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Conjugation-based genome engineering enables rapid prototyping and bioproduction in non-model bacteria

Abstract Non-model bacteria offer unique metabolic capabilities for sustainable bioproduction, yet their limited genetic accessibility hinders systematic strain development. Here we present conjugation-based serine recombinase-assisted genome engineering (cSAGE), a broad-host-range platform that enables predictable, iterative genomic integration in transformation-resistant bacteria. cSAGE combines conjugative DNA delivery, standardized low-copy vectors, orthogonal recombinases, and modular genetic parts to support rapid pathway assembly and cross-host benchmarking. Using purple nonsulfur bacteria as a testbed, we integrate promoter engineering, multi-payload genome modification, and genome-scale metabolic modeling to empirically evaluate host-dependent pathway performance. Applying this workflow, we identify strain-specific differences in photosynthetic conversion of lignin-derived p -coumarate to the thermoplastic precursor p -vinylphenol. By enabling genome engineering and functional comparison across diverse bacteria using a single plasmid system, cSAGE provides a general framework for non-model strain prototyping and biotransformation discovery.

Guzman, Michael S. [Department of Chemical Enginee↗

Introduction

It would be hard to argue against the fact that Integrated Computational Materials Engineering (ICME) is a fast growing discipline within material science and engineering. A quick scan of the proceedings from conferences such as Aeromat, Material Science and Technology, and the TMS Annual Meeting clearly shows it. What began a few years ago as one symposium has grown into multiple ICME related symposia at each of these conferences. As encouraging as the number of symposia being offered is the attendance at the symposia. For example, one of the ICME symposia at MS&T 10, the symposium in which this book is based, had five sessions which culminated in a panel discussion that was standing room only. In addition to the large, annual materials science and engineering conferences, smaller 1 to 2-day conferences/workshops sponsored by government agencies (e.g. AFRL and NIST) on specific aspects of ICME and by universities promoting their ICME work are regularly offered. And arguably the most significant news with regards to ICME and conferences is the July 2011 First World Congress on ICME. This five day TMS sponsored conference, specifically focused on ICME with an international advisory board of ICME leaders, shows how far ICME has spread across the globe. Evidence for the growth of ICME can also be found in Academia. The University Materials Council (UMC) is composed of department heads for material science and engineering from major U.S. and Canadian universities. Meeting twice a year to share best practices in order to strengthen both the engineering content [1] and the educational process, the UMC s agenda for their Spring 2010 meeting was dedicated to ICME [2]. This meeting was held in response to the growing awareness that the universities play a major role in the success of ICME and therefore need to develop ICME curriculum in order to meet that need. To aid educators in the development of ICME courses, NSF is funding a "Summer School" on ICME to be held at the University of Michigan in 2011 [3]. Northwestern University recently announced a MS Certificate Program in ICME [4]. Course work for this certificate begins in the Fall of 2011. Other signs that ICME is growing comes from the formation of ICME initiatives from work that did not start off with ICME in mind. One of the committees in ASM International is the Materials Properties Database Committee (MPDC). In the 2010 meeting of the MPDC, based on a study by ASM, the committee decided that it would create an ICME sub-committee in order to determine how ASM can meet the growing needs of the ICME community [5]. In 1999, the Air Force Research Laboratory (AFRL) created a consortium, the Metals Affordability Initiative (MAI), with members from both industry and government with a goal of reducing the cost and time to market of producing metal parts for aerospace applications [6].

Arnold, Steven M.↗

Educational Consortium for Energy-related Data Science & Computation in Building Engineering Programs

The project spearheaded by Pennsylvania State University aims to address the growing need for integrating energy-focused computation and data science into building engineering education. As the demand for energy-efficient building designs and operations increases, the educational sector must adapt to equip future engineers with the necessary skills. This initiative responds to this need by developing a consortium that unites multiple institutions to enhance curriculum development, dataset curation, and resource sharing, thereby ensuring students are well-prepared for the evolving energy sector. The primary goal of the project is to establish a consortium that will develop and disseminate educational materials and training programs focused on energy-related data science and computation. Key accomplishments include the creation of a beta website for resource sharing, the development of training programs and standalone modules, and the curation of datasets accessible to the public. This effort will culminate in a curriculum that incorporates advanced modeling technologies and data science skills into building engineering programs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

