Moreno, L.F; Casaregola, S; Mallet, S; Jacques, N; Roscini, L; Egidi, E; Bizet, C; Garcia-Hermoso, D; Martín, M.P; Deng, S; Groenewald, J.Z; Boekhout, T; Beer, Z.W. de; Barnes, I; Duong, T.A; Wingfield, M.J; Hoog, G.S. de; Crous, P.W; Lewis, C.T; Hambleton, S; Moussa, T.A.A; Al-Zahrani, H.S; Almaghrabi, O.A; Louis-Seize, G; Assabgui, R; McCormick, W; Omer, G; Dukik, K; Cardinali, G; Eberhardt, U; Vries, M. de; Robert, V

    2015-01-01

    The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode...

  6. Microsatellite Primers in the Foundation Tree Species Pinus edulis and P. monophylla (Pinaceae

    Directory of Open Access Journals (Sweden)

    Andrew L. Krohn

    2013-07-01

    Full Text Available Premise of the study: Microsatellite primers were developed in the foundational tree species Pinus edulis to investigate population differentiation of P. edulis and hybridization among closely related species. Methods and Results: Using a hybridization protocol, primer sets for 11 microsatellite loci were developed using megagametophyte tissue from P. edulis and scored for polymorphism in three populations of P. edulis and a single P. monophylla population. The primers amplified simple and compound di-, tri-, and pentanucleotide repeats with two to 18 alleles per locus. Conclusions: These results demonstrate the utility of the described primers for studies of population differentiation within and among P. edulis populations as well as across putative hybrid zones where P. edulis may coexist with sister species.

  7. Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers

    DEFF Research Database (Denmark)

    Balcells, Ingrid; Cirera, Susanna; Busk, Peter Kamp

    2011-01-01

    Background MicroRNAs are important regulators of gene expression at the post-transcriptional level and play an important role in many biological processes. Due to the important biological role it is of great interest to quantitatively determine their expression level in different biological...... settings. Results We describe a PCR method for quantification of microRNAs based on a single reverse transcription reaction for all microRNAs combined with real-time PCR with two, microRNA-specific DNA primers. Primer annealing temperatures were optimized by adding a DNA tail to the primers and could...... be designed with a success rate of 94%. The method was able to quantify synthetic templates over eight orders of magnitude and readily discriminated between microRNAs with single nucleotide differences. Importantly, PCR with DNA primers yielded significantly higher amplification efficiencies of biological...

  8. Recolectores, verificadores y reflexivos: perfiles de la competencia informacional en estudiantes universitarios de primer semestre

    National Research Council Canada - National Science Library

    Harold Castañeda-Peña; Liliana González Niño; Gloria Marciales Vivas; Jorge Winston Barbosa Chacón; Juan Carlos Barbosa Herrera

    2010-01-01

    Artículo de investigación que explora perfiles de la competencia informacional en estudiantes universitarios de primer semestre, a partir de un concepto renovado de competencia informacional desde la perspectiva...

  9. Primer retention owing to the absence of RNase H1 is catastrophic for mitochondrial DNA replication.

    Science.gov (United States)

    Holmes, J Bradley; Akman, Gokhan; Wood, Stuart R; Sakhuja, Kiran; Cerritelli, Susana M; Moss, Chloe; Bowmaker, Mark R; Jacobs, Howard T; Crouch, Robert J; Holt, Ian J

    2015-07-28

    Encoding ribonuclease H1 (RNase H1) degrades RNA hybridized to DNA, and its function is essential for mitochondrial DNA maintenance in the developing mouse. Here we define the role of RNase H1 in mitochondrial DNA replication. Analysis of replicating mitochondrial DNA in embryonic fibroblasts lacking RNase H1 reveals retention of three primers in the major noncoding region (NCR) and one at the prominent lagging-strand initiation site termed Ori-L. Primer retention does not lead immediately to depletion, as the persistent RNA is fully incorporated in mitochondrial DNA. However, the retained primers present an obstacle to the mitochondrial DNA polymerase γ in subsequent rounds of replication and lead to the catastrophic generation of a double-strand break at the origin when the resulting gapped molecules are copied. Hence, the essential role of RNase H1 in mitochondrial DNA replication is the removal of primers at the origin of replication.

  10. Incorporating travel-time reliability into the congestion management process : a primer.

    Science.gov (United States)

    2015-02-01

    This primer explains the value of incorporating travel-time reliability into the Congestion Management Process (CMP) : and identifies the most current tools available to assist with this effort. It draws from applied research and best practices : fro...

  11. Streamlining DNA barcoding protocols: automated DNA extraction and a new cox1 primer in arachnid systematics.

    Directory of Open Access Journals (Sweden)

    Nina Vidergar

    Full Text Available BACKGROUND: DNA barcoding is a popular tool in taxonomic and phylogenetic studies, but for most animal lineages protocols for obtaining the barcoding sequences--mitochondrial cytochrome C oxidase subunit I (cox1 AKA CO1--are not standardized. Our aim was to explore an optimal strategy for arachnids, focusing on the species-richest lineage, spiders by (1 improving an automated DNA extraction protocol, (2 testing the performance of commonly used primer combinations, and (3 developing a new cox1 primer suitable for more efficient alignment and phylogenetic analyses. METHODOLOGY: We used exemplars of 15 species from all major spider clades, processed a range of spider tissues of varying size and quality, optimized genomic DNA extraction using the MagMAX Express magnetic particle processor-an automated high throughput DNA extraction system-and tested cox1 amplification protocols emphasizing the standard barcoding region using ten routinely employed primer pairs. RESULTS: The best results were obtained with the commonly used Folmer primers (LCO1490/HCO2198 that capture the standard barcode region, and with the C1-J-2183/C1-N-2776 primer pair that amplifies its extension. However, C1-J-2183 is designed too close to HCO2198 for well-interpreted, continuous sequence data, and in practice the resulting sequences from the two primer pairs rarely overlap. We therefore designed a new forward primer C1-J-2123 60 base pairs upstream of the C1-J-2183 binding site. The success rate of this new primer (93% matched that of C1-J-2183. CONCLUSIONS: The use of C1-J-2123 allows full, indel-free overlap of sequences obtained with the standard Folmer primers and with C1-J-2123 primer pair. Our preliminary tests suggest that in addition to spiders, C1-J-2123 will also perform in other arachnids and several other invertebrates. We provide optimal PCR protocols for these primer sets, and recommend using them for systematic efforts beyond DNA barcoding.

  12. Adhesive bonding and the use of corrosion resistant primers. [for metal surface preparation

    Science.gov (United States)

    Hockridge, R. R.; Thibault, H. G.

    1972-01-01

    The use of an anti-corrosive primer has been shown to be essential to assure survival of a bonded structure in a hostile environment, particularly if a stress is to be applied to the adhesively bonded joint during the environmental exposure. For example, the Lockheed L-1011 TriStar assembly, after exhaustive evaluation tests specifies use of chromate filled inhibitive polysulfide sealants, and use of corrosion inhibiting adhesive primers prior to structural bonding with film adhesive.

  13. New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida)

    OpenAIRE

    Liu, Yingkui; Erséus, Christer

    2017-01-01

    Abstract Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate‐specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were devel...

  14. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates.

    Science.gov (United States)

    Folmer, O; Black, M; Hoeh, W; Lutz, R; Vrijenhoek, R

    1994-10-01

    We describe "universal" DNA primers for polymerase chain reaction (PCR) amplification of a 710-bp fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) from 11 invertebrate phyla: Echinodermata, Mollusca, Annelida, Pogonophora, Arthropoda, Nemertinea, Echiura, Sipuncula, Platyhelminthes, Tardigrada, and Coelenterata, as well as the putative phylum Vestimentifera. Preliminary comparisons revealed that these COI primers generate informative sequences for phylogenetic analyses at the species and higher taxonomic levels.

  15. MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool.

    Directory of Open Access Journals (Sweden)

    Bin Zou

    Full Text Available An understanding of microbial community structure is an important issue in the field of molecular ecology. The traditional molecular method involves amplification of small subunit ribosomal RNA (SSU rRNA genes by polymerase chain reaction (PCR. However, PCR-based amplicon approaches are affected by primer bias and chimeras. With the development of high-throughput sequencing technology, unbiased SSU rRNA gene sequences can be mined from shotgun sequencing-based metagenomic or metatranscriptomic datasets to obtain a reflection of the microbial community structure in specific types of environment and to evaluate SSU primers. However, the use of short reads obtained through next-generation sequencing for primer evaluation has not been well resolved. The software MIPE (MIcrobiota metagenome Primer Explorer was developed to adapt numerous short reads from metagenomes and metatranscriptomes. Using metagenomic or metatranscriptomic datasets as input, MIPE extracts and aligns rRNA to reveal detailed information on microbial composition and evaluate SSU rRNA primers. A mock dataset, a real Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST test dataset, two PrimerProspector test datasets and a real metatranscriptomic dataset were used to validate MIPE. The software calls Mothur (v1.33.3 and the SILVA database (v119 for the alignment and classification of rRNA genes from a metagenome or metatranscriptome. MIPE can effectively extract shotgun rRNA reads from a metagenome or metatranscriptome and is capable of classifying these sequences and exhibiting sensitivity to different SSU rRNA PCR primers. Therefore, MIPE can be used to guide primer design for specific environmental samples.

  16. Scour and Burial of Bottom Mines: a Primer for Fleet Use

    OpenAIRE

    Inman, Douglas L.; Jenkins, Scott A.

    2002-01-01

    This primer is for fleet use as a means of rapid access to information on scour, burial, and re-exposure of bottom mines placed in nearshore waters. The format is easily adapted to a computer slide show where sequential illustrations such as progressive mine scour and burial could be in animated form. The illustrations detail mechanisms and burial rates characteristic of coastal and sediment type. The primer also addresses the ranges of uncertainty in mine burial estimates by showing burial d...

  17. Recovery of the mitochondrial COI barcode region in diverse Hexapoda through tRNA-based primers

    OpenAIRE

    Oh Hyun-Woo; Suh Soo-Jung; Park Doo-Sang; Hebert Paul DN

    2010-01-01

    Abstract Background DNA barcoding uses a 650 bp segment of the mitochondrial cytochrome c oxidase I (COI) gene as the basis for an identification system for members of the animal kingdom and some other groups of eukaryotes. PCR amplification of the barcode region is a key step in the analytical chain, but it sometimes fails because of a lack of homology between the standard primer sets and target DNA. Results Two forward PCR primers were developed following analysis of all known arthropod mit...

  18. Development and evaluation of new primers for PCR-based identification of Prevotella intermedia.

    Science.gov (United States)

    Zhou, Yanbin; Liu, Dali; Wang, Yiwei; Zhu, Cailian; Liang, Jingping; Shu, Rong

    2014-08-01

    The aim of this study was to develop new Prevotella intermedia-specific PCR primers based on the 16S rRNA. The new primer set, Pi-192 and Pi-468, increased the accuracy of PCR-based P. intermedia identification and could be useful in the detection of P. intermedia as well as epidemiological studies on periodontal disease. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Peran Keluarga dalam Pengelolaan Kasus di Layanan Primer Melalui Five Family Oriented Questions

    OpenAIRE

    Retno Asti Werdhani; Elsa P. Setiawati; Fedri R. Rinawan

    2017-01-01

    Pengelolaan kasus di layanan primer dengan pendekatan kedokteran keluarga memperhatikan potensi keluarga sebagai sumber daya pendukung dan atau penghambat keberhasilan penatalaksanaan pasien. Penelitian ini bertujuan untuk melihat gambaran kasus di layanan primer dan persepsi keluarga mengenai pasien melalui five family oriented question (FFOQ). Pengambilan data dilakukan menggunakan kuesioner pada 162 pasien Puskesmas dan Klinik di DKI Jakarta pada tahun 2015–2016. Kuesioner terdiri a...

  20. Gold nanoparticle-assisted primer walking for closing the human chromosomal gap

    DEFF Research Database (Denmark)

    Li, H; Shi, B; Li, X

    2013-01-01

    NPs) to improve the efficiency in primer walking amplification. We used this strategy to close a gap in human chromosome 5 containing a DNA stretch composed of the 12SAT repeat. The obtained gap sequence is highly conserved among several mammalian genomes. The demonstrated AuNP-assisted primer walking strategy...... is capable of effectively improving the specificity of PCR amplification and enriching the yield of target DNA fragments; it offers a new avenue for closing gaps left by current sequencing methods...

  1. Target-cell-derived tRNA-like primers for reverse transcription support retroviral infection at low efficiency

    DEFF Research Database (Denmark)

    Schmitz, Alexander; Lund, Anders H; Hansen, Anette C

    2002-01-01

    Reverse transcription of a retroviral genome takes place in the cytoplasm of an infected cell by a process primed by a producer-cell-derived tRNA annealed to an 18-nucleotide primer-binding site (PBS). By an assay involving primer complementation of PBS-mutated vectors we analyzed whether tRNA...... primers derived from the target cell can sustain reverse transcription during murine leukemia virus (MLV) infection. Transduction efficiencies were 4-5 orders of magnitude below those of comparable producer-cell complementations. However, successful usage of a target-cell-derived tRNA primer was proven...... by cases of correction of single mismatches between Akv-MLV vectors and complementary tRNA primers toward the primer sequence in the integrated vector. Thus, target-cell-derived tRNA-like primers are able to initiate first-strand cDNA synthesis and plus-strand transfer leading to a complete provirus...

  2. GSP: a web-based platform for designing genome-specific primers in polyploids.

    Science.gov (United States)

    Wang, Yi; Tiwari, Vijay K; Rawat, Nidhi; Gill, Bikram S; Huo, Naxin; You, Frank M; Coleman-Derr, Devin; Gu, Yong Q

    2016-08-01

    The sequences among subgenomes in a polyploid species have high similarity, making it difficult to design genome-specific primers for sequence analysis. We present GSP, a web-based platform to design genome-specific primers that distinguish subgenome sequences in a polyploid genome. GSP uses BLAST to extract homeologous sequences of the subgenomes in existing databases, performs a multiple sequence alignment, and design primers based on sequence variants in the alignment. An interactive primers diagram, a sequence alignment viewer and a virtual electrophoresis are displayed as parts of the primer design result. GSP also designs specific primers from multiple sequences uploaded by users. GSP is a user-friendly and efficient web platform freely accessible at http://probes.pw.usda.gov/GSP Source code and command-line application are available at https://github.com/bioinfogenome/GSP CONTACTS: yong.gu@ars.usda.gov or devin.coleman-derr@ars.usda.gov Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  3. Family-Specific Degenerate Primer Design: A Tool to Design Consensus Degenerated Oligonucleotides

    Science.gov (United States)

    Goñi, Sandra Elizabeth; Lozano, Mario Enrique

    2013-01-01

    Designing degenerate PCR primers for templates of unknown nucleotide sequence may be a very difficult task. In this paper, we present a new method to design degenerate primers, implemented in family-specific degenerate primer design (FAS-DPD) computer software, for which the starting point is a multiple alignment of related amino acids or nucleotide sequences. To assess their efficiency, four different genome collections were used, covering a wide range of genomic lengths: Arenavirus (10 × 104 nucleotides), Baculovirus (0.9 × 105 to 1.8 × 105 bp), Lactobacillus sp. (1 × 106 to 2 × 106 bp), and Pseudomonas sp. (4 × 106 to 7 × 106 bp). In each case, FAS-DPD designed primers were tested computationally to measure specificity. Designed primers for Arenavirus and Baculovirus were tested experimentally. The method presented here is useful for designing degenerate primers on collections of related protein sequences, allowing detection of new family members. PMID:23533783

  4. Association of different primers and resin cements for adhesive bonding to zirconia ceramics.

    Science.gov (United States)

    Maeda, Fernando Akio; Bello-Silva, Marina Stella; de Paula Eduardo, Carlos; Miranda Junior, Walter Gomes; Cesar, Paulo Francisco

    2014-06-01

    To evaluate the shear bond strength (SBS) to zirconia ceramics using different associations of primers and resin cements. Two blocks of LAVA zirconia (3Y-TZP) were randomly submitted to an application of three different commercially available primers: Alloy Primer (AP), Z-Prime Plus (ZP), and Signum Zirconia Bond (SZB). Nonprimed specimens were considered controls. After treatment, the 80 specimens (5 mm × 5 mm × 2 mm) were randomly cemented with one of the resin cements: Panavia F, Multilink, seT, and NX3. For cementation, cylinders of resin cement were built on the ceramic surfaces using the SDI SBS apparatus. The specimens were submitted to the SBS test. Fractured surfaces were observed under stereomicroscopy to determine the failure mode, and mean bond strength values were analyzed using the Kruskal-Wallis and Mann-Whitney tests (α = 0.05). Signum Zirconia Bond had the highest SBS compared to all other primers and the control group, regardless of the resin cement used. The highest values were obtained when associating Panavia F with Signum Zirconia Bond. Alloy Primer increased bonding values when associated with seT cement only. When no primer was used, no statistical difference was observed among resin cements. All specimens fractured due to adhesive failure. Signum Zirconia Bond is capable of increasing bonding values of resin cements to zirconia ceramics. Its association with Panavia F shows enhanced results when considering short-term adhesion to zirconia.

  5. Survey of methanotrophic diversity in various ecosystems by degenerate methane monooxygenase gene primers.

    Science.gov (United States)

    Ghashghavi, Mohammad; Jetten, Mike S M; Lüke, Claudia

    2017-08-23

    Methane is the second most important greenhouse gas contributing to about 20% of global warming. Its mitigation is conducted by methane oxidizing bacteria that act as a biofilter using methane as their energy and carbon source. Since their first discovery in 1906, methanotrophs have been studied using a complementary array of methods. One of the most used molecular methods involves PCR amplification of the functional gene marker for the diagnostic of copper and iron containing particulate methane monooxygenase. To investigate the diversity of methanotrophs and to extend their possible molecular detection, we designed a new set of degenerate methane monooxygenase primers to target an 850 nucleotide long sequence stretch from pmoC to pmoA. The primers were based on all available full genomic pmoCAB operons. The newly designed primers were tested on various pure cultures, enrichment cultures and environmental samples using PCR. The results demonstrated that this primer set has the ability to correctly amplify the about 850 nucleotide long pmoCA product from Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobia and the NC10 phyla methanotrophs. The new primer set will thus be a valuable tool to screen ecosystems and can be applied in conjunction with previously used pmoA primers to extend the diversity of currently known methane-oxidizing bacteria.

  6. PRIMEGENSw3: a web-based tool for high-throughput primer and probe design.

    Science.gov (United States)

    Kushwaha, Garima; Srivastava, Gyan Prakash; Xu, Dong

    2015-01-01

    Highly specific and efficient primer and probe design has been a major hurdle in many high-throughput techniques. Successful implementation of any PCR or probe hybridization technique depends on the quality of primers and probes used in terms of their specificity and cross-hybridization. Here we describe PRIMEGENSw3, a set of web-based utilities for high-throughput primer and probe design. These utilities allow users to select genomic regions and to design primer/probe for selected regions in an interactive, user-friendly, and automatic fashion. The system runs the PRIMEGENS algorithm in the back-end on the high-performance server with the stored genomic database or user-provided custom database for cross-hybridization check. Cross-hybridization is checked not only using BLAST but also by checking mismatch positions and energy calculation of potential hybridization hits. The results can be visualized online and also can be downloaded. The average success rate of primer design using PRIMEGENSw3 is ~90 %. The web server also supports primer design for methylated sequences, which is used in epigenetic studies. Stand-alone version of the software is also available for download at the website.

  7. New primers for the class Actinobacteria: application to marine and terrestrial environments.

    Science.gov (United States)

    Stach, James E M; Maldonado, Luis A; Ward, Alan C; Goodfellow, Michael; Bull, Alan T

    2003-10-01

    In this study, we redesigned and evaluated primers for the class Actinobacteria. In silico testing showed that the primers had a perfect match with 82% of genera in the class Actinobacteria, representing a 26-213% improvement over previously reported primers. Only 4% of genera that displayed mismatches did so in the terminal three bases of the 3' end, which is most critical for polymerase chain reaction success. The primers, designated S-C-Act-0235-a-S-20 and S-C-Act-0878-a-A-19, amplified an approximately 640 bp stretch of the 16S rRNA gene from all actinobacteria tested (except Rubrobacter radiotolerans) up to an annealing temperature of 72 degrees C. An Actinobacteria Amplification Resource (http://microbe2.ncl.ac.uk/MMB/AAR.htm) was generated to provide a visual guide to aid the amplification of actinobacterial 16S rDNA. Application of the primers to DNA extracted from marine and terrestrial samples revealed the presence of actinobacteria that have not been described previously. The use of 16S rDNA similarity and DNA-DNA pairing correlations showed that almost every actinomycete clone represented either a new species or a novel genus. The results of this study reinforce the proposition that current culture-based techniques drastically underestimate the diversity of Actinobacteria in the environment and highlight the need to evaluate taxon-specific primers regularly in line with improvements in databases holding 16S rDNA sequences.

  8. Detection of Luminous Vibrio harveyi in Penaeid Shrimp Through Nested PCR Using Haemolysin Gene Primer

    Directory of Open Access Journals (Sweden)

    WAWAN ABDULLAH SETIAWAN

    2015-04-01

    Full Text Available Whiteleg shrimp (Litopenaeus vannamei is one of the most important aquaculture commodity in Indonesia. However, the luminous disease primarily caused by Vibrio harveyi bacteria still becomes an obstacle in penaeid shrimp farming, especially in shrimp hatchery. This study was aimed to identify the presence of V. harveyi in L. vannamei through nested PCR using haemolysin gene primer. First, initial primers were designed using V. harveyi VIB 391 haemolysin gene sequence (accession number: DQ640264, flanking the position 133 to 756. This primer pairs were used to identify haemolysin gene in both V. harveyi MR5339 and V. harveyi 275 strain. Sequencing results from each sample showed 99% similarity with haemolysin gene sequence in Genebank. Furthermore, the sequence of V. harveyi MR5339 haemolysin gene was used to design the nested PCR primers. The first primer pairs of nested PCR have successfully amplified the haemolysin gene fragment of all V. harveyi strains samples from position 52 to 405. The second primer pairs of nested PCR have amplified position 204 to 405 where it can detect all of V. harveyi strains used as sample sources in this study. The application of nested PCR technique in this study was able to identify V. harveyi strains at serial dilution of cells density as low as 100 cfu/mL, which is equal to a single cell or at DNA concentration up to 101 fg/µL.

  9. Enamel shear bond strength of different primers combined with an orthodontic adhesive paste.

    Science.gov (United States)

    Seeliger, Julia H; Botzenhart, Ute U; Gedrange, Tomasz; Kozak, Karol; Stepien, Lukas; Machoy, Monika

    2017-08-28

    The aim of this study was a comparison of shear bond strength (SBS) on tooth enamel of different primers combined with the adhesive paste Transbond XT. Forty bovine teeth were used in order to create 40 test blocks. The blocks were divided into four groups of 10 blocks each: group A - sample primer (SP); group B - Opal Seal (OS); group C - Transbond Plus SEP (TSEP); group D - Transbond XT Primer (TXT). After surface preparation and application of the primer, respectively, two stainless steel brackets were fixed on each tooth by using Transbond XT. Accordingly, 80 brackets were debonded (n=20). Shear bond strength and adhesive remnant index (ARI) scores were evaluated. Statistical analyses were performed by using the Student's t-test and Mann-Whitney U test. All tested groups revealed high shear bond strength in a similar size range. There were no significant differences between the groups concerning shear bond strength. The ARI scores of group C showed significantly lower ARI scores (0 and 1) than that of group D. Apart from that there was no statistical difference. In combination with the adhesive paste Transbond XT, all tested primers were suitable for fixing orthodontic brackets. The primers could be changed according to the clinical situation.

  10. A Primer on Population Health Management and Its Perioperative Application.

    Science.gov (United States)

    Boudreaux, Arthur M; Vetter, Thomas R

    2016-07-01

    The movement toward value-based payment models, driven by governmental policies, federal statutes, and market forces, is propelling the importance of effectively managing the health of populations to the forefront in the United States and other developed countries. However, for many anesthesiologists, population health management is a new or even foreign concept. A primer on population health management and its potential perioperative application is thus presented here. Although it certainly continues to evolve, population health management can be broadly defined as the specific policies, programs, and interventions directed at optimizing population health. The Population Health Alliance has created a particularly cogent conceptual framework and interconnected and very useful population health process model, which together identify the key components of population health and its management. Population health management provides a useful rationale for patients, providers, payers, and policymakers to move collectively away from the traditional system of individual, siloed providers to a more integrated, coordinated, team-based approach, thus creating a holistic view of the patient population. The goal of population health management is to keep the targeted patient population as healthy as possible, thus minimizing the need for costly interventions such as emergency department visits, acute hospitalizations, laboratory testing and imaging, and diagnostic and therapeutic procedures. Population health management strategies are increasingly more important to leaders of health care systems as the health of populations for which they care, especially in a strong cost risk-sharing environment, must be optimized. Most population health management efforts rely on a patient-centric team approach, coordination of care, effective communication, robust outcomes data analysis, and continuous quality improvement. Anesthesiologists have an opportunity to help lead these efforts in

  11. Konjungtivitis Viral: Diagnosis dan Terapi di Pelayanan Kesehatan Primer

    Directory of Open Access Journals (Sweden)

    Ratna Sitompul

    2017-04-01

    Full Text Available Konjungtiva adalah membran mukosa tipis transparan yang melapisi bagian anterior bola mata dan bagian dalam palpebral. Konjungtiva berfungsi sebagai salah satu komponen sistem perlindungan mata dari peradangan dan infeksi. Peradangan konjungtiva disebut konjungtivitis dan infeksi virus merupakan etiologi peradangan akut tersering pada konjungtiva. Virus yang menyebabkan konjungtivitis adalah adenovirus, herpes simpleks, herpes zoster, pox virus, myxovirus, paramyxovirus, dan arbovirus. Konjungtivitis sering terjadi bersama atau sesudah infeksi saluran napas dan umumnya terdapat riwayat kontak dengan pasien konjungtivitis viral. Gejala konjungtivitis viral berupa mata merah, sekret mata berair dan dapat disertai pembesaran kelenjar limfe. Gejala konjungtivitis viral biasanya ringan, dapat sembuh sendiri dan tidak disertai penurunan tajam penglihatan sehingga dapat ditatalaksana di pelayanan kesehatan primer. Meskipun demikian, terdapat kasus-kasus yang bersifat mengancam penglihatan sehingga perlu segera dirujuk ke rumah sakit atau dokter spesialis mata. Konjungtivitis viral sangat menular sehingga pasien perlu mendapat edukasi untuk mengurangi kontak langsung dan tidak langsung agar tidak menjadi sumber infeksi bagi lingkungannya. Konjungtivitis viral dapat sembuh sendiri, namun pemberian air mata buatan, antihistamin topikal, atau kompres dingin berguna untuk meredakan gejala. Terapi antiviral tidak diperlukan untuk konjungtivitis virus, kecuali untuk konjungtivitis herpetik. Kata kunci: epidemi, konjungtivitis, virus.     Viral Conjunctivitis: Diagnosis and Therapy in Primary Health Care   Abstract Conjunctivae is a transparent thin mucosal membrane covering the outer anterior eye and inner palpebrae. This structure is vital for eye defense from inflammation and infection. Inflammation occurring on the conjunctivae is called conjunctivitis and virus is one of the most common etiologic agent. Such viruses are adenovirus, herpes simplex virus

  12. The sorption of iodine by an inorganic zinc primer

    Energy Technology Data Exchange (ETDEWEB)

    Evans, G.J.; Bekeris, P.A. [Toronto Univ., ON (Canada). Dept. of Chemical Engineering and Applied Chemistry

    1996-12-01

    The purpose of this work was to identify and evaluate significant parameters in the sorption of I{sub 2}(g) onto Carbo Zinc 11 inorganic primer, a paint used in the containment structure of some CANDU reactors. Air containing known amounts of {sup 131}I{sub 2}(g) was passed through 0.64 cm diameter glass tubing coated on the inner surface with paint. The accumulation of iodine on the surface was continuously monitored using two scintillation detectors. The test parameters covered were relative humidity, flow rate, I{sub 2} concentration and paint temperature. Adsorption was rapid at 23{sup o}C and predominantly gas phase mass transfer limited: the deposition velocity of 0.7{+-}0.4 cm/s was similar to the gas phase mass transfer coefficient of 1.2 cm/s estimated for the system. The deposition velocity observed at a higher paint surface temperature was an order of magnitude smaller. A similar deposition velocity was observed at 23{sup o}C for adsorption of I{sub 2}(g) from essentially dry air suggesting that the low deposition velocity observed for high surface temperature was limited by the amount of water on the paint surface. The rate of adsorption on the paint was directly proportional to the I{sub 2}(g) concentration over the range in concentration studied. The majority of the iodine retained by the paint could not be removed by washing with methanol or chloroform, but it was removed by water indicating that it was in an ionic form. Analysis of the speciation of the iodine in the wash water indicated that only a third of it was in the form of I{sup -}; the form of the remaining iodine could not be resolved. Desorption from the paint was negligible at room temperature but was detectable at higher temperatures. These low desorption rates and the ionic nature of the surface iodine indicated that adsorption occurred predominantly through a chemisorption process. A number of possible mechanisms were proposed. (author) 5 figs., 2 tabs., 6 refs.

