Bacteriophage-based biosensors for detection of pathogenic microbes in wastewater

Wastewater is discarded from several sources, including industry, livestock, fertilizer application, and municipal waste. If the disposed of wastewater has not been treated and processed before discharge to the environment, pathogenic microorganisms and toxic chemicals are accumulated in the disposal area and transported into the surface waters. The presence of harmful microbes is responsible for thousands of human deaths related to water-born contamination every year. To be able to take the necessary step and quick action against the possible presence of harmful microorganisms and substances, there is a need to improve the effective speed of identification and treatment of these problems. Biosensors are such devices that can give quantitative information within a short period of time. There have been several biosensors developed to measure certain parameters and microorganisms. The discovered biosensors can be utilized for the detection of axenic and mixed microbial strains from the wastewaters. Biosensors can further be developed for specific conditions and environments with an in-depth understanding of microbial organization and interaction within that community. In this regard, bacteriophage-based biosensors have become a possibility to identify specific live bacteria in an infected environment. This paper has investigated the current scenario of microbial community analysis and biosensor development in identifying the presence of pathogenic microorganisms.

Designing and assessing a data literacy internship program for graduate health sciences students

This case study presents the results of a data internship and workshop series on data analysis in qualitative biomedical systematic reviews. In a newly developed librarian-led internship program, an intern was trained on data literacy concepts and data analysis tools and, in turn, helped recruit and train other graduate health sciences students. Due to COVID-19 restrictions, a flipped classroom model was applied to develop a completely virtual learning experience for both the intern and workshop attendees. Both the data intern and workshop participants reported improved confidence in data literacy competence at the end of the project. Assessment results suggest that while the workshop series improved participants' data literacy skills, participants might still benefit from additional data literacy instruction. This case also presents a model for student-led instruction that could be particularly useful for informing professional development opportunities for library interns, fellows, and student assistants.

Continuous improvement of a bioengineering CURE: Preparing students for a changing world

Based on recent education reform guidelines to prepare professionals who are able to handle new technological, economic, social, and environmental challenges, pedagogical modifications are deemed necessary by the educators. Specifically, in biology, the rapid changes in the content and biological products demand changes in the curriculum. We aim to address this current need by providing an example of a course that was redesigned to meet the current trends of biological engineering education. In this course-based undergraduate research experience (CURE), learning objectives and possible outcomes were developed and assessment mapping was performed to align the course objectives with the Accreditation Board for Engineering and Technology (ABET) recommendations. A description of how one can assess authentic inquiry courses while adhering to the recommendations are discussed. For example, in this particular course, students completed weekly reflection assignments, maintained lab notebooks that were graded every week, presented their research to their peers at the end of the semester, and submitted a final paper to be graded. "Holistic" engineering is crucial for the all-around development of a 21st century engineer. Altering the traditional lecturing with more hands-on learning is crucial for the development of professional and communication skills of students. Such alterations could lead to the production of well-rounded life-long learners to serve the upcoming world.

Salts and Polymorph Screens for Bedaquiline

Bedaquiline is used to treat multi-resistant tuberculosis in adults. The fumarate salt is commercially available and used in the product Sirturo. To provide open access to bedaquiline molecule once the patent on the chemical substance expires, new salts were screened. This work offers additional information on the bedaquiline system, as new salts may present better pharmacokinetic properties. The current studies focus on the attempted isolation of the acetate, benzoate, benzenesulfonate, hydrobromide, succinate, hydrochloride, tartrate, lactate, maleate, malate, and mesylate salts of bedaquiline. Potential salts were screened using a unique combination of conventional screening, and small-scale experiments supplemented by crystallographic analysis and infrared microspectroscopy. Salts were prepared on a larger scale by dissolving 1:1 ratios of the individual salt formers and bedaquiline base (30 mg, 0.055 mmol) in different solvents and allowing the solutions to evaporate or crystallize. X-ray diffraction (XRD) techniques and spectroscopic and thermal analyses were employed to characterize the salts. The benzoate and maleate salts were selected as lead candidates after reviewing preliminary characterization data. To determine the most stable forms for the leads, a polymorph screen was conducted using solvents of various polarities. These salt screens successfully generated five new salts of bedaquiline, namely, benzoate, maleate, hydrochloride, besylate, and mesylate. The existence of these salts was confirmed by powder XRD, proton NMR, and IR spectroscopies. TGA and DSC thermal analysis along with hot-stage optical microscopy were further used to characterize the salts. The polymorph screen conducted on the salts suggested the absence of additional polymorphs at 1 g scale.

