Douglas Clark - US grants

The objective of this research is to enhance understanding of reversible ethanol induced thrombocytopenia, a common and serious complication of alcoholism. I have developed a tissue culture system for the assay of human megakaryocyte progenitors (CFU-M) in vitro, to study the effects of ethanol on thrombocytopoiesis. Ethanol suppresses human platelet production independently of nutritional deficiency and inhibits proliferation of myeloid and erythroid progenitors in vitro. In have done preliminary experiments showing that both a cell closely related to human CFU-M and human megakaryocytes are sensitive to ethanol at or near concentrations occurring in vivo. To render this system more useful for studying the effects of ethanol, I propose to characterize it further as to the influence of cell-cell interactions on CFU-M proliferation. I then propose to delineate more fully the degree of ethanol sensitivity of human CFU-M and related cells. Bone marrow cells will be fractionated before exposure to ethanol to reveal the contribution of accessory cells (adherent leukocytes and T-lymphocytes) to ethanol sensitivity. Similar experiments will also be performed with acetaldehyde, the principal metabolite of ethanol. To investigate a possible basis for the effects of ethanol and acetaldehyde. I will attempt to reverse their inhibitory effect on CFU-M by supplementation of cultures with micronutrients (folinic acid, pyridoxine) or metabolites (a-ketoglutarate, L-asparate) implicated in the effects of ethanol on other hematopoietic cells or other tissues. Since platelet production may be regulated at two levels, I also propose to isolate human megakaryocytes from bone marrow by established techniques to determine the effect of ethanol and acetaldehyde on DNA and protein synthesis and maturation of these cells and its potential reversibility by micronutrients or metabolites. To study the effect of chronic alcoholism on CFU-M in vivo, I shall collect bone marrow and serum from consenting patients hospitalized with ethanol thrombocytopenia. Bone marrow will be assayed for CFU-M number and proportion in S-phase in comparison to assays for BFU-E and CFU-GM and with results from normal volunteers. Serum will be assayed for the possible presence of factors inhibitory to CFU-M proliferation in culture in an autologous system. These studies will increase knowledge of mechanism by which ethanol produces significant end-organ damage and will lead to increased understanding of normal thrombocytopoiesis by its contrast with the diseased state.

This research involves novel strategies to produce antibody polypeptides with optimal structures for immobilization to insoluble carriers. Each approach is designed to result in immobilized, monovalent antibody fragments with their combining sites facing out from the carrier surface, and attachment to the carrier will be achieved in a highly specific manner through a site on the polypeptide far removed from the combining site itself. Attachment in this fashion should allow complete retention of antibody binding activity and thus lead to improved techniques of affinity purification. In addition, immobilizing antibody fragments rather than the much large whole antibody should increase the number of antibody combining sites that can be immobilized on the carrier surface. In the case of Fv fragments, site-directed mutagenesis will be used to incorporate a single attachment site at a desired location on the polypeptide. The modified polypeptide will then be expressed in E. coli. Production of Fv fragments in E. coli may prove to be a superior alternative to present-day hybridoma technology, which is frequently the limiting factor in monoclonal antibody production and isolation. Moreover, both site- directed mutagenesis and random mutagenesis can be used to rapidly obtain antibody polypeptides with variant binding activities. Protein engineering may also be used to introduce pH or metal-regulated binding affinity into the combining site.

This collaborative project between workers at Berkeley and UCSF is designed to produce new polymeric peptides with useful properties. The investigators are all excellent scientists, although all well supported by other grants. In particular Dr. Craik has another NSF grant which duplicates his effort in this proposal. The P.I. has developed enzymatic methods for reacting amino acid esters in organic solvents with free amino acids to generate dipeptides. The approach has been extended to a tetra peptide, but the strategy seems unlikely to produce useful polymers, although it might be practical for short peptides. It should be noted that carboxypeptidase cannot be employed in such syntheses because it does not have and acyl enzyme intermediate. There are some interesting ideas in this proposal, but the practicality of synthesizing polypeptides by these approaches seems minimal.

9318821 Clark This Conference will highlight scientific as well as engineering aspects of enzyme technology. The program will include sessions devoted to new biocatalysts, advances in biosensor technology, metabolic and protein engineering, metal-based biocatalysts, and new biomolecules with enzyme-like properties. Industrial applications are also to be presented. ***

The University of California Berkeley will receive ARI Facilities support to create modern facilities for researchers working in a unique, integrated Program in Biological Chemistry and Engineering within the College of Chemistry. The renovated facilities will promote a strong interaction among bioinorganic chemists, biochemical engineers, and bioorganic chemists working in the areas of biotechnology and environmental research. The renovations activity funded by this award will be directed at the improvement of 1,305 square meters in 30-year old Latimer Hall and will consolidate researchers. Program activity will be enhanced as researchers are currently located in geographically distributed campus laboratories that are between 32 and 77 years old. A 7 month- long space assessment precedes the project which will involve gutting much of the interior space, installation of modular laboratory units and new fume hoods and upgrades to the mechanical, electrical and plumbing services for increased safety and improved efficiency. Provision of adequate facilities will enable the basic discovery processes to be linked more closely with the development process. Biochemical engineers will study separation techniques for the recovery of biological products, biomimetic adsorbents for metal removal and recovery and new approaches to bioremediation. Bioinorganic chemists will study metal ion transport that is essential to life processes, the use of chelating agents in the sequestration of heavy metals, and lanthanide complexes for possible use in enhancing MRI. A total of 8 professors and 117 graduate students and postdoctoral fellows will benefit from these improvements.

