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DOE OSTI2023

gRNA-SeqRET: a universal tool for targeted and genome-scale gRNA design and sequence extraction for prokaryotes and eukaryotes

High-throughput genetic screening is frequently employed to rapidly associate gene with phenotype and establish sequence-function relationships. With the advent of CRISPR technology, and the ability to functionally interrogate previously genetically recalcitrant organisms, non-model organisms can be investigated using pooled guide RNA (gRNA) libraries and sequencing-based assays to quantitatively assess fitness of every targeted locus in parallel. To aid the construction of pooled gRNA assemblies, we have developed an in silico design workflow for gRNA selection using the gRNA Sequence Region Extraction Tool (gRNA-SeqRET). Built upon the previously developed CCTop, gRNA-SeqRET enables automated, scalable design of gRNA libraries that target user-specified regions or whole genomes of any prokaryote or eukaryote. Additionally, gRNA-SeqRET automates the bulk extraction of any regions of sequence relative to genes or other features, aiding in the design of homology arms for insertion or deletion constructs. We also assess in silico the application of a designed gRNA library to other closely related genomes and demonstrate that for very closely related organisms Average Nucleotide Identity (ANI) > 95% a large fraction of the library may be of relevance. The gRNA-SeqRET web application pipeline can be accessed at https://grna.jgi.doe.gov. The source code is comprised of freely available software tools and customized Python scripts, and is available at https://bitbucket.org/berkeleylab/grnadesigner/src/master/ under a modified BSD open-source license (https://bitbucket.org/berkeleylab/grnadesigner).

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1992

Space Station Freedom assembly sequence - History, methods, and status

The goal of SSF assembly sequence design is to yield an operations-capable configuration at each stage of construction. Among the primary considerations of sequence designers are launcher payload-mass constraints, EVA time capabilities, and the ensuring of sufficient functionality at each construction stage. Trade studies are conducted to examine alternative hardware-delivery sequences; every iteration of this process either refines existing margins or reflects the redesign of one of the various elements.

Wanagas, John D.↗

NASA NTRS1993

Design methodology and projects for space engineering

NASA/USRA is an ongoing sponsor of space design projects in the senior design course of the Mechanical Engineering Department at The University of Texas at Austin. This paper describes the UT senior design sequence, consisting of a design methodology course and a capstone design course. The philosophical basis of this sequence is briefly summarized. A history of the Department's activities in the Advanced Design Program is then presented. The paper concludes with a description of the projects completed during the 1991-92 academic year and the ongoing projects for the Fall 1992 semester.

Nichols, S.↗

DOE OSTI2021

Designing Sequence-Defined Peptoids for Biomimetic Control over Inorganic Crystallization

Crystallization defines what the world is all about, ranging from biomineralization in living organisms to various materials in our lives. During these processes, biomineralization set a superexcellent example of the additive-controlled crystallization. However, the high complexity and low stability of peptides and proteins preclude their wide applications in controlling inorganic crystallization beyond the biological systems. Peptoids are one type of sequence-defined biomimetic polymers with a simple structure, high stability, protein-like molecular recognition, and distinctive self-assembly properties. They provide a promising alternative to mimic peptides and proteins for controlling inorganic crystallization and extend its application to predictive materials synthesis. In this review article, we extract the main concepts of peptoid engineering and highlight the recent advances in peptoid-controlled inorganic crystallization. Our focus is to understand the principles of sequence engineering that lead to the predictable physiochemical properties of these substances, which will give insights into other inorganic systems.

36 MATERIALS SCIENCE↗

NASA NTRS2003

Nanolayered Features of Collagen-like Peptides

We have been investigating collagen-like model oligopeptides as molecular bases for complex ordered biomimetic materials. The collagen-like molecules incorporate aspects of native collagen sequence and secondary structure. Designed modifications to native primary and secondary structure have been incorporated to control the nanostructure and microstructure of the collagen-like materials produced. We find that the collagen-like molecules form a number of lyotropic rod liquid crystalline phases, which because of their strong temperature dependence in the liquid state can also be viewed as solvent intercalated thermotropic liquid crystals. The liquid crystalline phases formed by the molecules can be captured in the solid state by drying off solvent, resulting in solid nanopatterned (chemically and physically) thermally stable (to greater than 100 C) materials. Designed sequences which stabilize smectic phases have allowed a variety of nanoscale multilayered biopolymeric materials to be developed. Preliminary investigations suggest that chemical patterns running perpendicular to the smectic layer plane can be functionalized and used to localize a variety of organic, inorganic, and organometallic moieties in very simple multilayered nanocomposites. The phase behavior of collagen-like oligopeptide materials is described, emphasizing the correlation between mesophase, molecular orientation, and chemical patterning at the microscale and nanoscale. In many cases, the textures observed for smectic and hexatic phase collagens are remarkably similar to the complex (and not fully understood) helicoids observed in biological collagen-based tissues. Comparisons between biological morphologies and collagen model liquid crystalline (and solidified materials) textures may help us understand the molecular features which impart order and function to the extracellular matrix and to collagen-based mineralized tissues. Initial studies have utilized synthetic collagen-like peptides while future work will also focus on similar sequences generated via genetic engineering methods.