  13. Primer-dependent and primer-independent initiation of double stranded RNA synthesis by purified Arabidopsis RNA-dependent RNA polymerases RDR2 and RDR6.

    Directory of Open Access Journals (Sweden)

    Anthony Devert

    Full Text Available Cellular RNA-dependent RNA polymerases (RDRs are fundamental components of RNA silencing in plants and many other eukaryotes. In Arabidopsis thaliana genetic studies have demonstrated that RDR2 and RDR6 are involved in the synthesis of double stranded RNA (dsRNA from single stranded RNA (ssRNA targeted by RNA silencing. The dsRNA is subsequently cleaved by the ribonuclease DICER-like into secondary small interfering RNAs (siRNAs that reinforce and/or maintain the silenced state of the target RNA. Models of RNA silencing propose that RDRs could use primer-independent and primer-dependent initiation to generate dsRNA from a transcript targeted by primary siRNA or microRNA (miRNA. However, the biochemical activities of RDR proteins are still partly understood. Here, we obtained active recombinant RDR2 and RDR6 in a purified form. We demonstrate that RDR2 and RDR6 have primer-independent and primer-dependent RNA polymerase activities with different efficiencies. We further show that RDR2 and RDR6 can initiate dsRNA synthesis either by elongation of 21- to 24- nucleotides RNAs hybridized to complementary RNA template or by elongation of self-primed RNA template. These findings provide new insights into our understanding of the molecular mechanisms of RNA silencing in plants.

  14. Comparison of the antibacterial activity of different self-etching primers and adhesives.

    Science.gov (United States)

    Korkmaz, Yonca; Ozalp, Meral; Attar, Nuray

    2008-11-01

    The aim of this study was to evaluate the antibacterial effects of different one-step and two-step self-etching primer/adhesives on Streptococcus mutans (S. mutans), Lactobacillus casei (L. casei), and Lactobacillus acidophilus (L. acidophilus). The antibacterial effects of Clearfil Protect Bond Primer and Bonding agent; AdheSE Primer and Bonding agent; Adper Prompt L-Pop; Futurabond NR; Clearfil Tri S Bond; and Cervitec (positive control, 1% chlorhexidine varnish) were tested against standard strains of S. mutans, L. Casei, and L. acidophilus using the disk diffusion method. Standard filter paper disks (n=5) impregnated with 20 microL of each material were prepared. After incubation at 37 masculineC for 48 hours in a 5-10% CO2 atmosphere, the diameter of inhibition zones were measured in millimeters. Data were analyzed using one way analysis of variance (ANOVA) and multivariate analysis of variance (MANOVA). Duncan's Multiple Range Test was used for pairwise comparison. The size of inhibition zones produced by primer/adhesives varied among the brands. AdheSE Primer: S. mutans (20.6+/-1.51); L. casei (14.8+/-1.78); L. acidophilus (11.4+/-0.54). Adper Prompt L-Pop: S. mutans (19.6+/-1.51); L. casei (13.8+/-1.64); L. acidophilus (13.8+/-1.09). Cervitec: S. mutans (23+/-0.00); L. casei (27+/-0.70); L. acidophilus (22.4+/-0.54). Clearfil Protect Bond Primer: S. mutans (17+/-0.00); L. casei (17.6+/-0.54); L. acidophilus (22.4+/-0.54). Futurabond NR was found effective only against S. mutans (14.6+/-1.67). Of all the materials tested, AdheSE Bonding agent, Clearfil Protect Bond Bonding agent, and Clearfil Tri S Bond exhibited no inhibition zone (-) for all bacteria tested. Among the adhesives tested Clearafil Protect Bond Primer based upon monomer methacryloyloxydodecylpyridiniium bromide (MDPB) was found to be the most potent material against L. acidophilus and L. casei. AdheSE Primer and Adper Prompt L-Pop are highly effective against S. mutans. Compared with other

  15. Circulating primers enhance platelet function and induce resistance to antiplatelet therapy

    Science.gov (United States)

    Blair, T A; Moore, S F; Hers, I

    2015-01-01

    Background Aspirin and P2Y12 antagonists are antiplatelet compounds that are used clinically in patients with thrombosis. However, some patients are ‘resistant’ to antiplatelet therapy, which increases their risk of developing acute coronary syndromes. These patients often present with an underlying condition that is associated with altered levels of circulating platelet primers and platelet hyperactivity. Platelet primers cannot stimulate platelet activation, but, in combination with physiologic stimuli, significantly enhance platelet function. Objectives To explore the role of platelet primers in resistance to antiplatelet therapy, and to evaluate whether phosphoinositide 3-kinase (PI3K) contributes to this process. Methods and Results We used platelet aggregation, thromboxane A2 production and ex vivo thrombus formation as functional readouts of platelet activity. Platelets were treated with the potent P2Y12 inhibitor AR-C66096, aspirin, or a combination of both, in the presence or absence of the platelet primers insulin-like growth factor-1 (IGF-1) and thrombopoietin (TPO), or the Gz-coupled receptor ligand epinephrine. We found that platelet primers largely overcame the inhibitory effects of antiplatelet compounds on platelet functional responses. IGF-1-mediated and TPO-mediated, but not epinephrine-mediated, enhancements in the presence of antiplatelet drugs were blocked by the PI3K inhibitors wortmannin and LY294002. Conclusions These results demonstrate that platelet primers can contribute to antiplatelet resistance. Furthermore, our data demonstrate that there are PI3K-dependent and PI3K-independent mechanisms driving primer-mediated resistance to antiplatelet therapy. PMID:26039631

  16. Family-specific vs. universal PCR primers for the study of mitochondrial DNA in plants

    Directory of Open Access Journals (Sweden)

    Aleksić Jelena M.

    2016-01-01

    Full Text Available Mitochondrial genomes (mtDNAs or mitogenomes of seed plants are characterized by a notoriously unstable organization on account of which available so-called universal or consensus primers may fail to fulfil their foreseen function - amplification of various mtDNA regions in a broad range of plant taxa. Thus, the primers developed for groups assumed to have similar organization of their mitogenomes, such as families, may facilitate a broader usage of more variable non-coding portions of these genomes in group members. Using in silico PCR method and six available complete mitogenomes of Fabaceae, it has been demonstrated that only three out of 36 published universal primer and three Medicago sativa-specific primer pairs that amplify various mtDNA regions are suitable for six representatives of the Fabaceae family upon minor modifications, and develop 21 Fabaceae-specific primer pairs for amplification of all 14 cis-splicing introns in genes of NADH subunits (nad genes which represent the most commonly used non-coding mtDNA regions in various studies in plants. Using the same method and six available complete mitogenomes of representatives of related families Cucurbitaceae, Euphorbiaceae and Rosaceae and a model plant, Arabidopsis thaliana, it has further been demonstrated that applicability of newly developed primer pairs for amplification of nad introns in more or less related taxa was dependent not only on species evolutionary distances but also on their genome sizes. A reported set of 24 primer pairs is a valuable resource which may facilitate a broader usage of mtDNA variability in future studies at both intra- and inter-specific levels in Fabaceae, which is the third largest family of flowering plants rarely studied at the mtDNA level, and in other more or less related taxa. [Projekat Ministarstva nauke Republike Srbije, br. 173005

  17. Profil Gangguan Kognitif pada Tumor Intrakranial Primer dan Metastasis

    Directory of Open Access Journals (Sweden)

    Kartika Maharani

    2015-12-01

    Full Text Available Gangguan kognitif sering menyertai pasien tumor intrakranial dan menjadi penyebab utama disabilitas. Perbedaan patofisiologi tumor intrakranial primer (TIP dan metastasis (TM menyebabkan perbedaan gambaran klinis dan derajat  gangguan kognitif. Tujuan penelitian ini untuk mengetahui prevalensi dan profil gangguan kognitif pasien TIP dan TM. Disain penelitian potong-lintang retrospektif menggunakan data sekunder dari Poliklinik Saraf RSCM pada bulan Januari 2011-Desember 2013. Subjek berusia 18-65 tahun yang didiagnosis TIP dan TM berdasarkan anamnesis, pemeriksaan fisik, CT scan atau MRI kepala, dan atau histopatologi. Terdapat 121 subjek, 79 TIP dan 27 TM; usia rerata TIP 43,7 tahun dan TM 50,9 tahun. Pada kelompok TM mayoritas (40,7% memiliki lesi di kedua hemisfer sedangkan TIP hanya di satu hemisfer. Lokasi tumor pada TM lebih dari 1 lobus (51,9%. Gangguan kognitif lebih banyak pada TM (81,5% dibandingkan TIK (52,5% dengan domain tersering gangguan visuospasial. Subjek TM mengalami gangguan kognitif lebih berat dibandingkan TIP (rerata MMSE 20,96 dan 22,61. Gangguan kognitif lebih banyak pada kelompok TM dibandingkan TIP dengan gangguan kognitif lebih berat karena mayoritas lesi tumor mengenai lebih dari 1 lobus. Kata kunci: gangguan kognitif, tumor intrakranial, neuro-onkologi.   Cognitve Impairment in Primary and Metastatic Brain Tumors Abstract Brain tumor patients are often accompanied by a wide range of cognitive impairment as a major cause of disablility. The different pathophysiology of primary and metastatic brain tumor influences patients’ clinical signs and symptoms, and also the severity of cognitive impairment. To determine the prevalence and profile of cognitive impairment in patients with primary and metastatic brain tumors, this cross-sectional study was done on subjects of 18 to 65 years old with the diagnosis of primary and metastatic brain tumors based on anamnesis, physical examination, imaging modalities, and

  18. methBLAST and methPrimerDB: web-tools for PCR based methylation analysis

    Directory of Open Access Journals (Sweden)

    Herzog Robert

    2006-11-01

    Full Text Available Abstract Background DNA methylation plays an important role in development and tumorigenesis by epigenetic modification and silencing of critical genes. The development of PCR-based methylation assays on bisulphite modified DNA heralded a breakthrough in speed and sensitivity for gene methylation analysis. Despite this technological advancement, these approaches require a cumbersome gene by gene primer design and experimental validation. Bisulphite DNA modification results in sequence alterations (all unmethylated cytosines are converted into uracils and a general sequence complexity reduction as cytosines become underrepresented. Consequently, standard BLAST sequence homology searches cannot be applied to search for specific methylation primers. Results To address this problem we developed methBLAST, a sequence similarity search program, based on the original BLAST algorithm but querying in silico bisulphite modified genome sequences to evaluate oligonucleotide sequence similarities. Apart from the primer specificity analysis tool, we have also developed a public database termed methPrimerDB for the storage and retrieval of validated PCR based methylation assays. The web interface allows free public access to perform methBLAST searches or database queries and to submit user based information. Database records can be searched by gene symbol, nucleotide sequence, analytical method used, Entrez Gene or methPrimerDB identifier, and submitter's name. Each record contains a link to Entrez Gene and PubMed to retrieve additional information on the gene, its genomic context and the article in which the methylation assay was described. To assure and maintain data integrity and accuracy, the database is linked to other reference databases. Currently, the database contains primer records for the most popular PCR-based methylation analysis methods to study human, mouse and rat epigenetic modifications. methPrimerDB and methBLAST are available at http

  19. Parâmetros digestivos, produção e qualidade do leite de cabras Saanen recebendo rações com casca do grão de soja em substituição ao milho = Digestive parameters, production and quality of milk from Saanen goats fed rations with soybean hulls as a replacement for ground corn

    Directory of Open Access Journals (Sweden)

    Maximiliane Alavarse Zambom

    2007-07-01

    Full Text Available O experimento objetivou avaliar os parâmetros digestivos, produção e qualidade do leite de cabras Saanen, recebendo rações com casca do grão de soja (CGS, em três níveis de substituição ao milho moído (0% CGS, 50% CGS e 100% CGS. Foram utilizadas três cabras Saanen (52,35 kg ± 7,46, primíparas, confinadas, distribuídas em quadrado latino 3 x 3. As rações apresentaram em média 14,70% de PB e 2,23 Mcal de EM kg-1 de MS ingerida. Foi realizado o controle diário da ingestão e produção de leite. As fezes foram coletadas para determinação da digestibilidade da matéria seca e dos nutrientes, e o líquido ruminal para determinação dos parâmetros ruminais. O leite foi coletado para análises físico-químicas e perfil de ácidos graxos. A maior (p 0,05 na digestibilidade da matéria seca e dos nutrientes, nem na produção e qualidade físico-química do leite. O tratamento 100% CGS proporcionou maior concentração de acetato ruminal, maior razão acetato:propionato e menores concentrações de propionato e butirato ruminal. Os tratamentos não alteraram (p > 0,05 o N-amoniacal e pH ruminal. O perfil de ácidos graxos do leite oscilou em função dos tratamentos. A casca do grão de soja pode substituir o milho moído em rações para cabras Saanen em lactação, sem alterações no processo digestivo, na produção e na qualidade do leite.The objective of this study was to evaluate digestive parameters, production and quality of milk from Saanen goats fed rations with soybean hulls (SBH as a replacement for ground corn. Three Saanen does (52.35 kg ± 7.46, confined and first-kidding, were allocated in a 3 x 3 Latin square. Treatments consisted of replacement levels of ground corn for SBH (0% SBH, 50% SBH and 100% SBH, with 14.70% of CP and 2.23 Mcal of ME kg-1 DMI as mean values. Intake and milk production were recorded daily. Feces were sampled for the determination of dry matter and nutrient digestibility, and ruminal

  20. Incorporação de farinhas de resíduos de Jundiá na dieta: bioquímica plasmática, parâmetros hepáticos e digestivos Addition of Jundiá waste meal in diet: plasmatic biochemistry, hepatic and digestive parameters

    Directory of Open Access Journals (Sweden)

    Suzete Rossato

    2013-06-01

    Full Text Available O objetivo deste estudo foi analisar a influência da adição de farinha de resíduos de jundiá (Rhamdia quelen na dieta de exemplares desta espécie sobre a bioquímica plasmática, parâmetros hepáticos e digestivos. No experimento I (EXP I, compararam-se dietas com 30% de farinha de carne e ossos suína (FCO, farinha de carcaça de jundiás com vísceras (FCJCV, farinha de carcaça de jundiá sem vísceras (FCJSV e farinha de jundiás inteiros (FJI. No experimento II (EXP II, níveis de inclusão de FCJCV foram testados (0; 3,75; 7,5; 15 e 30%. No plasma, foram quantificadas proteínas totais circulantes, colesterol total, triglicerídeos, glicose, albumina e aminoácidos. No fígado, analisou-se glicose, amônia, proteínas totais, glicogênio, aminoácidos e transaminases. No estômago, foi determinada a atividade de protease ácida e, no intestino, tripsina e quimotripsina. No EXP I, foram observados menores níveis de glicose no plasma e alanina aminotransferase (ALT no fígado, para o tratamento FCJSV, e maiores índices destes para FCO. A atividade da protease ácida e da quimotripsina foram menores para a FCO e maior para a FCJCV. No EXP II, os índices de aminoácidos livres e colesterol total no plasma aumentaram com a elevação dos níveis de inclusão da FCJCV na dieta. A incorporação de farinhas de resíduos de jundiá à dieta altera a bioquímica plasmática, os parâmetros hepáticos e digestivos dos juvenis de jundiá, porém essas alterações não influenciaram na saúde dos peixes, demonstrando sua qualidade nutricional e eficiência no uso em dietas para peixes.The objective of this study was to analyze the influence of the addition of jundiá (Rhamdia quelen waste meal in the diet of this species, on plasmatic biochemistry, liver and digestive parameters. Experiment I (EXP I compared diets with 30% of meat and swine bones (FCO, Jundiá carcass meal with viscera (FCJCV, Jundiá carcass meal without viscera (FCJSV and

  1. CloneAssistant 1.0: a stand-alone software for automated cloning primer design.

    Science.gov (United States)

    Shao, Chaogang; Meng, Yijun; Lv, Shaolei; Zhong, Wei; Wang, Zheyu; Chen, Ming

    2010-11-01

    "CloneAssistant 1.0" is a stand-alone software compatible with the current Windows operating systems, which can automatically design cloning primers with full consideration of the sequence information of vectors and genes, cloning strategies, the principles of primer design, reading frames, position effects, and enzymatic reaction conditions for users. Five internal XML (extensible markup language) databases [restriction enzymes, plasmids, universal buffers, PCR (polymerase chain reaction) protection bases, and an MCS (multiple cloning site) double digest interference database] were established to serve as the basic support for "CloneAssistant 1.0". The primer pairs designed are sorted according to the difficulty of the follow-up experiments. Once a primer pair is selected by the user, detailed experimental guidance for this primer pair will be provided. In addition, "CloneAssistant 1.0" can be used for restriction map analysis, ORF (open reading frame) finding, sequence alignment and complementary analysis, translation, restriction enzyme and universal buffer queries, and isocaudamer analysis. "CloneAssistant 1.0" makes gene clone design much easier, and it can be freely downloaded from http://bis.zju.edu.cn/clone. Copyright © 2010 Elsevier B.V. All rights reserved.

  2. Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans.

    Science.gov (United States)

    Lobo, Jorge; Costa, Pedro M; Teixeira, Marcos A L; Ferreira, Maria S G; Costa, Maria H; Costa, Filipe O

    2013-09-10

    Building reference libraries of DNA barcodes is relatively straightforward when specifically designed primers are available to amplify the COI-5P region from a relatively narrow taxonomic group (e.g. single class or single order). DNA barcoding marine communities have been comparatively harder to accomplish due to the broad taxonomic diversity and lack of consistently efficient primers. Although some of the so-called "universal" primers have been relatively successful, they still fail to amplify COI-5P of many marine animal groups, while displaying random success even among species within each group. Here we propose a new pair of primers designed to enhance amplification of the COI-5P region in a wide range of marine organisms. Amplification tests conducted on a wide range of marine animal taxa, rendered possible the first-time sequencing of DNA barcodes from eight separated phyla (Annelida, Arthropoda, Chordata, Cnidaria, Echinodermata, Mollusca, Nemertea and Platyhelminthes), comprising a total of 14 classes, 28 orders, 57 families, 68 genus and 76 species. These primers demonstrated to be highly cost-effective, which is of key importance for DNA barcoding procedures, such as for building comprehensive DNA barcode libraries of marine communities, where the processing of a large numbers of specimens from a wide variety of marine taxa is compulsory.

  3. Genus-specific PCR primers targeting intracellular parasite Euduboscquella (Dinoflagellata: Syndinea)

    Science.gov (United States)

    Jung, Jae-Ho; Choi, Jung Min; Kim, Young-Ok

    2017-12-01

    We designed a genus-specific primer pair targeting the intracellular parasite Euduboscquella. To increase target specificity and inhibit untargeted PCR, two nucleotides were added at the 3' end of the reverse primer, one being a complementary nucleotide to the Euduboscquella-specific SNP (single-nucleotide polymorphism) and the other a deliberately mismatched nucleotide. Target specificity of the primer set was verified experimentally using PCR of two Euduboscquella species (positive controls) and 15 related species (negative controls composed of ciliates, diatoms and dinoflagellates), and analytical comparison with SILVA SSU rRNA gene database (release 119) in silico. In addition, we applied the Euduboscquella-specific primer set to four environmental samples previously determined by cytological staining to be either positive or negative for Euduboscquella. As expected, only positive controls and environmental samples known to contain Euduboscquella were successfully amplified by the primer set. An inferred SSU rRNA gene phylogeny placed environmental samples containing aloricate ciliates infected by Euduboscquella in a cluster discrete from Euduboscquella groups a-d previously reported from loricate, tintinnid ciliates.

  4. RTPrimerDB: the real-time PCR primer and probe database, major update 2006.

    Science.gov (United States)

    Pattyn, Filip; Robbrecht, Piet; De Paepe, Anne; Speleman, Frank; Vandesompele, Jo

    2006-01-01

    The RTPrimerDB (http://medgen.ugent.be/rtprimerdb) project provides a freely accessible data retrieval system and an in silico assay evaluation pipeline for real-time quantitative PCR assays. Over the last year the number of user submitted assays has grown to 3500. Data conveyance from Entrez Gene by establishing an assay-to-gene relationship enables the addition of new primer assays for one of the 1.5 million different genes from 2300 species stored in the system. Easy access to the primer and probe data is possible by using multiple search criteria. Assay reports contain gene information, assay details (such as oligonucleotide sequences, detection chemistry and reaction conditions), publication information, users' experimental evaluation feedback and submitter's contact details. Gene expression assays are extended with a scalable assay viewer that provides detailed information on the alignment of primer and probe sequences on the known transcript variants of a gene, along with Single Nucleotide Polymorphisms (SNP) positions and peptide domain information. Furthermore, an mfold module is implemented to predict the secondary structure of the amplicon sequence, as this has been reported to impact the efficiency of the PCR. RTPrimerDB is also extended with an in silico analysis pipeline to streamline the evaluation of custom designed primer and probe sequences prior to ordering and experimental evaluation. In a secured environment, the pipeline performs automated BLAST specificity searches, mfold secondary structure prediction, SNP or plain sequence error identification, and graphical visualization of the aligned primer and probe sequences on the target gene.

  5. Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality.

    Directory of Open Access Journals (Sweden)

    Elvina Lee

    Full Text Available Next generation sequencing (NGS has rapidly become an invaluable tool for the detection, identification and relative quantification of environmental microorganisms. Here, we demonstrate two new 16S rDNA primer sets, which are compatible with NGS approaches and are primarily for use in water quality studies. Compared to 16S rRNA gene based universal primers, in silico and experimental analyses demonstrated that the new primers showed increased specificity for the Cyanobacteria and Proteobacteria phyla, allowing increased sensitivity for the detection, identification and relative quantification of toxic bloom-forming microalgae, microbial water quality bioindicators and common pathogens. Significantly, Cyanobacterial and Proteobacterial sequences accounted for ca. 95% of all sequences obtained within NGS runs (when compared to ca. 50% with standard universal NGS primers, providing higher sensitivity and greater phylogenetic resolution of key water quality microbial groups. The increased selectivity of the new primers allow the parallel sequencing of more samples through reduced sequence retrieval levels required to detect target groups, potentially reducing NGS costs by 50% but still guaranteeing optimal coverage and species discrimination.

  6. Novel Primer Sets for Next Generation Sequencing-Based Analyses of Water Quality.

    Science.gov (United States)

    Lee, Elvina; Khurana, Maninder S; Whiteley, Andrew S; Monis, Paul T; Bath, Andrew; Gordon, Cameron; Ryan, Una M; Paparini, Andrea

    2017-01-01

    Next generation sequencing (NGS) has rapidly become an invaluable tool for the detection, identification and relative quantification of environmental microorganisms. Here, we demonstrate two new 16S rDNA primer sets, which are compatible with NGS approaches and are primarily for use in water quality studies. Compared to 16S rRNA gene based universal primers, in silico and experimental analyses demonstrated that the new primers showed increased specificity for the Cyanobacteria and Proteobacteria phyla, allowing increased sensitivity for the detection, identification and relative quantification of toxic bloom-forming microalgae, microbial water quality bioindicators and common pathogens. Significantly, Cyanobacterial and Proteobacterial sequences accounted for ca. 95% of all sequences obtained within NGS runs (when compared to ca. 50% with standard universal NGS primers), providing higher sensitivity and greater phylogenetic resolution of key water quality microbial groups. The increased selectivity of the new primers allow the parallel sequencing of more samples through reduced sequence retrieval levels required to detect target groups, potentially reducing NGS costs by 50% but still guaranteeing optimal coverage and species discrimination.

  7. The use of a fluoropolymer containing primer to enhance adhesion of rotolined fluoropolymer coatings

    Energy Technology Data Exchange (ETDEWEB)

    Lech, L.M. [DuPont, Parkersburg, WV (United States)

    1999-11-01

    Fluoropolymers such as PFA and ETFE are often used in rotolining applications. A common source of failure for rotolined coatings is delamination from the metal substrate. Extensive thermal cycling of the coated part, permeation of the contained liquid to the substrate, or a combination of both thermal cycling and permeation causes this. Rotolined coatings are typically applied directly to the metal part. It has been found that applying an aqueous fluoropolymer based primer to the metal substrate prior to applying the rotolined resin increases the time before delamination is observed. The primer is applied by conventional spray techniques and can either be force dried at low temperature or air-dried under ambient conditions. The primer consists primarily of a fluoropolymer such as ETFE or PFA and a bonding agent such as polyamide-imide, polyphenylene sulfide, or polyether sulfone. After the primer is applied to the metal part, the fluoropolymer in the primer melt blends with the fluoropolymer rotolining resin during the rotolining process. The bonding agent enhances the adhesion of the entire coating system to the metal part. This extends the lifetime of the rotolined coatings.