9421862 Clark This project is on research to study the production of enzymes from extremophiles by expression of these enzymes in mesophiles, using recombinant DNA technology. The objective is to make available large quantities of these enzymes for biophysical and biochemical characterization and ultimately for enzymatic applications, without the need for culturing extremophiles directly. The specific objectives of this research include: (1) to clone and identify gene sequences from the hyperthermophile Pyrococcus furiosus and related thermophiles; (2) to express genes in heterologous systems at high pressure, and characterize recombinant enzymes under elevated pressure and temperature to establish optimal specific activity and assembly; and (3) to develop bioprocessing methods for obtaining enzymes in sufficient quantity for structural determination and biotechnological applications. ***

This project is building a high-performance multiprocessor from commodity desktop computer systems and off-the-shelf interconnects. Commercial Intel Pentium workstation boards, each with attached memory, disk, and I/O, are attached to a Paragon backplane. Communication uses a new mechanism called virtual memory-mapped communication, which disguises interprocessor communication as write operations to memory. The node interface maps physical pages in the memories of individual nodes to each other, so that a write to one mapped page results in messages to other nodes that share the mapped page. The operating systems on the individual nodes use their ordinary virtual memory mechanism to support virtual page mapping. In addition to this word-by-word communication, DMA transfers are available, with control registers located in the address space of individual processes. This allows high bandwidth communication that maintains user-level protection. Research to be addressed in the project includes the achievement of high-bandwith low-latency communication between processes, the structure of an I/O system supported by the new communication mechanism, and performance evaluation of the resulting system.

Caches and write buffers are becoming increasingly important to memory hierarchy designs since they are the key components for bridging the widening performance gap between microprocessors and DRAMs. This research studies the details of memory-referencing behavior in contemporary uniprocessors such as multiple referencing behavior . In particular, the research investigates the fine distinctions that characterize data references with respect to their cache and write-buffer behavior, and also studies possible architectural and organizational enhancements that will benefit writes.

DESCRIPTION: (Adapted from Applicant's Abstract) Cryptosporidium parvum is an important, poorly-understood protozoan parasite that causes refractory intestinal infection in HIV-infected persons. The clinical spectrum of cryptosporidiosis is broad, ranging from asymptomatic carriage to life-threatening diarrhea. Several small studies have suggested that clinical diversity is accompanied by genetic heterogeneity among different C. parvum isolates. The investigator will examine the correlation between the genotype and pathogenicity of C. parvum isolates using molecular genetic techniques. Isolates from a collection of stool samples and intestinal biopsies that have been previously collected will be studied. Genotypic data will be correlated with clinical information obtained from the infected patients. The specific aims of this proposal are to: (1) identify genetic polymorphism of the C. parvum elongation factor-2 and actin genes in human isolates. DNA sequence variation of these genes will be detected by restriction fragment length polymorphism (RFLP) analysis of PCR-generated gene fragments. (2) characterize the ribosomal RNA genes from C. parvum. The small subunit (18s) ribosomal RNA genes from the AUCp-1 isolate of C. parvum will be cloned, sequenced and used to identify genetic polymorphism within rRNA genes from the C. parvum isolates. (3) correlate the genotype of C. parvum isolates with their clinical behavior and histology. (4) identify genotype-specific C. parvum oocyst mRNAs.

9816490 Clark Hyperthermophilic microorganisms may be suitable models for ancestral, and possibly extraterrestrial, biosystems because their extraordinary adaptive capabilities allow them to colonize a wide range of subsurface volcanic areas on Earth. Deep sea hydrothermal vents and terrestrial hot springs support highly diverse ecosystems without access to solar energy, harboring autotrophic microorganisms and their dependant heterotrophic micro and macro communities in geochemical conditions similar to those that may exist below the surface of Mars or Europa. Hyperthermophiles also dominate most of the deeper branches of the universal phylogenetic tree, suggesting that ancestral microorganisms may have been thermophilic. The environmental limits for growth and survival of known hyperthermophilic species, as well as newly isolated strains will be established, using a combination of bioengineering, microbiology and molecular biology. This collaborative project with Dr. Frank T. Robb of the University of Maryland, Baltimore (Award MCB-9809352) emphasizes molecular adaptations to high pressure and high temperature, with the following objectives: 1. To determine the effects of supraoptimal temperatures and pressures on the survival and growth rates of existing hyperthermophilic microorganisms; 2. To utilize pressurized continuous fermentation systems for isolation and culture of new hyperthermophilic microbial strains and; 3. To examine physiological adaptations and genetic regulation of gene expression in response to transient challenges by heat and high pressure. The hypothesis being tested is that hydrostatic pressure may greatly extend the upper temperature limits of growth and survival of hyperthermophiles. Ongoing studies by these researchers have established that many enzymes from thermophiles display enhanced thermostability under pressure. Further, the growth rate of Methanococcus jannaschii accelerated five-fold and its maximum temperature for methane production rose by 6 degrees C in response to pressure, and the growth rate and ATP production of a newly characterized abyssal hyperthermophile, Pyrococcus horikoshii, were elevated under pressure. Novel equipment for incubating hyperthermophiles in continuous culture, under pressure and with thermal cycling, will be combined with molecular biology to explore the adaptive responses of hyperthermophiles in extremis. Gene expression, membrane lipid composition and morphology will be examined. The genes that are induced under conditions approaching lethality, will be identified by subtractive cloning and transcriptional assays. Upper survival limits of the abyssal hyperthermophiles as a function of pressure, using isolates from a shallow terrestrial sampling site to provide control data for pressure responses, will be determined. Enrichment cultures of hyperthermophiles from the vent systems of the back-arc region of the Northwest Pacific (Okinawa Trough and Uzzon Caldera on the Kamchatka Peninsula) will be incubated at temperatures and pressures exceeding those tolerated by known strains, thus using survival rather than rapid growth as the criterion for selection of new isolates. The phylogenetic positions and physiological requirements of the new strains will be determined. ***