Valluzzi, Regina↗

DOE OSTI2022

De Novo Design of a Highly Stable Ovoid TIM Barrel: Unlocking Pocket Shape towards Functional Design

The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrel fold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel protein has been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the fold remains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold) symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbone sampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequence design protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences are highly stable and fold to the designed barrel curvature as determined by a 2.1 Å resolution crystal structure. The designs show robustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in the hydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diverse hydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major step towards the de novo design of functional TIM barrels.

Chu, Alexander E.↗

DOE OSTI2025

Design and Development of the Handling Frame Assembly Table for the NIF Sustainment Project (Draft)

The Handling Frame Assembly Table is a custom designed piece of equipment developed to support the NIF Sustainment Project. The NIF Sustainment project's goal is to refurbish the National Ignition Facility (NIF), the world’s largest and most energetic laser, so it can continue advancing research in fusion energy, national security, and high energy density physics. A key aspect of this effort involves replacing all 1,728 blast shields on the NIF, which requires specialized equipment such as the Handling Frame Assembly Table to support the production of new blast shields. This project follows a systems engineering approach that guides the design sequence. This report documents the design process from initial concept through final design, including stakeholder analysis, requirements development, conceptual design, design analysis and validation, and final design. Future work will focus on building and commissioning the system.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2026

Design and Development of the Handling Frame Assembly Table for the National Ignition Facility Blast Shields

The Handling Frame Assembly Table is a custom designed piece of equipment developed to support the NIF Sustainment Project. The goal of the NIF Sustainment Project is to refurbish the National Ignition Facility (NIF), the world’s largest and most energetic laser, so it can continue advancing research in fusion energy, national security, and high energy density physics. A key aspect of this effort involves replacing all 1,728 blast shields on the NIF, which requires specialized equipment such as the Handling Frame Assembly Table to support the production of new blast shields. This project follows a systems engineering approach that guides the design sequence. This report documents the design process from initial concept through final design, including stakeholder analysis, requirements development, conceptual design, final design, and design validation. Future work will focus on building and commissioning the system.

42 ENGINEERING↗

DOE OSTI2026

Design and Development of the Handling Frame Assembly Table for the National Ignition Facility Blast Shields

42 ENGINEERING↗

NASA NTRS1991

Design concepts for pressurized lunar shelters utilizing indigenous materials

The objective is to design a pressurized shelter build of indigenous lunar material. The topics are presented in viewgraph form and include the following: lunar conditions which impact design; secondary factors; review of previously proposed concepts; cross section of assembly facility; rationale for indigenous materials; indigenous material choices; cast basalt properties; design variables; design 1, cylindrical segments; construction sequence; design 2, arch-slabs with post-tensioned ring girders; and future research.

Happel, John Amin↗

DOE OSTI2023

De novo design of knotted tandem repeat proteins

De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (3 1 ) and pentafoil (5 1 ) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein’s structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Populus VariantDB v3.2 facilitates CRISPR and functional genomics research

The success of CRISPR genome editing studies depends critically on the precision of guide RNA (gRNA) design. Sequence polymorphisms in outcrossing tree species pose design hazards that can render CRISPR genome editing ineffective. Despite recent advances in tree genome sequencing with haplotype resolution, sequence polymorphism information remains largely inaccessible to various functional genomics research efforts. The Populus VariantDB v3.2 addresses these challenges by providing a user-friendly search engine to query sequence polymorphisms of heterozygous genomes. The database accepts short sequences, such as gRNAs and primers, as input for searching against multiple poplar genomes, including hybrids, with customizable parameters. We provide examples to showcase the utilities of VariantDB in improving the precision of gRNA or primer design. The platform-agnostic nature of the probe search design makes Populus VariantDB v3.2 a versatile tool for the rapidly evolving CRISPR field and other sequence-sensitive functional genomics applications. The database schema is expandable and can accommodate additional tree genomes to broaden its user base.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1993

Space Engineering Projects in Design Methodology

NASA/USRA is an ongoing sponsor of space design projects in the senior design courses of the Mechanical Engineering Department at The University of Texas at Austin. This paper describes the UT senior design sequence, focusing on the first-semester design methodology course. The philosophical basis and pedagogical structure of this course is summarized. A history of the Department's activities in the Advanced Design Program is then presented. The paper includes a summary of the projects completed during the 1992-93 Academic Year in the methodology course, and concludes with an example of two projects completed by student design teams.