  8. Cytochrome c oxidase I primers for corbiculate bees: DNA barcode and mini-barcode.

    Science.gov (United States)

    Françoso, E; Arias, M C

    2013-09-01

    Bees (Apidae), of which there are more than 19 900 species, are extremely important for ecosystem services and economic purposes, so taxon identity is a major concern. The goal of this study was to optimize the DNA barcode technique based on the Cytochrome c oxidase (COI) mitochondrial gene region. This approach has previously been shown to be useful in resolving taxonomic inconsistencies and for species identification when morphological data are poor. Specifically, we designed and tested new primers and standardized PCR conditions to amplify the barcode region for bees, focusing on the corbiculate Apids. In addition, primers were designed to amplify small COI amplicons and tested with pinned specimens. Short barcode sequences were easily obtained for some Bombus century-old museum specimens and shown to be useful as mini-barcodes. The new primers and PCR conditions established in this study proved to be successful for the amplification of the barcode region for all species tested, regardless of the conditions of tissue preservation. We saw no evidence of Wolbachia or numts amplification by these primers, and so we suggest that these new primers are of broad value for corbiculate bee identification through DNA barcode. © 2013 John Wiley & Sons Ltd.

  9. A novel universal primer-multiplex-PCR method with sequencing gel electrophoresis analysis.

    Directory of Open Access Journals (Sweden)

    Wentao Xu

    Full Text Available In this study, a novel universal primer-multiplex-PCR (UP-M-PCR method adding a universal primer (UP in the multiplex PCR reaction system was described. A universal adapter was designed in the 5'-end of each specific primer pairs which matched with the specific DNA sequences for each template and also used as the universal primer (UP. PCR products were analyzed on sequencing gel electrophoresis (SGE which had the advantage of exhibiting extraordinary resolution. This method overcame the disadvantages rooted deeply in conventional multiplex PCR such as complex manipulation, lower sensitivity, self-inhibition and amplification disparity resulting from different primers, and it got a high specificity and had a low detection limit of 0.1 ng for single kind of crops when screening the presence of genetically modified (GM crops in mixture samples. The novel developed multiplex PCR assay with sequencing gel electrophoresis analysis will be useful in many fields, such as verifying the GM status of a sample irrespective of the crop and GM trait and so on.

  10. Synchrotron FTIR characterisation of automotive primer surfacer paint coatings for forensic purposes.

    Science.gov (United States)

    Maric, Mark; van Bronswijk, Wilhelm; Lewis, Simon W; Pitts, Kari

    2014-01-01

    Synchrotron FTIR microspectroscopy was used to characterise and assess the chemical diversity of electrocoat primer, primer surfacer and basecoats of automotive paint samples from 75 vehicles representing a range of international car manufacturers. Significant diversity was found in the synchrotron FTIR data from the primer surfacer coats. Classification using principal component analysis revealed 14 discrete groups, which could be associated with the country of manufacture, the specific manufacturer and manufacturing plant, the year of manufacture of the vehicle and in some instances the number of layers in the paint system. The model generated from the primer surfacer was significantly more discriminating than a previous model generated from FTIR analysis of clear coats of the same vehicles. Analysis of the primer surfacer also avoids issues of possible environmental degradation and component migration seen with FTIR analysis of automotive clear coats. Providing such information concerning vehicle origin would aid in the development of investigative leads from the analysis of questioned automotive paint samples located at the scene of a crime or on the body/clothing of a hit and run victim. © 2013 Published by Elsevier B.V.

  11. Polyadenylated Sequencing Primers Enable Complete Readability of PCR Amplicons Analyzed by Dideoxynucleotide Sequencing

    Directory of Open Access Journals (Sweden)

    Martin Beránek

    2012-01-01

    Full Text Available Dideoxynucleotide DNA sequencing is one of the principal procedures in molecular biology. Loss of an initial part of nucleotides behind the 3' end of the sequencing primer limits the readability of sequenced amplicons. We present a method which extends the readability by using sequencing primers modified by polyadenylated tails attached to their 5' ends. Performing a polymerase chain reaction, we amplified eight amplicons of six human genes (AMELX, APOE, HFE, MBL2, SERPINA1 and TGFB1 ranging from 106 bp to 680 bp. Polyadenylation of the sequencing primers minimized the loss of bases in all amplicons. Complete sequences of shorter products (AMELX 106 bp, SERPINA1 121 bp, HFE 208 bp, APOE 244 bp, MBL2 317 bp were obtained. In addition, in the case of TGFB1 products (366 bp, 432 bp, and 680 bp, respectively, the lengths of sequencing readings were significantly longer if adenylated primers were used. Thus, single strand dideoxynucleotide sequencing with adenylated primers enables complete or near complete readability of short PCR amplicons.

  12. An alternative suite of universal primers for genotyping in multiplex PCR.

    Directory of Open Access Journals (Sweden)

    Cheng Ge

    Full Text Available The universal primer three-primer approach can dramatically reduce the cost when genotyping the microsatellites. One former research reported four universal primers that can be used in singleplex and multiplex genotyping. In this study, we proposed an alternative suite of universal primers with four dyes for genotyping 8-12 loci in one single run. This multiplex method was tested on Tetranychus truncatus. Published microsatellite loci of T. kanzawai, Frankliniella occidentalis and Nilaparvata lugens were modified as needed and also tested. The robustness of the method was confirmed by comparing with singleplex using multiple fluorophores and genotyping two populations of T. truncatus. This method showed lower signal strength than the singleplex three-primer system, but it was still sufficient to determine the fragment length. The cost of such a project can be reduced dramatically when many loci of different species are involved. In this way, laboratories performing population genetic analyses or studying several different species may benefit from the use of this cost-effective protocol.

  13. Formulation and Assessment of a Wash-Primer Containing Lanthanum "Tannate" for Steel Temporary Protection

    Science.gov (United States)

    D'Alessandro, Oriana; Selmi, Gonzalo J.; Deyá, Cecilia; Di Sarli, Alejandro; Romagnoli, Roberto

    2017-12-01

    Tannins are polyphenols synthesized by plants and useful for the coating industry as corrosion inhibitors. In addition, lanthanum salts have a great inhibitory effect on steel corrosion. The aim of this study was to obtain lanthanum "tannate" with adequate solubility to be incorporated as the corrosion inhibitor in a wash-primer. The "tannate" was obtained from commercial "Quebracho" tannin and 0.1 M La(NO3)3. The soluble tannin was determined by the Folin-Denis reagent, while the concentration of Lanthanum was obtained by a gravimetric procedure. The protective action of "tannate" on SAE 1010 steel was evaluated by linear polarization curves and corrosion potential measurements. Lanthanum "tannate" was incorporated in a wash-primer formulation and tested by corrosion potential and ionic resistance measurements. The corrosion rate was also determined by the polarization resistance technique. Besides, the primer was incorporated in an alkyd paint system and its anticorrosion performance assessed in the salt spray cabinet and by electrochemical impedance spectroscopy. Results showed that lanthanum "tannate" primer inhibits the development of deleterious iron oxyhydroxides on the steel substrate and incorporated into a paint system had a similar behavior to the primer formulated with zinc tetroxychromate.

  14. Bonding of Resin Cement to Zirconia with High Pressure Primer Coating

    Science.gov (United States)

    Wang, Ying-jie; Jiao, Kai; Liu, Yan; Zhou, Wei; Shen, Li-juan; Fang, Ming; Li, Meng; Zhang, Xiang; Tay, Franklin R.; Chen, Ji-hua

    2014-01-01

    Objectives To investigate the effect of air-drying pressure during ceramic primer coating on zirconia/resin bonding and the surface characteristics of the primed zirconia. Methods Two ceramic primers (Clearfil Ceramic Primer, CCP, Kuraray Medical Inc. and Z-Prime Plus, ZPP, Bisco Inc.) were applied on the surface of air-abraded zirconia (Katana zirconia, Noritake) and dried at 4 different air pressures (0.1–0.4 MPa). The primed zirconia ceramic specimens were bonded with a resin-based luting agent (SA Luting Cement, Kuraray). Micro-shear bond strengths of the bonded specimens were tested after 3 days of water storage or 5,000× thermocycling (n = 12). Failure modes of the fractured specimens were examined with scanning electron miscopy. The effects of air pressure on the thickness of the primer layers and the surface roughness (Sa) of primed zirconia were evaluated using spectroscopic ellipsometry (n = 6), optical profilometry and environmental scanning electron microscopy (ESEM) (n = 6), respectively. Results Clearfil Ceramic Primer air-dried at 0.3 and 0.4 MPa, yielding significantly higher µSBS than gentle air-drying subgroups (pzirconia bond strength and durability significantly. Higher air-drying pressure (0.3-0.4 MPa) for CCP and intermediate pressure (0.2 MPa) for ZPP are recommended to produce strong, durable bonds between resin cement and zirconia ceramics. PMID:24992678

  15. Evaluation of genotypic diversity of Streptococcus mutans using distinct arbitrary primers

    Directory of Open Access Journals (Sweden)

    Cínthia Pereira Machado Tabchoury

    2008-12-01

    Full Text Available Streptococcus mutans has been considered one of the main etiological agents of dental caries and the genotypic diversity rather than its salivary counts may be considered as a virulence factor of this bacterium. For genotyping with polymerase chain reaction (PCR with arbitrary primers, several primers have been used in order to improve complexity and specificity of amplicon patterns. Thus, the aim of this study was to evaluate the degree of agreement of genotypic identification among AP-PCR reactions performed with 5 distinct arbitrary primers of S. mutans isolated from saliva. Stimulated saliva was collected from 11 adult volunteers for isolation of S. mutans, and a total of 88 isolates were genotyped with arbitrary primers OPA 02, 03, 05, 13 and 18. Fourteen distinct genotypes were identified in the saliva samples. Most volunteers (9 out of 11 presented only one genotype. The results of the present study suggest that primers OPA 02, 03, 05 and 13 were suitable for genotypic identification of S. mutans isolates of saliva from adult volunteers.

  16. Multicolor-based discrimination of 21 short tandem repeats and amelogenin using four fluorescent universal primers.

    Science.gov (United States)

    Asari, Masaru; Okuda, Katsuhiro; Hoshina, Chisato; Omura, Tomohiro; Tasaki, Yoshikazu; Shiono, Hiroshi; Matsubara, Kazuo; Shimizu, Keiko

    2016-02-01

    The aim of this study was to develop a cost-effective genotyping method using high-quality DNA for human identification. A total of 21 short tandem repeats (STRs) and amelogenin were selected, and fluorescent fragments at 22 loci were simultaneously amplified in a single-tube reaction using locus-specific primers with 24-base universal tails and four fluorescent universal primers. Several nucleotide substitutions in universal tails and fluorescent universal primers enabled the detection of specific fluorescent fragments from the 22 loci. Multiplex polymerase chain reaction (PCR) produced intense FAM-, VIC-, NED-, and PET-labeled fragments ranging from 90 to 400 bp, and these fragments were discriminated using standard capillary electrophoretic analysis. The selected 22 loci were also analyzed using two commercial kits (the AmpFLSTR Identifiler Kit and the PowerPlex ESX 17 System), and results for two loci (D19S433 and D16S539) were discordant between these kits due to mutations at the primer binding sites. All genotypes from the 100 samples were determined using 2.5 ng of DNA by our method, and the expected alleles were completely recovered. Multiplex 22-locus genotyping using four fluorescent universal primers effectively reduces the costs to less than 20% of genotyping using commercial kits, and our method would be useful to detect silent alleles from commercial kit analysis. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. A Novel Universal Primer-Multiplex-PCR Method with Sequencing Gel Electrophoresis Analysis

    Science.gov (United States)

    Huang, Kunlun; Zhang, Nan; Yuan, Yanfang; Shang, Ying; Luo, Yunbo

    2012-01-01

    In this study, a novel universal primer-multiplex-PCR (UP-M-PCR) method adding a universal primer (UP) in the multiplex PCR reaction system was described. A universal adapter was designed in the 5′-end of each specific primer pairs which matched with the specific DNA sequences for each template and also used as the universal primer (UP). PCR products were analyzed on sequencing gel electrophoresis (SGE) which had the advantage of exhibiting extraordinary resolution. This method overcame the disadvantages rooted deeply in conventional multiplex PCR such as complex manipulation, lower sensitivity, self-inhibition and amplification disparity resulting from different primers, and it got a high specificity and had a low detection limit of 0.1 ng for single kind of crops when screening the presence of genetically modified (GM) crops in mixture samples. The novel developed multiplex PCR assay with sequencing gel electrophoresis analysis will be useful in many fields, such as verifying the GM status of a sample irrespective of the crop and GM trait and so on. PMID:22272223

  18. Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas.

    Science.gov (United States)

    Taylor, D Lee; McCormick, Melissa K

    2008-01-01

    Despite advances owing to molecular approaches, several hurdles still obstruct the identification of fungi forming orchid mycorrhizas. The Tulasnellaceae exhibit accelerated evolution of the nuclear ribosomal operon, causing most standard primers to fail in polymerase chain reaction (PCR) trials. Insufficient sequences are available from well characterized isolates and fruitbodies. Lastly, taxon-specific PCR primers are needed in order to explore the ecology of the fungi outside of the orchid root. Here, progress in overcoming these hurdles is reported. Broad-spectrum basidiomycete internal transcribed spacer (ITS) primers that do not exclude most known Tulasnellaceae are presented. blast searches and empirical PCR tests support their wide utility within the Basidiomycota. Taxon-specific ITS primers are presented targeted to orchid-associated Tulasnella, and a core component of the Thelephora-Tomentella complex. The efficiency and selectivity of these primer sets are again supported by blast searches and empirical tests. Lastly, ITS DNA sequences are presented from several strains of Epulorhiza, Ceratorhiza, Ceratobasidium, Sistotrema, Thanatephorus and Tulasnella that were originally described in the landmark mycorrhizal studies of Currah and Warcup. Detailed phylogenetic analyses reveal some inconsistencies in species concepts in these taxonomically challenging resupinate basidiomycetes, but also help to place several sequences from environmental samples.

  19. SP-Designer: a user-friendly program for designing species-specific primer pairs from DNA sequence alignments.

    Science.gov (United States)

    Villard, Pierre; Malausa, Thibaut

    2013-07-01

    SP-Designer is an open-source program providing a user-friendly tool for the design of specific PCR primer pairs from a DNA sequence alignment containing sequences from various taxa. SP-Designer selects PCR primer pairs for the amplification of DNA from a target species on the basis of several criteria: (i) primer specificity, as assessed by interspecific sequence polymorphism in the annealing regions, (ii) the biochemical characteristics of the primers and (iii) the intended PCR conditions. SP-Designer generates tables, detailing the primer pair and PCR characteristics, and a FASTA file locating the primer sequences in the original sequence alignment. SP-Designer is Windows-compatible and freely available from http://www2.sophia.inra.fr/urih/sophia_mart/sp_designer/info_sp_designer.php. © 2013 John Wiley & Sons Ltd.

  20. Níveis decrescentes de proteína em dietas suplementadas com complexo enzimático, para coelhos em crescimento. 2. Parâmetros digestivos e composição química do conteúdo cecal

    Directory of Open Access Journals (Sweden)

    Santiago G.S.

    2000-01-01

    Full Text Available Estudou-se o efeito da redução do nível protéico da dieta, com e sem suplementação enzimática, sobre as características digestivas e composição do conteúdo cecal de coelhos em crescimento. Usou-se um delineamento inteiramente ao acaso, com 54 coelhos da raça Nova Zelândia Branco, de ambos os sexos, desmamados com 35 dias de idade, e divididos em cinco grupos (tratamentos, quatro de 11 e um de 10 coelhos. Os tratamentos constituíram-se de dietas calculadas como isoenergéticas e isoaminoacídicas, com 17, 16, 15 e 14% de proteína bruta (PB, suplementadas com 0,05% de um complexo enzimático comercial (Vegproâ com atividades de protease e celulase e uma dieta controle com 17% PB sem adição do complexo enzimático. Os pesos do trato digestivo cheio, ceco cheio, ceco vazio e conteúdo cecal foram significativamente afetados pelo nível de PB da dieta. Das frações químicas do conteúdo cecal (matéria seca, proteína bruta, fibra em detergente ácido, matéria orgânica e nitrogênio amoniacal, matéria orgânica, nitrogênio amoniacal e proporções molares dos ácidos acético e propiônico foram significativamente afetadas pelo nível de PB da dieta. Os resultados permitem concluir que a redução do nível de PB da dieta para 14 % não influenciou negativamente as características estudadas.

  1. Temas de Física para Ingeniería: Primer principio de la termodinámica

    OpenAIRE

    Beléndez Vázquez, Augusto

    1992-01-01

    Acústica, fluidos y termodinámica: "Primer principio de la termodinámica". Objetivos y caracteres generales de la termodinámica. Conceptos fundamentales de la termodinámica. Capacidad calorífica, calor específico y calor latente. Trabajo. Primer principio de la termodinámica: energía interna. Algunas aplicaciones del primer principio.

  2. MALDI-TOF mass spectrometric detection of multiplex single base extended primers

    DEFF Research Database (Denmark)

    Mengel-From, Jonas; Sanchez Sanchez, Juan Jose; Børsting, Claus

    2004-01-01

    One of the most promising techniques for typing of multiple single-nucleotide polymorphism (SNP) is detection of single base extension primers (SBE) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). We present a new MALDI-TOF MS protocol for typing...... triethylamine purification. The biotin-labeled ddNTPs contained linkers with different masses ensuring a clear separation of the alleles even for SBE primers with a mass of 10 300 Da. Furthermore, only 25-350 fmol of SBE primers were necessary in order to obtain reproducible MALDI-TOF spectra. Similar signal......, and the potential use of MALDI-TOF MS for SNP typing is discussed....

  3. Designing universal primers for the isolation of DNA sequences encoding Proanthocyanidins biosynthetic enzymes in Crataegus aronia

    Directory of Open Access Journals (Sweden)

    Zuiter Afnan

    2012-08-01

    Full Text Available Abstract Background Hawthorn is the common name of all plant species in the genus Crataegus, which belongs to the Rosaceae family. Crataegus are considered useful medicinal plants because of their high content of proanthocyanidins (PAs and other related compounds. To improve PAs production in Crataegus tissues, the sequences of genes encoding PAs biosynthetic enzymes are required. Findings Different bioinformatics tools, including BLAST, multiple sequence alignment and alignment PCR analysis were used to design primers suitable for the amplification of DNA fragments from 10 candidate genes encoding enzymes involved in PAs biosynthesis in C. aronia. DNA sequencing results proved the utility of the designed primers. The primers were used successfully to amplify DNA fragments of different PAs biosynthesis genes in different Rosaceae plants. Conclusion To the best of our knowledge, this is the first use of the alignment PCR approach to isolate DNA sequences encoding PAs biosynthetic enzymes in Rosaceae plants.

  4. Analysis of primer residue from lead free ammunition by X-ray microfluorescence.

    Science.gov (United States)

    Charpentier, B; Desrochers, C

    2000-03-01

    In forensic science, the analysis of gunshot residues was traditionally done by the detection of lead (Pb), antimony (Sb) and barium (Ba) usually found in a primer. However, the recent development of lead-free ammunition represents a new challenge for ballistic specialists. This analysis study gunshot residues from primers and ammunitions in the area surrounding bullet holes, a very important tool to determine the shooting distance. The ammunitions used were 9 mm Luger and .38 spl + p calibers, where lead in the primer was replaced with strontium (Sr) and where the lead bullet was plated with copper (Total Metal Jacket). Gunshot analysis results were obtained using an energy dispersive X-ray microfluorescence spectrometer. The method allows the detection and quantification of strontium residues on the target up to a distance of 45 cm.

  5. Development and characterization of microsatellite primers in the endangered Mediterranean shrub Ziziphus lotus (Rhamnaceae)1

    Science.gov (United States)

    González-Robles, Ana; Manzaneda, Antonio J.; Bastida, Jesús M.; Harvey, Nick; Jaime, Rafael; Salido, Teresa; Martínez, Luisa M.; Fernández-Ocaña, Ana; Alcántara, Julio M.; Rey, Pedro J.

    2016-01-01

    Premise of the study: Microsatellite primers were developed to characterize and evaluate patterns of genetic diversity and structure in the endangered Mediterranean shrub Ziziphus lotus (Rhamnaceae). Methods and Results: Twenty microsatellite primers were developed for Z. lotus, of which 14 were polymorphic. We evaluated microsatellite polymorphism in 97 specimens from 18 Spanish and seven Moroccan populations. Between two and eight alleles were found per locus, and the average number of alleles was 5.54. Observed heterozygosity and expected heterozygosity ranged from 0.08 to 0.90 and from 0.08 to 0.82, respectively. Nine of these primers also amplified microsatellite loci in Z. jujuba. Conclusions: The microsatellite markers described here will be useful in studies on genetic variation, population genetic structure, and gene flow in the fragmented habitat of this species. These markers are a valuable resource for designing appropriate conservation measures for the species in the Mediterranean range. PMID:28101436

  6. Searching for Beta-Haemolysin hlb Gene in Staphylococcus pseudintermedius with Species-Specific Primers.

    Science.gov (United States)

    Kmieciak, Wioletta; Szewczyk, Eligia M; Ciszewski, Marcin

    2016-07-01

    The paper presents an analysis of 51 Staphylococcus pseudintermedius clinically isolated strains from humans and from animals. Staphylococcus pseudintermedius strains' ability to produce β-haemolysin was evaluated with phenotypic methods (hot-cold effect, reverse CAMP test). In order to determine the hlb gene presence (coding for β-haemolysin) in a genomic DNA, PCR reactions were conducted with two different pairs of primers: one described in the literature for Staphylococcus aureus and recommended for analysing SIG group staphylococci and newly designed one in CLC Main Workbench software. Only reactions with newly designed primers resulted in product amplification, the presence of which was fully compatible with the results of phenotypic β-haemolysin test. Negative results for S. aureus and S. intermedius reference ATCC strains suggest that after further analysis the fragment of hlb gene amplified with primers described in this study might be included in the process of S. pseudintermedius strains identification.

  7. Designing universal primers for the isolation of DNA sequences encoding Proanthocyanidins biosynthetic enzymes in Crataegus aronia.

    Science.gov (United States)

    Zuiter, Afnan Saeid; Sawwan, Jammal; Al Abdallat, Ayed

    2012-08-10

    Hawthorn is the common name of all plant species in the genus Crataegus, which belongs to the Rosaceae family. Crataegus are considered useful medicinal plants because of their high content of proanthocyanidins (PAs) and other related compounds. To improve PAs production in Crataegus tissues, the sequences of genes encoding PAs biosynthetic enzymes are required. Different bioinformatics tools, including BLAST, multiple sequence alignment and alignment PCR analysis were used to design primers suitable for the amplification of DNA fragments from 10 candidate genes encoding enzymes involved in PAs biosynthesis in C. aronia. DNA sequencing results proved the utility of the designed primers. The primers were used successfully to amplify DNA fragments of different PAs biosynthesis genes in different Rosaceae plants. To the best of our knowledge, this is the first use of the alignment PCR approach to isolate DNA sequences encoding PAs biosynthetic enzymes in Rosaceae plants.

  8. Primer Based Approach for PCR Amplification of High GC Content Gene: Mycobacterium Gene as a Model

    Directory of Open Access Journals (Sweden)

    Arbind Kumar

    2014-01-01

    Full Text Available The genome of Mycobacterium is rich in GC content and poses problem in amplification of some genes, especially those rich in the GC content in terminal regions, by standard/routine PCR procedures. Attempts have been made to amplify three GC rich genes of Mycobacterium sp. (Rv0519c and Rv0774c from M. tuberculosis and ML0314c from M. leprae. Out of these three genes, Rv0774c gene was amplified with normal primers under standard PCR conditions, while no amplification was observed in case of Rv0519c and ML0314c genes. In the present investigation a modified primer based approach was successfully used for amplification of GC rich sequence of Rv0519c through codon optimization without changing the native amino acid sequence. The strategy was successfully confirmed by redesigning the standard primers with similar modifications followed by amplification of ML0314c gene.

  9. PCR bias associated with conserved primer binding sites, used to determine genotype diversity within Citrus tristeza virus populations.

    Science.gov (United States)

    Read, David Alan; Pietersen, Gerhard

    2016-11-01

    Citrus tristeza virus (CTV) is present in almost all of the major citrus production areas where it continues to reduce the profitability of citriculture. The accurate characterisation of CTV populations, which are usually made up of a number of disparate strains, requires the use of robust PCR protocols. Mismatches between primers and their corresponding binding sites may introduce primer-associated bias during amplification. The primer-associated bias of four sets of CTV specific primers, targeting the A and F regions and the p33 and p23 genes, were evaluated. This was done through the amplification of defined templates followed by their characterisation using the sequencing of multiple clones, as well as Illumina next generation sequencing. High levels of bias were found to be associated with the primer pairs targeting the A and F regions. The p33 gene primers were found to be biased against two genotypes and suggestions for preventing this apparent bias are discussed. The primer pair targeting the conserved p23 gene was found to have very little associated bias. Primers should undergo rigorous screening before being used to characterize virus populations that are known to exhibit high levels of variation, especially within primer binding sites. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. The corrosion protection of AISI(TM) 1010 steel by organic and inorganic zinc-rich primers

    Science.gov (United States)

    Danford, M. D.; Mendrek, M. J.

    1995-01-01

    The behavior of zinc-rich primer-coated AISI 1010 steel in 3.5-percent Na-Cl was investigated using electrochemical techniques. The alternating current (ac) method of electrochemical impedance spectroscopy (EIS), in the frequency range of 0.001 to 40,000 Hz, and the direct current (dc) method of polarization resistance (PR), were used to evaluate the characteristics of an organic, epoxy zinc-rich primer and an inorganic, ethyl silicate zinc-rich primer. A dc electromechanical galvanic corrosion test was also used to determine the corrosion current of each zinc-rich primer anode coupled to a 1010 steel cathode. Duration of the EIS/PR and galvanic testing was 21 days and 24 h, respectively. The galvanic test results demonstrated a very high current between the steel cathode and both zinc-rich primer anodes (38.8 and 135.2 microns A/sq cm for the organic and inorganic primers, respectively). The results of corrosion rate determinations demonstrated a much higher corrosion rate of the zinc in the inorganic primer than in the organic primer, due primarily to the higher porosity in the former. EIS equivalent circuit parameters confirmed this conclusion. Based on this investigation, the inorganic zinc-rich primer appears to provide superior galvanic protection and is recommended for additional study for application on solid rocket booster steel hardware.

  11. Primer fármaco antiepiléptico : patrón de uso y efectividad

    OpenAIRE

    Martínez Domeño, Alejandro

    2013-01-01

    Estudiem el primer fàrmac antiepileptic utlitzat en 430 pacients amb epilèpsia, per valorar la seva taxa de retenció, efectivitat i tolerabilitat en el primer any de tractament. El 81% van rebre àcid valproic, carbamazepina o feintoina com primer tractament, tot i que l'ús de la fenitoina ha disminuit significativamen en els últims anys. La taxa de retenció annual és del 87%, sent més altes amb levetiracetam i lamotrigina. Un 40% van presentar recurrències en el primer any, sent major el risc...

