Kennedy P.,Lewis And Clark College
New Phytologist | Year: 2010
The field of ectomycorrhizal fungal (EMF) ecology has largely developed outside the ecological mainstream, owing in large part to the challenges in studying the structure and dynamics of EMF communities. With advances in molecular identification and other research techniques, however, there has been growing interest among mycologists and ecologists in understanding how different ecological factors affect EMF community structure and diversity. While factors such as soil chemistry and host specificity have long been considered important, an increasing number of laboratory and field studies have documented that interspecific competition also has a major impact on EMF species interactions and may significantly influence EMF community structure. In this review, I examine the progress that has been made in understanding the nature of EMF competition. Currently, there are four conclusions that can be drawn: negative competitive effects are rarely reciprocal; competitive outcomes are environmentally context-dependent; field distributions often reflect competitive interactions; and timing of colonization influences competitive success. In addition, I highlight recent studies documenting links between competitive coexistence and EMF community structure, including checkerboard distributions, lottery models, storage effects, and colonization-competition tradeoffs. Finally, I discuss several aspects of EMF competition needing further investigation and some newer methods with which to address them. © The Author (2010). Journal compilation © New Phytologist Trust (2010).
Agency: NSF | Branch: Standard Grant | Program: | Phase: MAJOR RESEARCH INSTRUMENTATION | Award Amount: 306.12K | Year: 2013
An award is made to Lewis & Clark College (L&C) in Portland, Oregon to acquire a Zeiss LSM 710 Confocal Microscope, which will enable at least six different laboratories on campus (in Biology, Chemistry, and Physics Departments) as well as two collaborating labs at other institutions (in Molecular Biosciences and Neurology Departments) to expand and innovate their existing research programs. Confocal microscopy is an advanced fluorescence imaging technique that has a number of advantages over traditional fluorescence microscopy and is a particularly powerful tool for live imaging experiments. The enabled projects focus on live imaging, both in whole organisms (zebrafish, nematode, yeast) and in cultured neurons (mouse). Some of these include: 1) a powerful multicolor approach (Brainbow) to test how newborn cells in the immature brain transform into organized neuronal circuits; 2) fluorescence resonance energy transfer (FRET) to study interactions among ribosomal components in yeast; 3) photoconvertible proteins to study the regulated release of factors in hippocampal neurons during neuronal activity; and 4) in vivo imaging techniques in living zebrafish to study the behavior of proteins that underlie Parkinsons Disease in humans. The principal investigators have externally funded, active research programs that engage undergraduate students as partners in data generation and publications in peer-reviewed journals. Acquisition of a confocal microscope will help these laboratories to generate high-quality publications in areas that utilize and develop cutting-edge live imaging approaches.
The confocal acquisition will also have a number of important broader impacts. First, future generations of scientists will have the opportunity to master modern imaging approaches during their undergraduate training. Many L&C students go on to Ph.D. programs and careers in science after winning competitive research fellowships. In part this can be attributed to L&Cs strong focus on involving undergraduates in meaningful research; in the past five years, more than 90 undergraduate students have contributed as co-authors on publications. These dedicated and capable students will become trained in advanced microscopy by using the confocal system in their coursework and/or research laboratory. Second, L&C is a leader in the training of groups that are traditionally underrepresented in science. The natural sciences at L&C boast large numbers of women majors. In addition, L&C runs a successful, HHMI-funded summer research program that brings high school students from under-represented groups to campus for an intensive, 8-week laboratory experience. The confocal microscope will thus impact large numbers of young women who have chosen to pursue a career in science, as well as high school students who are just beginning to consider the direction of their future training. The opportunity to conduct live imaging experiments is often inspiring for students at this critical stage in their career path. Finally, the L&C Watzek Library Digital Initiatives staff will help design and construct an online public gallery that will showcase selected images and videos captured using the confocal microscope. The funded equipment thus has the potential to impact the broader community and to increase scientific literary among the public
Agency: NSF | Branch: Standard Grant | Program: | Phase: AMO Experiment/Atomic, Molecul | Award Amount: 195.01K | Year: 2015
Significant advancements in 21st century physics have relied on the discovery that properties of atoms are not fixed, but can be changed by interactions with laser light. The ability to understand and control these sensitive interactions is also the key to the creation of new atom-light based technologies. Some atom-light interactions are sensitive to the surrounding magnetic field. As an example, an atom is extremely selective about the precise colors of light it absorbs, but when it is placed in a magnetic field, the atoms color choices will shift depending on the strength of the field. Such interactions can be used as the foundation of a device, called an atomic magnetometer, that can measure unknown magnetic fields. This investigation studies interactions between laser light and a specially prepared gas of atoms that is sensitive to small variations in the surrounding magnetic field. The special preparation uses two lasers and a controlled magnetic field to temporarily but dramatically change how laser light travels through a gas of atoms. As a result, the laser lights brightness fluctuates, or flickers, in ways that are not yet fully understood. These fluctuations not only carry information about the atoms, but they are also especially sensitive to magnetic field variations. This research will further our scientific understanding of atom-light interactions, which is of broad interest for many technological applications. Simultaneously, the research will produce new techniques for detecting small, unknown magnetic fields, like the magnetic fields emitted from the human heart. The new detection methods will potentially impact a broad range of medical and scientific fields, and because they make use of low-cost and potentially portable laser systems, any resulting technological applications will be widely accessible and suitable for use outside of the laboratory environment. Undergraduate students will be involved at all stages of this research agenda, preparing them for careers in research science and other STEM-related fields.
