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At least 37 records · Page 2

A 1-year study on SARS-CoV-2 variant shifts in wastewater using dPCR: comparison with clinical and GISAID data

Wastewater testing can be used to monitor SARS-CoV-2 infections in communities. Data from PCR-based wastewater testing are usually available to public health authorities within 5–7 days after excreta and other body fluids enter the sewer. While PCR-based methods can accurately detect and quantify SARS-CoV-2, sequencing-based methods are usually required to distinguish between variants, delaying the results and adding cost to the process. We developed and assessed a novel, customizable digital PCR (dPCR)-based genotyping method for SARS-CoV-2 variant detection in wastewater, which is more cost-effective, faster, and more accessible than sequencing. This approach was applied to more than 1,400 wastewater samples

Wilton, Rose

Plant sulfate transporter protein sequences for phylogenetic analysis

Sulfur is an essential macronutrient that supports plant growth, development, and responses to environmental stress. Sulfate is the predominant inorganic form of sulfur in soils, and its uptake by roots and translocation to shoots are facilitated by the sulfate transporter (SULTR) family of proteins. Although the first plant SULTR gene was identified nearly three decades ago, several subfamily members, particularly those in the expansive and angiosperm-specific SULTR3 group, remain poorly characterized. To support comprehensive phylogenetic and sequence-based analyses, we compiled a curated dataset of 262 SULTR protein sequences from 22 plant species spanning the evolutionary breadth of land plants. This collection includes representatives from two basal lineages, two early-divergent angiosperms, six monocots, and ten dicots. All sequences were extracted from genome assemblies available in Phytozome v13 (Joint Genome Institute) and manually curated, with cross-referencing to additional databases such as NCBI when needed. This dataset provides a valuable resource for reconstructing the evolutionary history of the SULTR family, with particular emphasis on the diversification of SULTR3 transporters in flowering plants. This resource may also support functional annotation, comparative genomics, and structural modeling of sulfate transport proteins.

CBI

Development of a State Machine Sequencer for the Keck Interferometer: Evolution, Development and Lessons Learned using a CASE Tool Approach

This paper presents a discussion of the evolution of a sequencer from a simple EPICS (Experimental Physics and Industrial Control System) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a CASE (Computer Aided Software Engineering) tool approach. The main purpose of the sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Hare1 finite state machine, software program designed to orchestrate several lower-level hardware and software hard real time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORB A, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

interferometer

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

sequence

Machine learning approaches for integrating multi-omics data to expand microbiome annotation (Final Technical Report)

We fulfilled all original three aims of the proposal. Following the earlier release (during the first phase of the project at Montana) of software that identifies and fills gaps in the annotation of metabolic proteins within bacterial genomes, we have nearly completed a second gap-filling tool that improves accuracy and explainability. We completed software for alignment-based annotation of protein coding DNA, allowing for coding frameshifts caused by sequencing error. Finally, we completed a neural embedding model for identifying similarities between protein sequences based on amino-wise latent vectors.

59 BASIC BIOLOGICAL SCIENCES

Three-Dimensional, Transgenic Cell Models to Quantify Space Genotoxic Effects

The space environment contains radiation and chemical agents known to be mutagenic and carcinogenic to humans. Additionally, microgravity is a complicating factor that may modify or synergize induced genotoxic effects. Most in vitro models fail to use human cells (making risk extrapolation to humans more difficult), overlook the dynamic effect of tissue intercellular interactions on genotoxic damage, and lack the sensitivity required to measure low-dose effects. Currently a need exists for a model test system that simulates cellular interactions present in tissue, and can be used to quantify genotoxic damage induced by low levels of radiation and chemicals, and extrapolate assessed risk to humans. A state-of-the-art, three-dimensional, multicellular tissue equivalent cell culture model will be presented. It consists of mammalian cells genetically engineered to contain multiple copies of defined target genes for genotoxic assessment,. NASA-designed bioreactors were used to coculture mammalian cells into spheroids, The cells used were human mammary epithelial cells (H184135) and Stratagene's (Austin, Texas) Big Blue(TM) Rat 2 lambda fibroblasts. The fibroblasts were genetically engineered to contain -a high-density target gene for mutagenesis (60 copies of lacl/LacZ per cell). Tissue equivalent spheroids were routinely produced by inoculation of 2 to 7 X 10(exp 5) fibroblasts with Cytodex 3 beads (150 micrometers in diameter). at a 20:1 cell:bead ratio, into 50-ml HARV bioreactors (Synthecon, Inc.). Fibroblasts were cultured for 5 days, an equivalent number of epithelial cells added, and the fibroblast/epithelial cell coculture continued for 21 days. Three-dimensional spheroids with diameters ranging from 400 to 600 micrometers were obtained. Histological and immunohistochemical Characterization revealed i) both cell types present in the spheroids, with fibroblasts located primarily in the center, surrounded by epithelial cells; ii) synthesis of extracellular matrix; and iii,, mitotic cells located throughout the spheroids. Spheroidal integrity and cell viability were retained for the 30-day test period after removal of spheroids from the bioreactor. Potential utility of this three-dimensional, transgenic model for genotoxicity was initially assessed by exposure of spheroids to 0-2 Gy neon at dose rates of 0.3 to 1.5 Gy/min (National Institute of Radiological Sciences, Chiba, Japan). Quantification of mutation at the lacl gene revealed a linear dose response for mutation induction. Limited sequencing analysis of mutant clones revealed higher frequencies of deletions and multiple base sequence changes with increasing dose. These results suggest that our three-dimensional, transgenic model is applicable to a wide variety of studies involving the quantification, identification, and characterization of genotoxicity incurred in space and on Earth. This model uniquely allows investigation of the interaction of relevant factors, namely cell-to-cell interactions and the mechanistic interaction of microgravity with radiation insults and DNA repair. Using this three-dimensional model will allow us to obtain dual genotoxic information (i.e., mutation rate plus chromosome aberration data) from the same system so that one endpoint can be used to reference the other, thereby increasing the fidelity of the data set. Moreover, the tissue-equivalent nature of the three-dimensional model provides high confidence for relevance of risk assessment, i.e., the establishment of quality factors directly applicable to the microgravity environment.

