Gene Expression and Data Analysis Pipeline Using Cancer BioPortal in the Classroom.

At institutions with an emphasis on authentic research experiences as an integral part of the biology curriculum, COVID created a huge challenge for course instructors whose learning objectives were designed for such experiences. Moving such laboratory experiences online when remote learning became necessary has resulted in a new model for CUREs that utilizes free online databases to provide not only a novel research experience for students, but also the opportunity to engage in big data analysis. Cancer BioPortal (cBioPortal) is an open-access collective cancer research resource for storing and exploring clinical, genomic, proteomic, and transcriptomic data. cBioPortal eliminates the computational barrier of interpreting complex genomic data by providing easily understandable visualization that can be interpreted and translated into relevant biological insights. Because no prior computational knowledge is required, cBioPortal is an ideal educational tool for either in-person or distance learning environments. We developed a pedagogical approach, video tutorials, and data analysis workflows centered on using cBioPortal. Pedagogically, students develop an initial research outline that is continually updated and graded throughout the project. Progress during the project or course is assessed by a series of student presentations that are 5 to 15 minutes in length and are aimed at explaining the approach used in data acquisition, interpretation of the data, and relevance to the initial hypothesis. While cancer-specific, this analysis platform appeals to a wide range of classes and student interests. Further, the project has been successfully done both as an independent research experience and as part of a virtual class-based research project.

Calidad de control metabólico en pacientes ambulatorios con diabetes tipo 2 atendidos en una clínica privada / Quality of metabolic control in outpatients with type 2 diabetes seen in a private clinic

Objetivo: Evaluar la calidad de control metabólico en pacientes ambulatorios con diabetes mellitus tipo 2 (DM2) de una clínica privada en Lima, Perú. Materiales y métodos: Estudio de corte transversal en la consulta externa del Servicio de endocrinología de una clínica privada de Lima, Perú. Se recolectó información socio demográfica, historia de enfermedad, autorreporte de complicaciones y comorbilidades, medidas antropométricas y presión arterial. Además, se tomó muestras de sangre para análisis de prueba rápida de glucosa, hemoglobina glicosilada (HbA1c) y perfil lipídico. Se consideró pobre control metabólico si el participante tenía HbA1c >7%, colesterol LDL (LDL-c) =100 mg/dl, y presión arterial =130/80 mmHg. Se aplicaron cuestionarios adicionales, para medir la adherencia al tratamiento, actividad física, calidad de vida, autoeficacia y depresión. Resultados: Se incluyó a 60 participantes, 53,3% (32/60) fueron de sexo femenino y la media de edad fue 63,1 ±13,2 años. Se encontró pobre control metabólico en 85% (51/60) de los participantes; presión arterial controlada en 71,2% (42/60), LDL-c controlado en 10% (6/60) y HbA1c controlado en 48,3% (29/60) de los participantes respectivamente. Complicaciones crónicas como retinopatía se autorreportó en el 3,3% (2/60) participantes, neuropatía en 10% (6/60), nefropatía en 1,7% (1/60), presión arterial alta en 30% (18/60) y enfermedad cerebro vascular en 5% (3/60) de los participantes. Conclusión: La prevalencia de control metabólico no controlado es elevada, a pesar del contexto de atención en una clínica privada. Regulación y medidas para mejorar el control en centros privados es necesario