This proposal pursues an older observation that the lyophilization of certain enzyme catalysts in the presence of highly ionic, non-buffering salts, e.g., KCl, can increase the catalytic rate in non-aqueous systems by 3-4 orders of magnitude. This has been demonstrated primarily on subtilisin. The specific aims of the original proposal are:
To elucidate the mechanism(s) of enzyme activation in organic solvents with salts
To extend the concept to a broad range of enzymes and reactions. To utilize the activated enzymes for combinatorial biocatalysis. In the revised and funded proposal, Aim 3 has been dropped and a more detailed examination of the mechanism and scope of the phenomenon has been added.

The goal of this research is to reduce the cost and improve the
performance of observation-based branch characterization mechanisms in
the compiler and hardware. Often, correlation discovered at great cost
or missed entirely through execution can be determined in a simple
algebraic fashion at compile time. Relationships between program
structures can be inferred from these algebraic expressions and
subsequently conveyed to compiler optimizations and to the hardware
through appropriate mechanisms to be developed by this research. Once
employed, these relationships can refocus the efforts expended by
observation-based mechanisms, or can eliminate the need for them
altogether.

This award is for a project that involves coring and initial analysis of sediments in a deep, long-lived bog in the heart of the glaciated Sierra Nevada. The bog is unique in western North America because of its mountain location, depth, and potential to preserve sediments that date through most if not the entire last glacial cycle (~70,000-120,000 years). The location is particularly crucial, because the bog should record changes in sedimentology, slope stability, sediment geochemistry, paleomagnetism, and paleoecology in an environment that heretofore has not yielded a continuous record that dates past the last glacial maximum (~20,000 year B.P.) The investigators propose to drill through the Tioga outwash in the bog and into the underlying sediments recovering continuous core. They will then do basic analyses of the core sediments and obtain enough radiocarbon ages to demonstrate the kind of paleoclimate record that is potentially available from the bog.

The Biochemical Engineering Conference serves as the premier meeting for the Biochemical Engineering community. The focus of this Conference will include important core areas of Biochemical Engineering (fermentation/cell culture and downstream process development) as well as exciting new frontiers of Biochemical Engineering (nanotechnologies, the "omics" of proteomics, genomics and physiomics, marine and environmental biotechnology). The Conference will illustrate how the same engineering fundamentals (unit operations, mass and energy transport, thermodynamics, and kinetics) that form the basis of traditional areas of Biochemical Engineering are being applied to drive advances in both areas. In addition to the regular sessions, two workshops are planned. A workshop entitled "Biochemical Engineering Education: fundamentals versus state-of-the-art" will focus on the often-competing needs to incorporate engineering fundamental into the curriculum as well as state-of-the-art applications. This workshop will feature representatives from industry and academe. A second workshop entitled "New Directions in Biochemical Engineering Research" will focus on potentially new areas for research in Biochemical Engineering. The discussion will have as panelists both academic and industrial representatives. Each panelist will be asked to prepare a single transparency and speak for no longer than 5 minutes. Following the presentations, input from the audience will be requested.

The objective of this project is to improve recombinant expression systems. The major goals are to discover and characterize pathways that facilitate protein folding and subunit assembly in hyperthermophiles. The components of these pathways will be inserted into recombinant host cells to preempt induction of stress responses during recombinant expression, and to enhance the stabilization and solubilization of recombinant protein. Building on the approach and findings of the investigators previous research, the specific objectives are: (1) to determine the functions of interacting proteins encoded by the 23 genes in the heat shock regulon of the hyperthermophile, Pyrococcus furiosus, (2) to identify functional complexes of thermostable heat shock proteins and express them in E. coli, yeast and mammalian cells to enhance the durability of these cells, and (3) to determine the effects of combinations of chaperonins on high level recombinant expression of proteins in intact cells as well as cell-free transcription-translation systems.

The overall goals of this research are to achieve rate enhancements of several thousand fold, and to elucidate the underlying mechanism(s) for the activation process. This research will therefore provide new insights into the factors that govern enzyme activity in organic solvents, and will enable enzymes to play an expanded role in industrial processes, including chemicals and pharmaceuticals synthesis, polymer synthesis, drug discovery, and waste treatment, among other emerging applications of biocatalysis. Moreover, the same techniques that lead to improved enzyme function in organic solvents are likely to be of use in the stabilization of dehydrated protein systems, which is a critical issue in biotherapeutic protein formulation and delivery. Thus, this work has broad impact, ranging from biocatalysis to drug discovery to biopharmaceutical formulations.

Margaret Martonosi, Princeton University, Adaptive, Power-Efficeint Processors for Sensors and Embedded Systems

Sensor network systems have seen increasing research attention recently,
with a wide range of scientific and commercial applications. Sensor
processors need "agile" performance that responds quickly to
high-throughput bursts, with also lower-energy execution when
possible to minimize energy consumption. Sensor systems have
limited power budgets, with traditionally most energy going to
radio communications. But as radios improve and computational
demands increase, more of the energy budget is shifting back
to the processor.