Light intensity fluctuations derived from atomic coherence can encode valuable information about coherence dynamics in an atomic vapor. Furthermore, they provide a platform for a new class of compact and simple atomic magnetometers. This research agenda uses low-cost, free-running diode lasers with inherent frequency noise that is converted into information-rich intensity noise near an atomic resonance. The amplitude and phase of the intensity fluctuations are particularly sensitive to small magnetic field variations near an atomic coherence between Zeeman sublevels. Hanle effect Electromagnetically Induced Transparency will be induced in rubidium vapor and used to prototype and optimize a novel magnetometry technique relying on coherence-derived light fluctuations. The converted laser intensity noise will be studied using self-correlations and spectrum analysis. The findings will deepen our understanding of the relationship between the light fluctuations and the underlying atomic coherence, as well as give us the tools to build a new atomic magnetometer. Moreover, the results will provide useful insight for mitigating noise from imperfect lasers.
Agency: NSF | Branch: Standard Grant | Program: | Phase: Environmental Chemical Science | Award Amount: 220.12K | Year: 2014
The Environmental Chemical Sciences Program in the Division of Chemistry at the National Science Foundation supports the research of Professor Louis Y. Kuo at Lewis and Clark College that will involve undergraduate students. Inquiry-based research will be performed in diverse fields including organic synthesis, chemical catalysis, and coordination and phosphorus chemistry. With Professor Kuos guidance, undergraduates will actively participate in a hypothesis-based investigations driven by the collection of data and the analysis of results spanning different chemical disciplines. Written and oral dissemination of their results will be communicated at local and international venues. The PI has a proven track record of working with undergraduates on projects involving OP chemistry. In the past 20 years, the PI has mentored 37 undergraduate and high school students and has produced 21 publications with student coauthors. Another outstanding feature of this project is the outreach and involvement of high school students and a high school teacher through summer research. This collaboration will impact STEM education and potentially contribute to greater interest by students in sustainable environmental chemistry.
The research will examine the catalytic hydrolysis of sulfur-containing organophosphates (OP) by common, air stable and safe molybdenum oxide complexes. The OP under examination are sulfur-containing compounds that fall into two classes. The first class is the model compound O,S-diethylphenyl phosphonothioate (DEPP) in which further derivatizations are readily accomplished; DEPP also serves as a safe mimic of OP neurotoxins. The second class of compounds is live OP pesticides in common agricultural uses which are Phosmet, Chlorpyrifos and Malathion. This project provides mechanistic information on the hydrolytic degradation of sulfur-containing pesticides. This fundamental investigation focuses on OP hydrolysis through nucleophilic attack and phosphate activation by oxo-molybdates. It also tests how soil (i.e. clay) affects the various routes for OP hydrolysis by these new molybdenum complexes. The research results will provide fundamental understanding of soil-effects on important hydrolytic processes for pesticide degradation.