Objective: To assess the quality of metabolic control among outpatients with type 2 diabetes mellitus (DM2) in a private clinic in Lima, Peru. Materials and methods: This is a cross-sectional study in the outpatient endocrinology service of a private clinic in Lima, Peru. Socio-demographic information, history of diabetes, self-report of complications and comorbidities, anthropometric measures and blood pressure data were collected. Blood samples were taken for assessing fasting blood glucose, glycated hemoglobin (HbA1c) and lipid profile. A poor metabolic control was considered if the participant had HbA1c >7%, LDL cholesterol (LDL-c) =100 mg/dl, and blood pressure =130/80 mmHg. Additional questionnaires were administered for measuring adherence to therapy, physical activity, quality of life, self-efficacy and depression. Results: Sixty participants were included; 53.3% (32/60) were female and their mean age was 63.1 ±13.2 years. Poor metabolic control was found in 85% (51/60) of all participants; controlled blood pressure in 71.2% (42/60), controlled LDL-C levels in 10% (6/60), and controlled HbA1c values in 48.3% (29/60) participants, respectively. Chronic complications such as retinopathy were found in 3.33% (2/60) participants, neuropathy in 10% (6/60), nephropathy in 1.7% (1/60), high blood pressure in 30% (18/60) and cerebrovascular disease in 5% (3/60) of all participants. Conclusion: There is a high prevalence of poor metabolic control in patients with type 2 diabetes, despite being taken care of in a private clinic. It is necessary to take actions in order to improve the metabolic control in patients with type 2 diabetes attending the private health care sector

Brucellosis Transmission between Wildlife and Livestock in the Greater Yellowstone Ecosystem: Inferences from DNA Genotyping.

The wildlife of the Greater Yellowstone Ecosystem carries brucellosis, which was first introduced to the area by cattle in the 19th century. Brucellosis transmission between wildlife and livestock has been difficult to study due to challenges in culturing the causative agent, Brucella abortus . We examined B. abortus transmission between American bison ( Bison bison ), Rocky Mountain elk ( Cervus elaphus nelsoni), and cattle ( Bos taurus ) using variable number tandem repeat (VNTR) markers on DNA from 98 B. abortus isolates recovered from populations in Idaho, Montana, and Wyoming, US. Our analyses reveal interspecies transmission. Two outbreaks (2007, 2008) in Montana cattle had B. abortus genotypes similar to isolates from both bison and elk. Nevertheless, similarity in elk and cattle isolates from the 2008 outbreak suggest that elk are the likely source of brucellosis transmission to cattle in Montana and Wyoming. Brucella abortus isolates from sampling in Montana appear to be divided in two clusters: one found in local Montana elk, cattle, and bison; and another found mainly in elk and a bison from Wyoming, which is consistent with brucellosis having entered Montana via migration of infected elk from Wyoming. Our findings illustrate complex patterns of brucellosis transmission among elk, bison, and cattle as well as the utility of VNTRs to infer the wildlife species of origin for disease outbreaks in livestock.

Differential virus host-ranges of the Fuselloviridae of hyperthermophilic Archaea: implications for evolution in extreme environments.

An emerging model for investigating virus-host interactions in hyperthermophilic Archaea is the Fusellovirus-Sulfolobus system. The host, Sulfolobus, is a hyperthermophilic acidophile endemic to sulfuric hot springs worldwide. The Fuselloviruses, also known as Sulfolobus Spindle-shaped Viruses (SSVs), are "lemon" or "spindle"-shaped double-stranded DNA viruses, which are also found worldwide. Although a few studies have addressed the host-range for the type virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), using common Sulfolobus strains, a comprehensive host-range study for SSV-Sulfolobus systems has not been performed. Herein, we examine six bona fide SSV strains (SSV1, SSV2, SSV3, SSVL1, SSVK1, SSVRH) and their respective infection characteristics on multiple hosts from the family Sulfolobaceae. A spot-on-lawn or "halo" assay was employed to determine SSV infectivity (and host susceptibility) in parallel challenges of multiple SSVs on a lawn of a single Sulfolobus strain. Different SSVs have different host-ranges with SSV1 exhibiting the narrowest host-range and SSVRH exhibiting the broadest host range. In contrast to previous reports, SSVs can infect hosts beyond the genus Sulfolobus. Furthermore, geography does not appear to be a reliable predictor of Sulfolobus susceptibility to infection by any given SSV. The ability for SSVs to infect susceptible Sulfolobus host does not appear to change between 65°C and 88°C (physiological range); however, very low pH appears to influence infection. Lastly, for the virus-host pairs tested the Fusellovirus-Sulfolobus system appears to exhibit host-advantage. This work provides a foundation for understanding Fusellovirus biology and virus-host coevolution in extreme ecosystems.