Gonda, S. R.

Feasibility Criteria for Interval Management Operations as Part of Arrival Management Operations

Interval Management (IM) is a future airborne spacing concept that aims to provide more precise inter-aircraft spacing to yield throughput improvements and greater use of fuel efficient trajectories for arrival and approach operations. To participate in an IM operation, an aircraft must be equipped with avionics that provide speeds to achieve and maintain an assigned spacing interval relative to another aircraft. It is not expected that all aircraft will be equipped with the necessary avionics, but rather that IM fits into a larger arrival management concept developed to support the broader mixed-equipage environment. Arrival management concepts are comprised of three parts: a ground-based sequencing and scheduling function to develop an overall arrival strategy, ground-based tools to support the management of aircraft to that schedule, and the IM tools necessary for the IM operation (i.e., ground-based set-up, initiation, and monitoring, and the flight-deck tools to conduct the IM operation). The Federal Aviation Administration is deploying a near-term ground-automation system to support metering operations in the National Airspace System, which falls within the first two components of the arrival management concept. This paper develops a methodology for determining the required delivery precision at controlled meter points for aircraft that are being managed to a schedule and aircraft being managed to a relative spacing interval in order to achieve desired flow rates and adequate separation at the meter points.

Levitt, Ian M.

Environmental Control Of A Genetic Process

E. coli bacteria altered to contain DNA sequence encoding production of hemoglobin made to produce hemoglobin at rates decreasing with increases in concentration of oxygen in culture media. Represents amplification of part of method described in "Cloned Hemoglobin Genes Enhance Growth Of Cells" (NPO-17517). Manipulation of promoter/regulator DNA sequences opens promising new subfield of recombinant-DNA technology for environmental control of expression of selected DNA sequences. New recombinant-DNA fusion gene products, expression vectors, and nucleotide-base sequences will emerge. Likely applications include such aerobic processes as manufacture of cloned proteins and synthesis of metabolites, production of chemicals by fermentation, enzymatic degradation, treatment of wastes, brewing, and variety of oxidative chemical reactions.

Khosla, Chaitan

LinkFinder: An expert system that constructs phylogenic trees

An expert system has been developed using the C Language Integrated Production System (CLIPS) that automates the process of constructing DNA sequence based phylogenies (trees or lineages) that indicate evolutionary relationships. LinkFinder takes as input homologous DNA sequences from distinct individual organisms. It measures variations between the sequences, selects appropriate proportionality constants, and estimates the time that has passed since each pair of organisms diverged from a common ancestor. It then designs and outputs a phylogenic map summarizing these results. LinkFinder can find genetic relationships between different species, and between individuals of the same species, including humans. It was designed to take advantage of the vast amount of sequence data being produced by the Genome Project, and should be of value to evolution theorists who wish to utilize this data, but who have no formal training in molecular genetics. Evolutionary theory holds that distinct organisms carrying a common gene inherited that gene from a common ancestor. Homologous genes vary from individual to individual and species to species, and the amount of variation is now believed to be directly proportional to the time that has passed since divergence from a common ancestor. The proportionality constant must be determined experimentally; it varies considerably with the types of organisms and DNA molecules under study. Given an appropriate constant, and the variation between two DNA sequences, a simple linear equation gives the divergence time.