This research examines processor architectures for agile,
energy-efficient, stream-based processing in sensor networks
and other embedded systems. A particular focus is on using
parallelism (through tiled processing units) for energy management.
Another key aspect is investigating the interconnect between on-chip
processing units, and exploring design techniques that let different
processing elements run at different clock rates. Connecting processing elements by
a system of hardware queues, for example, allows the chip to exploit
a thread-based, producer-consumer model to adapt processor settings
to running threads; this enables efficient energy and speed control
via dynamic voltage/frequency scaling. By exposing
queue/memory status to near neighbors, processors can use
control theoretic approaches to coordinate performance/energy
needs across local and broader regions.

Major research questions include: (i) How much on-chip parallelism
best balances application performance and energy? (ii) What range of applications
are applicable to this model? (iii) How to design performance and
power-efficient speed-control models based on local and global
control approaches? (iv) What are the roles of distributed and
hierarchical control techniques? (v) Can control theoretic
approaches be devised that offer good responsiveness and stability
in the face of sensing errors and sensing/actuation delays?

David Walker
Princeton University
0627650
Panel: 060970
Well-typed trustworthy computing in the presence of transient faults

Abstract



In recent decades, microprocessor performance has been increasing
exponentially, due in large part to smaller and faster transistors
enabled by improved fabrication technology. While such transistors
yield performance enhancements, their lower threshold voltages and
tighter noise margins make them less reliable, rendering processors
that use them more susceptible to transient faults caused by energetic
particles striking the chip. Such faults can corrupt computations,
crash computers, and cause heavy economic damages. Indeed,
Sun Microsystems, Cypress Semiconductor and Hewlett-Packard
have all recently acknowledged massive failures at client sites
due to transient faults.

This project addresses several basic scientific questions: How does one
build software systems that operate on faulty hardware, yet provide
ironclad reliability guarantees? For what fault models can these
guarantees be provided? Can one prove that a given implementation does
indeed tolerate all faults described by the model? Driven in part by
the answers to these scientific questions, this project will produce a
trustworthy, flexible and efficient computing platform that tolerates
transient faults. The multidisciplinary project team will do this by
developing: (1) programming language-level reliability specifications so
consumers can dictate the level of reliability they need, (2)
reliability-preserving compilation and optimization techniques to
improve the performance of reliable code but ensure correctness (3)
automatic, machine-level verifiers so compiler-generated code can be
proven reliable, (4) new software-modulated fault tolerance techniques
at the hardware/software boundary to implement the reliability
specifications, and finally (5) microarchitectural optimizations that
explore trade-offs between reliability, performance, power, and cost.

This award will use funds made available under the auspices of the Small Grants for Exploratory Research (SGER) program to deploy an experimental and mobile coring apparatus to obtain ice cores from an alpine site atop Mt. Waddington in the British Columbia Coast Range.

The site holds the promise, but not the certainty, of obtaining a continuous record of inter-annual variability in net annual snowfall over the last 200-1,000 years. This is important because if the drill works as planned, it will open up a new archive of paleoclimate data to use by climate researchers. At present, most paleoclimate research from ice cores is conducted from large base stations in polar regions.

Annual snow accumulation records, which can be well preserved even in areas with significant summer melt-layer formation, have been shown to be useful quantitative indicators of large-scale atmospheric circulation patterns. Snow accumulation records from the North Pacific region are of particular interest because of their potential to contribute to the documentation and reconstruction of multi-decadal climate variability. The ice divide at Combatant Col, below the summit of Mt. Waddington, contains approximately 150 meters of ice and rarely experiences melt at the surface.

The funds from this award will be leveraged against funds from the Canadian Foundation for Climate and Atmospheric Sciences (CFCAS), who will bear the majority of the expedition costs (i.e., helicopter support, drill shipment, drill preparations and repair) and provide satellite imagery and analysis, installation of a weather station near Mt. Waddington, mesoscale climate modeling, and glacier ice flow modeling. The co-funding between the US NSF and the CFCAS is an attractive feature of this SGER request because it effectively leverages US funds to derive a bigger bang for the US buck.

Besides field testing a new strategy in ice core drilling that could have broad impact on the wider science community, the data from project will aid in the quantitative reconstruction of climate variability in western North America and the North Pacific as well as improved understanding of glacier mass balance and hydrological variability.