  12. DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies

    National Research Council Canada - National Science Library

    Hugerth, Luisa W; Wefer, Hugo A; Lundin, Sverker; Jakobsson, Hedvig E; Lindberg, Mathilda; Rodin, Sandra; Engstrand, Lars; Andersson, Anders F

    2014-01-01

    .... We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem...

  13. Transfer of primer binding site-mutated simian immunodeficiency virus vectors by genetically engineered artificial and hybrid tRNA-like primers

    DEFF Research Database (Denmark)

    Hansen, A C; Grunwald, T; Lund, Anders Henrik

    2001-01-01

    could be obtained by cotransfection of a gene for an engineered tRNA(Pro)-tRNA hybrid with a match to PBS-Pro. The importance of tRNA backbone identity was further analyzed by complementing the PBS-X2 vector with a gene for a matching x2 primer with a tRNA backbone, which led to three- to fourfold...

  14. Hubungan Stres dengan Kejadian Dismenore Primer pada Mahasiswi Pendidikan Dokter Fakultas Kedokteran Universitas Andalas

    Directory of Open Access Journals (Sweden)

    Diana Sari

    2015-05-01

    Full Text Available AbstrakDismenore primer merupakan nyeri menstruasi yang dijumpai tanpa kelainan yang nyata pada alat-alat genital. Lebih dari 50% wanita mengalami dismenore primer dan 15% diantaranya mengalami nyeri yang hebat.Tujuan penelitian ini adalah untuk menentukan hubungan tingkat stres dengan derajat dismenore primer. Penelitian dilakukan pada mahasiswi pendidikan dokter Fakultas Kedokteran Universitas Andalas angkatan 2009 dan 2010. Desain penelitian ini menggunakan cross sectional study dengan jumlah subjek 165 orang. Pengumpulan data dari responden dilakukan dengan wawancara terpimpin (pengisian kuesioner. Analisa statistik yang digunakan adalah uji chi-square dan uji koefisien korelasi sederhana. Uji chi-square menunjukan ada hubungan yang bermakna antara stres dengan kejadian dismenore primer dan uji statistik koefisien korelasi sederhana menunjukkan ada hubungan yang bermakna dengan korelasi agak lemah antara tingkat stres dengan derajat dismenore primer.Kata kunci: stres, dismenore primer, mahasiswi fakultas kedokteran AbstractPrimary dysmenorrhoea is menstrual pain founded without real abnormalities in genital organs. More than 50% woman experiance it and 15% had severe pain. The objective of this study was to determine relationship between stress and primary dysmenorrhoea. Research was executed to education medical female students medical faculty of Andalas University class of 2009 and 2010. This research use cross sectional study design with 165 subjects. Data was collected by guided interview. Statistic analysis use chi-square test and simple correlation test. Chi-square test show there is significant relationship between stress and primary dysmenorrhoea and simple coefficient test show there is weak correlation between stress levels and degree of primary dysmenorrhoea.Keywords: stress, primary dysmenorrhoea, female student of medical faculty

  15. Pengembangan Sejumlah Primer untuk Reverse Transcriptase Polymerase Chain Reaction Guna Melacak Virus Flu Burung di Indonesia (DEVELOPMENt OF PRIMERS FOR REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION TO DETECT AVIAN INFLUENZA VIRUS IN INDONESIA

    Directory of Open Access Journals (Sweden)

    Ni Luh Putu Indi Dharmayanti

    2016-07-01

    Full Text Available Until recently, two clades of of avian influenza viruses (AIVs designated as 2.3.2 and 2.2.3 havebeen circulating in Indonesia. Mutations of AIV genes have cretaed many more variants of the virus. It istherefore important to evaluate the appropriate methods used for the detection and diagnosis of AI virusin the field. Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR have been used as a standardmethod for detection of AIV in many laboratories in Indonesia. The success of RT-PCR for detection ofAIV virus is dependent on the nucleotide sequences of primer that match with the circulating of AIVs. Theaims of this study was to develop RT-PCR by designing primers for H5 subtype specific to the circulatingAIVs in the field. The primers were designed using Primer Design software, and optimization andvalidation of the primer were conducted using AIVs that have been characterized in the previous study.The primers were then used RT-PCR using AIV isolates from field samples and their sensitivity andspecificity were then determined. The results showed that the H5 primers designed in this study, H5-IDand H5-NLP, was able to detect the AIVs in field samples better than the H5-specific primers have beenused previously. In conclusion, H5 primers designed based on recent viruses in the field showed betterresults in the detection of AI virus as compared to the previous primers. As AIV-H5N1 subtype in the fieldwill continue to change and evolve, the use of primers designed in this study is recommended for diagnosisof H5 AIV.

  16. Deformación en flexión plantar del primer radio

    OpenAIRE

    Blasco García, Carlos; García Carrasco, Julián; Pardo Ríos, Manuel; Romero Soto, Manuel; Santaya Borreiros, Fátima; Vergés Salas, Carles

    2010-01-01

    La posición del primer radio tanto desde el plano frontal como desde el plano sagital, es de vital importancia para la consecución de una correcta y adecuada marcha, así como para mantener la estructura anatómica del pie durante la bipedestación estática. La deformidad en flexión plantar del primer radio modifica estos parámetros creando mecanismos compensatorios que pueden afectar a otras unidades funcionales articulares, tanto del mediopié como del retropié, lo que puede dar lugar a un patr...

  17. Assessment of fungal diversity in deep-sea sediments by multiple primer approach

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, P.; Raghukumar, C.; Verma, P.; Shouche, Y.

    constructed based on fungal ITS gene sequences obtained using fungal specific primer set ITS1F/ITS4. Topology was built using Mega v.5.03 from a ClustalW 1.83 alignment. Numbers below branches indicate bootstrap values (>50 %) from 1,000 replicates. New...S rDNA gene sequences obtained using universal fungal 18S rDNA primer set, NS1/NS2. Topology was built using Mega v.5.03 from a ClustalW 1.83 alignment. Numbers below branches indicate bootstrap values (>50 %) from 1,000 replicates. New sequence...

  18. One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes.

    Science.gov (United States)

    Stielow, J B; Lévesque, C A; Seifert, K A; Meyer, W; Iriny, L; Smits, D; Renfurm, R; Verkley, G J M; Groenewald, M; Chaduli, D; Lomascolo, A; Welti, S; Lesage-Meessen, L; Favel, A; Al-Hatmi, A M S; Damm, U; Yilmaz, N; Houbraken, J; Lombard, L; Quaedvlieg, W; Binder, M; Vaas, L A I; Vu, D; Yurkov, A; Begerow, D; Roehl, O; Guerreiro, M; Fonseca, A; Samerpitak, K; van Diepeningen, A D; Dolatabadi, S; Moreno, L F; Casaregola, S; Mallet, S; Jacques, N; Roscini, L; Egidi, E; Bizet, C; Garcia-Hermoso, D; Martín, M P; Deng, S; Groenewald, J Z; Boekhout, T; de Beer, Z W; Barnes, I; Duong, T A; Wingfield, M J; de Hoog, G S; Crous, P W; Lewis, C T; Hambleton, S; Moussa, T A A; Al-Zahrani, H S; Almaghrabi, O A; Louis-Seize, G; Assabgui, R; McCormick, W; Omer, G; Dukik, K; Cardinali, G; Eberhardt, U; de Vries, M; Robert, V

    2015-12-01

    The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1-D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β -tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5-6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.

  19. The Universal Primer - An open source solution for archiving, organizing and streaming live lectures

    DEFF Research Database (Denmark)

    Christoffersen, Marc Juul; Panton, Hans Christian Hansen; Krajowski-Kukiel, Maciej

    2011-01-01

    . The goal of the Universal Primer is to address these problems, and allow anyone, anywhere, to teach or learn anything that can be reasonably taught or learned through a computer. The Universal Primer is 1: A fully open source solution for streaming live lectures. And 2: A Wikipedia-like website......Many disparate projects providing open access to educational videos are currently available or under development. These projects lack a unifying interface for accessing content, employ differing content licenses, and provide little or no infrastructure for user-contribution or live teaching...... for uploading and organizing open-licensed communitycontributed educational material....

  20. Alteraciones del primer radio en el plano sagital. Tratamiento ortopodológico

    OpenAIRE

    Prats Climent, Baldiri; Alcorisa Rodero, Olga; Verdaguer Sanmartí, Josefina; Vázquez Amela, F. Xavier (Francesc Xavier); Vergés Salas, Carles; Vila Espinalt, Rosa M.

    2004-01-01

    Las alteraciones posicionales del primer radio en un plano sagital, dorsiflexionado o plantarflexionado, son causas de alteraciones en el funcionamiento de la articulación subastragalina y en consecuencia de la posición resultado del retropié. Esta relación causa-efecto depende de la movilidad (flexible, semiflexible o rígido) y de la adaptación del primer radio al suelo en la fase de apoyo total durante la marcha. Dependiendo de ello el tratamiento ortopodólogico será diferente, ...

  1. PEROLEHAN SUHU AIR PENDINGIN PRIMER REAKTOR TRIGA 2000 KETIKA PENAMBAHAN CEROBONG DAN PELAT PENUKAR PANAS

    Directory of Open Access Journals (Sweden)

    Reinaldy Nazar

    2015-03-01

    Full Text Available Kesinambungan operasi reaktor TRIGA 2000 di antaranya ditentukan oleh suhu bahan bakar dan suhu air pendingin primer. Sebagai contoh pengoperasian reaktor TRIGA 2000 saat ini sulit mencapai daya 2000 kW, karena suhu di pusat elemen bahan bakar di dalam teras reaktor mencapai 675 oC, suhu pendingin primer yang masuk ke teras reaktor mencapai 41,3 oC, suhu pendingin primer yang ke luar dari tangki reaktor mencapai 48,2 oC. Tingginya suhu elemen bahan bakar dan suhu pendingin primer di dalam teras telah meningkatkan pendidihan dan menambah pembentukan gelembung uap di dalam teras reaktor, sehingga menurunkan moderasi neutron oleh pendingin primer di dalam teras dan reaktor tidak mampu mencapai daya 2000 KW. Beberapa kegiatan yang dapat dilakukan untuk menurunkan suhu bahan bakar dan air pendingin primer di dalam teras reaktor TRIGA 2000, di antaranya dengan menempatkan cerobong di atas teras reaktor dan menambah pelat penukar panas. Mengingat studi kasus ini tidak memungkinkan untuk dilakukan secara eksperimen, maka analisis dilakukan melalui kajian teoritik menggunakan program komputer CFD. Berdasarkan hasil kajian yang telah dilakukan diketahui bahwa dengan menambah tinggi cerobong menjadi 2 m, pelat penukar panas menjadi 384 lembar, laju alir pendingin primer 950 gpm, dan laju alir pendingin sekunder menjadi 1200 gpm, mampu menurunkan suhu pendingin primer yang ke luar dari penukar panas atau suhu pendingin primer yang masuk ke teras reaktor menjadi 30,48 oC. Jika kondisi ini digunakan tentunya akan menurunkan suhu maksimum kelongsong bahan bakar, dan suhu pendingin primer di dalam teras, sehingga akan mengurangi pendidihan di dalam teras reaktor, meskipun hal ini akan menaikkan konsentrasi N-16 di permukaan tangki reaktor menjadi 49,41%. Kata kunci: cerobong, pelat penukar panas, suhu bahan bakar, suhu pendingin primer.   Continuation of the TRIGA 2000 reactor operation is determined by the fuel and primary cooling water temperature. For

  2. Greedy Algorithms for Finding a Small Set of Primers Satisfying Cover and Length Resolution Conditions in PCR Experiments.

    Science.gov (United States)

    Doi; Imai

    1997-01-01

    Selecting a good collection of primers is very important for polymerase chain reaction (PCR) experiments. Most existing algorithms for primer selection are concerned with computing a primer pair for each DNA sequence. In generalizing the arbitrarily primed PCR, etc., to the case that all DNA sequences of target objects are already known, like about 6000 ORFs of yeast, we may design a small set of primers so that all the targets are PCR amplified and resolved electrophoretically in a series of experiments. This is quite useful because deceasing the number of primers greatly reduces the cost of experiments. Pearson et al. (ISMB 1995: 285-291, 1995; Discrete Appl. Math. 71: 231-246, 1996) consider finding a minimum set of primers covering all given DNA sequences, but their method does not meet necessary biological conditions such as primer amplification and electrophoresis resolution. In this paper, based on the modeling and computational complexity analysis by Doi, we propose algorithms for this primer selection problem. These algorithms do not necessarily minimize the number of primers, but, since basic versions of these problems are shown to be computationally intractable, especially even for approximability with the length resolution condition, this is inevitable. In the algorithms, the amplification condition by a primer pair and the length resolution condition by electrophoresis are incorporated. These algorithms are based on the theoretically well-founded greedy algorithm for the set cover in computer science. Preliminary computational results are presented to show the validity of this approach. The number of computed primers is much less than a half of the number of targets, and hence is less than one forth of the number needed in the multiplex PCR.

  3. Primer registro de Serratospiculum tendo (Nematoda: Diplotriaenidae para el Perú

    Directory of Open Access Journals (Sweden)

    Luis A. Gomez-Puerta

    2014-05-01

    Full Text Available Reportamos por primera vez la presencia del nematodo, Serratospiculum tendo Nitzsch, 1819, parasitando los sacos aéreos de un halcón peregrino (Falco peregrinus Tunstall, 1771. Seis nematodos (2 machos y 4 hembras fueron colectados e identificados como S. tendo. El hallazgo de este nematodo constituye el primer registro en el Perú.

  4. Hemorragias obstétricas en el primer y segundo trimestre del embarazo

    OpenAIRE

    García Rodríguez, Blanca

    2013-01-01

    Se aborda el tema de las hemorragias obstétricas en el primer y segundo trimestre del embarazo. Diagnóstico precoz de las mismas, la identificación de factores de riesgo, las causas y el tratamiento terapéutico

  5. Optimisation of the PCR-invA primers for the detection of Salmonella ...

    African Journals Online (AJOL)

    A polymerase chain reaction (PCR)-based method for the detection of Salmonella species in water samples was optimised and evaluated for speed, specificity and sensitivity. Optimisation of Mg2+ and primer concentrations and cycling parameters increased the sensitivity and limit of detection of PCR to 2.6 x 104 cfu/m.

  6. Detection of three porcine vesicular viruses using multiplex real-time primer-probe energy transfer

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Uttenthal, Åse; Aguero, M.

    2006-01-01

    Rapid identification of the etiologic agent in infected animals is important for the control of an outbreak of vesicular disease in livestock. We have in the present study developed a multiplex real-time reverse transcription-PCR, based on primer-probe energy transfer (PriProET), for simultaneous...

  7. Discovery of EST-derived microsatellite primers in the legume Lens culinaris (Fabaceae)1

    Science.gov (United States)

    Jain, Neelu; Dikshit, H. K.; Singh, D.; Singh, Akanksha; Kumar, Harish

    2013-01-01

    • Premise of the study: We developed microsatellite markers in the legume Lens culinaris from publicly available databases to enrich the limited marker resource available for the crop. • Methods and Results: Eighty-two primer sets were identified using expressed sequence sets of L. culinaris available in the National Center for Biotechnology Information (NCBI) database and were characterized in six species of Lens. Among them, 20 simple sequence repeat (SSR) primers produced no amplification product, 43 produced monomorphic products, and 19 were polymorphic. The primers amplified mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats with one to four alleles. These SSR loci successfully amplified in five related wild species, with a total of 61 primer pairs in L. nigricans and L. odemensis (98.39%), 59 in L. tomentosus (95.1%), and 60 in L. ervoides and L. orientalis (96.7%), respectively. • Conclusions: The microsatellite markers discovered in this study will be useful in genetic mapping, marker-assisted breeding, and characterization of germplasm. PMID:25202567

  8. A new set of validated SSR primers for application in mulberry ...

    Indian Academy of Sciences (India)

    user

    2018-01-11

    Jan 11, 2018 ... Cluster analysis was performed using the data generated by 15. MulSatG primers with Rp >2 by Neighbour Joining method to check for the degree of resolution that could be achieved. Results and discussion. Sericulture is a cottage industry that employs 8.03 million people across India and generates.

  9. PCR Conditions for 16S Primers for Analysis of Microbes in the Colon of Rats.

    Science.gov (United States)

    Guillen, I A; Camacho, H; Tuero, A D; Bacardí, D; Palenzuela, D O; Aguilera, A; Silva, J A; Estrada, R; Gell, O; Suárez, J; Ancizar, J; Brown, E; Colarte, A B; Castro, J; Novoa, L I

    2016-09-01

    The study of the composition of the intestinal flora is important to the health of the host, playing a key role in maintaining intestinal homeostasis and the evolution of the immune system. For these studies, various universal primers of the 16S rDNA gene are used in microbial taxonomy. Here, we report an evaluation of 5 universal primers to explore the presence of microbial DNA in colon biopsies preserved in RNAlater solution. The DNA extracted was used for the amplification of PCR products containing the variable (V) regions of the microbial 16S rDNA gene. The PCR products were studied by restriction fragment length polymorphism (RFLP) analysis and DNA sequence, whose percent of homology with microbial sequences reported in GenBank was verified using bioinformatics tools. The presence of microbes in the colon of rats was quantified by the quantitative PCR (qPCR) technique. We obtained microbial DNA from rat, useful for PCR analysis with the universal primers for the bacteria 16S rDNA. The sequences of PCR products obtained from a colon biopsy of the animal showed homology with the classes bacilli (Lactobacillus spp) and proteobacteria, normally represented in the colon of rats. The proposed methodology allowed the attainment of DNA of bacteria with the quality and integrity for use in qPCR, sequencing, and PCR-RFLP analysis. The selected universal primers provided knowledge of the abundance of microorganisms and the formation of a preliminary test of bacterial diversity in rat colon biopsies.

  10. Detection of Ophiocordyceps sinensis and Its Common Adulterates Using Species-Specific Primers

    Directory of Open Access Journals (Sweden)

    Yang Liu

    2017-06-01

    Full Text Available Ophiocordyceps sinensis is a fungus that infects Hepialidae caterpillars, mummifying the larvae and producing characteristic fruiting bodies (stromata that are processed into one of the most valued traditional Chinese medicines (TCM. The product commands a very high price due to a high demand but a very limited supply. Adulteration with other fungi is a common problem and there is a need to test preparation for the presence of the correct fungus. In the current study, a PCR-based approach for the identification of O. sinensis based on a segment of the internal transcribed spacer (ITS region was developed. The segments is 146-bp in size and is likely to be amplified even in materials where processing led to DNA fragmentation. Primer development was based on the alignment of sequence data generated from a total of 89 samples of O. sinensis and potential adulterants as well as sequences date from 41 Ophiocordyceps species and 26 Cordyceps species available in GenBank. Tests with primer pair, DCF4/DCR4, demonstrated generation of an amplicon from DNA extracted from O. sinensis stromata, but not from extracts derived from adulterants. Species-specific primer pairs were also developed and tested for detection of the common adulterants, Cordyceps gunnii, Cordyceps cicadae, Cordyceps militaris, Cordyceps liangshanensis and Ophiocordyceps nutans. The collection of primers developed in the present study will be useful for the authentication of preparation claiming to only contain O. sinensis and for the detection of fungi used as adulterants in these preparations.

  11. Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification▿†

    OpenAIRE

    Berry, David; Ben Mahfoudh, Karim; Wagner, Michael; Loy, Alexander

    2011-01-01

    “Barcode-tagged” PCR primers used for multiplex amplicon sequencing generate a thus-far-overlooked amplification bias that produces variable terminal restriction fragment length polymorphism (T-RFLP) and pyrosequencing data from the same environmental DNA template. We propose a simple two-step PCR approach that increases reproducibility and consistently recovers higher genetic diversity in pyrosequencing libraries.

  12. Detection of Ophiocordyceps sinensis and Its Common Adulterates Using Species-Specific Primers.

    Science.gov (United States)

    Liu, Yang; Wang, Xiao-Yue; Gao, Zi-Tong; Han, Jian-Ping; Xiang, Li

    2017-01-01

    Ophiocordyceps sinensis is a fungus that infects Hepialidae caterpillars, mummifying the larvae and producing characteristic fruiting bodies (stromata) that are processed into one of the most valued traditional Chinese medicines (TCM). The product commands a very high price due to a high demand but a very limited supply. Adulteration with other fungi is a common problem and there is a need to test preparation for the presence of the correct fungus. In the current study, a PCR-based approach for the identification of O. sinensis based on a segment of the internal transcribed spacer (ITS) region was developed. The segments is 146-bp in size and is likely to be amplified even in materials where processing led to DNA fragmentation. Primer development was based on the alignment of sequence data generated from a total of 89 samples of O. sinensis and potential adulterants as well as sequences date from 41 Ophiocordyceps species and 26 Cordyceps species available in GenBank. Tests with primer pair, DCF4/DCR4, demonstrated generation of an amplicon from DNA extracted from O. sinensis stromata, but not from extracts derived from adulterants. Species-specific primer pairs were also developed and tested for detection of the common adulterants, Cordyceps gunnii, Cordyceps cicadae, Cordyceps militaris, Cordyceps liangshanensis and Ophiocordyceps nutans. The collection of primers developed in the present study will be useful for the authentication of preparation claiming to only contain O. sinensis and for the detection of fungi used as adulterants in these preparations.

  13. Magnesium-Based Sacrificial Anode Cathodic Protection Coatings (Mg-Rich Primers for Aluminum Alloys

    Directory of Open Access Journals (Sweden)

    Michael D. Blanton

    2012-09-01

    Full Text Available Magnesium is electrochemically the most active metal employed in common structural alloys of iron and aluminum. Mg is widely used as a sacrificial anode to provide cathodic protection of underground and undersea metallic structures, ships, submarines, bridges, decks, aircraft and ground transportation systems. Following the same principle of utilizing Mg characteristics in engineering advantages in a decade-long successful R&D effort, Mg powder is now employed in organic coatings (termed as Mg-rich primers as a sacrificial anode pigment to protect aerospace grade aluminum alloys against corrosion. Mg-rich primers have performed very well on aluminum alloys when compared against the current chromate standard, but the carcinogenic chromate-based coatings/pretreatments are being widely used by the Department of Defense (DoD to protect its infrastructure and fleets against corrosion damage. Factors such as reactivity of Mg particles in the coating matrix during exposure to aggressive corrosion environments, interaction of atmospheric gases with Mg particles and the impact of Mg dissolution, increases in pH and hydrogen gas liberation at coating-metal interface, and primer adhesion need to be considered for further development of Mg-rich primer technology.

  14. Discovery of EST-Derived Microsatellite Primers in the Legume Lens culinaris (Fabaceae

    Directory of Open Access Journals (Sweden)

    Neelu Jain

    2013-06-01

    Full Text Available Premise of the study: We developed microsatellite markers in the legume Lens culinaris from publicly available databases to enrich the limited marker resource available for the crop. Methods and Results: Eighty-two primer sets were identified using expressed sequence sets of L. culinaris available in the National Center for Biotechnology Information (NCBI database and were characterized in six species of Lens. Among them, 20 simple sequence repeat (SSR primers produced no amplification product, 43 produced monomorphic products, and 19 were polymorphic. The primers amplified mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats with one to four alleles. These SSR loci successfully amplified in five related wild species, with a total of 61 primer pairs in L. nigricans and L. odemensis (98.39%, 59 in L. tomentosus (95.1 %, and 60 in L. ervoides and L. orientalis (96.7%, respectively. Conclusions: The microsatellite markers discovered in this study will be useful in genetic mapping, marker-assisted breeding, and characterization of germplasm.

  15. What Are the Odds of that? A Primer on Understanding Logistic Regression

    Science.gov (United States)

    Huang, Francis L.; Moon, Tonya R.

    2013-01-01

    The purpose of this Methodological Brief is to present a brief primer on logistic regression, a commonly used technique when modeling dichotomous outcomes. Using data from the National Education Longitudinal Study of 1988 (NELS:88), logistic regression techniques were used to investigate student-level variables in eighth grade (i.e., enrolled in a…

  16. Identification of sex in Cetaceans by multiplexing with three ZFX and ZFY specific primers

    NARCIS (Netherlands)

    Berube, M; Palsboll, P

    We sequenced 540 nucleotides of the last exon in the ZFY/ZFX gene in two males and two females for eight cetacean species; four odontocetes (toothed whales) and four mysticetes (baleen whales). Based upon the obtained nucleotide sequences, we designed two sets of oligonucleotide primers for specific

  17. A paint removal concept with side-chain liquid crystalline polymers as primer material

    NARCIS (Netherlands)

    Wielen, van der M.W.J.; Cohen Stuart, M.A.; Fleer, G.J.; Nieuwhof, R.P.; Marcelis, A.T.M.; Sudhölter, E.J.R.

    2001-01-01

    A new paint removal concept is introduced making use of a polymer primer layer with a sharp softening temperature. For this, a new class of side-chain liquid crystalline polymers with polar moieties in the backbone has been developed and studied in thin films. These polymers form lamellar-ordered

  18. Pedagogia de l'oprimit, capítols primer i segon

    OpenAIRE

    Freire, Paulo

    2006-01-01

    El document forma part dels materials docents programats mitjançant l'ajut del Servei de Política Lingüística de la Universitat de València Traducció al català dels capítols primer i segon del llibre Pedagogia de l'oprimit, de Paulo Freire

  19. New primers for promising single-copy genes in fungal phylogenetics and systematics

    NARCIS (Netherlands)

    Schmitt, I.; Crespo, A.; Divakar, P.K.; Fankhauser, J.D.; Herman-Sackett, E.; Kalb, K.; Nelsen, M.P.; Nelson, N.A.; Rivas-Plata, E.; Shimp, A.D.; Widhelm, T.; Lumbsch, H.T.

    2009-01-01

    Developing powerful phylogenetic markers is a key concern in fungal phylogenetics. Here we report degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota). Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes,

  20. Book review: Estimation of parameters for animal populations: A primer for the rest of us

    Science.gov (United States)

    Post van der Burg, Max

    2016-01-01

    No abstract available.Estimation of Parameters for Animal Populations: A Primer for the Rest of Us. Larkin A. Powell and George A. Gale. 2015. Caught Napping Publications, Lincoln, Nebraska, USA. 239 pages. (http://larkinpowell.wixsite.com/larkinpowell/estimationof-parameters-for-animal-pop). ISBN: 978-329-06151-4.

  1. Historia del primer templo mayor de Tunja, nombrado de Nuestra Señora de Guadalupe

    Directory of Open Access Journals (Sweden)

    Ernesto Porras Collantes

    2004-01-01

    Full Text Available Gonzalo Suárez Rendón Sarmiento, fundador de Tunja, bautizó con el nombrede Nuestra Señora de Guadalupe al primer templo mayor de la ciudad. Elcarpintero Gregorio López estuvo a cargo de la construcción de la obra, desdefebrero hasta la navidad del año de

  2. A web-based adaptive tutor to teach PCR primer design

    NARCIS (Netherlands)

    van Seters, Janneke R.; Wellink, Joan; Tramper, Johannes; Goedhart, Martin J.; Ossevoort, Miriam A.