Inglehart, James

Computer-Controlled Cylindrical Polishing Process for Development of Grazing Incidence Optics for Hard X-Ray Region

The presentation includes grazing incidence X-ray optics, motivation and challenges, mid spatial frequency generation in cylindrical polishing, design considerations for polishing lap, simulation studies and experimental results, future scope, and summary. Topics include current status of replication optics technology, cylindrical polishing process using large size polishing lap, non-conformance of polishin lap to the optics, development of software and polishing machine, deterministic prediction of polishing, polishing experiment under optimum conditions, and polishing experiment based on known error profile. Future plans include determination of non-uniformity in the polishing lap compliance, development of a polishing sequence based on a known error profile of the specimen, software for generating a mandrel polishing sequence, design an development of a flexible polishing lap, and computer controlled localized polishing process.

Khan, Gufran Sayeed

Solution to a gene divergence problem under arbitrary stable nucleotide transition probabilities

A nucleic acid chain, L nucleotides in length, with the specific base sequence B(1)B(2) ... B(L) is defined by the L-dimensional vector B = (B(1), B(2), ..., B(L)). For twelve given constant non-negative transition probabilities that, in a specified position, the base B is replaced by the base B' in a single step, an exact analytical expression is derived for the probability that the position goes from base B to B' in X steps. Assuming that each base mutates independently of the others, an exact expression is derived for the probability that the initial gene sequence B goes to a sequence B' = (B'(1), B'(2), ..., B'(L)) after X = (X(1), X(2), ..., X(L)) base replacements. The resulting equations allow a more precise accounting for the effects of Darwinian natural selection in molecular evolution than does the idealized (biologically less accurate) assumption that each of the four nucleotides is equally likely to mutate to and be fixed as one of the other three. Illustrative applications of the theory to some problems of biological evolution are given.

Holmquist, R.

Viromics approaches for the study of viral diversity and ecology in microbiomes

Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.

Ecology

Software Architecture to Support the Evolution of the ISRU RESOLVE Engineering Breadboard Unit 2 (EBU2)

The In-Situ Resource Utilization (ISRU) Regolith & Environmental Science and Oxygen & Lunar Volatiles Extraction (RESOLVE) software provides operation of the physical plant from a remote location with a high-level interface that can access and control the data from external software applications of other subsystems. This software allows autonomous control over the entire system with manual computer control of individual system/process components. It gives non-programmer operators the capability to easily modify the high-level autonomous sequencing while the software is in operation, as well as the ability to modify the low-level, file-based sequences prior to the system operation. Local automated control in a distributed system is also enabled where component control is maintained during the loss of network connectivity with the remote workstation. This innovation also minimizes network traffic. The software architecture commands and controls the latest generation of RESOLVE processes used to obtain, process, and quantify lunar regolith. The system is grouped into six sub-processes: Drill, Crush, Reactor, Lunar Water Resource Demonstration (LWRD), Regolith Volatiles Characterization (RVC) (see example), and Regolith Oxygen Extraction (ROE). Some processes are independent, some are dependent on other processes, and some are independent but run concurrently with other processes. The first goal is to analyze the volatiles emanating from lunar regolith, such as water, carbon monoxide, carbon dioxide, ammonia, hydrogen, and others. This is done by heating the soil and analyzing and capturing the volatilized product. The second goal is to produce water by reducing the soil at high temperatures with hydrogen. This is done by raising the reactor temperature in the range of 800 to 900 C, causing the reaction to progress by adding hydrogen, and then capturing the water product in a desiccant bed. The software needs to run the entire unit and all sub-processes; however, throughout testing, many variables and parameters need to be changed as more is learned about the system operation. The Master Events Controller (MEC) is run on a standard laptop PC using Windows XP. This PC runs in parallel to another laptop that monitors the GC, and a third PC that monitors the drilling/ crushing operation. These three PCs interface to the process through a CompactRIO, OPC Servers, and modems.

Moss, Thomas

wavess 1.2: presenting an HLA-aware within-host virus sequence simulation framework

Motivation Understanding how virus sequences are shaped by selection can inform vaccine design and transmission inference. Modeling within-host evolution to interrogate these questions requires a detailed mechanistic framework that accurately captures sequence diversification. The CD8 + cytotoxic T-lymphocyte (CTL) response plays an important role in immune-mediated selection and can leave strong signatures in virus sequences; however, existing sequence-based within-host virus modeling frameworks do not explicitly include a human leukocyte antigen (HLA)-aware CTL response. Results We extended our previously published within-host sequence evolution simulator, wavess, to include an explicit CTL response, and share a method for identifying HLA-specific CTL epitopes given a founder virus sequence. We also updated the model to permit a variable recombination rate, which allows for modeling non-adjacent genes, segmented genomes, and recombination hotspots. These extensions to wavess allow for more accurate simulation of viruses and virus genes, particularly in regions of the genome where the immune response is dominated by CTLs (rather than antibodies). It also provides the foundation for investigations of how these newly-added biological mechanisms influence within-host evolution. Availability and implementation The core of wavess is written in Python 3, with helper functions written in R. It is available at https://github.com/MolEvolEpid/wavess.