NASA Environmental Justice Data Search Interface Overview

NASA’s Earth Science Division (ESD) is committed to empower Environmental Justice (EJ) communities by expanding awareness, accessibility, and use of Earth science data to enable contributions to Earth science research and applications. To that end, the NASA Earth Science Data Systems (ESDS) Program developed an EJ Data Catalog, a simple guide to NASA datasets and socioeconomic datasets that may be useful in EJ research. The EJ Data Catalog is divided by topics—such as disasters, urban flooding, extreme heat, food availability, water availability, climate, and health and air quality—and possible use cases for each dataset. The new version of the EJ Data Catalog is now integrated into NASA’s Science Discovery Engine (SDE), an open-source science infrastructure to enable collaborative and interdisciplinary science. In this workshop you will learn about NASA’s Equity and Environmental Justice (EEJ) activities and opportunities as well as participate on an interactive live demo of the new Science Discovery Engine for Environmental Justice.

environmental justice↗

NASA's Elementary and Secondary Education Program: Review and Critique

The federal role in precollege science, technology, engineering, and mathematics (STEM) education is receiving increasing attention in light of the need to support public understanding of science and to develop a strong scientific and technical workforce in a competitive global economy. Federal science agencies, such as the National Aeronautics and Space Administration (NASA), are being looked to as a resource for enhancing precollege STEM education and bringing more young people to scientific and technical careers. For NASA and other federal science agencies, concerns about workforce and public understanding of science also have an immediate local dimension. The agency faces an aerospace workforce skewed toward those close to retirement and job recruitment competition for those with science and engineering degrees. In addition, public support for the agency s missions stems in part from public understanding of the importance of the agency s contributions in science, engineering, and space exploration.

Quinn, Helen R.↗

Sense and Sensibility: The Case for the Nationwide Inclusion of Engineering in the K-12 Curriculum

The competitive status of the United States is inextricably linked to innovation just as innovation is inseparable from science, technology, engineering, and mathematics. To stay competitive in innovation requires that the United States produce a 21st century workforce complete with requisite education, training, skills, and motivation. If we accept a priori that science, technology, engineering, and mathematics education are crucial to competitiveness and innovation and that, in terms of innovation, mathematics, science, and engineering are interdependent, why are mathematics and science uniformly ubiquitous in the K-12 curriculum while engineering is conspicuously absent? We are passionate in our belief that the uniform addition of engineering to the K-12 curriculum will help ensure that the nation has "the right" 21st Century workforce. Furthermore, we believe that a nationwide effort, led by a coalition of engineering academics, practitioners, and societies is required to turn this goal into reality. However, accomplishing this goal necessitates, as we are reminded by the title of Jane Austen's timeless novel, "Sense and Sensibility", a workable solution that seeks the "middle ground" between passion and reason. We begin our paper by making two essential points: Engineers are not scientists. Engineering exists separate from science, has its own specialized knowledge community apart from science, and it is largely responsible for many of the most significant advancements and improvements in the quality of our life. Our workable solution requires that K-12 education, nationwide, accommodate the inclusion of engineering as a stand alone curriculum and we offer three reasons to support our position: (1) workforce development, (2) stimulating interest in STEM (science, technology, engineering, and mathematics) courses and careers, and (3) creating a technologically literate society. We conclude with some thoughts on how this important goal can be accomplished.

Lindberg, Robert E.↗

Enhancing Global Food Security: Opportunities for the American Meteorological Society

Food security is a key pillar of environmental security yet remains one of the world’s greatest challenges. Its obverse, food insecurity, negatively impacts health and well-being, drives mass migration, and undermines national security and global sustainable development. Ensuring food security is a delicate balance of myriad concerns within the atmospheric and Earth sciences, agronomy and agriculture engineering, social sciences, economics, monitoring, and policymaking. A Food Security Presidential Session at the American Meteorological Society’s (AMS) 2022 Annual Meeting brought together experts across disciplines to tackle issues at the nexus of weather, climate, and food security. The starkest takeaway was the realization that, despite its importance and clear roles for the atmospheric and climate sciences, food security has not been a focus for the AMS community. The aim of this paper is to build on the perspectives shared by this expert panel and to identify overlapping issues and key points of intersection between the food-security community and AMS. We examine 1) the interactions between weather, climate, and the food system and how they influence food security; 2) the time and spatial scales of food security decision support that match weather and climate phenomena; 3) the role of both providers and users of information as well as decision-makers in improving research to operations for food security; and 4) the opportunities for the AMS community to address food security. We conclude that, moving forward, the AMS community is well-positioned to scale up its engagement across the global food system to address existing scientific needs and technology gaps to improve global food security.