    2012-01-01

    When students have varying prior knowledge, personalized instruction is desirable. One way to personalize instruction is by using adaptive e-learning to offer training of varying complexity. In this study, we developed a web-based adaptive tutor to teach PCR primer design: the PCR Tutor. We used

  3. The fidelity of reverse transcription differs in reactions primed with RNA versus DNA primers

    NARCIS (Netherlands)

    Oude Essink, B. B.; Berkhout, B.

    1999-01-01

    Reverse transcriptase enzymes (RT) convert single-stranded retroviral RNA genomes into double-stranded DNA. The RT enzyme can use both RNA and DNA primers, the former being used exclusively during initiation of minus- and plus-strand synthesis. Initiation of minus-strand DNA synthesis occurs by

  4. Designing Polymerase Chain Reaction (PCR) Primer Multiplexes in the Forensic Laboratory

    Science.gov (United States)

    Elkins, Kelly M.

    2011-01-01

    The polymerase chain reaction (PCR) is a common experiment in upper-level undergraduate biochemistry, molecular biology, and forensic laboratory courses as reagents and thermocyclers have become more affordable for institutions. Typically, instructors design PCR primers to amplify the region of interest and the students prepare their samples for…

  5. Application of nonsense-mediated primer exclusion (NOPE) for preparation of unique molecular barcoded libraries.

    Science.gov (United States)

    Shagin, Dmitriy A; Turchaninova, Maria A; Shagina, Irina A; Shugay, Mikhail; Zaretsky, Andrew R; Zueva, Olga I; Bolotin, Dmitriy A; Lukyanov, Sergey; Chudakov, Dmitriy M

    2017-06-05

    Recently we proposed efficient method to exclude undesirable primers at any stage of amplification reaction, here termed NOPE (NOnsense-mediated Primer Exclusion). According to this method, added oligonucleotide overlapping with the 3'-end of unwanted amplification primer (NOPE oligo) simultaneously provides a template for its elongation. This elongation disrupts specificity of unwanted primer, preventing its further participation in PCR. The suggested approach allows to rationally manage the course of PCR reactions in order to facilitate analysis of complex DNA mixtures as well as to perform multistage PCR bypassing intermediate purification steps. Here we apply NOPE method to DNA library preparation for the high-throughput sequencing (HTS) with the PCR-based introduction of unique molecular identifiers (UMI). We show that NOPE oligo efficiently neutralizes UMI-containing oligonucleotides after introduction of UMI into sample DNA molecules, thus allowing to proceed with further amplification steps without purification and associated loss of starting material. At the same time, NOPE oligo does not affect the efficiency of target PCR amplification. We describe a simple, robust and cheap modification of UMI-labeled HTS libraries preparation procedure, that allows to bypass purification step and thus to preserve starting material which may be limited, e.g. circulating tumor DNA, circulating fetal DNA, or small amounts of isolated cells of interest. Furthermore, demonstrated simplicity and robustness of NOPE method should make it popular in various PCR protocols.

  6. Following Reading Primers the Wrong Way: Pedagogical Nonsense in Dr. Seuss

    Science.gov (United States)

    Yang, Lichung

    2017-01-01

    A well-versed writer on the limitations and possibilities of the English language, Seuss follows the conventional primers the wrong way, not by retracing the tradition of the genre, but by working his way against the current. Drawing upon Jean-Jacques Lecercle's notion of nonsense, this essay is a small attempt to examine three of Dr. Seuss's…

  7. Specific and sensitive primers for the detection of predated olive fruit flies, Bactrocera oleae (Diptera: Tephritidae

    Directory of Open Access Journals (Sweden)

    Esther Lantero

    2017-07-01

    Full Text Available Bactrocera oleae, the olive fruit fly, is a major pest of olive (Olea europaea L. trees worldwide. Its presence can cause important losses, with consequences for the economies of countries that produce and export table olives and olive oil. Efforts to control olive fruit fly populations have, however, been insufficient. Now more than ever, environmentally friendly alternatives need to be considered in potential control programs. Generalist predators could provide a way of managing this pest naturally. However, the identification of candidate predator species is essential if such a management system is to be introduced. The present paper describes a set of species-specific primers for detecting the presence of B. oleae DNA in the gut of predatory arthropods. All primers were tested for checking cross-reactive amplification of other fruit fly DNA and evaluated in heterospecific mixes of nucleic acids. All were found to be very sensitive for B. oleae. Subsequent feeding trials were conducted using one of the most abundant species of ground dwelling carabids in olive groves in south-eastern Madrid, Spain. These trials allowed determining that 253F-334R and 334F-253R primer pairs had the highest detection efficiency with an ID50 of around 78 h. These primers therefore provide a very useful tool for screening the gut contents of potential predators of B. oleae, and can thus reveal candidate species for the pest's biological control

  8. Medication Interventions for ADHD Youth: A Primer for School and Mental Health Counselors.

    Science.gov (United States)

    Hall, Alex S.; Gushee, Arlinn G.

    2002-01-01

    This primer on the medical aspects of treating Attention Deficit Hyperactivity Disorder (ADHD) youth will help counselors feel better informed about the types of medications available, possible side effects, and the advantages and disadvantages for use. It also offers a discussion of the consequences for using interventions requiring medication…

  9. Screening for Residual Disease in Pediatric Burkitt Lymphoma Using Consensus Primer Pools

    Directory of Open Access Journals (Sweden)

    Melissa Agsalda

    2009-01-01

    Full Text Available Assessing molecular persistent or minimal residual disease (PD/MRD in childhood Burkitt lymphoma (BL is challenging because access to original tumor is usually needed to design patient-specific primers (PSPs. Because BL is characterized by rearranged immunoglobulin heavy chain (IgVH genes, IgVH primer pools from IgVH1–IgVH7 regions were tested to detect PD/MRD, thus eliminating the need for original tumor. The focus of the current study was to assess the feasibility of using IgVH primer pools to detect disease in clinical specimens. Fourteen children diagnosed with B-NHL had follow-up repository specimens available to assess PD/MRD. Of the 14 patients, 12 were PD/MRD negative after 2 months of therapy and remained in remission at the end of therapy; 2/14 patients were PD/MRD positive at 2-3 months and later relapsed. PSP-based assays from these 14 patients showed 100% concordance with the current assay. This feasibility study warrants further investigation to assess PD/MRD using IgVH primer pools, which could have clinical significance as a real-time assessment tool to monitor pediatric BL and possibly other B-cell non-Hodgkin lymphoma therapy.

  10. A blocking primer increases specificity in environmental DNA detection of bull trout (Salvelinus confluentus)

    Science.gov (United States)

    Taylor M. Wilcox; Michael K. Schwartz; Kevin S. McKelvey; Michael K. Young; Winsor H. Lowe

    2014-01-01

    Environmental DNA (eDNA) is increasingly applied as a highly sensitive way to detect aquatic animals non-invasively. However, distinguishing closely related taxa can be particularly challenging. Previous studies of ancient DNA and genetic diet analysis have used blocking primers to enrich target template in the presence of abundant, non-target DNA. Here we apply a...

  11. Optimisation of the PCR-invA primers for the detection of Salmonella ...

    African Journals Online (AJOL)

    2007-04-02

    Apr 2, 2007 ... ile distilled water and quantified by UV spectrophotometry at ... Cell dilution: Tenfold serial cell dilutions of S. enteritidis ATCC .... tration of primers and the annealing conditions also affect the .... ble to light-induced decay and predation than S. typhimurium ..... recombinant DNA from bacteria and a yeast.

  12. A Primer on a Domestic Catastrophic Disaster Response for the Joint Logistics Enterprise

    Science.gov (United States)

    2017-04-30

    COVERED (From - To) 4. TITLE AND SUBTITLE (U) A Primer on a Domestic Catastrophic Disaster Response 5a. CONTRACT NUMBER N00014-16-D-5003 for the...3  National Response Framework and the Post -Katrina Emergency...level responses to local incidents, all disaster responses begin and end at the local level. National Response Framework and the Post - Katrina Emergency

  13. LOMA: A fast method to generate efficient tagged-random primers despite amplification bias of random PCR on pathogens

    Directory of Open Access Journals (Sweden)

    Lee Wah

    2008-09-01

    Full Text Available Abstract Background Pathogen detection using DNA microarrays has the potential to become a fast and comprehensive diagnostics tool. However, since pathogen detection chips currently utilize random primers rather than specific primers for the RT-PCR step, bias inherent in random PCR amplification becomes a serious problem that causes large inaccuracies in hybridization signals. Results In this paper, we study how the efficiency of random PCR amplification affects hybridization signals. We describe a model that predicts the amplification efficiency of a given random primer on a target viral genome. The prediction allows us to filter false-negative probes of the genome that lie in regions of poor random PCR amplification and improves the accuracy of pathogen detection. Subsequently, we propose LOMA, an algorithm to generate random primers that have good amplification efficiency. Wet-lab validation showed that the generated random primers improve the amplification efficiency significantly. Conclusion The blind use of a random primer with attached universal tag (random-tagged primer in a PCR reaction on a pathogen sample may not lead to a successful amplification. Thus, the design of random-tagged primers is an important consideration when performing PCR.

  14. Design of phylum-specific hybrid primers for DNA barcoding: addressing the need for efficient COI amplification in the Echinodermata.

    Science.gov (United States)

    Hoareau, T B; Boissin, E

    2010-11-01

    Recent research has shown the usefulness of the Folmer region of the cytochrome oxidase I (COI) as a genetic barcode to assist in species delimitation of echinoderms. However, amplification of COI is often challenging in echinoderms (low success or pseudogenes). We present a method that allows the design of phylum-specific hybrid primers, and use this to develop COI primers for the Echinodermata. We aligned COI sequences from 310 echinoderm species and designed all possible primers along the consensus sequence with two methods (standard degenerate and hybrid). We found much lower degeneracy for hybrid primers (4-fold degeneracy) than for standard degenerate primers (≥48-fold degeneracy). We then designed the most conserved hybrid primers to amplify a >500-bp region within COI. These primers successfully amplified this gene region in all tested taxa (123 species across all echinoderm classes). Sequencing of 30 species among these confirmed both the quality of the sequences (>500 bp, no pseudogenes) and their utility as a DNA barcode. This method should be useful for developing primers for other mitochondrial genes and other phyla. The method will also be of interest for the development of future projects involving both community-based genetic assessments on macroorganisms and biodiversity assessment of environmental samples using high-throughput sequencing. © 2010 Blackwell Publishing Ltd.

  15. In silico vs in vitro analysis of primer specificity for the detection of Gardnerella vaginalis, Atopobium vaginae and Lactobacillus spp.

    Directory of Open Access Journals (Sweden)

    Henriques Ana

    2012-11-01

    Full Text Available Abstract Background Bacterial vaginosis (BV is a common pathology of women in reproductive age that can lead to serious health complications, and is associated with shifts in the normal microflora from predominance of Lactobacillus spp. to a proliferation of other anaerobes such as G. vaginalis and A vaginae, which can be detected by PCR. The optimal PCR pathogen detection assay relies mainly on the specificity and sensitivity of the primers used. Findings Here we demonstrate that in silico analytical testing of primer specificity is not a synonym to in vitro analytical specificity by testing a range of published and newly designed primers with both techniques for the detection of BV-associated microorganisms. Conclusions By testing primer in vitro specificity with a sufficient range of bacterial strains, we were able to design primers with higher specificity and sensitivity. Also by comparing the results obtained for the newly designed primers with other previously published primers, we confirmed that in silico analysis is not sufficient to predict in vitro specificity. As such care must be taken when choosing the primers for a detection assay.

  16. Electrochemical primer extension for the detection of single nucleotide polymorphisms in the cardiomyopathy associated MYH7 gene.

    Science.gov (United States)

    Debela, A M; Thorimbert, S; Hasenknopf, B; O'Sullivan, C K; Ortiz, M

    2016-01-14

    We report the labelling of dideoxy nucleotides (ddNTPs) for use in electrochemical array based primer extension for the detection of single nucleotide polymorphisms (SNPs). The results confirm the extension of the immobilised primers for each of the four ddNTPs, representing a significant advance in achieving a cost-effective platform for screening of disease-specific SNPs.

  17. Effect of clearfil protect bond and transbond plus self-etch primer on shear bond strength of orthodontic brackets

    Directory of Open Access Journals (Sweden)

    S Hamid Raji

    2011-01-01

    Conclusion: The shear bond strength of clearfil protect bond and transbond plus self-etch primer was enough for bonding the orthodontic brackets. The mode of failure of bonded brackets with these two self-etch primers is safe for enamel.

  18. Evaluation of 16S rRNA gene primer pairs for monitoring microbial community structures showed high reproducibility within and low comparability between datasets generated with multiple archaeal and bacterial primer pairs

    Directory of Open Access Journals (Sweden)

    Martin Alexander Fischer

    2016-08-01

    Full Text Available The application of next-generation sequencing technology in microbial community analysis increased our knowledge and understanding of the complexity and diversity of a variety of ecosystems. In contrast to Bacteria, the archaeal domain was often not particularly addressed in the analysis of microbial communities. Consequently, established primers specifically amplifying the archaeal 16S ribosomal gene region are scarce compared to the variety of primers targeting bacterial sequences. In this study, we aimed to validate archaeal primers suitable for high throughput next generation sequencing. Three archaeal 16S primer pairs as well as two bacterial and one general microbial 16S primer pairs were comprehensively tested by in-silico evaluation and performing an experimental analysis of a complex microbial community of a biogas reactor. The results obtained clearly demonstrate that comparability of community profiles established using different primer pairs is difficult. 16S rRNA gene data derived from a shotgun metagenome of the same reactor sample added an additional perspective on the community structure. Furthermore, in-silico evaluation of primers, especially those for amplification of archaeal 16S rRNA gene regions, does not necessarily reflect the results obtained in experimental approaches. In the latter, archaeal primer pair ArchV34 showed the highest similarity to the archaeal community structure compared to observed by the metagenomic approach and thus appears to be the appropriate for analyzing archaeal communities in biogas reactors. However, a disadvantage of this primer pair was its low specificity for the archaeal domain in the experimental application leading to high amounts of bacterial sequences within the dataset. Overall our results indicate a rather limited comparability between community structures investigated and determined using different primer pairs as well as between metagenome and 16S rRNA gene amplicon based community

  19. A degenerate pair of primers for simultaneous detection of four alpha- and betanecroviruses.

    Science.gov (United States)

    Varanda, C M R; Cardoso, J M S; Oliveira, M D M; Oliveira, S; Clara, M I E; Félix, M R F

    2014-11-01

    The high infection levels due to Olive latent virus 1 (OLV-1), Olive mild mosaic virus (OMMV) (alphanecrovirus) and Tobacco necrosis virus D (TNV-D) (betanecrovirus) in Portuguese olive orchards prompted us to develop a rapid PCR-based assay for the simultaneous detection of these viruses aimed at the sanitary selection and marketing of plant material in compliance with European Union regulations. A pair of degenerate oligonucleotide primers, parRdRp5' and parCoat3' was designed based on conserved regions located in the RNA-dependent RNA polymerase (RdRp) and coat protein (CP) genes of these viruses and one other alphanecrovirus, Tobacco necrosis virus A. Its use in RT-PCR assays generated a product of ca. 2000 bp for the 4 viral species tested. These primers were compared with virus specific primers in multiplex RT-PCR, and identical results were obtained. Its application to dsRNA extracted from 54 olive field growing trees originated the expected ca. 2000 bp amplicon in 17 trees. The virus identity was determined by sequencing the cloned RT-PCR products. No TNV-A was found. The RT-PCR assay using the degenerate primers described in this study were shown to be reliable in detecting any of the above-mentioned alpha- and betanecroviruses, and it is as sensitive as that which uses virus specific primers in multiplex assays. Therefore, this assay is well suited for the rapid screen of virus-free plant material in selection and improvement crop programmes. Additionally, it has the potential to reveal virus diversity and the presence of new viruses, provided the RT-PCR generated amplicon is further sequenced. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. A method for automatically extracting infectious disease-related primers and probes from the literature

    Directory of Open Access Journals (Sweden)

    Pérez-Rey David

    2010-08-01

    Full Text Available Abstract Background Primer and probe sequences are the main components of nucleic acid-based detection systems. Biologists use primers and probes for different tasks, some related to the diagnosis and prescription of infectious diseases. The biological literature is the main information source for empirically validated primer and probe sequences. Therefore, it is becoming increasingly important for researchers to navigate this important information. In this paper, we present a four-phase method for extracting and annotating primer/probe sequences from the literature. These phases are: (1 convert each document into a tree of paper sections, (2 detect the candidate sequences using a set of finite state machine-based recognizers, (3 refine problem sequences using a rule-based expert system, and (4 annotate the extracted sequences with their related organism/gene information. Results We tested our approach using a test set composed of 297 manuscripts. The extracted sequences and their organism/gene annotations were manually evaluated by a panel of molecular biologists. The results of the evaluation show that our approach is suitable for automatically extracting DNA sequences, achieving precision/recall rates of 97.98% and 95.77%, respectively. In addition, 76.66% of the detected sequences were correctly annotated with their organism name. The system also provided correct gene-related information for 46.18% of the sequences assigned a correct organism name. Conclusions We believe that the proposed method can facilitate routine tasks for biomedical researchers using molecular methods to diagnose and prescribe different infectious diseases. In addition, the proposed method can be expanded to detect and extract other biological sequences from the literature. The extracted information can also be used to readily update available primer/probe databases or to create new databases from scratch.

  1. Identification of Pork Adulteration in Processed Meat Products Using the Developed Mitochondrial DNA-Based Primers.

    Science.gov (United States)

    Ha, Jimyeong; Kim, Sejeong; Lee, Jeeyeon; Lee, Soomin; Lee, Heeyoung; Choi, Yukyung; Oh, Hyemin; Yoon, Yohan

    2017-01-01

    The identification of pork in commercially processed meats is one of the most crucial issues in the food industry because of religious food ethics, medical purposes, and intentional adulteration to decrease production cost. This study therefore aimed to develop a method for the detection of pork adulteration in meat products using primers specific for pig mitochondrial DNA. Mitochondrial DNA sequences for pig, cattle, chicken, and sheep were obtained from GenBank and aligned. The 294-bp mitochondrial DNA D-loop region was selected as the pig target DNA sequence and appropriate primers were designed using the MUSCLE program. To evaluate primer sensitivity, pork-beef-chicken mixtures were prepared as follows: i) 0% pork-50% beef-50% chicken, ii) 1% pork-49.5% beef-49.5% chicken, iii) 2% pork-49% beef-49% chicken, iv) 5% pork-47.5% beef-47.5% chicken, v) 10% pork-45% beef-45% chicken, and vi) 100% pork-0% beef-0% chicken. In addition, a total of 35 commercially packaged products, including patties, nuggets, meatballs, and sausages containing processed chicken, beef, or a mixture of various meats, were purchased from commercial markets. The primers developed in our study were able to detect as little as 1% pork in the heat treated pork-beef-chicken mixtures. Of the 35 processed products, three samples were pork positive despite being labeled as beef or chicken only or as a beef-chicken mix. These results indicate that the developed primers could be used to detect pork adulteration in various processed meat products for application in safeguarding religious food ethics, detecting allergens, and preventing food adulteration.

  2. Effect of MMA-PMMA resin polymerization initiators on the bond strengths of adhesive primers for noble metal.

    Science.gov (United States)

    Yoshida, K; Atsuta, M

    1999-09-01

    This study was conducted to investigate the effect of MMA-PMMA resin polymerization initiators on the bond strengths of two adhesive metal primers by evaluating the shear bond strengths of resins of silver-palladium-copper-gold (Ag-Pd-Cu-Au) alloy. Three types of MMA-PMMA resins for which the polymerization initiators were TBB, BPO-amine and CQ-amine, and two adhesive primers, Metal PrimerII and V-Primer, were used. A brass ring placed over the nonprimed or primed casting alloy disk surface was filled with each resin. The half specimens were stored in water at 37 degrees C for 24 h. In addition, another half specimens were then immersed alternately in water baths at 4 degrees C and 60 degrees C for 1 min each for 20,000 thermal cycles before shear mode testing at a crosshead speed of 0.5 mm/min. There were no significant differences (p > 0.05) in bond strength between the three types of resins with or without thermal cycling when Metal PrimerII was used. However, when Ag-Pd-Cu-Au alloy was primed with V-Primer, the bond strength of CQ-amine resin was significantly weaker than that of TBB resin. Metal PrimerII was more effective for enhancing the bond strength and the bond strength was not affected by thermal cycling, in contrast to V-Primer. The effectiveness of Metal PrimerII to enhance the bond strength is not influenced by polymerization mode of MMA-PMMA resin, in contrast to V-Primer when the resin is bonded to Ag-Pd-Cu-Au alloy.

  3. Schrodinger's scat: a critical review of the currently available tiger (Panthera Tigris) and leopard (Panthera pardus) specific primers in India, and a novel leopard specific primer.

    Science.gov (United States)

    Maroju, Pranay Amruth; Yadav, Sonu; Kolipakam, Vishnupriya; Singh, Shweta; Qureshi, Qamar; Jhala, Yadvendradev

    2016-02-09

    Non-invasive sampling has opened avenues for the genetic study of elusive species, which has contributed significantly to their conservation. Where field based identity of non-invasive sample is ambiguous (e.g. carnivore scats), it is essential to establish identity of the species through molecular approaches. A cost effective procedure to ascertain species identity is to use species specific primers (SSP) for PCR amplification and subsequent resolution through agarose gel electrophoresis. However, SSPs if ill designed can often cross amplify non-target sympatric species. Herein we report the problem of cross amplification with currently published SSPs, which have been used in several recent scientific articles on tigers (Panthera tigris) and leopards (Panthera pardus) in India. Since these papers form pioneering research on which future work will be based, an early rectification is required so as to not propagate this error further. We conclusively show cross amplification of three of the four SSPs, in sympatric non-target species like tiger SSP amplifying leopard and striped hyena (Hyaena hyaena), and leopard SSP amplifying tiger, lion (Panthera leo persica) and clouded leopard (Neofelis nebulosa), with the same product size. We develop and test a non-cross-amplifying leopard specific primer pair within the mitochondrial cytochrome b region. We also standardize a duplex PCR method to screen tiger and leopard samples simultaneously in one PCR reaction to reduce cost and time. These findings suggest the importance of an often overlooked preliminary protocol of conclusive identification of species from non-invasive samples. The cross amplification of published primers in conspecifics suggests the need to revisit inferences drawn by earlier work.

  4. One Primer To Rule Them All: Universal Primer That Adds BBa_B0034 Ribosomal Binding Site to Any Coding Standard 10 BioBrick

    OpenAIRE

    Bryksin, Anton V.; Bachman, Haylee N.; Cooper, Spencer W.; Balavijayan, Tilak; Blackstone, Rachael M.; Du, Haoli; Jenkins, Jackson P.; Haynes, Casey L.; Siemer, Jessica L.; Fiore, Vincent F.; Barker, Thomas H.

    2014-01-01

    Here, we present a universal, simple, efficient, and reliable way to add small BioBrick parts to any BioBrick via PCR that is compatible with BioBrick assembly standard 10. As a proof of principle, we have designed a universal primer, rbs_B0034, that contains a ribosomal binding site (RBS; BBa_B0034) and that can be used in PCR to amplify any coding BioBrick that starts with ATG. We performed test PCRs with rbs_B0034 on 31 different targets and found it to be 93.6% efficient. Moreover, when s...

  5. PERAN DATA PRIMER PADA PEMBENTUKAN SKEMA KONSEPTUAL YANG FAKTUAL (STUDI KASUS: SKEMA KONSEPTUAL BASISDATA SIMBUMIL

    Directory of Open Access Journals (Sweden)

    Titin Pramiyati

    2017-11-01

    Full Text Available Sumber  data  yang  diperoleh  secara  langsung  dari  sumber  asli  disebut  sebagai  data  primer. Penggunaan data primer umumnya untuk kebutuhan menghasilkan informasi yang mencerminkan kebenaran sesuai dengan kondisi faktual, sehingga informasi yang dihasilkan dapat berguna dalam pengambilan  keputusan.Kebenaran  data  merupakan  aspek  penting  pada  sistem  informasi  kesehatan, terlebih terhadap data yang berkaitan dengan data klinis ibu hamil. Ketersediaan data klinis ibu hamil yang digunakan secara bersama oleh unit layanan kesehatan membutuhkan ketersediaan sistem informasi yang memberikan kelengkapan data klinis dengan akurat untuk pencegahan timbulnya penyulit kehamilan yang berujung pada kematian ibu dan bayi. Bagaimana peran data primer dalam pembangunan skema konseptual  basisdata  SIMBUMIL  yang  faktual  adalahtopik  yang  dibahas  pada  paper  ini.  Skema konseptual basisdata yang dibangun dengan cara melakukan peninjauan ulang terhadap skema yang telah dibangun  sebelumnya  menggunakan  sumber  data sekunder  yang  diambil  dari  beberapa  situs asuhan kehamilan.Peninjauan ulang yang dilakukan menggunakan data primer dan penelusuran pustaka. Penelusuran pustaka dilakukan bertujuan untuk memahami istilah yang digunakan sebagai nama atribut.Langkah   yang  dilakukan  dalam  pembangunan  skema  konseptual  ini  terdiri  dari  langkah identifikasi  entitasasuhan  kehamilan,  tinjauan  fungsi atribut pada setiap entitas,  dan  perbaikan/revisi skema konseptual untuk menghasilkan skema konseptual yang faktual. Studi lapangan dan wawancara kepada narasumber  yang  kompeten  adalah  metode  yang digunakan  untuk  mendapatkan  data  primer sebagai dasar peninjauan ulang. Hasil dari pembangunan skema konseptual diperoleh struktur basisdata yang mewakili kondisi faktual rekam medis asuhan kehamilan. Peran data primer sangat berpengaruh pada pembangunan basisdata SIMBUMIL

  6. Improved efficiency and robustness in qPCR and multiplex end-point PCR by twisted intercalating nucleic acid modified primers.

    Directory of Open Access Journals (Sweden)

    Uffe Vest Schneider

    Full Text Available We introduce quantitative polymerase chain reaction (qPCR primers and multiplex end-point PCR primers modified by the addition of a single ortho-Twisted Intercalating Nucleic Acid (o-TINA molecule at the 5'-end. In qPCR, the 5'-o-TINA modified primers allow for a qPCR efficiency of 100% at significantly stressed reaction conditions, increasing the robustness of qPCR assays compared to unmodified primers. In samples spiked with genomic DNA, 5'-o-TINA modified primers improve the robustness by increased sensitivity and specificity compared to unmodified DNA primers. In unspiked samples, replacement of unmodified DNA primers with 5'-o-TINA modified primers permits an increased qPCR stringency. Compared to unmodified DNA primers, this allows for a qPCR efficiency of 100% at lowered primer concentrations and at increased annealing temperatures with unaltered cross-reactivity for primers with single nucleobase mismatches. In a previously published octaplex end-point PCR targeting diarrheagenic Escherichia coli, application of 5'-o-TINA modified primers allows for a further reduction (>45% or approximately one hour in overall PCR program length, while sustaining the amplification and analytical sensitivity for all targets in crude bacterial lysates. For all crude bacterial lysates, 5'-o-TINA modified primers permit a substantial increase in PCR stringency in terms of lower primer concentrations and higher annealing temperatures for all eight targets. Additionally, crude bacterial lysates spiked with human genomic DNA show lesser formation of non-target amplicons implying increased robustness. Thus, 5'-o-TINA modified primers are advantageous in PCR assays, where one or more primer pairs are required to perform at stressed reaction conditions.