Agency: NSF | Branch: Standard Grant | Program: | Phase: | Award Amount: 200.00K | Year: 2012
This project provides general and organic chemistry students with hands-on education using single crystal X-ray crystallography (SC-XRD) at Lewis and Clark College and a consortium of three other campuses - George Fox University, Willamette University and the University of Portland. Curricular materials using SC-XRD to analyze samples and determine accurate and precise measurements of the full three dimensional structure of a molecule, including bond distances and angles, are designed, implemented, evaluated and diseminated. SC-XRD is an emerging topic in the undergraduate chemistry curriculum and this projects helps to fill a gap in available curricular materials. Faculty members from participating campuses participate in workshops where they both refine their skills using the instrumentation and develop the new teaching materials. Structural information is available to other institutions through online data sharing. Curricular materials and evaluation outcomes are disseminated through a sponsored regional meeting, project web site and publications. Evaluation of the technical component of developed materials is performed by an experienced crystallographer, while evaluation of the faculty professional development and the projects impact on student attitudes and learning outcomes, is performed by a faculty member from the Lewis and Clark Graduate School of Education and Counseling.
Agency: NSF | Branch: Standard Grant | Program: | Phase: FED CYBER SERV: SCHLAR FOR SER | Award Amount: 166.53K | Year: 2015
The EDURange project, a collaboration between Evergreen State College and Lewis and Clark College, will support faculty teaching cyber security by providing hands-on exercises, a student-staffed help-desk, and webinars. These resources will be designed to be easy to deploy and will be interactive, competitive and collaborative to ensure student engagement. The availability of these resources will make it easier for computer science faculty with little prior background to teach security across, and will increase the number of schools teaching cyber security concepts. As a result this project will produce more students with the analytical skills required to secure computing assets in the Pacific Northwest and in turn will help to ensure American technical competitiveness in the future.
The resources will be linked to the concepts and learning outcomes defined in the IEEE/ACM CS Curricula 2013 report. Support for these resources will be provided by a student-run help desk and a user interface that will allow faculty to modify exercises to fit the content and level of difficulty of their classes. Background material will be provided for students to make the exercises applicable to a variety of computer science classes. These resources will fulfill four important needs: (1) expanding and disseminating technology ? improving exercises using EDURange, a flexible, cloud-based teaching infrastructure, (2) faculty development ? helping them use hands-on security exercises in their classrooms and providing curricular resources, (3) student engagement ? developing their skills, leveraging their talent and knowledge, and mentoring them to become the next generation of teachers and researchers, and (4) education research --investigating the acquisition of analytical skills.
Assessment of the resources will focus on four activities: (1) a quantitative evaluation and summary of how often and how widely the resources are used, (2) a qualitative assessment of how well exercises map or express the cyber security knowledge units of CS2013, (3) an assessment of faculty experience using the resources in their courses, and (4) an evaluation of the experience using the resources by security faculty, professionals, and students.
Agency: NSF | Branch: Standard Grant | Program: | Phase: Cellular Dynamics and Function | Award Amount: 469.41K | Year: 2016
The project will investigate how compartments are generated within some cell types but not others in multicellular animals. The cells of complex organisms contain compartments called organelles that endow cells with their specific functional properties. While many organelles are common to all of the cells within an organism, some are only generated in a subset of cell types. One of these, called a lysosome-related organelle (LRO), plays varied and important roles, however only certain animal cells generate them. The research will investigate how this is achieved and identify factors that promote the formation of LROs. Many undergraduates (25-55/year)will be mentored in collaborative, investigative, and original research as part of the project. Many of these students will come from underrepresented groups in the sciences. The work will provide hands on scientific training for a large and diverse group of students, most of who will progress on to careers in science and education.
In many cell types, lysosome-related organelles LROs co-exist with conventional lysosomes due to the activity of conserved LRO-specific trafficking pathways that divert cargo away from endolysosomes. The emergence of LRO biogenesis pathways likely result from the poorly understood interplay of general endolysosome trafficking factors expressed in all cells with key regulators that are only present and active within LRO-containing cells. To identify and investigate the function of these regulators, the project is analyzing the biogenesis of C. elegans gut granules, cell type-specific LROs that co-exist with conventional lysosomes. Some LRO biogenesis factors identified in this system have cell type restricted expression and likely regulate the diversion of cargo to LROs. The research addresses the function of one of these, GLO-3, which is proposed to redirect the function of CCZ-1, a RAB-7 guanine nucleotide exchange factor (GEF), away from conventional endolysosomal pathways, toward the GLO-1 Rab to regulate LRO biogenesis. The research will involve detailed phenotypic analysis of mutants, yeast 2-hybrid screens, and in vitro GEF assays. The research will examine whether expressing GLO-3 and other LRO biogenesis factors are sufficient to direct the trafficking of LRO cargo away from conventional endosomes in cell types that do not normally generate LROs. The research will employ a novel genetic resource to identify nearly all of the genes necessary for LRO biogenesis in C. elegans.