Geology (42) This project investigates the value of incorporating chronotopographic analysis across a range of undergraduate geology courses using terrestrial laser scanning (TLS) to improve student understanding of the rates and styles of geomorphic processes. Repeat high-resolution TLS surveys have begun to track, in detail, the evolution of active landscapes, including investigations of active faulting, glaciation, landslides, fluvial systems and coastal dynamics. This project is investigating the hypothesis that undergraduate geology students who collect and analyze positional data for locally-important, active landscapes develop a better sense of the critical (and non-steady) geomorphic processes affecting landscape change. A collaborative faculty team from three institutions (regional university, community college, and tribal college) are acquiring and being trained on a TLS system and are collecting baseline scans of actively evolving landscapes identified in cooperation with local land-use agencies. The team is developing inquiry activities for each site and for classes at each institution, and assessing their impact using rigorous evaluation procedures. The 2-year college faculty and students are especially interested in monitoring rapid retreat of coastal bluffs near their campus. The tribal college faculty and students are integrating the TLS monitoring into their BA degree program and into a high school mentoring program with the support of the Lummi Nation School physics teacher. The university faculty are incorporating the TLS scanning into upper division geomorphology courses. In small research teams, students are: partnering with a local land-use agency to identify and evaluate an actively evolving landform; defining target zones for TLS surveying; designing and conducting a TLS survey; conducting basic TLS data processing, including deformation analysis with past surveys; quantifying variability in rates and modes of landscape change at several time and length scales; and identifying uncertainties and limits of TLS data, and their value relative to qualitative assessments (e.g., geomorphic mapping, repeat photography, etc.). Pre- and post-instruction data on student understanding of geological rates are being collected. Questionnaires and interviews are designed to measure preconceptions and then evaluate change after students complete the chronotopographic activities. The results of this project are being disseminated through the "On the Cutting Edge Teaching Geomorphology" web site (cross-referenced with NSDL), and the processed chronotopographic sequences are being posted on the WWU Landscape Observatory web site. The results of this project benefit research universities that may already have a TLS system, and regional and liberal arts institutions, which may be evaluating the value of incorporating this 'revolutionary' technology into their undergraduate curricula.

Scaffolding Understanding by Redesigning Games for Education (SURGE) is a three year exploratory project focusing on the redesign of popular commercial video games to support students? understanding of Newtonian mechanics. In support of this goal, SURGE develops and implements design principles for game-based learning environments integrating research on conceptual change, cognitive processing-based design, and socio-cognitive scripting.

The initial development enhances ?marble? virtual obstacle course games with visual signaling techniques to help make explicit underlying physics properties and processes present in the games. SURGE augments this popular type of game to help learners extend and connect the rich tacit understandings that video games typically support with broader explicit formalized knowledge structures to facilitate transfer across contexts. These enhanced games thus bridge the gap between student learning in non-formal game environments and the formalized knowledge structures learned in school by leveraging and integrating the strengths of each. As a consequence, school learning is more attainable and more broadly applicable.

The project strategies and assessment focus on closing achievement, motivation, and self-efficacy gaps among female students, English language learners, and students with low prior success in science. Various methods are used to assess learning such as the Force Concept Inventory, the Patterns for Adaptive Learning Survey, and the Test of Science Related Attitudes. An iterative design and test process is used with full experimental design and random assignments in late phases.

Funding is provided to obtain new ice core accumulation records from Combatant Col, Mt. Waddington, in southwestern British Columbia (BC), Canada. Combatant Col is located significantly farther south than other existing ice core sites along the west coast of North America and variations in precipitation tend to be out of phase with those in Alaska and the Yukon.

Combatant Col sits at 3000 meters and contains more than 200 meters of ice. The net annual snow accumulation is ~2.5 meters/year and the mean annual temperature -5°C. A 65-meter core from the site shows that clear annual layering is preserved in the geochemistry and in dust and black carbon. The age of the ice near bedrock is estimated to be between 200 years and 1000 years old. It is anticipated that an annually-resolved record of layer thickness will be recovered at the site to allow for a record of snow accumulation covering the last 200-1000 years.

The Combatant Col record, in combination with other existing records of precipitation variability along the western margin of North America, will be used to develop an updated and improved reconstruction of precipitation variability in this region over the last 200-1000 years to address fundamental questions about Pacific decadal scale variability.

The broader impacts involve supporting an early career female investigator and strengthening international collaborations with researchers from institutions in Canada.

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

This Small Business Technology Transfer (STTR) Phase II project will address further development and commercialization of a multi-enzyme lead optimization chip (Multizyme Chip) for high-throughput generation of lead compound analogs coupled with cell-based screening for the rapid identification of biologically active derivatives. Such a capability directly impacts a key bottleneck in drug discovery; namely, the efficient optimization of lead compounds to develop drugs with optimal pharmacological properties. Solidus Biosciences, Inc. proposes to combine six biocatalysis with pharmacological screening to provide rapid identification of biologically active compounds against cell-specific targets, which is a new paradigm for lead optimization. Moreover, the Multizyme Chip platform will be well-suited for lead optimization in related industries, including agrochemicals, cosmetics, and cosmeceuticals. The Solidus technology will thus improve the competitiveness and efficiency of the pharmaceutical, cosmetics, and chemical industries, and will serve as a rich source of new and improved commercial products.

The broader impacts of this research are the advances that Solidus Biosciences will achieve toward generating better and safer drugs, reducing the cost to develop these drugs, and increasing the overall efficiency of the pharmaceutical industry. Solidus will generate Multizyme Chips for purchase by pharmaceutical and biotechnology companies to facilitate their lead optimization programs, particularly those involving natural product-derived and complex synthetic small molecule leads. Cryopreservation techniques developed in Phase II will enable the sale of chips and chip-handling devices produced during Phase I, and will allow seamless penetration of the Solidus technology platform into the company's target markets.

This project's investigation is at the nexus between scientific thinking, computational thinking, modeling as an investigative endeavor, and visual programming tools. The PIs are infusing middle-school science with efforts to promote computational thinking, doing that through making modeling a more significant part of science activities. The modeling experiences learners have become progressively more complex throughout each module and more complex across modules, with the increases in complexity informed by complexities of becoming a computational thinker. Modeling and computational thinking are foregrounded in each module, with each becoming more fluid over time as a result of the repetition of increasingly complex modeling experiences in a variety of situations, all of which build on each other. The mental model building, computational thinking, modeling, and science education literatures all inform the endeavor. The technological innovation includes creating and refining a modeling environment appropriate to middle schoolers, including an appropriate visual programming language. Research questions address issues in learning computational thinking in the context of learning to model and use models for investigation (and vice versa) and trajectories towards competency in computational thinking and modeling as their research questions.