60 APPLIED LIFE SCIENCES

Molecular information theory meets protein folding

We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone configurational entropy, secondary structure content, residue burial layers, and mutational studies of protein stability changes. We found that the average information contained in the sequences of evolved proteins is very close to the average information needed to specify a fold ~2.2 ± 0.3 bits/(site operation). The effective alphabet size in evolved proteins equals the effective number of conformations of a residue in the compact unfolded state at around 5. We calculated an energy-to-information conversion efficiency upon folding of around 50%, lower than the theoretical limit of 70%, but much higher than human built macroscopic machines. We propose a simple mapping between molecular information theory and energy landscape theory and explore the connections between sequence evolution, configurational entropy and the energetics of protein folding.

Ignacio E. Sánchez

Air Traffic Management Technology Demonstration (ATD-1) - Concept to Operations

In order to enable arrival management concepts and solutions in a NextGen environment, ground-based sequencing and scheduling functions have been developed to support metering operations in the National Airspace System. These sequencing and scheduling algorithms as well as tools are designed to aid air traffic controllers in developing an overall arrival strategy. The research presented provides an outline of the challenge of bringing time based scheduling to the terminal environment and the steps that were taken to bring the technology from concept to testing in an operational environment, and finally acquisition by the FAA. ATM Technology Demonstration-1 (ATD-1), is a set of technologies that provides an efficient solution for managing arrival aircraft beginning from just prior to top-of-descent and continuing down to the runway. The ATD-1 suite of technologies has been tested separately, and each has demonstrated benefits in throughput, delay, and fuel-efficiency. Together, the integration of terminal arrival tools allow arrival aircraft to safely fly closer together on more fuel-efficient routes to increase capacity, and reduce delay, fuel burn, noise, and greenhouse gas emissions.

DEMO

Geologic Characterization of the South Georgia Rift Basin for Source Proximal CO2 Storage

The project Geologic Characterization of the South Georgia Rift Basin for Source Proximal CO2 Storage is one of 9 site characterization projects that were implemented as part of ARRA (American Recovery and Reinvestment Act). Data from this project was used to improve resolution of data in NATCARB in the area of study. Data related to this study has already been incorporated in NATCARB Atlas. The South Carolina Research Foundation and partners evaluated the feasibility of CCS in the Jurassic/ Triassic (J / TR) saline formations of the buried Mesozoic South Georgia Rift (SGR) Basin that extends from South Carolina into Georgia. The J / TR sequence, based on preliminary assessment of limited geologic and geophysical data, appears to have both the appropriate areal extent and multiple horizons to permanently and safely store CO2 The presence of several igneous rock layers within the sequence may potentially provide adequate seals to prevent upward CO2 migration into the Coastal Plain aquifer systems. Approximately 81 kilometers of 2-D seismic reflection data were collected by Bay Geophysical, Inc. to explore a portion of the SGR located in southern Georgia. The 81 kilometers were divided into two lines approximately 40.5 kilometers each, with Line 1 intersecting Georgia well GGS 3457. Line 2 intersects Line 1 at the southern portion of Line 1 to maximize the extent of coverage away from GGS-3457 (a deep well drilled in the 1980s for oil and gas exploration). This well had a set of usable logs, including gamma and neutron logs that provided promising results related to CO2 storage. Results showed sandstone with porosity values greater than 10 percent and a thickness of 120 meters. The design of the seismic shot was to extrapolate information away from the well and to better define the extent of the SGR and the necessary reservoir and caprock for a successful CO2 injection. A numerical simulation model of CO2 Injection and migration was developed based on the geology log for the GGS-3457 well. The simulation model was used to investigate the feasibility of injecting 30 million metric tons of CO2 into SGR J / TA sediments and integrity of the diabase layers as seals to prevent CO2 migration.

2-D seismic

Application of State Analysis and Goal-Based Operations to a MER Mission Scenario

State Analysis is a model-based systems engineering methodology employing a rigorous discovery process which articulates operations concepts and operability needs as an integrated part of system design. The process produces requirements on system and software design in the form of explicit models which describe the behavior of states and the relationships among them. By applying State Analysis to an actual MER flight mission scenario, this study addresses the specific real world challenges of complex space operations and explores technologies that can be brought to bear on future missions. The paper describes the tools currently used on a daily basis for MER operations planning and provides an in-depth description of the planning process, in the context of a Martian day's worth of rover engineering activities, resource modeling, flight rules, science observations, and more. It then describes how State Analysis allows for the specification of a corresponding goal-based sequence that accomplishes the same objectives, with several important additional benefits.

mission planning