Integrated analysis of epigenomic and genomic changes by DNA methylation dependent mechanisms provides potential novel biomarkers for prostate cancer

Epigenetic silencing mediated by CpG methylation is a common feature of many cancers. Characterizing aberrant DNA methylation changes associated with tumor progression may identify potential prognostic markers for prostate cancer (PCa). We treated two PCa cell lines, 22Rv1 and DU-145 with the demethylating agent 5-Aza 2’–deoxycitidine (DAC) and global methylation status was analyzed by performing methylation-sensitive restriction enzyme based differential methylation hybridization strategy followed by genome-wide CpG methylation array profiling. In addition, we examined gene expression changes using a custom microarray. Gene Set Enrichment Analysis (GSEA) identified the most significantly dysregulated pathways. In addition, we assessed methylation status of candidate genes that showed reduced CpG methylation and increased gene expression after DAC treatment, in Gleason score (GS) 8 vs. GS6 patients using three independent cohorts of patients; the publically available The Cancer Genome Atlas (TCGA) dataset, and two separate patient cohorts. Our analysis, by integrating methylation and gene expression in PCa cell lines, combined with patient tumor data, identified novel potential biomarkers for PCa patients. These markers may help elucidate the pathogenesis of PCa and represent potential prognostic markers for PCa patients.

Elevated level of inhibin-α subunit is pro-tumourigenic and pro-metastatic and associated with extracapsular spread in advanced prostate cancer

The biological function of inhibin-a subunit (INHa) in prostate cancer (PCa) is currently unclear. A recent study associated elevated levels of INHa in PCa patients with a higher risk of recurrence. This prompted us to use clinical specimens and functional studies to investigate the pro-tumourigenic and pro-metastatic function of INHa. We conducted a cross-sectional study to determine a link between INHa expression and a number of clinicopathological parameters including Gleason score, surgical margin, extracapsular spread, lymph node status and vascular endothelial growth factor receptor-3 expression, which are well-established prognostic factors of PCa. In addition, using two human PCa cell lines (LNCaP and PC3) representing androgen-dependent and -independent PCa respectively, we investigated the biological function of elevated levels of INHa in advanced cancer. Elevated expression of INHa in primary PCa tissues showed a higher risk of PCa patients being positive for clinicopathological parameters outlined above. Overexpressing INHa in LNCaP and PC3 cells demonstrated two different and cell-type-specific responses. INHa-positive LNCaP demonstrated reduced tumour growth whereas INHa-positive PC3 cells demonstrated increased tumour growth and metastasis through the process of lymphangiogenesis. This study is the first to demonstrate a pro-tumourigenic and pro-metastatic function for INHa associated with androgen-independent stage of metastatic prostate disease. Our results also suggest that INHa expression in the primary prostate tumour can be used as a predictive factor for prognosis of PCa.

Versatility of polymethacrylate monoliths for chromatographic purification of biomolecules

Polymethacrylate monoliths, specifically poly(glycidyl methacrylate-co-ethylene dimethacrylate) or poly(GMA-co-EDMA) monoliths, are a new generation of chromatographic supports and are significantly different from conventional particle-based adsorbents, membranes, and other monolithic supports for biomolecule purification. Similar to other monoliths, polymethacrylate monoliths possess large pores which allow convective flow of mobile phase and result in high flow rates at reduced pressure drop, unlike particulate supports. The simplicity of the adsorbent synthesis, pH resistance, and the ease and flexibility of tailoring their pore size to that of the target biomolecule are the key properties which differentiate polymethacrylate monoliths from other monoliths. Polymethacrylate monoliths are endowed with reactive epoxy groups for easy functionalization (with anion-exchange, hydrophobic, and affinity ligands) and high ligand retention. In this review, the structure and performance of polymethacrylate monoliths for chromatographic purification of biomolecules are evaluated and compared to those of other supports. The development and use of polymethacrylate monoliths for research applications have grown rapidly in recent times and have enabled the achievement of high through-put biomolecule purification on semi-preparative and preparative scales.