Agency: NSF | Branch: Standard Grant | Program: | Phase: ORGANIZATION | Award Amount: 823.01K | Year: 2016
The remarkable function of the brain requires proper growth and formation in the embryo. First, a small cluster of cells increases dramatically in number, then transforms into an exquisitely organized organ with a complicated pattern of connections. Most of the time, this process results in brains that are perfectly normal, with the right number of nerve cells. Surprisingly little is known, though, about how the growing brain decides how many cells to produce. This research project will look at the control of cell number in the growing brains of transparent living zebrafish during the first few days of life. The PI has developed techniques for watching clusters of dividing cells over time in special zebrafish embryos whose brain cells glow with unique combinations of colors (called Brainbow). This coloring allows new cells to be followed as they divide off from their mother cell. So far it appears that families of cells (mother cell with her set of daughter cells) compete with other families to survive in the growing brain. This type of competition has not been seen before in the brain, and may be responsible for controlling growth - not only in the brain, but in other organs as well. The PI will test which genes are important for cell families to survive this competition. The work will generate a number of new research tools that will be shared with the scientific community. Undergraduate students will perform and analyze the experiments themselves, providing rich opportunities for research training early in developing scientists careers. By also transforming the data they have personally collected into an interactive, educational website, students will learn various digital media approaches to making scientific material understandable to traditional and non-traditional audiences. The colorful images produced by this research have great appeal to both scientists and non-scientists, making it easier for students to learn how to engage the public with their work.
To study dynamic cellular behavior in the living brain, the PI has developed an approach using in vivo time-lapse confocal imaging and multicolor fluorescent protein (Brainbow) expression in zebrafish. Using this technique, the PI has shown that programmed cell death occurs non-randomly in the living brain, with specific neural progenitor cells and their neuronal progeny (entire clones) undergoing cell death in a coordinated manner, while neighboring clones appear normal. If whole clones of dividing cells are in fact competing with one another, increases or decreases in cellular fitness should influence a clones competitive edge. The planned research will use a mosaic approach to alter gene expression in individual cells, coupled with global Brainbow expression to simultaneously follow dynamics within multiple clones of dividing cells. Cellular fitness will be targeted via both cell-intrinsic mechanisms (cell cycle, c-myc activity) and cell-extrinsic mechanisms (access to extracellular BMP signaling). These experiments will test directly whether cellular fitness influences a clone?s ability to survive in the developing brain. Overall this may support the hypothesis that competition among clones of dividing cells helps regulate neuronal production and growth in the developing nervous system.
Agency: NSF | Branch: Standard Grant | Program: | Phase: | Award Amount: 199.57K | Year: 2012
Lewis and Clark Community College (L&C) is developing a STEM-based outreach program using hands-on activities for the design and construction of trebuchets. Project activities include constructing STEM-based learning objectives for the trebuchet competition, expanding an existing trebuchet contest to a broader and diverse number of high schools, building collaborative relationships with schools of engineering at regional universities, arranging strategies for tracking the enrollment histories of engineering students, and building partnerships with regional industries to support STEM-based engineering and engineering technology programs. L&C is expanding the level of participation of high schools to at least 25 schools (and 80 teams). Collaborating partners are the Schools of Engineering at Southern Illinois University Edwardsville (SIUE) and Missouri University of Science & Technology (MST). Industrial partners include Covidien Pharmaceutical and Boeing (both of St. Louis). A freshman-level course to introduce students to engineering is also being developed. The project consults with leaders of a related project at Sierra College (CA) and their NSF/ATE Center for Applied Competitive Technologies.
Lewis And Clark College | Date: 2013-05-30
Degradation of phosphate esters, particularly neurotoxins and pesticides, is performed using high oxidative state molybdenum complexes, more particularly molybdenum(VI) complexes. A molybdenum(VI) complex is dissolved in water and then reacted with a phosphate ester. The phosphate esters can include, but are not limited to, VX, VE, VG, VM, GB, GD, GA, GF, parathion, paraoxon, triazophos, oxydemeton-methyl, chlorpyrifos, fenitrothion and pirimiphos-methyl, representing both chemical warfare agents as well as pesticides and insecticides.