R Crawford↗

DOE OSTI2023

De novo design of small beta barrel proteins

Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy–based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2011

High-Payoff Space Transportation Design Approach with a Technology Integration Strategy

A general architectural design sequence is described to create a highly efficient, operable, and supportable design that achieves an affordable, repeatable, and sustainable transportation function. The paper covers the following aspects of this approach in more detail: (1) vehicle architectural concept considerations (including important strategies for greater reusability); (2) vehicle element propulsion system packaging considerations; (3) vehicle element functional definition; (4) external ground servicing and access considerations; and, (5) simplified guidance, navigation, flight control and avionics communications considerations. Additionally, a technology integration strategy is forwarded that includes: (a) ground and flight test prior to production commitments; (b) parallel stage propellant storage, such as concentric-nested tanks; (c) high thrust, LOX-rich, LOX-cooled first stage earth-to-orbit main engine; (d) non-toxic, day-of-launch-loaded propellants for upper stages and in-space propulsion; (e) electric propulsion and aero stage control.

McCleskey, C. M.↗

NASA NTRS2006

Anomaly Recovery and the Mars Exploration Rovers

The premise of the design of operations for the Mars Exploration Rovers (MER) is that the vehicles will drive each day. As a result, they will encounter some aspect of the terrain environment that cannot be anticipated or otherwise accommodated by the sequences linked onboard that day. The operations team then must correct the problem by planning then commanding the execution of a different drive the next day. Often other aspects of the operation on the surface of Mars: environmental changes, component degradation, errors in sequence design or execution, etc., lead to anomalies which must be addressed before normal operations can resume. The operational design that makes it possible to recover from a driving error each day also reduces the time needed to recover from anomalies. As an example of the efficiency achieved, less than 5% (about 30 sols out of 700 sols of operations) of the time on the surface has been devoted to recovery from anomalies for each vehicle. In this paper the major anomalies experienced by the MER rovers will be recounted and the streamlined approaches to addressing these problems described. The operational flexibility developed for these missions is also a function of the system design that anticipated a number of likely faults and conditions arising from uncertainty in sequence execution and environmental change. This design will be described as well as the considerations in operation that motivated this design. These considerations will likely be present in any future surface mission.

rovers↗

NASA NTRS1994

Small scale sequence automation pays big dividends

Galileo sequence design and integration are supported by a suite of formal software tools. Sequence review, however, is largely a manual process with reviewers scanning hundreds of pages of cryptic computer printouts to verify sequence correctness. Beginning in 1990, a series of small, PC based sequence review tools evolved. Each tool performs a specific task but all have a common 'look and feel'. The narrow focus of each tool means simpler operation, and easier creation, testing, and maintenance. Benefits from these tools are (1) decreased review time by factors of 5 to 20 or more with a concomitant reduction in staffing, (2) increased review accuracy, and (3) excellent returns on time invested.

Nelson, Bill↗

NASA NTRS1994

SEQ-POINTER: Next generation, planetary spacecraft remote sensing science observation design tool

Since Mariner, NASA-JPL planetary missions have been supported by ground software to plan and design remote sensing science observations. The software used by the science and sequence designers to plan and design observations has evolved with mission and technological advances. The original program, PEGASIS (Mariners 4, 6, and 7), was re-engineered as POGASIS (Mariner 9, Viking, and Mariner 10), and again later as POINTER (Voyager and Galileo). Each of these programs were developed under technological, political, and fiscal constraints which limited their adaptability to other missions and spacecraft designs. Implementation of a multi-mission tool, SEQ POINTER, under the auspices of the JPL Multimission Operations Systems Office (MOSO) is in progress. This version has been designed to address the limitations experienced on previous versions as they were being adapted to a new mission and spacecraft. The tool has been modularly designed with subroutine interface structures to support interchangeable celestial body and spacecraft definition models. The computational and graphics modules have also been designed to interface with data collected from previous spacecraft, or on-going observations, which describe the surface of each target body. These enhancements make SEQ POINTER a candidate for low-cost mission usage, when a remote sensing science observation design capability is required. The current and planned capabilities of the tool will be discussed. The presentation will also include a 5-10 minute video presentation demonstrating the capabilities of a proto-Cassini Project version that was adapted to test the tool. The work described in this abstract was performed by the Jet Propulsion Laboratory, California Institute of Technology, under contract to the National Aeronautics and Space Administration.

Boyer, Jeffrey S.↗