Designing libraries of chimeric proteins using SCHEMA recombination and RASPP

SCHEMA is a method for designing libraries of novel proteins by recombination of homologous sequences. The goal is to maximize the number of folded proteins while simultaneously generating significant sequence diversity. Here, we use the RASPP algorithm to identify optimal SCHEMA designs for shuffling contiguous elements of sequence. To exemplify the method, SCHEMA is used to recombine five fungal cellobiohydrolases (CBH1s) to produce a library of more than 390,000 novel CBH1 sequences

The Drosophila Anion Exchanger (DAE) lacks a detectable interaction with the spectrin cytoskeleton

<p>Abstract</p> <p>Background</p> <p>Current models suggest that the spectrin cytoskeleton stabilizes interacting ion transport proteins at the plasma membrane. The human erythrocyte anion exchanger (AE1) was the first membrane transport protein found to be associated with the spectrin cytoskeleton. Here we evaluated a conserved anion exchanger from Drosophila (DAE) as a marker for studies of the downstream effects of spectrin cytoskeleton mutations.</p> <p>Results</p> <p>Sequence comparisons established that DAE belongs to the SLC4A1-3 subfamily of anion exchangers that includes human AE1. Striking sequence conservation was observed in the C-terminal membrane transport domain and parts of the N-terminal cytoplasmic domain, but not in the proposed ankyrin-binding site. Using an antibody raised against DAE and a recombinant transgene expressed in <it>Drosophila </it>S2 cells DAE was shown to be a 136 kd plasma membrane protein. A major site of expression was found in the stomach acid-secreting region of the larval midgut. DAE codistributed with an infolded subcompartment of the basal plasma membrane of interstitial cells. However, spectrin did not codistribute with DAE at this site or in anterior midgut cells that abundantly expressed both spectrin and DAE. Ubiquitous knockdown of DAE with dsRNA eliminated antibody staining and was lethal, indicating that DAE is an essential gene product in <it>Drosophila</it>.</p> <p>Conclusions</p> <p>Based on the lack of colocalization and the lack of sequence conservation at the ankyrin-binding site, it appears that the well-characterized interaction between AE1 and the spectrin cytoskeleton in erythrocytes is not conserved in <it>Drosophila</it>. The results establish a pattern in which most of the known interactions between the spectrin cytoskeleton and the plasma membrane in mammals do not appear to be conserved in <it>Drosophila</it>.</p

Bed bug deterrence

A recent study in BMC Biology has determined that the immature stage of the bed bug (the nymph) signals its reproductive status to adult males using pheromones and thus avoids the trauma associated with copulation in this species. The success of this nymphal strategy of deterrence is instructive. Against the background of increasing problems with bed bugs, this research raises the question whether pheromones might be used to control them

Cross-sectional associations between sleep duration, sedentary time, physical activity, and adiposity indicators among Canadian preschool-aged children using compositional analyses

