Foundations of Translational Ecology

Ecologists who specialize in translational ecology (TE) seek to link ecological knowledge to decision making by integrating ecological science with the full complement of social dimensions that underlie today\u27s complex environmental issues. TE is motivated by a search for outcomes that directly serve the needs of natural resource managers and decision makers. This objective distinguishes it from both basic and applied ecological research and, as a practice, it deliberately extends research beyond theory or opportunistic applications. TE is uniquely positioned to address complex issues through interdisciplinary team approaches and integrated scientist–practitioner partnerships. The creativity and context-specific knowledge of resource managers, practitioners, and decision makers inform and enrich the scientific process and help shape use-driven, actionable science. Moreover, addressing research questions that arise from on-the-ground management issues – as opposed to the top-down or expert-oriented perspectives of traditional science – can foster the high levels of trust and commitment that are critical for long-term, sustained engagement between partners

Pathogenetics of alveolar capillary dysplasia with misalignment of pulmonary veins.

Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal lung developmental disorder caused by heterozygous point mutations or genomic deletion copy-number variants (CNVs) of FOXF1 or its upstream enhancer involving fetal lung-expressed long noncoding RNA genes LINC01081 and LINC01082. Using custom-designed array comparative genomic hybridization, Sanger sequencing, whole exome sequencing (WES), and bioinformatic analyses, we studied 22 new unrelated families (20 postnatal and two prenatal) with clinically diagnosed ACDMPV. We describe novel deletion CNVs at the FOXF1 locus in 13 unrelated ACDMPV patients. Together with the previously reported cases, all 31 genomic deletions in 16q24.1, pathogenic for ACDMPV, for which parental origin was determined, arose de novo with 30 of them occurring on the maternally inherited chromosome 16, strongly implicating genomic imprinting of the FOXF1 locus in human lungs. Surprisingly, we have also identified four ACDMPV families with the pathogenic variants in the FOXF1 locus that arose on paternal chromosome 16. Interestingly, a combination of the severe cardiac defects, including hypoplastic left heart, and single umbilical artery were observed only in children with deletion CNVs involving FOXF1 and its upstream enhancer. Our data demonstrate that genomic imprinting at 16q24.1 plays an important role in variable ACDMPV manifestation likely through long-range regulation of FOXF1 expression, and may be also responsible for key phenotypic features of maternal uniparental disomy 16. Moreover, in one family, WES revealed a de novo missense variant in ESRP1, potentially implicating FGF signaling in the etiology of ACDMPV

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Journal on Excellence in College Teaching: Volume 25, Numbers 3 & 4

Small-Group Learning in Higher Education - Cooperative, Collaborative, Problem-Based, and Team-Based Learning - Neil Davidson, Claire Howell Major, & Larry K. Michaelsen Boundary Crossings: Cooperative Learning, Collaborative Learning, and Problem-Based Learning - Neil Davidson & Claire Howell Major Team-Based Learning Practices and Principles in Comparison with Cooperative Learning and Problem-Based Learning - Larry K. Michaelsen, Neil Davidson, & Claire Howell Major Cooperative Learning: Improving University Instruction by Basing Practice on Validated Theory - David W. Johnson, Roger T. Johnson, & Karl A. Smith Kagan Structures, Processing, and Excellence in College Teaching - Spencer Kagan Using Cooperative Structures to Promote Deep Learning - Barbara J. Millis Using Classroom Assessment and Cognitive Scaffolding to Enhance the Power of Small-Group Learning - James Cooper & Pamela Robinson Examining the Influence of Structured Collaborative Learning Experiences for Graduate Studies - Elizabeth A. Jones Integrating Collaborative Learning Inside and Outside of the Classroom - Anne Goodsell Love, Alexa Dietrich, Jason Fitzgerald, & David Gordon Why Problem-Based Learning Works: Theoretical Foundations - Rose M. Marra, David H. Jonassen, Betsy Palmer, & Steve Luft Problem-Based Learning: Outcomes Evidence from the Health Professions - Mark A. Albanese & Laura dast Now, What Happens During Class? Using Team-Based Learning to Optimize the Role of Expertise Within the Flipped Classroom - Michael L. Wallace, Joshua D. Walker, Anne M. Braseby, & Michael S. Sweet Effective Task Design for the TBL Classroom - Bill Roberson & Billie Franchini Analysis of the Team-Based Learning Literature: TBL Comes of Age - Paul Haidet, Karla Kubitz, & Wayne T. McCormac

Journal on Excellence in College Teaching, Volume 7, Number 3

A Message from the Editors - Laurie Richlin & Milton D. Cox Changing Methods and Metaphors: A Case Study of Growth in University Teaching - Cheryl Amundsen, Alenoush Saroyan, & Myron Frankman Professors\u27 Assumptions About Students\u27 Critical Thinking Dispositions and Epistemological Beliefs - Geoffrey Scheurman Student Ratings of 10 Strategies for Using Humor in College Teaching - Ronald A. Berk Abandoning the Lecture in Biology - Robert C. Evans & Nancy Omaha Boy Strategies for Enhancing Teaching and Learning in an Undergraduate Course - Bruce W. Tuckman A Team-Based Approach to Problem-Based Learning: An Evaluation of Structured Team Problem Solving - Michael Peterson White Males Teaching for Diversity: How and Why - Robert M. Schaible & Paul Burli