Abstract A26: Shotgun lipidomics analysis of temozolomide-treated glioblastoma

Glioblastoma (GBM) is the most common and aggressive form of primary brain tumor. Due to its extremely malignant and invasive nature, the mean survival period of GBM patients is only 12-15 months from diagnosis. GBM patients rely on current treatment options, including surgery, radiation and chemotherapy (temozolomide). However, these treatment options fail to improve quality of patients' lives. After the treatment of temozolomide (TMZ) chemotherapy, more than 80% of the GBM tumors relapse. One of the most significant issues with the standard treatment strategy is that these secondary tumors have usually developed a chemoresistance to TMZ. This indicates that the secondary tumors have different tumor characteristics than primary tumors. Our goal is to examine the TMZ-treated and non-treated tumors in order to investigate the lipid expression changes in GBM samples by shotgun lipidomics. Lipids are known to play a critical role in cancer cell initiation and progression governed by oncogenic signaling pathways. Our previous study showed that more than 90% of identified lipids from orthotopic GBM tumors were significantly under-expressed compared to the control samples, which suggests that studying changes of lipids in tumor environment might help us better develop better strategies to overcome chemoresistance.

We hypothesize that temozolomide promotes tumor heterogeneity and a mutagenic microenvironment in GBM, and lipid profiles of GBM can be a potential key biomarker for chemoresistance and cancer development. Our study focuses on investigating changes in lipid expression between TMZ-treated and non-treated GBM tumors by shotgun lipidomics.

Intracerebral implants of the GBM10 cell line were performed in the right cerebral hemisphere in NOD/SCID/gchainnull mice obtained from the In Vivo Therapeutics Core Indiana University School of Medicine (IUSCC/IUSM). Ten mice received three rounds of TMZ treatment, and ten mice received no treatment. Tumors were harvested approximately 25 days after the implants and stored in -80C immediately.

We plan to investigate lipid biomarkers of GBM by utilizing shotgun lipidomics to examine changes in the tumor lipid composition as a result of temozolomide treatment. In order to visualize the data, our group will utilize supervised statistical analysis methods (principal component analysis - PCA), univariate statistics and receiver operating characteristics (ROC) curve to show the differences of lipid profiles and define prospective biomarkers. Our findings could contribute to the development or the monitoring of therapeutic intervention strategies for tumors that recur after standard care of treatment in glioblastoma.

Citation Format: Soo Jung Ha, Lauren Bailey, Christina Ferreira, Haiyan Wang, Barbara Bailey, Jixin Ding, M Reza Saadatzadeh, Karen E. Pollok, Kari Clase. Shotgun lipidomics analysis of temozolomide-treated glioblastoma. [abstract]. In: Proceedings of the AACR Special Conference on Engineering and Physical Sciences in Oncology; 2016 Jun 25-28; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2017;77(2 Suppl):Abstract nr A26.

A broadly implementable research course in phage discovery and genomics for first-year undergraduate students

Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students' interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training.

IMPORTANCE

Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

A survey of scholarly literature describing the field of bioinformatics education and bioinformatics educational research

Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the potential advancement of research and development in complex biomedical systems has created a need for an educated workforce in bioinformatics. However, effectively integrating bioinformatics education through formal and informal educational settings has been a challenge due in part to its cross-disciplinary nature. In this article, we seek to provide an overview of the state of bioinformatics education. This article identifies: 1) current approaches of bioinformatics education at the undergraduate and graduate levels; 2) the most common concepts and skills being taught in bioinformatics education; 3) pedagogical approaches and methods of delivery for conveying bioinformatics concepts and skills; and 4) assessment results on the impact of these programs, approaches, and methods in students' attitudes or learning. Based on these findings, it is our goal to describe the landscape of scholarly work in this area and, as a result, identify opportunities and challenges in bioinformatics education.

A course-based research experience: how benefits change with increased investment in instructional time

There is widespread agreement that science, technology, engineering, and mathematics programs should provide undergraduates with research experience. Practical issues and limited resources, however, make this a challenge. We have developed a bioinformatics project that provides a course-based research experience for students at a diverse group of schools and offers the opportunity to tailor this experience to local curriculum and institution-specific student needs. We assessed both attitude and knowledge gains, looking for insights into how students respond given this wide range of curricular and institutional variables. While different approaches all appear to result in learning gains, we find that a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. An alumni survey revealed that time spent on a research project is also a significant factor in the value former students assign to the experience one or more years later. We conclude: 1) implementation of a bioinformatics project within the biology curriculum provides a mechanism for successfully engaging large numbers of students in undergraduate research; 2) benefits to students are achievable at a wide variety of academic institutions; and 3) successful implementation of course-based research experiences requires significant investment of instructional time for students to gain full benefit.