  7. One primer to rule them all: universal primer that adds BBa_B0034 ribosomal binding site to any coding standard 10 BioBrick.

    Science.gov (United States)

    Bryksin, Anton V; Bachman, Haylee N; Cooper, Spencer W; Balavijayan, Tilak; Blackstone, Rachael M; Du, Haoli; Jenkins, Jackson P; Haynes, Casey L; Siemer, Jessica L; Fiore, Vincent F; Barker, Thomas H

    2014-12-19

    Here, we present a universal, simple, efficient, and reliable way to add small BioBrick parts to any BioBrick via PCR that is compatible with BioBrick assembly standard 10. As a proof of principle, we have designed a universal primer, rbs_B0034, that contains a ribosomal binding site (RBS; BBa_B0034) and that can be used in PCR to amplify any coding BioBrick that starts with ATG. We performed test PCRs with rbs_B0034 on 31 different targets and found it to be 93.6% efficient. Moreover, when supplemented with a complementary primer, addition of RBS can be accomplished via whole plasmid site-directed mutagenesis, thus reducing the time required for further assembly of composite parts. The described method brings simplicity to the addition of small parts, such as regulatory elements to existing BioBricks. The final product of the PCR assembly is indistinguishable from the standard or 3A BioBrick assembly.

  8. In silico assessment of primers for eDNA studies using PrimerTree and application to characterize the biodiversity surrounding the Cuyahoga River

    Science.gov (United States)

    Cannon, M. V.; Hester, J.; Shalkhauser, A.; Chan, E. R.; Logue, K.; Small, S. T.; Serre, D.

    2016-03-01

    Analysis of environmental DNA (eDNA) enables the detection of species of interest from water and soil samples, typically using species-specific PCR. Here, we describe a method to characterize the biodiversity of a given environment by amplifying eDNA using primer pairs targeting a wide range of taxa and high-throughput sequencing for species identification. We tested this approach on 91 water samples of 40 mL collected along the Cuyahoga River (Ohio, USA). We amplified eDNA using 12 primer pairs targeting mammals, fish, amphibians, birds, bryophytes, arthropods, copepods, plants and several microorganism taxa and sequenced all PCR products simultaneously by high-throughput sequencing. Overall, we identified DNA sequences from 15 species of fish, 17 species of mammals, 8 species of birds, 15 species of arthropods, one turtle and one salamander. Interestingly, in addition to aquatic and semi-aquatic animals, we identified DNA from terrestrial species that live near the Cuyahoga River. We also identified DNA from one Asian carp species invasive to the Great Lakes but that had not been previously reported in the Cuyahoga River. Our study shows that analysis of eDNA extracted from small water samples using wide-range PCR amplification combined with high-throughput sequencing can provide a broad perspective on biological diversity.

  9. [Effect of a chemical primer on the bond strength of a zirconia ceramic with self-adhesive resin cement].

    Science.gov (United States)

    Zhang, Hong; Jing, Ye; Nie, Rongrong; Meng, Xiangfeng

    2015-10-01

    To evaluate the bond strength and durability of a self-adhesive resin cement with a zirconia ceramic pretreated by a zirconia primer. Zirconia ceramic (Vita Inceram YZ) plates with a thickness of 2.5 mm were fired, polished, and then cleaned. Half of the polished ceramic plates were sandblasted with 50 μm alumina particles at 0.3 MPa for 20 s. The surface compound weight ratios were measured via X-ray fluorescence microscopy. The polished and sandblasted ceramic plates were directly bonded with self-adhesive resin cement (Biscem) or were pretreated by a zirconia primer (Z Primer Plus) before bonding with Biscem. The specimens of each test group were divided into two subgroups (n=10) and subjected to the shear test after 0 and 10,000 thermal cycles. The data were analyzed via three-way ANOVA. After air abrasion, 8.27% weight ratio of alumina attached to the zirconia surface. Compared with air abrasion, primer treatment more significantly improved the primary resin bond strength of the zirconia ceramic. The primary resin bond strength of the zirconia ceramic with no primer treatment was not affected by thermocycling (P>0.05). However, the primary resin bond strength of the zirconia ceramic with primer treatment was significantly decreased by thermocycling (Pzirconia ceramics. However, the bond interface of the primer is not stable and rapidly degraded during thermocycling.

  10. Detection of Xanthomonas arboricola pv. pruni by PCR using primers based on DNA sequences related to the hrp genes.

    Science.gov (United States)

    Park, So Yeon; Lee, Young Sun; Koh, Young Jin; Hur, Jae-Sun; Jung, Jae Sung

    2010-10-01

    Efficient control of Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot on stone fruit, requires a sensitive and reliable diagnostic tool. A PCR detection method that utilizes primers to target the hrp gene cluster region was developed in this study. The nucleotide sequence of the PCR product amplified with primers specific for the hrp region of the xanthomonads and genomic DNA of X. arboricola pv. pruni was determined, and the sequence was aligned with that of X. campestris pv. campestris, which was obtained from the GenBank database. On the basis of the sequence of the amplified hrp region, a PCR primer set of XapF/R specific to X. arboricola pv. pruni was designed. This primer set yielded a 243-bp product from the genomic DNA of X. aboricola pv. pruni strains, but no products from other 21 strains of Xanthomonas or from two epiphytic bacterial species. Southern blot hybridization with the probe derived from the PCR product with the primer set and X. aboricola pv. pruni DNA confirmed the PCR results. The Xap primer system was successfully applied to detect the pathogen from infected peach fruits. When it was applied in field samples, the primer set was proved as a reliable diagnostic tool for specific detection of X. aboricola pv. pruni from peach orchards.

  11. Detection of N2O-producing fungi in environment using nitrite reductase gene (nirK)-targeting primers.

    Science.gov (United States)

    Chen, Huaihai; Yu, Fangbo; Shi, Wei

    2016-12-01

    Fungal denitrification has been increasingly investigated, but its community ecology is poorly understood due to the lack of culture-independent tools. In this work, four pairs of nirK-targeting primers were designed and evaluated for primer specificity and efficiency using thirty N2O-producing fungal cultures and an agricultural soil. All primers amplified nirK from fungi and soil, but their efficiency and specificity were different. A primer set, FnirK_F3/R2 amplified ∼80 % of tested fungi, including Aspergillus, Fusarium, Penicillium, and Trichoderma, as compared to ∼40-70 % for other three primers. The nirK fragments of fungal and soil DNA amplified by FnirK_F3/R2 were phylogenetically related to denitrifying fungi in the orders Eurotiales, Hypocreales, and Sordariales; and clone sequences were also distributed in the clusters of Chaetomium, Metarhizium, and Myceliophthora that were uncultured from soil in our previous work. This proved the wide-range capability of primers for amplifying diverse denitrifying fungi from environment. However, our primers and recently-developed other primers amplified bacterial nirK from soil and this co-amplification of fungal and bacterial nirK was theoretically discussed. The FnirK_F3/R2 was further compared with published primers; results from clone libraries demonstrated that FnirK_F3/R2 was more specifically targeted on fungi and had broader taxonomical coverage than some others. Copyright © 2016 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  12. Barcoding the kingdom Plantae: new PCR primers for ITS regions of plants with improved universality and specificity.

    Science.gov (United States)

    Cheng, Tao; Xu, Chao; Lei, Li; Li, Changhao; Zhang, Yu; Zhou, Shiliang

    2016-01-01

    The internal transcribed spacer (ITS) of nuclear ribosomal DNA is one of the most commonly used DNA markers in plant phylogenetic and DNA barcoding analyses, and it has been recommended as a core plant DNA barcode. Despite this popularity, the universality and specificity of PCR primers for the ITS region are not satisfactory, resulting in amplification and sequencing difficulties. By thoroughly surveying and analysing the 18S, 5.8S and 26S sequences of Plantae and Fungi from GenBank, we designed new universal and plant-specific PCR primers for amplifying the whole ITS region and a part of it (ITS1 or ITS2) of plants. In silico analyses of the new and the existing ITS primers based on these highly representative data sets indicated that (i) the newly designed universal primers are suitable for over 95% of plants in most groups; and (ii) the plant-specific primers are suitable for over 85% of plants in most groups without amplification of fungi. A total of 335 samples from 219 angiosperm families, 11 gymnosperm families, 24 fern and lycophyte families, 16 moss families and 17 fungus families were used to test the performances of these primers. In vitro PCR produced similar results to those from the in silico analyses. Our new primer pairs gave PCR improvements up to 30% compared with common-used ones. The new universal ITS primers will find wide application in both plant and fungal biology, and the new plant-specific ITS primers will, by eliminating PCR amplification of nonplant templates, significantly improve the quality of ITS sequence information collections in plant molecular systematics and DNA barcoding. © 2015 John Wiley & Sons Ltd.

  13. Effect of dentin primer on shear bond strength of composite resin to moist and dry enamel.

    Science.gov (United States)

    Jain, P; Stewart, G P

    2000-01-01

    The etched enamel-composite resin bond is the most reliable bond known to us. Moisture and dentin primers are the two most important variables that can interfere with this bond. This study investigated the effect of dentin primer on bond strengths of composite resin to moist and dry enamel. One hundred freshly extracted molar teeth were used for shear bond strength testing. The teeth were mounted in phenolic rings with an approximal enamel surface exposed. The exposed enamel surface on each tooth was flattened using 320- 400- and 600-grit silicon carbide papers and etched using 34-38% phosphoric acid gel. The teeth were then divided into 10 groups (n = 10). Four groups were assigned to each of the two dentin bonding systems, Scotchbond Multi-Purpose and OptiBond FL. Two groups were assigned to the single-bottle bonding agent (Single Bond). Each bonding system was tested on moist and dry enamel. OptiBond FL and Scotchbond MP were tested with and without the use of primer. All samples were thermocycled and tested in shear. Fracture analysis was performed using a binocular microscope. For scanning electron microscopy, approximal samples of enamel (1 mm thick) were flattened, etched, and bonded with and without primer on moist and dry enamel. A 1 mm-thick layer of Z100 was bonded to the specimens, which were then immersed in 10% HCl for 24 hours to dissolve the enamel. The specimens were viewed under a scanning electron microscope. Results indicated that the use of primer on dry enamel did not significantly affect (P > 0.05) shear bond strengths for the two bonding systems, Scotchbond MP (primed 24.10 +/- 4.83 MPa, unprimed 29.57 +/- 7.49 MPa) and OptiBond FL (primed 26.82 +/- 4.44, unprimed 25.66 +/- 2.95). However, the use of primer was found to be essential on moist enamel to obtain acceptable bond strengths with both Scotchbond MP (primed 25.61 +/- 10.29 MPa, unprimed 3.26 +/- 0.95 MPa) and OptiBond FL (primed 30.28 +/- 3.49 MPa, unprimed 8.37 +/- 3.31 MPa

  14. Primers for low-copy nuclear genes in Metrosideros and cross-amplification in Myrtaceae1

    Science.gov (United States)

    Pillon, Yohan; Johansen, Jennifer; Sakishima, Tomoko; Chamala, Srikar; Barbazuk, W. Brad; Stacy, Elizabeth A.

    2014-01-01

    • Premise of the study: Primers were developed to amplify low-copy nuclear genes in Hawaiian Metrosideros (Myrtaceae). • Methods and Results: Data from a pooled 454 Titanium run of the partial transcriptomes of four Metrosideros taxa were used to identify the loci of interest. Ten exon-primed intron-crossing (EPIC) markers were amplified and sequenced directly with success in Metrosideros, as well as in a representative selection of Myrtaceae, including Syzygium, Psidium, and Melaleuca for most of the markers. The loci amplified ranged between 500 and 1100 bp, and up to 117 polymorphic sites were observed within an individual gene alignment. Two introns contained microsatellites in some of the species. • Conclusions: These novel primer pairs should be useful for phylogenetic analysis and population genetics of a broad range of Myrtaceae, particularly the diverse fleshy-fruited tribes Syzygieae and Myrteae. PMID:25309837

  15. Primers for low-copy nuclear genes in Metrosideros and cross-amplification in Myrtaceae.

    Science.gov (United States)

    Pillon, Yohan; Johansen, Jennifer; Sakishima, Tomoko; Chamala, Srikar; Barbazuk, W Brad; Stacy, Elizabeth A

    2014-10-01

    Primers were developed to amplify low-copy nuclear genes in Hawaiian Metrosideros (Myrtaceae). • Data from a pooled 454 Titanium run of the partial transcriptomes of four Metrosideros taxa were used to identify the loci of interest. Ten exon-primed intron-crossing (EPIC) markers were amplified and sequenced directly with success in Metrosideros, as well as in a representative selection of Myrtaceae, including Syzygium, Psidium, and Melaleuca for most of the markers. The loci amplified ranged between 500 and 1100 bp, and up to 117 polymorphic sites were observed within an individual gene alignment. Two introns contained microsatellites in some of the species. • These novel primer pairs should be useful for phylogenetic analysis and population genetics of a broad range of Myrtaceae, particularly the diverse fleshy-fruited tribes Syzygieae and Myrteae.

  16. STITCHER: A web resource for high-throughput design of primers for overlapping PCR applications.

    Science.gov (United States)

    O'Halloran, Damien M

    2015-06-01

    Overlapping PCR is routinely used in a wide number of molecular applications. These include stitching PCR fragments together, generating fluorescent transcriptional and translational fusions, inserting mutations, making deletions, and PCR cloning. Overlapping PCR is also used for genotyping by traditional PCR techniques and in detection experiments using techniques such as loop-mediated isothermal amplification (LAMP). STITCHER is a web tool providing a central resource for researchers conducting all types of overlapping PCR experiments with an intuitive interface for automated primer design that's fast, easy to use, and freely available online (http://ohalloranlab.net/STITCHER.html). STITCHER can handle both single sequence and multi-sequence input, and specific features facilitate numerous other PCR applications, including assembly PCR, adapter PCR, and primer walking. Field PCR, and in particular, LAMP, offers promise as an on site tool for pathogen detection in underdeveloped areas, and STITCHER includes off-target detection features for pathogens commonly targeted using LAMP technology.

  17. Human DNA polymerase θ grasps the primer terminus to mediate DNA repair.

    Science.gov (United States)

    Zahn, Karl E; Averill, April M; Aller, Pierre; Wood, Richard D; Doublié, Sylvie

    2015-04-01

    DNA polymerase θ protects against genomic instability via an alternative end-joining repair pathway for DNA double-strand breaks. Polymerase θ is overexpressed in breast, lung and oral cancers, and reduction of its activity in mammalian cells increases sensitivity to double-strand break-inducing agents, including ionizing radiation. Reported here are crystal structures of the C-terminal polymerase domain from human polymerase θ, illustrating two potential modes of dimerization. One structure depicts insertion of ddATP opposite an abasic-site analog during translesion DNA synthesis. The second structure describes a cognate ddGTP complex. Polymerase θ uses a specialized thumb subdomain to establish unique upstream contacts to the primer DNA strand, including an interaction with the 3'-terminal phosphate from one of five distinctive insertion loops. These observations demonstrate how polymerase θ grasps the primer to bypass DNA lesions or extend poorly annealed DNA termini to mediate end-joining.

  18. Resin adhesion strengths to zirconia ceramics after primer treatment with silane coupling monomer or oligomer.

    Science.gov (United States)

    Okada, Masahiro; Inoue, Kazusa; Irie, Masao; Taketa, Hiroaki; Torii, Yasuhiro; Matsumoto, Takuya

    2017-09-26

    Resin bonding to zirconia ceramics is difficult to achieve using the standard methods for conventional silica-based dental ceramics, which employ silane coupling monomers as primers. The hypothesis in this study was that a silane coupling oligomer -a condensed product of silane coupling monomers- would be a more suitable primer for zirconia. To prove this hypothesis, the shear bond strengths between a composite resin and zirconia were compared after applying either a silane coupling monomer or oligomer. The shear bond strength increased after applying a non-activated ethanol solution of the silane coupling oligomer compared with that achieved when applying the monomer. Thermal treatment of the zirconia at 110°C after application of the silane coupling agents was essential to improve the shear bond strength between the composite resin cement and zirconia.

  19. Book Review: The Basics of Digital Forensics: The Primer for Getting Started in Digital Forensics

    Directory of Open Access Journals (Sweden)

    Stephen Larson

    2014-03-01

    Full Text Available Sammons, John. (2012. The Basics of Digital Forensics: The Primer for Getting Started in Digital Forensics. Waltham, MA: Syngress, 208 pages, Print Book ISBN: 9781597496612.eBook ISBN : 9781597496629. Print: US $29.95. eBook: US$20.97. Includes exercises, case studies, references, and index.Reviewed by Stephen Larson, PhD. Assistant Professor, Slippery Rock University of PAThe Basics of Digital Forensics: The Primer for Getting Started in Digital Forensics is well-named–it really is very basic. And it should be, as the book’s intended audience includes entry-level digital forensics professionals and complimentary fields such as law enforcement, legal, and general information security. Though the copyright is 2012, some of the data is from 2009, and there is mention of estimates for 2010.(see PDF for full review

  20. Mineralogical Transformation and Electrochemical Nature of Magnesium-Rich Primers during Natural Weathering

    Directory of Open Access Journals (Sweden)

    Shashi S. Pathak

    2014-07-01

    Full Text Available Magnesium-rich primers (MgRP have generated great interest as a promising alternative to chromium-based primers for the protection of aluminum substrates but their performance during exterior exposure has not been well documented. This paper focuses on the evaluation of MgRP during natural weathering to gain insight into its mineralogical phase transformation and electrochemical nature. Control studies were conducted on Mg and AA2024-T3 coupons. The results indicate that Mg particles in MgRP transform into a variety of hydroxide, carbonate, and hydroxy carbonates. During natural weathering, CO2 inhibited the dissolution of both Mg and AA2024-T3 as a result of protective carbonate layer formation in the coating.

  1. El arte de cozina de Diego Granado (1599), primer libro de cocina en lengua castellana

    OpenAIRE

    Redondo Buey, Patricia

    2014-01-01

    El Siglo de Oro es un periodo histórico que abarca desde el Renacimiento del siglo XVI hasta el Barroco del siglo XVII, durante el cual se publicó el primer tratado gastronómico de España. En este trabajo científico haremos un estudio meticuloso y minucioso sobre lo que se considera el primer recetario del Siglo de Oro español y así analizar las fuentes primarias de la cocina española, cosa que nunca se había hecho. Departamento de Pediatría e Inmunología, Obstetricia y Ginecología, Nutric...

  2. Crecimiento longitudinal posnatal del primer metatarsiano. [Longitudinal postnatal growth of the first metatarsal bone

    OpenAIRE

    Julio J. Masquijo; Victoria Allende; Luis M. Herrera; Armando Torres Gómez

    2014-01-01

    Introducción: si bien el crecimiento prenatal y posnatal del pie ha sido documentado hace varios años, el crecimiento longitudinal del primer metatarsiano en particular no ha sido estudiado previamente. El objetivo del estudio es determinar el patrón de crecimiento longitudinal posnatal de este hueso y compararlo con el del pie y los huesos largos del miembro inferior. Materiales y Métodos: mediante una búsqueda informatizada, se identificaron pacientes

  3. Designing clinical interviewing training courses for psychiatric residents: a practical primer for interviewing mentors.

    Science.gov (United States)

    Shea, Shawn Christopher; Green, Ron; Barney, Christine; Cole, Stephen; Lapetina, Graciana; Baker, Bruce

    2007-06-01

    This article provides a no-nonsense primer for the design of effective clinical interviewing programs and the use of interviewing mentors. Principles for smoothly integrating educational tools such as direct observation, role-playing, the use of videotaping and facilic supervision are described. A sample core curriculum syllabus is provided including a comprehensive listing of core educational goals with regard to clinical interviewing skills.

  4. PIPEMicroDB: microsatellite database and primer generation tool for pigeonpea genome

    Science.gov (United States)

    Sarika; Arora, Vasu; Iquebal, M. A.; Rai, Anil; Kumar, Dinesh

    2013-01-01

    Molecular markers play a significant role for crop improvement in desirable characteristics, such as high yield, resistance to disease and others that will benefit the crop in long term. Pigeonpea (Cajanus cajan L.) is the recently sequenced legume by global consortium led by ICRISAT (Hyderabad, India) and been analysed for gene prediction, synteny maps, markers, etc. We present PIgeonPEa Microsatellite DataBase (PIPEMicroDB) with an automated primer designing tool for pigeonpea genome, based on chromosome wise as well as location wise search of primers. Total of 123 387 Short Tandem Repeats (STRs) were extracted from pigeonpea genome, available in public domain using MIcroSAtellite tool (MISA). The database is an online relational database based on ‘three-tier architecture’ that catalogues information of microsatellites in MySQL and user-friendly interface is developed using PHP. Search for STRs may be customized by limiting their location on chromosome as well as number of markers in that range. This is a novel approach and is not been implemented in any of the existing marker database. This database has been further appended with Primer3 for primer designing of selected markers with left and right flankings of size up to 500 bp. This will enable researchers to select markers of choice at desired interval over the chromosome. Furthermore, one can use individual STRs of a targeted region over chromosome to narrow down location of gene of interest or linked Quantitative Trait Loci (QTLs). Although it is an in silico approach, markers’ search based on characteristics and location of STRs is expected to be beneficial for researchers. Database URL: http://cabindb.iasri.res.in/pigeonpea/ PMID:23396298

  5. Applied Ecosystem Analysis - - a Primer : EDT the Ecosystem Diagnosis and Treatment Method.

    Energy Technology Data Exchange (ETDEWEB)

    Lestelle, Lawrence C.; Mobrand, Lars E.

    1996-05-01

    The aim of this document is to inform and instruct the reader about an approach to ecosystem management that is based upon salmon as an indicator species. It is intended to provide natural resource management professionals with the background information needed to answer questions about why and how to apply the approach. The methods and tools the authors describe are continually updated and refined, so this primer should be treated as a first iteration of a sequentially revised manual.

  6. Avulsión de canino y subluxación del primer premolar superiores derechos

    OpenAIRE

    Berástegui, Esther

    1996-01-01

    Se presenta un caso clínico de avulsión de canino y subluxación del primer remolar, superiores derechos, secundario a traumatismo por piedra lanzada al aire. El tiempo extraoral fue de cuatro horas en medio seco. Se trató con reimplante, ferulización y tratamiento endodóncico. Los controles posteriores a los cuatro años del tratamiento mostraron la evolución favorable del caso.

  7. Novel primers for complete mitochondrial cytochrome b gene sequencing in mammals.

    Science.gov (United States)

    Naidu, Ashwin; Fitak, Robert R; Munguia-Vega, Adrian; Culver, Melanie

    2012-03-01

    Sequence-based species identification relies on the extent and integrity of sequence data available in online databases such as GenBank. When identifying species from a sample of unknown origin, partial DNA sequences obtained from the sample are aligned against existing sequences in databases. When the sequence from the matching species is not present in the database, high-scoring alignments with closely related sequences might produce unreliable results on species identity. For species identification in mammals, the cytochrome b (cyt b) gene has been identified to be highly informative; thus, large amounts of reference sequence data from the cyt b gene are much needed. To enhance availability of cyt b gene sequence data on a large number of mammalian species in GenBank and other such publicly accessible online databases, we identified a primer pair for complete cyt b gene sequencing in mammals. Using this primer pair, we successfully PCR amplified and sequenced the complete cyt b gene from 40 of 44 mammalian species representing 10 orders of mammals. We submitted 40 complete, correctly annotated, cyt b protein coding sequences to GenBank. To our knowledge, this is the first single primer pair to amplify the complete cyt b gene in a broad range of mammalian species. This primer pair can be used for the addition of new cyt b gene sequences and to enhance data available on species represented in GenBank. The availability of novel and complete gene sequences as high-quality reference data can improve the reliability of sequence-based species identification. © 2011 Blackwell Publishing Ltd.

  8. An anti-steroidogenic inhibitory primer pheromone in male sea lamprey (Petromyzon marinus)

    Science.gov (United States)

    Chung-Davidson, Yu-Wen; Wang, Huiyong; Bryan, Mara B.; Wu, Hong; Johnson, Nicholas S.; Li, Weiming

    2013-01-01

    Reproductive functions can be modulated by both stimulatory and inhibitory primer pheromones released by conspecifics. Many stimulatory primer pheromones have been documented, but relatively few inhibitory primer pheromones have been reported in vertebrates. The sea lamprey male sex pheromone system presents an advantageous model to explore the stimulatory and inhibitory primer pheromone functions in vertebrates since several pheromone components have been identified. We hypothesized that a candidate sex pheromone component, 7α, 12α-dihydroxy-5α-cholan-3-one-24-oic acid (3 keto-allocholic acid or 3kACA), exerts priming effects through the hypothalamic-pituitary-gonadal (HPG) axis. To test this hypothesis, we measured the peptide concentrations and gene expressions of lamprey gonadotropin releasing hormones (lGnRH) and the HPG output in immature male sea lamprey exposed to waterborne 3kACA. Exposure to waterborne 3kACA altered neuronal activation markers such as jun and jun N-terminal kinase (JNK), and lGnRH mRNA levels in the brain. Waterborne 3kACA also increased lGnRH-III, but not lGnRH-I or -II, in the forebrain. In the plasma, 3kACA exposure decreased all three lGnRH peptide concentrations after 1 h exposure. After 2 h exposure, 3kACA increased lGnRHI and -III, but decreased lGnRH-II peptide concentrations in the plasma. Plasma lGnRH peptide concentrations showed differential phasic patterns. Group housing condition appeared to increase the averaged plasma lGnRH levels in male sea lamprey compared to isolated males. Interestingly, 15α-hydroxyprogesterone (15α-P) concentrations decreased after prolonged 3kACA exposure (at least 24 h). To our knowledge, this is the only known synthetic vertebrate pheromone component that inhibits steroidogenesis in males.