Abstract Background Sleep duration, sedentary behaviour, and physical activity are three co-dependent behaviours that fall on the movement/non-movement intensity continuum. Compositional data analyses provide an appropriate method for analyzing the association between co-dependent movement behaviour data and health indicators. The objectives of this study were to examine: (1) the combined associations of the composition of time spent in sleep, sedentary behaviour, light-intensity physical activity (LPA), and moderate- to vigorous-intensity physical activity (MVPA) with adiposity indicators; and (2) the association of the time spent in sleep, sedentary behaviour, LPA, or MVPA with adiposity indicators relative to the time spent in the other behaviours in a representative sample of Canadian preschool-aged children. Methods Participants were 552 children aged 3 to 4 years from cycles 2 and 3 of the Canadian Health Measures Survey. Sedentary time, LPA, and MVPA were measured with Actical accelerometers (Philips Respironics, Bend, OR USA), and sleep duration was parental reported. Adiposity indicators included waist circumference (WC) and body mass index (BMI) z-scores based on World Health Organization growth standards. Compositional data analyses were used to examine the cross-sectional associations. Results The composition of movement behaviours was significantly associated with BMI z-scores (p = 0.006) but not with WC (p = 0.718). Further, the time spent in sleep (BMI z-score: γ sleep  = −0.72; p = 0.138; WC: γ sleep  = −1.95; p = 0.285), sedentary behaviour (BMI z-score: γ SB  = 0.19; p = 0.624; WC: γ SB  = 0.87; p = 0.614), LPA (BMI z-score: γ LPA  = 0.62; p = 0.213, WC: γ LPA  = 0.23; p = 0.902), or MVPA (BMI z-score: γ MVPA  = −0.09; p = 0.733, WC: γ MVPA  = 0.08; p = 0.288) relative to the other behaviours was not significantly associated with the adiposity indicators. Conclusions This study is the first to use compositional analyses when examining associations of co-dependent sleep duration, sedentary time, and physical activity behaviours with adiposity indicators in preschool-aged children. The overall composition of movement behaviours appears important for healthy BMI z-scores in preschool-aged children. Future research is needed to determine the optimal movement behaviour composition that should be promoted in this age group

Mental health screening using the MINI test in medical students

Introducción: Los trastornos de salud mental constituyen un problema prevalente en alumnos de educación superior, siendo los estudiantes de medicina una población especialmente vulnerable. Objetivos: Determinar la frecuencia de trastornos de salud mental en los alumnos de una escuela de medicina. Diseño: Estudio descriptivo, transversal. Institución: Escuela de Medicina, Universidad Católica Santo Toribio de Mogrovejo, Chiclayo, Lambayeque, Perú. Participantes: Alumnos de una escuela de medicina. Intervenciones: En el semestre académico 2010-I, se evaluó la frecuencia de trastornos de salud mental en los alumnos utilizando el test Mini International Neuropsychiatric Interview (MINI), validado en español, como método de tamizaje. Principales medidas de resultados: Frecuencia de problemas de salud mental. Resultados: Se evaluó 159 estudiantes, 94 del sexo femenino (59,1%) y 65 de sexo masculino (40,8%); la media de la edad fue de 18,6+/- 2,1 años; 35 alumnos (22%) tuvieron al menos un trastorno mental. Los diagnósticos más frecuentes fueron: episodio hipomaniaco pasado (16 alumnos; 10,2%), riesgo suicida (11; 6,9%), trastorno depresivo actual (9; 5,6%), trastorno de angustia actual (8; 5%), agorafobia (8; 5%). En 20 (12,6%) y 11 estudiantes (6,9%), respectivamente, algún profesional de la salud le había diagnosticado previamente ansiedad y depresión. Conclusiones: Los problemas de salud mental fueron frecuentes en esta población de estudiantes, siendo el episodio hipomaniaco pasado, el riesgo suicida y el episodio depresivo actual los más frecuentes.Introduction: Mental health disorders are prevalent in higher education students and medical students are especially vulnerable. Objectives: To determine mental health problems frequency in students of Medicine. Design: Descriptive, transversal study. Setting: School of Medicine, Universidad Catolica Santo Toribio de Mogrovejo, Chiclayo, Lambayeque, Peru. Participants: Medical students. Interventions: During the 2010-I academic semester, frequency of mental health problems were determined using the Mini International Neuropsychiatric Interview (MINI) test, validated in Spanish, as a screening test for mental health. Main outcome measures: Frequency of mental health problems. Results: From 159 students interviewed, 94 were women (59,1%) and 65 men (40,8%). Average age was 18,7+/- 2,1 years; 35 students (22%) had at least one mental disorder. There were 16 (10,2%) students with history of hypomania episode, 11 with suicide risk (6,9%), 9 with current depressive disorder (5,6%), 8 with agoraphobia (4,8%), 8 with current anxiety disorder (4,8%); 20 (12,6%) and 11 (6,9%) students respectively mentioned that a health care provider had previously diagnosed anxiety and depression. Conclusions: Mental health disorders were frequent in these medical students; past hypomania episode, suicidal risk and current depressive disorder were the most frequently diagnosed mental health disorders