Computational thinking is becoming a more and more important required expertise of scientists -- both those who work at the high levels of computational science and engineering and those who support them and apply computational science. In addition, as computation becomes more and more ubiquitous in a whole variety of disciplines and workplace responsibilities, the rest of the population, too, needs to be more expert at computational thinking and at using computational tools. Infusing computational thinking and the use of computational tools into the curriculum in appropriate ways is the right way to promote this cross-cutting expertise. Science is one place in the curriculum where computational thinking can easily be integrated, and doing so not only holds the promise for readying more of the population for careers and jobs that require computational thinking and use of computational tools but also making middle school science more exciting to more of the population.

This development and research project from Vanderbilt University, Facet Innovations, and Filament Games, designs, develops, and tests a digital game-based learning environment for supporting, assessing and analyzing middle school students' conceptual knowledge in learning physics, specifically Newtonian mechanics. This research integrates work from prior findings and refines computer assisted testing and Hidden Markov Modeling to develop a new methodology to engage students in deep learning while diagnosing and scaffolding the learning of Newtonian mechanics.

The project uses a randomized experimental 2 x 1 design comparing a single control condition to a single experimental condition with multiple iterations to test the impact of the game on the learning of Newtonian physics. Using designed based research with teachers and students, the researchers are iteratively developing and testing the interactions and knowledge acquisition of students through interviews, pre and post tests and stealth assessment. Student learner action logs are recorded during game-play along with randomized student interviews. Students' explanations and game-play data are collected and analyzed for changes in domain understanding using pre-post tests assessment.

The project will afford the validation of EGAME as an enabler of new knowledge in the fields of cognition, conceptual change, computer adaptive testing and Hidden Markov Modeling as 90 to 300 middle school students learn Newtonian mechanics, and other science content in game-based learning and design. The design of this digital game platform encompasses a very flexible environment that will be accessible to a diverse group of audiences, and have a transformational affect that will advance theory, design and practice in game-based learning environments.

The Cyberlearning and Future Learning Technologies Program funds efforts that support envisioning the future of learning technologies and advance what we know about how people learn in technology-rich environments. Development and Implementation (DIP) Projects build on proof-of-concept work that shows the possibilities of the proposed new type of learning technology, and PI teams build and refine a minimally-viable example of their proposed innovation that allows them to understand how such technology should be designed and used in the future and that allows them to answer questions about how people learn, how to foster or assess learning, and/or how to design for learning. An important issue in education is helping learners understand scientific phenomena, especially those that are too small or large, fast or slow, dangerous or inconvenient to experience and manipulate first hand. A way of helping learners experience such phenomena is through modeling -- building a model of the phenomenon or process and then manipulating it to see what happens in different circumstances. Computer tools are available for creating such models, but model building, though very useful for learning, is a complex and difficult task for many learners. In this team's Cyberlearning Exploration (EXP) Project, they developed what looks like a promising way to help middle school students learn to build computational models of scientific phenomena. They designed a visual language for expressing models and showed how progressing from less to more sophisticated models across several phenomena could help middle schoolers not only learn targeted science content but also learn how to design and build models and how to interpret and learn from models. In this follow-on project, they build on that approach, aiming to extend the technology to cover more sciences, automate some of the help teachers provide to students as they engage in model building and interpretation, systematically study the challenges learners face in learning through model building and interpretation, and identify pedagogical approaches that will foster successful learning in these circumstances.


The goal of this proposal is to improve middle schoolers' computational thinking and scientific modeling capabilities in parallel with each other and in a way that prepares young learners for the computational sciences of the future. The PIs' earlier Cyberlearning EXP project explored the potential of using what is known about learning to be a computational thinker to guide sequencing of activities for fostering model-building and interpretation capabilities in science. The sequencing they proposed has middle schoolers building models of phenomena that they gradually make more sophisticated over the course of a science unit, then in the next unit, repeating that sequencing again, but with different content requiring more sophisticated or different modeling practices. They designed a language for model specification that they hoped would foster computational thinking and model-building capabilities. CTSIM, the software that supports the approach, is a visual programming platform for modeling scientific modeling that includes discipline-specific constructs, provides a scalable architecture that seamlessly weaves together model construction, simulation, testing, experimentation, and verification, is usable across science domains, and connects to NetLogo, which runs the simulations. In this project, the team will extend the technology to cover more sciences, add adaptive scaffolding based on what they saw teachers providing to help students build and learn from models, identify pedagogical approaches for promoting learning from model building, and systematically study the challenges students face and how to address those challenges. Their research questions focus on students' abilities to simultaneously learn science content and computational thinking skills involved in modeling, the ins and outs of using linked representations, the kinds of feedback needed for scaffolding the approach, and scaling issues for teachers.

As computing has become integral to the practice of science, technology, engineering and mathematics (STEM), the STEM + Computing Partnerships program seeks to address emerging challenges in computational STEM areas through the applied integration of computational thinking (CT) and computing activities within STEM teaching and learning in early childhood education through high school. This project is a research and development effort aimed at developing a yearlong science curriculum aligned to the Next Generation Science Standards (NGSS) with a focus on English learners (ELs) that integrates computational modeling. The project will integrate computational models in online environments using StarLogo Nova to allow all students, including ELs, to model causal relationships that explain the studied phenomena. Plans are to enhance and integrate StarLogo Nova, a block-based programming environment with an agent-based simulation engine for modeling complex systems. Using the enhanced StarLogo Nova, the project will embed CT throughout the yearlong NGSS-aligned curriculum for students and teachers.

