Biological Pathways Associated with Wild and Domestic Animals

Background: Zoonotic diseases are problematic, in that, they impact both wild and domestic animals alike. Thus, there is a need to investigate the genomes of wild and domestic. Gene ontology (GO) is a major bioinformatics initiative, whereby descriptions of gene products across the database are developed and unified to describe all species. This process is performed by biocurators, who gather, annotate, and validate information on the databases, consequently affording easy access to accurate and updated data. In this study, we investigated the biocuration of two biological processes, DNA integration, which is used for DNA coding, and the tricarboxylic acid (TCA) cycle that occurs in all aerobic organisms. The objective of this study was to compare the genomes of 271 mammals, birds, reptiles and some aquatic animals to determine the number of wild versus domesticated animals, where DNA integration and the TCA cycle have annotations. We hypothesized that there would be more annotations on domesticated animals than wild animals because of easier access to domesticated animal genomes. Methods: To test this hypothesis, we first accessed the National Center of Biotechnology Information (NCBI) to retrieve the taxonomy ID for 271 species of animals found in this study. Then the European Bioinformatics Institute (EBI) database, QuickGO, was accessed to retrieve all annotations associated with the taxonomy ID of the species. Data was assembled into a wiki-database that is now publicly available online. Results and Conclusion: Data indicated that more annotations for DNA integration and the TCA cycle were 22% higher in domestic animals than in wild animals. Therefore, we propose that more biocuration needs to be done for wild animals. The number of wild animals’ sequences available are growing, but if they are not annotated, detailed investigations are not possible. If more resources are dedicated to the investigation of the genomes of wild animals, more work can be done to study the genetic factors affecting zoonotic diseases

A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics

In their 2012 report, the President\u27s Council of Advisors on Science and Technology advocated replacing standard science laboratory courses with discovery-based research courses -a challenging proposition that presents practical and pedagogical difficulties. In this paper, we describe our collective experiences working with the Genomics Education Partnership, a nationwide faculty consortium that aims to provide undergraduates with a research experience in genomics through a scheduled course (a classroom-based undergraduate research experience, or CURE). We examine the common barriers encountered in implementing a CURE, program elements of most value to faculty, ways in which a shared core support system can help, and the incentives for and rewards of establishing a CURE on our diverse campuses. While some of the barriers and rewards are specific to a research project utilizing a genomics approach, other lessons learned should be broadly applicable. We find that a central system that supports a shared investigation can mitigate some shortfalls in campus infrastructure (such as time for new curriculum development, availability of IT services) and provides collegial support for change. Our findings should be useful for designing similar supportive programs to facilitate change in the way we teach science for undergraduates

Synthesis and characterization of chitosan-carbon nanotube composites

Acid functionalized single walled carbon nanotubes were covalently grafted to chitosan by first reacting the oxidized carbon nanotubes with thionyl chloride to form acyl-chlorinated carbon nanotubes which are subsequently dispersed in chitosan and covalently grated to form composite material, CNT-chitosan, 1, which was washed several times to remove un-reacted materials. This composite has been characterized by FTIR, 13C NMR, TGA, SEM and TEM and has been shown to exhibit enhanced thermal stability. The reaction of 1, with poly lactic acid has also been accomplished to yield CNTchitosan-g-poly(LA), 2 and fully characterized by the above techniques. Results showed covalent attachment of chitosan and chitosan-poly lactic acid to the carbon nanotubes. © 2008 Elsevier B.V. All rights reserved

Hydroxyapatite grafted carbon nanotubes and graphene nanosheets: Promising bone implant materials

In the present study, hydroxyapatite (HA) was successfully grafted to carboxylated carbon nanotubes (CNTs) and graphene nanosheets. The HA grafted CNTs and HA-graphene nanosheets were characterized using FT-IR, TGA, SEM and X-ray diffraction. The HA grafted CNTs and graphene nanosheets (CNTs-HA and Gr-HA) were further used to examine the proliferation and differentiation rate of temperature-sensitive human fetal osteoblastic cell line (hFOB 1.19). Total protein assays and western blot analysis of osteocalcin expression were used as indicators of cell proliferation and differentiation. Results indicated that hFOB 1.19 cells proliferate and differentiate well in treatment media containing CNTs-HA and graphene-HA. Both CNTs-HA and graphene-HA could be promising nanomaterials for use as scaffolds in bone tissue engineering. © 2014 Elsevier B.V. All rights reserved

Innovative professional development and community building activity program improves STEM URM graduate student experiences

BACKGROUND: Strong consensus exists on the need to expand participation of URM doctoral students in STEM fields, to increase their retention, reduce their average time to degree, and provide these students with the preparation necessary to compete for faculty positions. This paper provides a model for implementing effective strategies to support the success of URM STEM graduate students across a system with various types of institutions. An innovative professional development, participation incentive, and community building program for underrepresented minority (URM) Graduate students in STEM (science, technology, engineering, and mathematics) fields was instrumental in preparing them to secure academic positions, navigating graduate school successfully, and form a support network that helped them excel at the next level. The program provided sustained support and several activities in a collaborative environment for 84 Ph.D. and 84 Master’s students, in over 43 graduate programs. Data were collected using evaluation questionnaires containing open-ended responses and responses to specific items sent to the students after each activity, and a survey seeking their feedback on the program. RESULTS: In only 4 years, the program helped 13 students to secure faculty or post-doctoral positions, and improved the opinion of the professoriate career as thirteen students transitioned to the Ph.D. program and are now more interested in applying for faculty positions. The program was successful in developing and sustaining large-scale, distributed, yet interconnected STEM communities among the diverse Alliance system institutions and increased participation (from 58 in 2013 to 98 in 2017), reduced barriers, and promoted the success of URM doctoral students preparing for careers in the professoriate. CONCLUSIONS: We have developed activities that connected students and faculty across institutions, providing multiple paths to the professoriate that align with students’ diverse academic career aspirations. This article illustrates that professional development, incentives, and community building interventions are essential in generating URM STEM education transformation

Thermal stability of functionalized carbon nanotubes studied by in situ transmission electron microscopy

The thermal stability of functionalized carbon nanotubes (CNTs) has been studied experimentally by direct in situ observations using a heating stage in a transmission electron microscope, from room temperature (RT) to about 1000 °C. It was found that the thermal stability of the functionalized CNTs was significantly reduced during the in situ heating process. Their average diameter dramatically expanded from RT to about 500 °C, and then tended to be stable until about 1000 °C. The X-ray energy dispersive spectroscopy analysis suggested that the diameter expansion was associated with coalescence of the carbon structure instead of deposition with additional foreign elements during the heating process. © 2011 Elsevier B.V. All rights reserved

Synthesis, characterization and stability of chitosan and poly(methyl methacrylate) grafted carbon nanotubes

The single walled carbon nanotubes (CNTs) were effectively functionalized through grafting with chitosan (CTS) and poly(methyl methacrylate) (PMMA). Prior to grafting reaction, the carboxylated SWNCTs (SWNCTs-COOH) were obtained by treating pristine CNTs with a mixture of 3:1 (v/v) H2SO4 and HNO3, and the successive treatment of SWNCTs-COOH with SOCl 2 yielded the acylated CNTs (CNTs-COCl). The functionalized derivatives of CNTs were characterized using Fourier transform infrared spectroscopy, thermogravimetric analysis, atomic force microscopy, scanning electron microscopy and transmission electron microscopy. Both CTS and PMMA grafted CNTs showed better dispersability in acetic acid and tetrahydrofuran, in addition to higher stability in solution. © 2012 Elsevier B.V. All rights reserved

The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students