High-temperature, low-H₂O silicic magmas of the Yellowstone Hotspot: an experimental study of Rhyolite from the Bruneau-Jarbidge eruptive center, Central Snake River Plain, USA

The phase relations have been investigated experimentally at 200 and 500 MPa as a function of water activity for one of the least evolved (Indian Batt Rhyolite) and of a more evolved rhyolite composition (Cougar Point Tuff XV) from the 12·8-8·1 Ma Bruneau-Jarbidge eruptive center of the Yellowstone hotspot. Particular priority was given to accurate determination of the water content of the quenched glasses using infrared spectroscopic techniques. Comparison of the composition of natural and experimentally synthesized phases confirms that high temperatures (>900°C) and extremely low melt water contents (<1·5 wt % H₂O) are required to reproduce the natural mineral assemblages. In melts containing 0·5-1·5 wt % H₂O, the liquidus phase is clinopyroxene (excluding Fe-Ti oxides, which are strongly dependent on fO₂), and the liquidus temperature of the more evolved Cougar Point Tuff sample (BJR; 940-1000°C) is at least 30°C lower than that of the Indian Batt Rhyolite lava sample (IBR2; 970-1030°C). For the composition BJR, the comparison of the compositions of the natural and experimental glasses indicates a pre-eruptive temperature of at least 900°C. The composition of clinopyroxene and pigeonite pairs can be reproduced only for water contents below 1·5 wt % H₂O at 900°C, or lower water contents if the temperature is higher. For the composition IBR2, a minimum temperature of 920°C is necessary to reproduce the main phases at 200 and 500 MPa. At 200 MPa, the pre-eruptive water content of the melt is constrained in the range 0·7-1·3 wt % at 950°C and 0·3-1·0 wt % at 1000°C. At 500 MPa, the pre-eruptive temperatures are slightly higher (by 30-50°C) for the same ranges of water concentration. The experimental results are used to explore possible proxies to constrain the depth of magma storage. The crystallization sequence of tectosilicates is strongly dependent on pressure between 200 and 500 MPa. In addition, the normative Qtz-Ab-Or contents of glasses quenched from melts coexisting with quartz, sanidine and plagioclase depend on pressure and melt water content, assuming that the normative Qtz and Ab/Or content of such melts is mainly dependent on pressure and water activity, respectively. The combination of results from the phase equilibria and from the composition of glasses indicates that the depth of magma storage for the IBR2 and BJR compositions may be in the range 300-400 MPa (13 km) and 200-300 MPa (10 km), respectively.

Making an IMPACT: Campus-wide collaboration for course and learning space transformation

At Purdue University, the Libraries participate in a provost-initiated, campus-wide course redesign program called Instruction Matters: Purdue Academic Course Transformation (IMPACT). This initiative aims to bring active-learning to foundational courses traditionally taught through lectures. Purdue librarians recognized the IMPACT initiative as one way to enter the conversations blooming on our campus about the nature of learning, curriculum design, and how space design impacts potential learning. This article presents three perspectives: 1) the information literacy coordinator, 2) a libraries’ administrator with a gift for space planning, and; 3) an in-the-trenches liaison to course redesign projects. Each discusses the IMPACT initiative from his or her unique perspective and view of its impact on librarian roles. Collectively, the article explains why we think it is essential that this kind of campus effort is supported by libraries.

Statistical literacy social media project for the masses

This article examines a social media assignment used to teach and practice statistical literacy with over 400 students each semester in large-lecture traditional, fully online, and flipped sections of an introductory-level statistics course. Following the social media assignment, students completed a survey on how they approached the assignment. Drawing from the authors’ experiences with the project and the survey results, this article offers recommendations for developing social media assignments in large courses that focus on the interplay between the social media tool and the implications of assignment prompts.

“It’s in the syllabus”: Identifying information literacy and data information literacy opportunities using a grounded theory approach

Developing innovative library services requires a real world understanding of faculty members' desired curricular goals. This study aimed to develop a comprehensive and deeper understanding of Purdue's nutrition science and political science faculties' expectations for student learning related to information and data information literacies. Course syllabi were examined using grounded theory techniques that allowed us to identify how faculty were addressing information and data information literacies in their courses, but it also enabled us to understand the interconnectedness of these literacies to other departmental intentions for student learning, such as developing a professional identity or learning to conduct original research. The holistic understanding developed through this research provides the necessary information for designing and suggesting information literacy and data information literacy services to departmental faculty in ways supportive of curricular learning outcomes.