The project will take place in Elizabeth Public Schools in Elizabeth, New Jersey (NJ), and Metro Nashville Public Schools in Nashville, Tennessee (TN). These are two distinct sites with diverse student populations. NJ adopted the NGSS and is currently working out implementation plans, whereas TN represents states that have not adopted the NGSS. The study has two main goals: (1) to investigate feasibility of implementation of the curriculum model in classrooms; and (2) to investigate the extent to which the curriculum promotes student learning outcomes. To achieve the first goal in terms of feasibility of classroom implementation, the project will examine the following research questions: (1) To what extent and how do elementary school teachers support students' engagement in computational modeling?; (2) To what extent and how do students engage in computational modeling?; and (3) What design features of the curriculum and software support students' engagement in computational modeling? Data gathering strategies will include focus groups, field notes to document teachers' feedback, and classroom observations, including videotaping. To achieve the second goal in terms of student learning outcomes, the project will examine the following questions: (4) How do students' understanding of the causal relationships underlying phenomena evolve as they engage in physical, diagrammatic, and computational modeling over the year?; and (5) How do students' understanding of key aspects of CT (e.g., abstraction, pattern generalization, representational competence, modularization, algorithmic notions of flow of control, and conditional logic) evolve as they engage in computational modeling over the full-year curriculum? To measure student learning outcomes, the project will use student assessments of science and CT. A principal outcome of this project will be a field-tested and research-informed model that integrates (a) science learning, (b) language learning, and (c) infusion of critical CT constructs and ideas. An external evaluation will include formative and summative components to provide an independent perspective on the project's work, contributions, and quality of outcomes in terms of design critique, research audit, products review, and collaboration assessment.

The project will design and study new learning environments integrating mathematical and computational thinking. While integrating content has been suggested as a strategy for students' learning, there has been limited investigation about how mathematics and computational thinking should be connected in learning experiences. Computational thinking is an essential skill for STEM careers including concepts such as algorithms and programming, data collection and analysis, using abstractions, and problem solving. These computational thinking concepts and practices can be related to mathematics concepts. This project will examine how to design learning modules that place mathematics concepts. By exploring how different kinds of designs support learning and engagement, the project will establish a set of design principles for supporting mathematical and computational thinking. The project is funded by the STEM+Computing program, which seeks to address emerging challenges in computational STEM areas through the applied integration of computational thinking and computing activities within disciplinary STEM teaching and learning in early childhood education through high school (preK-12). The Discovery Research K-12 program (DRK-12) seeks to significantly enhance the learning and teaching of science, technology, engineering and mathematics (STEM) by preK-12 students and teachers, through research and development of innovative resources, models and tools (RMTs). Projects in the DRK-12 program build on fundamental research in STEM education and prior research and development efforts that provide theoretical and empirical justification for proposed projects.

Using design-based research as a methodology to support iterative design and research, the project will explore two core tensions that are relevant to the integration of mathematics and computational thinking. Each tension deals with how to balance competing goals, and investigates the influence of foregrounding one goal over another. Specifically, the project will design, test, and begin to apply in schools a set of modules that contrast: 1) foregrounding mathematics vs. computational thinking; and 2) foregrounding agency vs. structure. The model of implementation includes two summers of camp sessions for middle school students, and a year of implementation in classrooms, thus allowing exploration beyond the potential for math and computational thinking to be integrated, and extending into what such integration looks like in the institutional context of schools. The research questions to be investigated include: (1) What are the advantages of modules that teach mathematics through computational thinking (foregrounding mathematics) vs. those that teach computational thinking through mathematics (foregrounding computational thinking)? (2) What are the advantages of modules that teach computational thinking through open exploration (agency) vs. game play (structure)? (3) What kinds of instructional supports do math teachers need or request as they are teaching students at the intersection of computational thinking and mathematics? The project will result in (a) a set of instructional sequences for middle school that propose productive intersections of computational thinking and mathematics, (b) an understanding of how and why these instructional sequences support diverse participation, and (c) conjectures about the support math teachers need to integrate computational thinking in their classrooms. Different sections for students will be created to compare different conditions that will foreground mathematics, computational thinking, structure or agency. Data collected will include measures of student learning, interviews, analysis of student work, and video analysis to examine student engagement and interest.

Part 1
Despite decades of work on diversity, equity and inclusion (DEI) at the national level, the geosciences remain the least diverse of STEM fields. Welcoming geoscientists with diverse backgrounds and abilities into this field requires multi-directional action by all members of geology departments. The Geology Department at Western Washington University (WWU) seeks to develop its capacity to address issues of DEI through several targeted interventions. In order to build a more inclusive Geology Department at WWU, we will create a comprehensive
program consisting of five components: 1) Development of a new Lab Camp capstone course option in addition to traditional Field Camp; 2) Ongoing renovation of the Field Camp capstone to make the course more accessible; 3) Workshops for graduate student Teaching Assistants
focused on inclusive teaching practices; 4) Professional development opportunities for WWU Geology faculty focused on DEI; and 5) Department seminar speakers who focus on topics related to DEI. This program emphasizes the development of a new Lab Camp because doing
so will create a more accessible alternative to the traditional Field Camp model and it will provide students with opportunities to develop high-impact lab-based research skills that are increasingly valuable in geoscience professions. Creating a more inclusive and accessible department will result in the recruitment and retention of a more diverse population of undergraduate and graduate students. Once implemented, this model for change can be adapted and transferred to other geology programs nationwide.