Food security↗

2019 Budget Request for the DOE Computational Science Graduate Fellowship (CSGF) Grant

The Department of Energy Computational Science Graduate Fellowship (DOE CSGF) is necessary to meet the continual challenging national workforce needs that arise as computational science and engineering problems continue to grow in scope and complexity. Computational science and engineering (CSE) is a multidisciplinary approach that uses scientific computing to solve practical problems methods and to supply technical tools across the scientific discovery spectrum. In particular, the DOE CSGF emphasizes high-performance computing (HPC) that enables CSE that advances science and engineering in directions important to the DOE and the economy in general. Over the past half-century, HPC has been an essential tool for DOE’s success. During this period, important missions, such as nuclear stockpile stewardship, have turned to HPC as an essential technology. Entire science disciplines, such as biology and cosmology, have been transformed through the augmentation of scientific observation via HPC. At government laboratories and in industry, DOE CSGF alumni are helping push traditional HPC boundaries while contributing to discoveries in high-energy physics, renewable energy, fusion-reactor design, additive manufacturing, nanomaterials for next-generation batteries and transistors, and turbine and advanced nuclear reactor modeling. In addition, HPC is used to address national health needs that will eventually point to cures both by helping cancer researchers manage and analyze huge troves of data, by simulating biological mechanisms, and by accelerating drug development — including continuing to rise to the challenge of pandemic-related research. A 2023 report from the ASCAC Subcommittee on American Competitiveness and Innovation to the ASCR office, “Can the United States Maintain Its Leadership in High-Performance Computing?” says of the Program, “The CSGF program provides a barometer for disciplines that will be of interest to future DOE computing.” An explosion in scientific and technological data has driven the need for increasingly sophisticated HPC to transform those data into scientific understanding. With access to more and more data and the proliferation of HPC, Machine Learning and Artificial Intelligence are experiencing a renaissance, complementing the now well-established use of computational simulation. Indeed, in its September 2020 subcommittee report on “AI/ML, Data Intensive Science and High-Performance Computing”, the DOE Advanced Scientific Computing Advisory Committee (ASCAC) explicitly called for a fellowship program to train computational and data scientists to tackle exascale and data-intensive computing challenges. This collaboration of empirical and theory-based modeling will increasingly inform federal policymakers whose decisions affect American society and future generations, and it requires highly skilled and intellectually agile computational scientists who can support the fast-moving DOE National Laboratory research environment. In fact, the DOE CSGF program has explicitly and consistently addressed this need.

97 MATHEMATICS AND COMPUTING↗

NASA's New Wildland Fire Earth Observation Science & Applications Programmatic Developments

In 2021, the U.S. National Aeronautics & Space Administration (NASA) initiated new programmatic elements within the Science Mission Directorate (SMD) and the Aeronautics Research Mission Directorate (ARMD) focused on supporting wildland fire science and applications improvements, employing the vast array of NASA scientific knowledge, airborne and space-borne Earth Observations (EO) capabilities, technology development (sensor systems, etc.), and large framework modeling efforts. Within the Science Mission Directorate, the NASA Earth Science Division (ESD) will focus on improving our understanding of wildland fire through EO tools and applying rigorous-tested modeling and results of that research into operational use. The ESD Wildfire strategy is to invest in new technology and to better integrate NASA’s satellite, airborne, and ground-based observations with wildfire models to provide the wildfire stakeholders with the information they need to make informed decisions about the pre-, active-, and post-fire conditions. The Applied Science Program has restarted the Wildland Fire Applications Program with a focus on engaging wildland fire management and the fire science community in transitioning EO science efforts into routine use by land management entities at the local, state, national and international level. The NASA Aeronautics Research Mission Directorate will focus on arenas where their aeronautics science and engineering outcomes can benefit the fire management community as well, specifically in the innovative development of Uncrewed Aircraft systems, congested mixed-use platform airspace management issues, new platform configurations supporting wildland fire missions, and other aeronautics-related science / engineering capabilities which may benefit the fire management community. In total, these developments represent a major thrust forward, supporting the goals of utilizing NASA science to benefit humankind. This presentation will highlight the various wildland fire science focus areas identified through collaborations with the wildland fire science and management community and highlight the plans of this new NASA focus area.

NASA↗

Learning nonlinear operators in latent spaces for real-time predictions of complex dynamics in physical systems

Abstract Predicting complex dynamics in physical applications governed by partial differential equations in real-time is nearly impossible with traditional numerical simulations due to high computational cost. Neural operators offer a solution by approximating mappings between infinite-dimensional Banach spaces, yet their performance degrades with system size and complexity. We propose an approach for learning neural operators in latent spaces, facilitating real-time predictions for highly nonlinear and multiscale systems on high-dimensional domains. Our method utilizes the deep operator network architecture on a low-dimensional latent space to efficiently approximate underlying operators. Demonstrations on material fracture, fluid flow prediction, and climate modeling highlight superior prediction accuracy and computational efficiency compared to existing methods. Notably, our approach enables approximating large-scale atmospheric flows with millions of degrees, enhancing weather and climate forecasts. Here we show that the proposed approach enables real-time predictions that can facilitate decision-making for a wide range of applications in science and engineering.