  9. Low Volatile Organic Compound Containing Wash Primer for Letterkenny Army Depot

    Science.gov (United States)

    2012-09-01

    is working with Sustainable Painting Operations for the Total Army to test chromate containing wash primers with lower VOC emissions compared to the...PRF-23377 has an extremely low viscosity and required two coats to prevent sagging and running. Also, Letterkenny painters have had no experience...test for 20 cycles. Afterward, these panels were visually examined for surface defects and signs of galvanic corrosion. 26 Figure 5. Sample

  10. Facebook targeted advertisement for research recruitment: A primer for nurse researchers.

    Science.gov (United States)

    Carter-Harris, Lisa

    2016-11-01

    Recruiting participants for research studies can be challenging and costly. Innovative recruitment methods are needed. Facebook targeted advertisement offers a low-cost alternative to traditional methods that has been successfully used in research study recruitment. This primer offers nurse researchers a method utilizing social media as a recruitment tool and details Facebook targeted advertisement for research recruitment. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. FONZIE: An optimized pipeline for minisatellite marker discovery and primer design from large sequence data sets

    Directory of Open Access Journals (Sweden)

    Balesdent Marie-Hélène

    2010-11-01

    Full Text Available Abstract Background Micro-and minisatellites are among the most powerful genetic markers known to date. They have been used as tools for a large number of applications ranging from gene mapping to phylogenetic studies and isolate typing. However, identifying micro-and minisatellite markers on large sequence data sets is often a laborious process. Results FONZIE was designed to successively 1 perform a search for markers via the external software Tandem Repeat Finder, 2 exclude user-defined specific genomic regions, 3 screen for the size and the percent matches of each relevant marker found by Tandem Repeat Finder, 4 evaluate marker specificity (i.e., occurrence of the marker as a single copy in the genome using BLAST2.0, 5 design minisatellite primer pairs via the external software Primer3, and 6 check the specificity of each final PCR product by BLAST. A final file returns to users all the results required to amplify markers. A biological validation of the approach was performed using the whole genome sequence of the phytopathogenic fungus Leptosphaeria maculans, showing that more than 90% of the minisatellite primer pairs generated by the pipeline amplified a PCR product, 44.8% of which showed agarose-gel resolvable polymorphism between isolates. Segregation analyses confirmed that the polymorphic minisatellites corresponded to single-locus markers. Conclusion FONZIE is a stand-alone and user-friendly application developed to minimize tedious manual operations, reduce errors, and speed up the search for efficient minisatellite and microsatellite markers departing from whole-genome sequence data. This pipeline facilitates the integration of data and provides a set of specific primer sequences for PCR amplification of single-locus markers. FONZIE is freely downloadable at: http://www.versailles-grignon.inra.fr/bioger/equipes/leptosphaeria_maculans/outils_d_analyses/fonzie

  12. Myalgic Encephalomyelitis/Chronic Fatigue Syndrome Diagnosis and Management in Young People: A Primer

    OpenAIRE

    Rowe, Peter C.; Underhill, Rosemary A.; Friedman, Kenneth J.; Alan Gurwitt; Medow, Marvin S.; Malcolm S. Schwartz; Nigel Speight; Stewart, Julian M.; Rosamund Vallings; Katherine S. Rowe

    2017-01-01

    Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex disease that affects children and adolescents as well as adults. The etiology has not been established. While many pediatricians and other health-care providers are aware of ME/CFS, they often lack essential knowledge that is necessary for diagnosis and treatment. Many young patients experience symptoms for years before receiving a diagnosis. This primer, written by the International Writing Group for Pediatric ME/CFS, p...

  13. Variety discrimination of Tigridia pavonia (L.f.) DC. assesed by different length RAPD primers

    OpenAIRE

    José Luis Piña-Escutia

    2010-01-01

    Tigridia pavonia (L.f.) DC. is one of the important phytogenetic resources of México. This species is used as ornamental, food and medicinal purposes. Despite its ornamental and economic potential, there is little information about the genetic variability. In this study, randomly amplified polymorphic DNA (RAPD) primers of 10, 15 and 20 bases were used to assess the level of genetic variation among nine botanical varieties of Tigridia pavoniacollected in three localities within State of Méxic...

  14. New mitochondrial and nuclear primers for the Mediterranean marine bivalve Pinna nobilis

    OpenAIRE

    Sanna, D.; G.L. DEDOLA; Scarpa, F.; Lai, T.; Cossu, P.; Curini-Galletti, M.; Francalacci, P.; Casu, M

    2014-01-01

    Pinna nobilis is the largest endemic Mediterranean marine bivalve. During past centuries, various human activities led to the regression of its populations. As a consequence of stringent standards of protection, demographic expansions are currently reported in many sites. We designed a set of four mitochondrial- and two nuclear- specific PCR-primers with the aim to provide molecular tools to gather new insights into the genetic variability of this species. A total of 54 specimens were sampled...

  15. The potential of novel primers and universal adhesives to bond to zirconia.

    Science.gov (United States)

    Amaral, Marina; Belli, Renan; Cesar, Paulo Francisco; Valandro, Luiz Felipe; Petschelt, Anselm; Lohbauer, Ulrich

    2014-01-01

    To investigate the adhesive potential of novel zirconia primers and universal adhesives to surface-treated zirconia substrates. Zirconia bars were manufactured (3.0mm×3.0mm×9.0mm) and treated as follows: no treatment (C); air abrasion with 35μm alumina particles (S); air abrasion with 30μm silica particles using one of two systems (Rocatec or SilJet) and; glazing (G). Groups C and S were subsequentially treated with one of the following primers or adhesives: ZP (Z-Prime Plus), AZ (AZ Primer); MP (Monobond Plus); SU (ScotchBond Universal) and; EA (an Experimental Adhesive). Groups Rocatec and SilJet were silanized prior to cementation. Samples form group G were further etched and silanized. Bars were cemented (Multilink) onto bars of a silicate-based ceramic (3.0mm×3.0mm×9.0mm) at 90° angle, thermocycled (2.500 cycles, 5-55°C, 30s dwell time), and tested in tensile strength test. Failure analysis was performed on fractured specimens to measure the bonding area and crack origin. Specimens from group C did not survive thermocycling, while CMP, CSU and CEA groups survived thermocycling but rendered low values of bond strength. All primers presented a better bond performance after air abrasion with Al2O3 particles. SilJet was similar to Rocatec, both presenting the best bond strength results, along with SMP, SSU and CEA. G promoted intermediate bond strength values. Failure mode was predominately adhesive on zirconia surface combined to cohesive of the luting agent. Universal adhesives (MP, SU, EA) may be a considerable alternative for bonding to zirconia, but air abrasion is still previously required. Air abrasion with silica particles followed by silane application also presented high bond strength values. Copyright © 2013 Elsevier Ltd. All rights reserved.

  16. Identification of Pork Adulteration in Processed Meat Products Using the Developed Mitochondrial DNA-Based Primers

    OpenAIRE

    Ha, Jimyeong; Kim, Sejeong; Lee, Jeeyeon; Lee, Soomin; Lee, Heeyoung; Choi, Yukyung; Oh, Hyemin; Yoon, Yohan

    2017-01-01

    The identification of pork in commercially processed meats is one of the most crucial issues in the food industry because of religious food ethics, medical purposes, and intentional adulteration to decrease production cost. This study therefore aimed to develop a method for the detection of pork adulteration in meat products using primers specific for pig mitochondrial DNA. Mitochondrial DNA sequences for pig, cattle, chicken, and sheep were obtained from GenBank and aligned. The 294-bp mitoc...

  17. Review of "Conducting Educational Research: A primer for teachers and administrators"

    OpenAIRE

    Keirl, S; Edwards-Leis, Christine E

    2011-01-01

    Book Title: Conducting Educational Research: A primer for teachers and administrators\\ud Book Authors: Morrell, P.D. and Carroll, J.B.\\ud Publisher: Sense Publishers\\ud Reviewers: Steve Keirl (Goldsmiths, University of London) and Christine Edwards-Leis (St Mary's University College)\\ud ISBN: 978-94-6091-202-3 (paperback)\\ud ISBN: 978-94-6091-204-7 (e-book)

  18. A primer on governance and performance in small and medium-sized enterprises

    OpenAIRE

    Yacuzzi, Enrique

    2005-01-01

    This paper is a primer on corporate performance, corporate governance, and their interrelationships and measurement systems, with particular focus on Small and Medium- Sized Enterprises (SMEs). This is the first report of a larger on going research project. In the domain of performance measurement the paper describes the trend from financial to non-financial measures, as well as a taxonomy of measures and the impact of the TQM movement on measurement practices. In the domain of governance, go...

  19. Construction of "small-intelligent" focused mutagenesis libraries using well-designed combinatorial degenerate primers.

    Science.gov (United States)

    Tang, Lixia; Gao, Hui; Zhu, Xuechen; Wang, Xiong; Zhou, Ming; Jiang, Rongxiang

    2012-03-01

    Site-saturation mutagenesis is a powerful tool for protein optimization due to its efficiency and simplicity. A degenerate codon NNN or NNS (K) is often used to encode the 20 standard amino acids, but this will produce redundant codons and cause uneven distribution of amino acids in the constructed library. Here we present a novel "small-intelligent" strategy to construct mutagenesis libraries that have a minimal gene library size without inherent amino acid biases, stop codons, or rare codons of Escherichia coli by coupling well-designed combinatorial degenerate primers with suitable PCR-based mutagenesis methods. The designed primer mixture contains exactly one codon per amino acid and thus allows the construction of small-intelligent mutagenesis libraries with one gene per protein. In addition, the software tool DC-Analyzer was developed to assist in primer design according to the user-defined randomization scheme for library construction. This small-intelligent strategy was successfully applied to the randomization of halohydrin dehalogenases with one or two randomized sites. With the help of DC-Analyzer, the strategy was proven to be as simple as NNS randomization and could serve as a general tool to efficiently randomize target genes at positions of interest.

  20. Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA

    Energy Technology Data Exchange (ETDEWEB)

    Mosley, Ralph T.; Edwards, Thomas E.; Murakami, Eisuke; Lam, Angela M.; Grice, Rena L.; Du, Jinfa; Sofia, Michael J.; Furman, Philip A.; Otto, Michael J. (Pharmasset); (Emerald)

    2012-08-01

    The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory {beta}-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory {beta}-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.

  1. Conserved primers for DNA barcoding historical and modern samples from New Zealand and Antarctic birds.

    Science.gov (United States)

    Patel, Selina; Waugh, John; Millar, Craig D; Lambert, David M

    2010-05-01

    Our ability to DNA barcode the birds of the world is based on the effective amplification and sequencing of a 648 base pair (bp) region of the mitochondrial cytochrome c oxidase (COI or cox1) gene. For many geographic regions the large numbers of vouchered specimens necessary for the construction of a DNA barcoding database have already been collected and are available in museums and other institutions. However, many of these specimens are old (>20 years) and are stored as either fixed study skins or dried skeletons. DNA extracted from such historical samples is typically degraded and, generally, only short DNA fragments can be recovered from such specimens making the recovery of the barcoding region as a single fragment difficult. We report two sets of conserved primers that allow the amplification of the entire DNA barcoding region in either three or five overlapping fragments. These primer sets allow the recovery of DNA barcodes from valuable historical specimens that in many cases are unique in that they are unable or unlikely to be collected again. We also report three new primers that in combination allow the effective amplification from modern samples of the entire DNA barcoding region as a single DNA fragment for 17 orders of Southern Hemisphere birds. © 2009 Blackwell Publishing Ltd.

  2. A new set of primers for COI amplification from freshwater microcrustaceans.

    Science.gov (United States)

    Prosser, Sean; Martínez-Arce, Arely; Elías-Gutiérrez, Manuel

    2013-11-01

    Despite the contribution of DNA barcoding towards understanding the biodiversity and distribution of species, the success of COI amplification has been quite variable when it comes to freshwater zooplankton (Elías-Gutiérrez & Valdez-Moreno 2008; Jeffery et al. 2011). Some genera of microcrustaceans seem to be more difficult to amplify than others. For example, Macrothrix, Scapholeberis, Diaphanosoma and cyclopoids have yielded limited results. Among several possible reasons for the inability to barcode freshwater microcrustaceans is that there does not exist a specific set of primers for COI amplification. To this end, we developed a zooplankton - specific set of primers, which significantly increased average amplification success (20% increase). With these primers, we observed an overall success of over 70% for Sididae and Chydoridae, and more than 80% for Daphniidae, Moinidae, Bosminidae, Macrothricidae, Ilyocryptidae and Diaptomidae. We also demonstrate a simple alteration to a common specimen fixation method that increases the overall recovery of barcodes from freshwater zooplankton. Collectively, we believe our results will greatly aid the recovery of barcodes from these difficult groups. © 2013 John Wiley & Sons Ltd.

  3. Meeting the challenge of DNA barcoding Neotropical amphibians: polymerase chain reaction optimization and new COI primers.

    Science.gov (United States)

    Lyra, Mariana L; Haddad, Célio F B; de Azeredo-Espin, Ana Maria L

    2017-09-01

    Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here, we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1, we were able to recover COI sequences for 100% of the species analysed (N = 161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species. © 2016 John Wiley & Sons Ltd.

  4. Thermal stability of quadruplex primers for highly versatile isothermal DNA amplification.

    Science.gov (United States)

    Mathias, Jordan; Okyere, Robert; Lomidze, Levan; Gvarjaladze, David; Musier-Forsyth, Karin; Kankia, Besik

    2014-01-01

    Quadruplex priming amplification (QPA) allows isothermal amplification of nucleic acids with improved yield and simplified detection. This assay is based on a DNA quadruplex, GGGTGGGTGGGTGGG (G3T), which in the presence of specific cations possesses unusually high thermal stability. QPA employs truncated G3T sequences as primers, which upon polymerase elongation, self-dissociate from the binding site and allow the next round of priming without thermal unfolding of amplicons. The rate of amplification strongly depends on the thermal stability of the primer/primer binding site (PBS) complex and to date QPA has been demonstrated to work over a narrow temperature range. To expand the capabilities of QPA, in the present study, we studied the fold and thermodynamic properties of the wild-type G3T and variants containing sequence modifications or extensions at the 5'-end. Circular dichroism studies demonstrate that the substitution of thymidines by other nucleotides or GC addition at the 5'-end does not change the parallel fold of G3T. Thermal unfolding experiments revealed that purine bases incorporated at loop positions and 5'-end dinucleotide extension significantly destabilize the quadruplex, while loop pyrimidines have almost no effect. Overall, the results of these studies suggest that linear isothermal QPA can be performed over a wide temperature range to accommodate both thermophilic and mesophilic DNA polymerases. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. A set of 100 chloroplast DNA primer pairs to study population genetics and phylogeny in monocotyledons.

    Directory of Open Access Journals (Sweden)

    Nora Scarcelli

    Full Text Available Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC. Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding (exon and non-coding regions (intron and intergenic spacer. They span the different chloroplast regions: 72 are located in the LSC, 13 in the Small Single Copy (SSC and 15 in the Inverted Repeat region (IR. Amplification and sequencing were tested in 13 species of Monocotyledons: Dioscorea abyssinica, D. praehensilis, D. rotundata, D. dumetorum, D. bulbifera, Trichopus sempervirens (Dioscoreaceae, Phoenix canariensis, P. dactylifera, Astrocaryum scopatum, A. murumuru, Ceroxylon echinulatum (Arecaceae, Digitaria excilis and Pennisetum glaucum (Poaceae. The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR. We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA are located in the SSC. Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies.

  6. Degenerate PCR primer design for the specific identification of rhinovirus C.

    Science.gov (United States)

    Nam, Young Ran; Lee, Uk; Choi, Han Seok; Lee, Kyoung Jin; Kim, Nari; Jang, Yong Ju; Joo, Chul Hyun

    2015-03-01

    Human rhinovirus (HRV)-A and -B is a common cause of upper respiratory tract infections. Recently, a third species, HRV-C, was categorized based on molecular typing studies. The results showed that the HRV-C genome had diverged from that of HRV-A and -B. Despite its late identification, increasing evidence suggests that HRV-C causes more severe pathogenic infections than HRV-A or -B; however, a large amount of epidemiological data is required to confirm this association in different clinical settings. Consequently, a simple and rapid method for identifying HRV-C is required to expedite such epidemiological studies. Here, two degenerate primer sets (HEV and HRVC) were designed based on bioinformatic analyses. The HEV set targeting the fifth IRES domain sequence within the 5'-UTR, which is highly conserved among enteroviruses, was designed to detect all enteroviruses, whereas the HRVC set, which targeted the VP2 coding region, was designed to detect HRV-C alone. Both primer sets were tested against a panel of standard enteroviruses and clinical lavage samples. HEV detected all enteroviruses tested whereas HRVC was specific for HRV-C. Although the primer design strategy was confirmed with a limited number of samples, extensive tests are required to be applied in clinical settings. Copyright © 2014 Elsevier B.V. All rights reserved.

  7. Analysis of telomerase activity based on a spired DNA tetrahedron TS primer.

    Science.gov (United States)

    Li, Yan; Wen, Yanli; Wang, Lele; Liang, Wen; Xu, Li; Ren, Shuzhen; Zou, Ziying; Zuo, Xiaolei; Fan, Chunhai; Huang, Qing; Liu, Gang; Jia, Nengqin

    2015-05-15

    The development of sensitive telomerase biosensors is hindered by the restricted accessibility of telomere strand (TS) primer and the limited enzyme reaction space, which is mainly confined by the vertical distance. In this work, we designed an electrochemical telomerase biosensor based on a spired DNA tetrahedron TS primer (STTS). By adding a rigid dsDNA spire onto the top of the DNA tetrahedron, we successfully regulated the distance between the TS primer and the surface, and thus greatly facilitated the telomerase elongation on surface. The signal-to-noise ratio was 2 times higher than TSP without the spire structure. The limit of detection was calculated to be lower than 10 HeLa cells, which is at least 2 magnitudes lower than other surface extension-based electrochemical telomerase sensors without amplification. The practicability of STTS sensor was also demonstrated by analysing various other cell lines including cancer cells, stem cells of high telomerase activity and somatic cells of low telomerase activity. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. Identifying krill eggs in the central California current using novel multiplex PCR primers: Applications and limitations

    Science.gov (United States)

    Carrion, C. N.; Slesinger, E.; Marinovic, B.

    2016-02-01

    Euphausiids, otherwise known as krill, are an important link between primary producers and higher trophic levels within the central California current upwelling system. Euphausia pacifica and Thysanoessa spinifera, two of the most common euphausiid species along the central California coast, are both broadcast spawners and have some overlap in habitat, e.g. near marine life hotspots like the Monterey Bay and Gulf of Farallones. Species composition of euphausiid egg population within these regions is currently unknown. Distinct morphological differences between their eggs are lost once the egg dies or is preserved via formalin, alcohol, or freezing. In this project we designed genus specific DNA primers (mtCOI) for use in a multiplex PCR to distinguish among spawned euphausiid eggs of Euphausia spp. and Thysanoessa spp. in central California current surface waters. Effective and ineffective application of primers in a multiplex versus single-plex PCR is discussed, with an emphasis on primer design limitations in reference to the available barcoded regions of mitochondrial cytochrome oxidase subunit I (mtCOI) for each species in GenBank. This new protocol expands current monitoring efforts into sampling a non-swimming portion of the population which has the potential to improve euphausiid biomass estimates.

  9. Remineralization Property of an Orthodontic Primer Containing a Bioactive Glass with Silver and Zinc

    Directory of Open Access Journals (Sweden)

    Seung-Min Lee

    2017-10-01

    Full Text Available White spot lesions (WSLs are irreversible damages in orthodontic treatment due to excessive etching or demineralization by microorganisms. In this study, we conducted a mechanical and cell viability test to examine the antibacterial properties of 0.2% and 1% bioactive glass (BAG and silver-doped and zinc-doped BAGs in a primer and evaluated their clinical applicability to prevent WSLs. The microhardness statistically significantly increased in the adhesive-containing BAG, while the other samples showed no statistically significant difference compared with the control group. The shear bond strength of all samples increased compared with that of the control group. The cell viability of the control and sample groups was similar within 24 h, but decreased slightly over 48 h. All samples showed antibacterial properties. Regarding remineralization property, the group containing 0.2% of the samples showed remineralization properties compared with the control group, but was not statistically significant; further, the group containing 1% of the samples showed a significant difference compared with the control group. Among them, the orthodontic bonding primer containing 1% silver-doped BAG showed the highest remineralization property. The new orthodontic bonding primer used in this study showed an antimicrobial effect, chemical remineralization effect, and WSL prevention as well as clinically applicable properties, both physically and biologically.

  10. Una experiencia con QSB+ en Matemáticas de primer curso

    Directory of Open Access Journals (Sweden)

    Ordás Amo, Pilar

    2001-01-01

    Full Text Available Nuestro objetivo con este trabajo es presentar una experiencia que hemos llevado a cabo con los alumnos de primer curso, en la asignatura de Matemáticas, de las Licenciaturas en Ciencias Económicas y Administración y Dirección de Empresas, durante los cursos 1999/2000 y 2000/2001. El propósito de la experiencia es que los alumnos de primer curso vean una parte de la optimización matemática, como es la programación lineal, y el método del Símplex, a través de un software informático sencillo como es el QSB+, en el aula de ordenadores. Para llevar a cabo la experiencia, se añadió una hora lectiva al horario de los alumnos implicados y de los profesores de Matemáticas de primer curso, con plan nuevo (plan 99, durante el segundo semestre, de forma totalmente voluntaria para los alumnos, aunque la materia explicada en estas clases “extras” formaba parte del examen final de la asignatura. El nombre oficial de la experiencia fue Seminario de Programación Lineal, y tuvo una duración aproximada de quince horas lectivas.

  11. Crecimiento longitudinal posnatal del primer metatarsiano. [Longitudinal postnatal growth of the first metatarsal bone

    Directory of Open Access Journals (Sweden)

    Julio J. Masquijo

    2014-10-01

    Full Text Available Introducción: si bien el crecimiento prenatal y posnatal del pie ha sido documentado hace varios años, el crecimiento longitudinal del primer metatarsiano en particular no ha sido estudiado previamente. El objetivo del estudio es determinar el patrón de crecimiento longitudinal posnatal de este hueso y compararlo con el del pie y los huesos largos del miembro inferior. Materiales y Métodos: mediante una búsqueda informatizada, se identificaron pacientes <18 años de edad con radiografías informadas como “normal” por el radiólogo. Se analizó una muestra de 886 pacientes divididos en 18 grupos según la edad (0-11 meses, 1 año, 2 años, etc. y el sexo. El análisis de las imágenes se realizó con un software de imágenes Kodak Carestream PACS. Resultados: el largo promedio en el primer grupo fue de 19,91 mm (3,20; 15,22-25,62. El largo promedio en el último grupo fue de 66,13 mm (5,33; 52,50-77,18. La tasa de crecimiento anual fue de 2,71 mm. La edad promedio al momento del cierre de la fisis fue de 14.85 años (± 1.64 para los varones y 14.77 años (± 3.63 para las niñas. Conclusión: el crecimiento del primer metatarsiano acompaña el crecimiento longitudinal del pie, pero no el de los huesos largos del miembro inferior. Las curvas de crecimiento del primer metatarsiano descritas en este artículo pueden ser aplicadas en patologías que afectan el desarrollo del pie o que requieren cirugía de corrección sobre el primer metatarsiano, o se las puede emplear como estándar de referencia en futuros estudios.

  12. Telecommunications Primer

    Directory of Open Access Journals (Sweden)

    Joseph Becker

    2013-05-01

    Full Text Available A description of modern telecommunications devices which can be useful in inter-library communications, including their capacities, types of signals and carriers. Described are telephone lines, radio broadcasting, coaxial cable, microwave and communications satellites. This article, and the one following, were presented as tutorials by the author's to participants at the American Library Association's Atlantic City Convention on June 25, 1969.

  13. Hyperelasticity primer

    CERN Document Server

    Hackett, Robert M

    2016-01-01

    This book introduces the subject of hyperelasticity in a concise manner mainly directed to students of solid mechanics who have a familiarity with continuum mechanics.  It focuses on important introductory topics in the field of nonlinear material behavior and presents a number of example problems and solutions to greatly aid the student in mastering the difficulty of the subject and gaining necessary insight.  Professor Hackett delineates the concepts and applications of hyperelasticity in such a way that a new student of the subject can absorb the intricate details without having to wade through excessively complicated formulations.  The book further presents significant review material on intricately related subjects such as tensor calculus and introduces some new formulations.

  14. MATLAB Primer

    CERN Document Server

    Davis, Timothy A

    2010-01-01

    The eighth edition of this popular book provides a hands-on introduction to MATLAB[registered] that can be used at the undergraduate level. The new edition features the use of MATLAB 8.0, which will be introduced to the market in March 2010. It covers object-oriented programming in MATLAB and the improvements that have been made to the MATLAB desktop and programming tools. There is a new chapter that discusses MATLAB Central, a supporting website where users can exchange files, blogs, and links. In addition, the appendix of help topics has been updated to reflect only the most frequently used

  15. Analisis psicometrico de la escala autoeficacia en conductas de cuidado de la salud fisica en universitarios de primer ingreso

    National Research Council Canada - National Science Library

    Ornelas, Martha; Blanco, Humberto; Rodriguez, Judith M; Flores, Francisco J

    2011-01-01

    .... La muestra fue de 2089 sujetos; 902 mujeres y 1187 hombres, alumnos de primer ingreso a las licenciaturas que se ofrecen en la Universidad Autonoma de Chihuahua en Mexico, con una edad media de 18.23 anos...

  16. Razonamiento cientifico y conocimientos conceptuales de mecanica: un diagnostico de alumnos de primer ingreso a licenciaturas en ingenieria

    National Research Council Canada - National Science Library

    Rodriguez, Maria D; Mena, Daniel A; Rubio, Carlos M

    2010-01-01

    Se presenta un diagnostico del grado de razonamiento cientifico de cinco grupos de estudiantes de primer ingreso a licenciaturas en ingenieria aplicando la prueba de aula de razonamiento cientifico de Lawson...

  17. Prevalencia y factores asociados al consumo de citrato de sildenafil en estudiantes universitarios colombianos, durante el primer semestre de 2013

    National Research Council Canada - National Science Library

    Javier Martínez-Torres; Ingrid Katherine Duarte-Corredor; Gaby Johanna García-Vásquez; Gissely Dimarhy Jáuregui-Rodríguez

    2015-01-01

    ... a la disminución de enfermedades de transmisión sexual y embarazos no deseados. Determinar la prevalencia del consumo de Citrato de Sildenafil y sus factores asociados en estudiantes universitarios, durante el primer semestre de 2013...

  18. Molecular diagnosis of cryptococcal meningitis in cerebrospinal fluid: comparison of primer sets for Cryptococcus neoformans and Cryptococcus gattii species complex

    Directory of Open Access Journals (Sweden)

    Marilena dos Anjos Martins

    2015-01-01

    Conclusions: These data suggest that the CN4/CN5 primer set was highly sensitive for the identification of C. neoformans/C. gattii species complex in cerebrospinal fluid samples from patients with clinical suspicion of cryptococcal meningitis.

  19. PLASMA POLYMER FILMS AS ADHESION PROMOTING PRIMERS FOR ALUMINUM. PART II: STRENGTH AND DURABILITY OF LAP JOINTS

    Science.gov (United States)

    Plasma polymerized hexamethyldisiloxane (HMDSO) films (~800 A in thickness) were deposited onto 6111-T4 aluminum substrates in radio frequency and microwave powered reactors and used as primers for structural adhesive bonding. Processing variables such as substrate pre-treatment,...