Caracterización del HLA en una familia colombiana endogámica con síndrome de Usher

Resumen El síndrome de Usher es una enfermedad autosómica recesiva que se caracteriza por presentar retinitis pigmentosa, hipoacusia neurosensorial congénita y disfunción vestibular. El propósito de este trabajo es realizar la caracterización de hla en una familia colombiana endogámica que presenta síndrome de Usher. La metodología consiste en que con un previo consentimiento informado se realizó una genealogía de la familia y a cuatro pacientes confirmados clínicamente con síndrome de Usher y a cuatro fenotípicamente sanos se les tomó 5 ml de sangre periférica en tubos de venopunción con edta para luego realizar el aislamiento del dna por la técnica de salting out, conservados en buffer te a -8 °C y ajustada la muestra a una concentración de 8 μg/ml. Posteriormente a través de la técnica de pcr-ssp de mediana resolución se caracterizaron los antígenos de hla *a, *b, *drb1 y *dqb1. Los resultados obtenidos indican que la familia oriunda del Departamento del Huila presenta una marcada endogamia detectándose que todos los hermanos afectados, sus padres son hermanos también y una de las parejas a su vez tuvo una niña afectada, por lo que sus abuelos y padres son hermanos. En lo referente al hla, los alelos más frecuentemente encontrados fueron a30 b42 dr1 dq5 y a3 b45 dr12 y dq7, que no están asociados a la enfermedad. Estos resultados sugieren que dada la endogamia que muestra esta familia se presenta una gran acumulación de polimorfismos y mutaciones, por lo que es necesario realizar un proceso de asesoría genética para disminuir el riesgo de recurrencia. Abstract Usher syndrome is an autosomal recessive disease characterized by retinitis pigmentosa, congenital sensorineural hearing loss and vestibular dysfunction. The purpose of this work was to characterize hla in an inbred Colombian family that presents Usher Syndrome. The Methodology consisted in that a genealogy of the family was made and previous informed consent, from four patients clinically confirmed with Usher Syndrome and four phenotypically healthy patients 5 ml of peripheral blood were taken in venipuncture tubes with edta and then the dna isolation was performed with the technique of salting out, preserved in te buffer at -8 °C and adjusted the sample to a concentration of 8 μg/ml. The hla *A, *B, *DRB1 and *DQB1 antigens were then characterized by the medium-resolution pcr-ssp techniqu

Paleo-landscapes of the Northern Patagonian Massif, Argentina

Fil: Aguilera, Emilia Yolanda. Instituto de Geomorfología y Suelos (IGS). Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; ArgentinaFil: Rabassa, Jorge. Laboratorio de Geomorfología y Cuaternario. CADIC. Universidad Nacional de Tierra del Fuego; ArgentinaFil: Aragón, Eugenio. Centro de Investigaciones Geológicas (CIG). Facultad de Ciencias Naturales y Museo. Universidad Nacional de La Plata; Argentin

Caracterización del HLA en una familia colombiana endogámica con síndrome de Usher