Part 2
Field Camp is the most common form of capstone course offered in undergraduate geoscience programs in the United States. About half of all geoscience students participate in some version of field camp while earning their bachelor's degree, and those who do not are often encouraged to participate in other types of field experiences. Most undergraduate geoscience programs also emphasize learning in the field by including a range of field experiences in regular coursework. However, little research has been conducted on the learning benefits of field-based geoscience capstone courses. This project will examine the learning benefits of field camp capstone courses
by (1) characterizing the educational impact of field-based and lab-based courses and (2) comparing the two experiences. To evaluate this, we will use pre- and post-course assessments of learning gains. The research team will also measure accessibility and inclusion in field and lab camp courses by leading students in ongoing qualitative analysis activities. Focus groups and interviews will be used to evaluate the impact of the program on faculty and graduate student instructors? views on accessibility and inclusion.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

Microbes can make organic molecules with complex structures. Many of these molecules or their analogs are central ingredients in a variety of products, but the diversity of these molecules is limited by the range of the reactions catalyzed by natural enzymes. Engineering cells to produce artificial metalloenzymes (AMEs) will expand the range of possible reactions. Novel biosynthetic pathways will be created by complementing natural enzymes with AMEs. Graduate students and postdoctoral associates will be trained in this convergent field of synthetic chemistry and synthetic biology. Outreach activities to encompass topics related to artificial biosynthesis will be offered to underserved high school students and teachers, as well as to K-8 students.


This project will build upon the general concept of creating artificial biosynthetic pathways containing artificial metalloenzymes and preliminary results showing the feasibility of creating these pathways in bacteria. We will increase the numbers and types of microorganisms that can host the chemistry catalyzed by artificial metalloenzymes to expand the range of natural products that react with AMEs; expand the types of metallo-cofactors that are incorporated intracellularly into AMEs to increase the scope of unnatural reactions in these pathways; and combine the abiotic chemistry with natural biosynthesis in varying sequences. Specifically, we will 1) introduce AMEs into Streptomyces strains and test activity on heterologously produced terpenes and polyketides; 2) incorporate new cofactors into AMEs expressed in E. coli and Streptomyces; 3) broaden the scope of transformations catalyzed by AMEs in the artificial biosynthetic pathways to encompass abiotic C-H bond functionalizations; 4) create pathways in which the unnatural chemistry occurs in the middle of the artificial biosynthesis; and 5) elucidate the pathways for diazo-containing small molecules. By doing so, we will generate the fundamental knowledge and demonstrate guiding principles to create artificial biosynthetic pathways that convert simple carbon sources to valuable unnatural products in whole microorganisms.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

This project is funded, under the auspices of the EArly Concept Grant For Exploratory Research (EAGER) award concept, to test ideas on late-Pleistocene through late-Holocene climate change in southeastern Australia based on multiproxy analyses of sediment cores collected from three alpine tarns (lakes) in the highest portions of the Snowy Mountains, New South Wales, Australia. Despite recent efforts to reconstruct the magnitude and spatial distribution of major post-glacial climate events in the Southern Hemisphere (e.g., Antarctic Climate Reversal, Little Ice Age), key gaps in proxy data, most notably in Australia, hinder these reconstructions; this gap reflects a dearth of sites on the continent that preserve high resolution, continuous paleoclimate records. The alpine tarns in Kosciuszko National Park (KNP), New South Wales, represent notable exceptions to this problem: five tarns have acted as continuous sediment traps since deglaciation 18,000-20,000 years ago

All lakes in KNP freeze during the peak of the Austral winter (July-September), which provides stable surfaces for deep coring. Blue Lake was previously cored in the 1970?s, and although analyses of those cores were limited, they indicated that the lake has trapped sediment continuously since deglaciation (>18,000 years ago).

With a small grant from Western Washington University (WWU), the researchers collected a pilot core from the lake in 2016 in order to test the viability of collecting continuous records from the lake. Initial analysis of the core on an ITRAX multi-scanner demonstrates that the sediments are well preserved and highly structured. Both visual and X-ray imagery indicate sub-centimeter scale strata throughout the core; based on the age estimates from above, this stratigraphy would provide sub-centennial resolution (ca. 20 year/cm) throughout the core. If borne out by dating, such resolution would be unprecedented in southern Australia.

This single core demonstrates the exceptional stratigraphic record preserved in Blue Lake alone, and implies that similar, complementary records likely exist in the other, smaller tarns in the park. To test this, the researchers propose to core two additional tarns in the park: Lake Albina, and Club Lake; although shallower than Blue Lake, both occupy bedrock basins and so are less susceptible to lake-level fluctuations related to droughts than sediment dammed lakes. Their differing sizes, depths, and basin geometries might provide complementary records to Blue Lake, allowing the researchers to distinguish between local and regional signals based on correlation testing of the cores.

In addition to collecting cores, a suite of analyses to test the paleoclimate potential of cores from these lakes will be conducted at University of Canterbury/University of Queensland by Australian collaborators under existing Australian funding.

The Broader Impacts include providing new data and insights into the frequency and magnitude of possible past droughts and temperature variations as well as informing resource managers in local agencies and water and power utility companies. The project will also provide valuable training of early career scientists and undergraduates and graduate students.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.