Challenges Associated with Eradicating Invasive Rodents from Islands: Lessons Learned

Removal of introduced rats from islands is a proven and powerful conservation tool that can help restore ecosystem functioning and/or processes. Haida Gwaii, British Columbia, Canada, is an isolated marine archipelago with distinct flora and fauna that have evolved during 14,000 years of isolation from the mainland. Approximately 1.5 million seabirds from 13 species nest on the islands of Haida Gwaii, including 50% of the global ancient murrelet population, a federally designated species at risk in Canada. Within Gwaii Haanas National Park Reserve and Haida Heritage Site (located at the southern end of Haida Gwaii) there are 9 designated Important Bird Areas (IBAs), established primarily to denote important seabird nesting sites. However, unintentional historical introductions of rats to islands within IBAs and throughout Haida Gwaii have led to the demise of several seabird nesting colonies. In September 2013, Parks Canada Agency, in partnership with Coastal Conservation and Island Conservation, implemented Canada’s first aerial broadcast eradication of black rats from two islands within the Ramsay Island and Northern Juan Perez Sound Islands IBA, where seabird colonies and ecosystem processes have been negatively impacted by this species. The eradication of black rats from Murchison and Faraday Islands posed several challenges including ensuring adequate bait density to maximize the probability of eradication success while minimizing risks to native species. Our planning efforts focused on addressing bait competition by non-target species, the consequence of bait interception by the forest canopy, minimizing bait entering the marine environment, mitigating potential negative impacts to non-target species, and determining the ideal timing for the eradication operation. We present here a summary of these challenges and the measures that were implemented to address them

Journal on Excellence in College Teaching: Volume 25, Numbers 2

How Are We Doing? Evaluating Facutly Teaching and Assesing Student Learning: A Message from the Editors - Laurie Richlin, Gregg W. Wentzell, & Milton D. Cox Differences in Student Evaluations of Limited-Term Lecturers and Full-Time Faculty - Jeong-Il Cho, Koichiro Otani, & B. Joon Kim First-Year Students\u27 Perceptions of Instruction in Large Lectures: The Top-10 Mistakes Made by Instructors - K. Andrew R. Richards & Juan D. Velasquez Student Evaluations of Faculty Members: A Call for Analytical Prudence - Darryl J. Mitry & David E. Smith Metacognition: Student Reflections on Problem Solving - Shelly Wismath, Doug Orr, & Brandon Good The Impact of Peer Review on Writing in a Psychology Course: Lessons Learned - Naureen Bhullar, Karen C. Rose, Janine M. Utell, & Kathryn N. Healey Using Formative Assessment and Self-Regulated Learning to Help Developmental Mathematics Students Achieve: A Multi-Campus Program - John Hudesman, Sara Crosby, Niesha Ziechmke, Howard Everson, Sharlene Isaac, Bert Flugman, Barry Zimmerman, & Adam Moylan Intellectual Curiosity in Action: A Framework to Assess First-Year Seminars in Liberal Arts Settings - Kenneth H. Kolb, Kyle C. Longest, & Jenna C. Barnet

Journal on Excellence in College Teaching, Volume 7, Number 2

A Message from the Editors - Laurie Richlin & Milton D. Cox Promoting Student Learning Through Questioning: A Study of Classroom Questions - Sandra Edwards & Mary Ann Bowman From Student Narratives to Case Studies: Diversity from the Bottom Up - Diane Gillespie, Jeannette Seaberry, & Joseph Valades Relational Pedagogy: Investigating Together in a Project Discovery Mathematics Course - Marcia B. Baxter Magolda & Jennifer Buckley Energizing the Introduction to Education Classroom Through Experiential Learning - Kathleen Montgomery, Cathleen Deery, & Susan Brown Students\u27 Perceptions of Excellent Lecturers and Discussion Leaders - Gary S. Goldstein & Victor A. Benassi Teaching Strategies for a Barrier-Free Classroom - Rachelle Waksler Breathing the Words: What Students Have Taught Me - Susan Streeter Carpente

Journal on Excellence in College Teaching: Volume 25, Numbers 1

Teaching for Civic Engagement: A Message from the Guest Editor - C. Lee Harrington Lessons in Citizenship: Using Collaboration in the Classroom to Build Community, Foster Academic Integrity, and Model Civic Responsibility - Ann E. Biswas Solving Real Community Problems to Improve the Teaching of Public Affairs - Abdulfattah yaghi & Madalla Alibeli Teaching Evidence-Based Practice in Service-Learning: A Model for Education and Service - John D. Terry, Bradley H. Smith, & Samuel D. McQuillin The Impact of a Service-Learning Experience in Mentoring At-Risk Youth - Leah Wasburn-Moses, Jay Fry, & Kari Sanders Speak Out Loud: Deconstructing Shame and Fear through Theater in a Community-Based Service-Learning Project - Karina Vazquez Teaching Diversity Through Service-Learning: An Integrative Praxis Pedagogical Apprach - Julie Steinkipf Rice & Terri Horn Service-Learning: A Tool to Develop Competencies for College Student