97 MATHEMATICS AND COMPUTING↗

JESNET Expert Assistant

The Johnson Space Center Engineering and Science Network (JESNET) supports the JSC Engineering and Space and Life Sciences Directorates by providing a network of interconnected ETHERNETS with a wide diversity of processing and routing nodes throughout the Johnson Space Center and off-site contractor locations. The JESNET provides the primary method of communication between the various computers that support the Directorates. Lockheed Engineering and Sciences Co. (LESC) is tasked with the operation and maintenance of certain primary portions of this network. Since maintenance of this network depends on the timely identification and subsequent repair of problems on the network, the decision was made to develop a JESNET Expert Assistant (JEA) to assist LESC personnel in the operation and maintenance of the JESNET. The JEA is being implemented in CLIPS, DEC Graphical Kernal System (GKS(TM)) and C on a DEC MicroVAX(TM) with VMS(TM).

Hansen, Roger F.↗

A Summer Research Program of NASA/Faculty Fellowships at the Jet Propulsion Laboratory

The NASA Faculty Fellowship Program (NFFP) is designed to give college and university faculty members a rewarding personal as well as enriching professional experience. Fellowships are awarded to engineering and science faculty for work on collaborative research projects of mutual interest to the fellow and his or her JPL host colleague. The Jet Propulsion Laboratory (JPL) and the California Institute of Technology (Caltech) have participated in the NASA Faculty Fellowship Program for more than 25 years. Administrative offices are maintained both at the Caltech Campus and at JPL; however, most of the activity takes place at JPL. The Campus handles all fiscal matters. The duration of the program is ten continuous weeks. Fellows are required to conduct their research on-site. To be eligible to participate in the program, fellows must be a U.S. citizen and hold a teaching or research appointment at a U.S. university or college. The American Society of Engineering Education (ASEE) contracts with NASA and manages program recruitment. Over the past several years, we have made attempts to increase the diversity of the participants in the NFFP Program. A great deal of attention has been given to candidates from minority-serving institutions. There were approximately 100 applicants for the 34 positions in 2002. JPL was the first-choice location for more than half of them. Faculty from 16 minority-serving institutions participated as well as four women. The summer began with an orientation meeting that included introduction of key program personnel, and introduction of the fellows to each other. During this welcome, the fellows were briefed on their obligations to the program and to their JPL colleagues. They were also given a short historical perspective on JPL and its relationship to Caltech and NASA. All fellows received a package, which included information on administrative procedures, roster of fellows, seminar program, housing questionnaire, directions to JPL, maps of the local area, and a copy of the JPL Universe (a JPL newsletter). A calendar of events for the 2002 NFFP Program was designed to expose the fellows to the full range of JPL activities, seminars, tours, and trips to NASA Dryden, Goldstone, and Palomar Observatory. Weekly brown-bag lunches were also scheduled. The lunches provided a time for airing problems that may have arisen during the previous week, soliciting suggestions for program enhancement, announcements, and general socializing. Professor and Mrs. Albee also hosted the annual Summer Faculty Welcome Party at their home. During their ten-week tenure at JPL, the visiting faculty carried out projects in a wide variety of JPL's science, engineering, and technology disciplines, including communication, planetary science, materials research, reliability and quality assurance, astronomy, guidance and control, and micro-sensors. At the end of the NFFP Program, all fellows were required to complete a one-page summary of their summer s work. This was in addition to any documentation required by their host organization. Distribution of the final paycheck was dependent upon submission of this one-page summary and completion of NASA's NFFP evaluation in the EdCATS system. Fellows were also asked to complete a questionnaire for JPL, which enables the program administrators to make any appropriate changes to make the program more beneficial and effective for all involved. The 2002 NFFP Program at JPUCaltech was considered unanimously highly successful by both fellows and JPL colleagues. It provided a significant experience to most faculty members and fresh ideas to JPL researchers. Each year, suggestions for improvement include expansion of the program, longer terms, larger stipends, funds to support graduate students, and funds to continue collaborative research. The NASA Faculty Fellowship Program continues to occupy a significant place in JPL programs and serves to strengthen the ties between NASA, JPL, Caltech, and t academic community. This program is an important part of NASA's commitment to education. No inventions or patents were created during this program.

Albee, Arden↗