Circulating tumor cell detection in high-risk non-metastatic prostate cancer

Purpose The detection of circulating tumor cells (CTCs) provides important prognostic information in men with metastatic prostate cancer. We aim to determine the rate of detection of CTCs in patients with high-risk non-metastatic prostate cancer using the CellSearch® method. Method Samples of peripheral blood (7.5 mL) were drawn from 36 men with newly diagnosed high-risk non-metastatic prostate cancer, prior to any initiation of therapy and analyzed for CTCs using the CellSearch® method. Results The median age was 70 years, median PSA was 14.1, and the median Gleason score was 9. The median 5-year risk of progression of disease using a validated nomogram was 39 %. Five out of 36 patients (14 %, 95 % CI 5–30 %) had CTCs detected in their circulation. Four patients had only 1 CTC per 7.5 mL of blood detected. One patient had 3 CTCs per 7.5 mL of blood detected, which included a circulating tumor microemboli. Both on univariate analysis and multivariate analysis, there were no correlations found between CTC positivity and the classic prognostic factors including PSA, Gleason score, T-stage and age. Conclusion This study demonstrates that patients with high-risk, non-metastatic prostate cancer present infrequently with small number of CTCs in peripheral blood. This finding is consistent with the limited literature available in this setting. Other CTC isolation and detection technologies with improved sensitivity and specificity may enable detection of CTCs with mesenchymal phenotypes, although none as yet have been validated for clinical use. Newer assays are emerging for detection of new putative biomarkers for prostate cancer. Correlation of disease control outcomes with CTC detection will be important.

Informed learning in the undergraduate classroom: The role of information experiences in shaping outcomes

This research aimed to inform the design of effective information literacy lessons in higher education. Phenomenography, a research approach designed to study human experience, was used to explore the experiences of a teacher and undergraduate students using information to learn about language and gender issues. The findings show that the way learners use information influences content-focused learning outcomes, and reveal an instructional pattern for enabling students to use information while becoming aware of the topic they are investigating. Based on the findings, a design model is offered in which learning outcomes are realized through targeted information literacy activities.

Designing rich information experiences to shape learning outcomes

Students in higher education typically learn to use information as part of their course of study, which is intended to support ongoing academic, personal and professional growth. Informing the development of effective information literacy education, this research uses a phenomenographic approach to investigate the experiences of a teacher and students engaged in lessons focused on exploring language and gender topics by tracing and analyzing their evolution through scholarly discourse. The findings suggest that the way learners use information influences content-focused learning outcomes, and reveal how teachers may enact lessons that enable students to learn to use information in ways that foster a specific understanding of the topic they are investigating.

Crossing literacy and informed learning boundaries with Manga

This research investigated high school students’ experiences of informed learning in a literacy development workshop. It was conducted in the library of an Australian high school with a low socio-economic population. Building upon students’ fascination with Manga fiction and artwork, the workshop was part of a larger university-community engagement project Crossing Boundaries with Reading which aimed to address widespread literacy challenges at the school. The paper first provides a brief literature review that introduces the concept of informed learning, or the experience of using information to learn. In practice, informed learning fosters simultaneous learning about using information and learning about a topic. Thus, information is a transformative force that extends beyond functional information literacy skills. Then, the paper outlines the phenomenographic methodology used in this study, the workshop context and the research participants. The findings reveal three different ways that students experienced the workshop: as an art lesson; as a life lesson; and as an informed learning lesson. The discussion highlights the power of informed learning as a holistic approach to information literacy education. The study’s findings are significant as students from low socio-economic backgrounds are often at risk of experiencing disadvantage throughout their lives if they do not develop a range of literacies including the ability to use information effectively. Responding to this problem, the paper provides an empirically-based example of informed learning to support further research and develop professional practice. While the research context is limited to one high school library, the findings are of potential value for teacher-librarians, educators and information professionals elsewhere.