  20. Pre-treatment of radicular dentin by self-etch primer containing chlorhexidine can improve fiber post bond durability.

    Science.gov (United States)

    Zhou, Jianfeng; Yang, Xu; Chen, Li; Liu, Xiaoqiang; Ma, Lin; Tan, Jianguo

    2013-01-01

    We evaluated whether the pre-treatment of radicular dentin by ED Primer containing different concentrations of chlorhexidine can improve the bond durability of fiber post to radicular dentin. Experimental ED primers containing different concentrations of chlorhexidine (0%, 0.5% and 1.0%) were prepared. Thirty extracted maxillary anterior teeth were divided into 3 groups, each group corresponding to different chlorhexidine concentrations. Fiber posts were cemented in endodontically treated teeth with experimental ED primers and Panavia F. The bonded teeth were transversally sectioned into six slices and then were processed for thin slice push-out test 24 h later or after 18-months water storage. Eighteen-month storage resulted in significant bond strength reduction of all groups (pchlorhexidine into ED primer can extend the bond longevity of fiber post to radicular dentin.

  1. Çoklu Primer Tümörler - Tek Merkez Deneyimi

    Directory of Open Access Journals (Sweden)

    Gökşen İnanç İmamoğlu

    2017-12-01

    Full Text Available Amaç: Onkolojik hastalıkların erken tanı ve tedavisinde yeni gelişmeler hayatta kalma oranlarının artmasına neden olsa da, artmış sağ kalım oranlarına bağlı olarak gelişen uzun takipler sırasında ikinci primer maligniteler ortaya çıkabilmektedir. İkincil primer tümörlerin gelişimi için birçok faktör vardır. En önemlisi, yaşlı hastalar ın uzun vadede kanserojenlere maruz kalma olasılıkları daha yüksektir. Çoklu primer tümörler, genellikle iki malignite tanısı arasındaki zaman çizelgesine bağlı olarak metakron veya senkron olarak görülür. Senkron hastalıklar sıklıkla benzer karsinojenlere maruz kalma sonucu oluşsa da, metakron olanlar daha çok primer tümörün tedavisine bağlı advers etkilerle ilişkili olabilir. Bu tek merkezli çalışma, Ocak 2007 ile Aralık 2016 arasında multipl primer tümörlü hastaların klinikopatolojik özelliklerini araştırmayı amaçladı ve bunlardan 20'si senkron, 36'sı metakron olarak toplam 56 hasta dahil edildi. En yaygın kanser çiftlerinin erkeklerde kolon-akciğer ve prostat-mesane, kadınlarda meme-kolon ve meme-tiroid olduğu tespit edilmiştir. Yöntemler: Ocak 2007 ile Aralık 2017 tarihleri arasında merkezimizde takip edilen ÇPT’ lü hastaların dosyaları retrospektif olarak incelendi, 56 hastada multiple primer tümör olduğu tespit edildi. Hastaların cinsiyetler, yaşları tespit edildi. Tümörün hangi organlarda oluştuğu, ne zaman geliştiği, bulunabilen etyolojik veriler, sağ kalım oranları araştırıldı. Tüm istatistiksel analizler Package for Social Sciences (SPSS v 15.0, SPSS Inc., Chicago, IL, USA ile yapıldı. Sonuç: Senkron hastalıklar genellikle benzer kanserojenlere maruz kalmanın bir sonucu olarak ortaya çıkarken, metakronöz hastalıkların primer tümörlerin tedavisinin yan etkileri ile ilişkili olması muhtemeldir

  2. Effect of Metal Primers on Bond Strength of a Composite Resin to Nickel-Chrome Metal Alloy.

    Science.gov (United States)

    Nima, Gabriel; Ferreira, Paulo Vitor Campos; Paula, Andreia Bolzan de; Consani, Simonides; Giannini, Marcelo

    2017-01-01

    This study evaluated the effects of three metal primers and one multi-mode adhesive system on the shear bond strength (SBS) of a flowable composite resin to nickel-chrome metal alloy (Ni-Cr). Ninety plates were cast from Ni-Cr and divided in nine groups (n=10). The surfaces were sandblasted with Al2O3 and primed with three adhesive primers: Alloy Primer (AP), Universal Primer (TP) and RelyX Ceramic Primer (CP), and a multi-mode adhesive (Scotchbond Universal, SU). The Adper Single Bond Plus (SB) and SU adhesives were also combined with adhesive primers. Control group did not have any surface treatment. The groups were: AP, AP+SB, AP+SU, TP+SB, TP+SU, CP+SB, CP+SU and SU. Composite cylinders were built on alloy surface. After 24 h, half the specimens were subjected to SBS and the other half to thermal cycling before testing. Data were analyzed by two-way ANOVA and Tukey's test (a=0.05). Failure modes were assessed by SEM observation. Higher SBS were obtained with AP and TP combined with adhesives at 24 h and the lowest one for control group. Thermocycling reduced SBS for AP, CP+SU and SU. Combination between TP and SU resulted in the highest SBS after the thermocycling. TP groups showed all types of failures and high incidence of mixed failures. The use of AP and UP metal primers before application of SU and SB adhesive systems increased the SBS of composite to Ni-Cr. These combinations between metal primers and adhesives had the highest SBS after thermocycling.

  3. The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

    DEFF Research Database (Denmark)

    Binladen, Jonas; Gilbert, M Thomas P; Bollback, Jonathan P

    2007-01-01

    to the correct source once sequencing anomalies are accounted for (miss-assignment ratebias in the distribution of the differently tagged...... primers that is dependent on the 5' nucleotide of the tag. In particular, primers 5' labelled with a cytosine are heavily overrepresented among the final sequences, while those 5' labelled with a thymine are strongly underrepresented. A weaker bias also exists with regards to the distribution...

  4. Bonding durability of using self-etching primer with 4-META/ MMA-TBB resin cement to bond orthodontic brackets.

    Science.gov (United States)

    Saito, Kayo; Sirirungrojying, Somsak; Meguro, Daijiro; Hayakawa, Tohru; Kasai, Kazutaka

    2005-03-01

    This study determines the bonding durability when a self-etching primer is used with Superbond C&B (a 4-methacryloxyethyl trimellitate anhydride/methyl methacrylate-tri-n-butyl borane resin) to bond orthodontic brackets to enamel. Thermocycling test was used to assess bonding durability. Metal brackets were bonded to the phosphoric acid-etched or Megabond self-etching primer-treated enamel surface of human premolars using Superbond C&B. The shear bond strengths were measured after immersion in water at 37 degrees C for 24 hours or after 2000 or 5000 cycles of thermocycling between 5 degrees C and 55 degrees C. Data were analyzed using 2-way analysis of variance and Fisher's protected least significant difference test for multiple comparisons. There was no significant difference in shear bond strength between phosphoric acid and Megabond self-etching primer treatment before the thermocycling test. After 2000 and 5000 thermal cycles, significant decreases in shear bond strength were observed with phosphoric acid etching. On the contrary, no significant differences in shear bond strength were observed after 2000 and 5000 thermal cycles with Megabond self-etching primer. The adhesive remnant indices were not significantly different between phosphoric acid etching and Megabond self-etching primer treatment either before or after thermal cycles. This study suggested that when used with Superbond C&B in bonding orthodontic brackets, Megabond self-etching primer is superior to phosphoric acid as an enamel preparation agent in providing durable bond strength.

  5. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability.

    Science.gov (United States)

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization.

  6. Effect of clearfil protect bond and transbond plus self-etch primer on shear bond strength of orthodontic brackets

    Science.gov (United States)

    Raji, S. Hamid; Ghorbanipour, Reza; Majdzade, Fateme

    2011-01-01

    Background: The aim of this study was to evaluate the shear bond strength of an antimicrobial and fluoride-releasing self-etch primer (clearfil protect bond) and compare it with transbond plus self-etch primer and conventional acid etching and priming system. Materials and Methods: Forty-eight extracted human premolars were divided randomly to three groups. In group 1, the teeth were bonded with conventional acid etching and priming method. In group 2, the teeth were bonded with clearfil protect bond self-etch primer, and transbond plus self-etch primer was used to bond the teeth in group 3. The samples were stored in 37°C distilled water and thermocycled. Then, the SBS of the sample was evaluated with Zwick testing machine. Descriptive statistics and the analysis of variances (ANOVA) and Tukey's test and Kruskal-Wallis were used to analyze the data. Results: The results of the ANOVA showed that the mean of group 3 was significantly lower than that of other groups. Most of the sample showed a pattern of failure within the adhesive resin. Conclusion: The shear bond strength of clearfil protect bond and transbond plus self-etch primer was enough for bonding the orthodontic brackets. The mode of failure of bonded brackets with these two self-etch primers is safe for enamel. PMID:23372605

  7. Genome-Wide Characterization of Simple Sequence Repeat (SSR Loci in Chinese Jujube and Jujube SSR Primer Transferability.

    Directory of Open Access Journals (Sweden)

    Jing Xiao

    Full Text Available Chinese jujube (Ziziphus jujuba, an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization.

  8. Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

    Science.gov (United States)

    Xiao, Jing; Zhao, Jin; Liu, Mengjun; Liu, Ping; Dai, Li; Zhao, Zhihui

    2015-01-01

    Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization. PMID:26000739

  9. Effect of the type of acidic monomer on the bond durability of two-bottle type ceramic primer.

    Science.gov (United States)

    Tanimura, Hideki

    2017-01-01

    Ceramic primers consisting of γ-methacryloxypropyl trimethoxysilane (γ-MPS) and either 4-methacryloyloxyethyl trimellitate (4-MET) or 10-methacryloyloxydecyl dihydrogen phosphate (MDP) are useful for facilitating bonding of resin cement to silica-based ceramic surfaces. However, bond stability at the resin-ceramic interface differs among commercial ceramic primers. To determine the ability of 4-MET or MDP to hydrolyze the methoxy group in γ-MPS, the author designed two-bottle experimental ceramic primers comprising γ-MPS solution and an activator solution of 4-MET or MDP. The effects of the type of acidic monomer on contact angle and ceramic bond durability of resin were investigated. MDP and 4-MET promoted chemisorption of γ-MPS on the ceramic surface and enhanced the ceramic bond strength of the resin. However, thermocycling decreased ceramic bond strengths, as reflected by the increased number of bonded specimens that exhibited interfacial resin failure. Bond strength was greater for 4-MET-activated ceramic primer than for the MDP-activated ceramic primer, although most bonded specimens exhibited interfacial resin failure. Degradation behavior differed between the 4-MET-activated and MDP-activated ceramic primers.

  10. A tool for design of primers for microRNA-specific quantitative RT-qPCR. BMC Bioinformatics

    DEFF Research Database (Denmark)

    Busk, Peter Kamp

    2014-01-01

    by this method have been distributed to several labs and used successfully in published studies. Conclusions The software miRprimer is an automatic and easy method for design of functional primers for miR-specific RT-qPCR. The application is available as stand-alone software that will work on the MS Windows...... at a high price and the sequences of the primers are not disclosed. An alternative to commercial assays is to manually design primers but this work is tedious and, hence, not practical for the design of primers for a larger number of targets. Results I have developed the software miRprimer for automatic...... design of primers for the method miR-specific RT-qPCR, which is one of the best performing microRNA qPCR methods available. The algorithm is based on an implementation of the previously published rules for manual design of miR-specific primers with the additional feature of evaluating the propensity...

  11. High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples.

    Directory of Open Access Journals (Sweden)

    Hirokazu Toju

    Full Text Available The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the diversity and ecology of this huge kingdom, DNA barcoding targeting the internal transcribed spacer (ITS region of the nuclear ribosomal repeat has been regarded as a prerequisite procedure. By extensively surveying ITS sequences in public databases, we designed new ITS primers with improved coverage across diverse taxonomic groups of fungi compared to existing primers. An in silico analysis based on public sequence databases indicated that the newly designed primers matched 99% of ascomycete and basidiomycete ITS taxa (species, subspecies or varieties, causing little taxonomic bias toward either fungal group. Two of the newly designed primers could inhibit the amplification of plant sequences and would enable the selective investigation of fungal communities in mycorrhizal associations, soil, and other types of environmental samples. Optimal PCR conditions for the primers were explored in an in vitro investigation. The new primers developed in this study will provide a basis for ecological studies on the diversity and community structures of fungi in the era of massive DNA sequencing.

  12. High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples.

    Science.gov (United States)

    Toju, Hirokazu; Tanabe, Akifumi S; Yamamoto, Satoshi; Sato, Hirotoshi

    2012-01-01

    The kingdom Fungi is estimated to include 1.5 million or more species, playing key roles as decomposers, mutualists, and parasites in every biome on the earth. To comprehensively understand the diversity and ecology of this huge kingdom, DNA barcoding targeting the internal transcribed spacer (ITS) region of the nuclear ribosomal repeat has been regarded as a prerequisite procedure. By extensively surveying ITS sequences in public databases, we designed new ITS primers with improved coverage across diverse taxonomic groups of fungi compared to existing primers. An in silico analysis based on public sequence databases indicated that the newly designed primers matched 99% of ascomycete and basidiomycete ITS taxa (species, subspecies or varieties), causing little taxonomic bias toward either fungal group. Two of the newly designed primers could inhibit the amplification of plant sequences and would enable the selective investigation of fungal communities in mycorrhizal associations, soil, and other types of environmental samples. Optimal PCR conditions for the primers were explored in an in vitro investigation. The new primers developed in this study will provide a basis for ecological studies on the diversity and community structures of fungi in the era of massive DNA sequencing.

  13. PCR primers specific for the genus Tuber reveal the presence of several truffle species in a truffle-ground.

    Science.gov (United States)

    Zampieri, Elisa; Mello, Antonietta; Bonfante, Paola; Murat, Claude

    2009-08-01

    Truffles are hypogeous Ascomycete fungi belonging to the genus Tuber and forming fruiting bodies highly prized for their taste and aroma. The identification of the genus Tuber and its species is important to investigate their ecology and avoid fraud in the food market. As genus-specific primers are not available, the aims of this work were (1) to assess the usefulness of the beta-tubulin gene as a DNA barcoding region for designing Tuber genus-specific primers, (2) to test the primers on a range of fruiting bodies, representing a large part of truffle biodiversity and (3) to check their ecological usefulness, applying them to truffle-ground soil. The new primers designed on the beta-tubulin gene were specific to the Tuber genus in nested PCR. When applied to DNA from soils, they gave a positive signal for 23 of 32 soils. Phylogenetic analysis confirmed that the bands corresponded to Tuber and that at least five Tuber species were present in the truffle-ground. beta-tubulin was found to be a good barcoding region for designing Tuber genus-specific primers, detecting a high Tuber diversity in a natural environment. These primers will be useful for understanding truffle ecology and for practical needs in plantation management.

  14. Typing of human rotaviruses: Nucleotide mismatches between the VP7 gene and primer are associated with genotyping failure

    Directory of Open Access Journals (Sweden)

    Zaman Khalequz

    2005-03-01

    Full Text Available Abstract Background Rotavirus genotyping is performed by using reverse transcription PCR with type-specific-primers. Because the high rotavirus mutation rate generates an extensive genomic variation, different G-type-specific primer sets are applied in different geographical locations. In Bangladesh, a significant proportion (36.9% of the rotavirus strains isolated in 2002 could not be G-typed using the routinely used primer set. To investigate the reason why the strains were untypeable, nucleotide sequencing of the VP7 genes was performed. Results Four nucleotide substitutions at the G1 primer-binding site of the VP7 gene of Bangladeshi G1 rotaviruses rendered a major proportion of circulating strains untypeable using the routine primer set. Using an alternative primer set, we could identify G1 rotaviruses as the most prevalent genotype (44.8%, followed by G9 (21.7%, G2 (15.0% and G4 (13.8%. Conclusion Because of the natural variation in the rotaviral gene sequences, close monitoring of rotavirus genotyping methods is important.

  15. Fatores preditivos da transfusão de concentrado de hemácias em pacientes submetidos a cirurgias eletivas do aparelho digestivo: uma análise interinstitucional Predictive factors associated with packed red cell transfusions in patients submitted to elective surgery of the digestive tract: an inter-institutional analysis

    Directory of Open Access Journals (Sweden)

    Antonio Sergio Barcala Jorge

    2010-01-01

    Full Text Available O objetivo desse estudo foi compreender os fatores determinantes da prática transfusional de concentrado de hemácias em cirurgias eletivas do aparelho digestivo em quatro unidades hospitalares em Montes Claros, Minas Gerais, Brasil. Foi realizado um estudo descritivo, analítico e retrospectivo através do levantamento de dados em prontuários clínicos de quatro unidades hospitalares de onde foram catalogados os dados de pacientes a partir de junho de 2007 a dezembro de 2008, referentes às cirurgias citadas. Os resultados evidenciaram 81 casos, sendo 42% do gênero feminino e 58% do masculino. A idade média foi de 55,5 anos (±19,11 anos. As enfermidades de base reportadas mais comuns foram os processos neoplásicos (42%. Desses 81 pacientes, 38 (47% foram hemotransfundidos no pré-operatório imediato, 28 (18% foram transfundidos no transcirúrgico e 37 (45,7% no pós-operatório imediato. Na análise univariada houve diferenças entre a prática transfusional pré-cirúrgica interinstitucional. Na fase cirúrgica houve relação entre a prática transfusional com a citação de motivos, fator RH (Rhesus, prática institucional e doença de base. Na fase pós-cirúrgica não foram demonstradas relações. Em todas as fases, não houve associação da prática transfusional com os tipos de procedimentos cirúrgicos, com o índice ASA (American Society of Anesthesiology e valores de hemoglobina e hematócrito. Concluindo, esse estudo revelou que a prática transfusional foi heterogênea entre instituições hospitalares, careceu de valores laboratoriais específicos, relacionou-se com a patologia de base mas não com o tipo de procedimento cirúrgico e foi norteada pelo critério de escolha do profissional.The objective of this study was to understand the determinative factors for packed red cell transfusions in elective digestive tract surgeries in four hospital units in Montes Claros, Minas Gerais, Brazil. Retrospective analyses were

  16. A novel photoinduced electron transfer (PET) primer technique for rapid real-time PCR detection of Cryptosporidium spp

    Energy Technology Data Exchange (ETDEWEB)

    Jothikumar, N., E-mail: jin2@cdc.gov; Hill, Vincent R.

    2013-06-28

    Highlights: •Uses a single-labeled fluorescent primer for real-time PCR. •The detection sensitivity of PET PCR was comparable to TaqMan PCR. •Melt curve analysis can be performed to confirm target amplicon production. •Conventional PCR primers can be converted to PET PCR primers. -- Abstract: We report the development of a fluorescently labeled oligonucleotide primer that can be used to monitor real-time PCR. The primer has two parts, the 3′-end of the primer is complimentary to the target and a universal 17-mer stem loop at the 5′-end forms a hairpin structure. A fluorescent dye is attached to 5′-end of either the forward or reverse primer. The presence of guanosine residues at the first and second position of the 3′ dangling end effectively quenches the fluorescence due to the photo electron transfer (PET) mechanism. During the synthesis of nucleic acid, the hairpin structure is linearized and the fluorescence of the incorporated primer increases several-fold due to release of the fluorescently labeled tail and the absence of guanosine quenching. As amplicons are synthesized during nucleic acid amplification, the fluorescence increase in the reaction mixture can be measured with commercially available real-time PCR instruments. In addition, a melting procedure can be performed to denature the double-stranded amplicons, thereby generating fluorescence peaks that can differentiate primer dimers and other non-specific amplicons if formed during the reaction. We demonstrated the application of PET-PCR for the rapid detection and quantification of Cryptosporidium parvum DNA. Comparison with a previously published TaqMan® assay demonstrated that the two real-time PCR assays exhibited similar sensitivity for a dynamic range of detection of 6000–0.6 oocysts per reaction. PET PCR primers are simple to design and less-expensive than dual-labeled probe PCR methods, and should be of interest for use by laboratories operating in resource

  17. A set of primers for analyzing chloroplast DNA diversity in Citrus and related genera.

    Science.gov (United States)

    Cheng, Yunjiang; de Vicente, M Carmen; Meng, Haijun; Guo, Wenwu; Tao, Nengguo; Deng, Xiuxin

    2005-06-01

    Chloroplast simple sequence repeat (cpSSR) markers in Citrus were developed and used to analyze chloroplast diversity of Citrus and closely related genera. Fourteen cpSSR primer pairs from the chloroplast genomes of tobacco (Nicotiana tabacum L.) and Arabidopsis were found useful for analyzing the Citrus chloroplast genome (cpDNA) and recoded with the prefix SPCC (SSR Primers for Citrus Chloroplast). Eleven of the 14 primer pairs revealed some degree of polymorphism among 34 genotypes of Citrus, Fortunella, Poncirus and some of their hybrids, with polymorphism information content (PIC) values ranging from 0.057 to 0.732, and 18 haplotypes were identified. The cpSSR data were analyzed with NTSYS-pc software, and the genetic relationships suggested by the unweighted pair group method based on arithmetic means (UPGMA) dendrogram were congruent with previous taxonomic investigations: the results showed that all samples fell into seven major clusters, i.e., Citrus medica L., Poncirus, Fortunella, C. ichangensis Blanco, C. reticulata Swingle, C. aurantifolia (Christm.) Swingle and C. grandis (L.) Osbeck. The results of previous studies combined with our cpSSR analyses revealed that: (1) Calamondin (C. madurensis Swingle) is the result of hybridization between kumquat (Fortunella) and mandarin (C. reticulata), where kumquat acted as the female parent; (2) Ichang papeda (C. ichangensis) has a unique taxonomic status; and (3) although Bendiguangju mandarin (C. reticulata) and Satsuma mandarin (C. reticulata) are similar in fruit shape and leaf morphology, they have different maternal parents. Bendiguangju mandarin has the same cytoplasm as sweet orange (C. sinensis), whereas Satsuma mandarin has the cytoplasm of C. reticulata. Seventeen PCR products from SPCC1 and 21 from SPCC11 were cloned and sequenced. The results revealed that mononucleotide repeats as well as insertions and deletions of small segments of DNA were associated with SPCC1 polymorphism, whereas polymorphism

  18. Microleakage of self-etching primers after thermal and flexural load cycling.

    Science.gov (United States)

    Kubo, S; Yokota, H; Sata, Y; Hayashi, Y

    2001-06-01

    To evaluate the adhesive properties of a one-bottle self-etching primer system. 150 wedge-shaped cervical cavities on bovine teeth were restored with Clearfil Liner Bond 2 (LB), Clearfil Liner Bond 2V (LV) or Clearfil SE Bond (SE), according to the manufacturer's instructions. Twenty specimens of each adhesive system were finished 15 mins after light curing and 30 specimens were finished after a 24-hr storage period in water. From each group, 10 restorations were immediately immersed in 0.5% basic fuchsin solution and kept there for 24 hrs to examine microleakage. The other 10 restorations were thermocycled (5-60 degrees C, 15 s dwell time, 5,000 cycles), and then immersed in the dye solution. The remaining 10 specimens of the 24-hr storage group were subjected to flexural load cycling (0.5 mm labio-lingual displacement at the incisal edge, 10,000 cycles, 1 cps) prior to immersion in the dye solution. The data was analyzed using the Mann-Whitney U-test and the Kruskal-Wallis test. The tensile bond strengths of the adhesive systems to bovine enamel and dentin were also determined. The data was analyzed using the Student's t-test and ANOVA. In addition, SEM examinations were made to evaluate the effects of self-etching primers on enamel and dentin surfaces. LV and SE showed significantly better marginal sealing than LB (Pintegrity of SE did not deteriorate even after immediate finishing, thermal stresses or flexural loads. There were no significant differences in bond strengths among the adhesive systems tested. All adhesive systems showed similar bond strengths to enamel and dentin. The enamel etching patterns using LV and SE systems were obscure and difficult to assess. Although the smear plugs were not fully removed, no smear layer was observed on the treated dentin surfaces, regardless of the self-etching primer system used. Clearfil SE bond could possibly improve the clinical performance of cervical cavities.

  19. Analysis of ancient human DNA and primer contamination: one step backward one step forward.

    Science.gov (United States)

    Deguilloux, Marie-France; Ricaud, Séverine; Leahy, Rachael; Pemonge, Marie-Hélène

    2011-07-15

    The analysis of DNA from archaeological human remains is plagued by a unique set of methodological problems concerning contamination with modern exogenous DNA. Through an original approach, we propose complementary methods to identify all potential sources of contamination and complete guidelines for the validation of ancient human sequences. The study presented was conducted on non-European human samples (Polynesian and Amerindian) which were collected with all precautions during excavation. This permitted us to distinguish without ambiguity authentic and contaminant sequences. The samples' origins and histories were perfectly known, allowing us to trace all potential contamination sources and to determine the efficiency of precautions followed during all steps of the study. The data obtained confirm that precautions taken during sampling effectively prevent contamination. However, we demonstrate that human contamination can also be introduced during genetic analyses even if all precautions are strictly followed. Indeed, numerous human contaminations were detected in template-PCR products and negative controls, resulting in a striking diversity of contaminant mitochondrial DNA sequences. We argue that this contamination partly derives from the primers. To our knowledge, no previous experiment has been performed to investigate primers as a possible source of human contamination despite the fact that this specific type of contamination poses a real problem in terms of validating ancient human DNA studies. Finally, we confirm that the detection of contaminants in negative controls is clearly related to the number of PCR cycles used. This study enhances our understanding of contamination processes and confirms that, in reality, an absolutely contamination-free situation cannot be obtained. As a consequence, we propose improvements to the guidelines usually followed in the field in order to take the highly probable contamination of PCR reagents, including primers, into

  20. Recolectores, verificadores y reflexivos: perfiles de la competencia informacional en estudiantes universitarios de primer semestre

    Directory of Open Access Journals (Sweden)

    Harold Castañeda-Peña

    2010-01-01

    Full Text Available Artículo de investigación que explora perfiles de la competencia informacional en estudiantes universitarios de primer semestre, a partir de un concepto renovado de competencia informacional desde la perspectiva sociocultural, donde se entiende perfil como una práctica habitual que es situada y variada. Se analiza el caso de 285 estudiantes provenientes de dos universidades colombianas, por medio de un instrumento observacional (cuestionario de perfil, protocolos en voz alta y entrevistas. Se encuentra que el 55% de los estudiantes de primer año de una universidad con carreras profesionales tiende a recolectar información y que el 78% de los estudiantes de primer año de una universidad con carreras tecnológicas tiende a contrastar y verificar información, en tanto que sólo entre 3% y 4% tiende a manejar la información críticamente. Se discute que, al asumir una tarea académica, estos estudiantes vinculan sus prácticas de competencia informacional a sus propias historias de vida y escolares, y que la edad y los antecedentes académicos parecen influir en tales prácticas. Los casos analizados se ubican dentro de perfiles de competencia informacional: recolectores, verificadores y reflexivos. Estos perfiles no son fijos, sino más bien fluidos, y se concretan de manera diferente según la tarea académica. Se recomienda realizar estudios de perfiles informacionales en estudiantes tanto de secundaria como universitarios, para diseñar políticas educativas sobre competencia informacional.