Resumen El síndrome de Usher es una enfermedad autosómica recesiva que se caracteriza por presentar retinitis pigmentosa, hipoacusia neurosensorial congénita y disfunción vestibular. El propósito de este trabajo es realizar la caracterización de hla en una familia colombiana endogámica que presenta síndrome de Usher. La metodología consiste en que con un previo consentimiento informado se realizó una genealogía de la familia y a cuatro pacientes confirmados clínicamente con síndrome de Usher y a cuatro fenotípicamente sanos se les tomó 5 ml de sangre periférica en tubos de venopunción con edta para luego realizar el aislamiento del dna por la técnica de salting out, conservados en buffer te a -8 °C y ajustada la muestra a una concentración de 8 μg/ml. Posteriormente a través de la técnica de pcr-ssp de mediana resolución se caracterizaron los antígenos de hla *a, *b, *drb1 y *dqb1. Los resultados obtenidos indican que la familia oriunda del Departamento del Huila presenta una marcada endogamia detectándose que todos los hermanos afectados, sus padres son hermanos también y una de las parejas a su vez tuvo una niña afectada, por lo que sus abuelos y padres son hermanos. En lo referente al hla, los alelos más frecuentemente encontrados fueron a30 b42 dr1 dq5 y a3 b45 dr12 y dq7, que no están asociados a la enfermedad. Estos resultados sugieren que dada la endogamia que muestra esta familia se presenta una gran acumulación de polimorfismos y mutaciones, por lo que es necesario realizar un proceso de asesoría genética para disminuir el riesgo de recurrencia. Abstract Usher syndrome is an autosomal recessive disease characterized by retinitis pigmentosa, congenital sensorineural hearing loss and vestibular dysfunction. The purpose of this work was to characterize hla in an inbred Colombian family that presents Usher Syndrome. The Methodology consisted in that a genealogy of the family was made and previous informed consent, from four patients clinically confirmed with Usher Syndrome and four phenotypically healthy patients 5 ml of peripheral blood were taken in venipuncture tubes with edta and then the dna isolation was performed with the technique of salting out, preserved in te buffer at -8 °C and adjusted the sample to a concentration of 8 μg/ml. The hla *A, *B, *DRB1 and *DQB1 antigens were then characterized by the medium-resolution pcr-ssp techniqu

Oncogenic hijacking of a developmental transcription factor evokes vulnerability toward oxidative stress in Ewing sarcoma.

Ewing sarcoma (EwS) is an aggressive childhood cancer likely originating from mesenchymal stem cells or osteo-chondrogenic progenitors. It is characterized by fusion oncoproteins involving EWSR1 and variable members of the ETS-family of transcription factors (in 85% FLI1). EWSR1-FLI1 can induce target genes by using GGAA-microsatellites as enhancers.Here, we show that EWSR1-FLI1 hijacks the developmental transcription factor SOX6 - a physiological driver of proliferation of osteo-chondrogenic progenitors - by binding to an intronic GGAA-microsatellite, which promotes EwS growth in vitro and in vivo. Through integration of transcriptome-profiling, published drug-screening data, and functional in vitro and in vivo experiments including 3D and PDX models, we discover that constitutively high SOX6 expression promotes elevated levels of oxidative stress that create a therapeutic vulnerability toward the oxidative stress-inducing drug Elesclomol.Collectively, our results exemplify how aberrant activation of a developmental transcription factor by a dominant oncogene can promote malignancy, but provide opportunities for targeted therapy

Deep Sequencing of Pyrethroid-Resistant Bed Bugs Reveals Multiple Mechanisms of Resistance within a Single Population

A frightening resurgence of bed bug infestations has occurred over the last 10 years in the U.S. and current chemical methods have been inadequate for controlling this pest due to widespread insecticide resistance. Little is known about the mechanisms of resistance present in U.S. bed bug populations, making it extremely difficult to develop intelligent strategies for their control. We have identified bed bugs collected in Richmond, VA which exhibit both kdr-type (L925I) and metabolic resistance to pyrethroid insecticides. Using LD50 bioassays, we determined that resistance ratios for Richmond strain bed bugs were ∼5200-fold to the insecticide deltamethrin. To identify metabolic genes potentially involved in the detoxification of pyrethroids, we performed deep-sequencing of the adult bed bug transcriptome, obtaining more than 2.5 million reads on the 454 titanium platform. Following assembly, analysis of newly identified gene transcripts in both Harlan (susceptible) and Richmond (resistant) bed bugs revealed several candidate cytochrome P450 and carboxylesterase genes which were significantly over-expressed in the resistant strain, consistent with the idea of increased metabolic resistance. These data will accelerate efforts to understand the biochemical basis for insecticide resistance in bed bugs, and provide molecular markers to assist in the surveillance of metabolic resistance