Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Adaptation, Biological”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Marine phytoplankton resilience may moderate oligotrophic ecosystem responses and biogeochemical feedbacks to climate change

Are the oceans turning into deserts? Rising temperature, increasing surface stratification, and decreasing vertical inputs of nutrients are expected to cause an expansion of warm, nutrient deplete ecosystems. Such an expansion is predicted to negatively affect a trio of key ocean biogeochemical features: phytoplankton biomass, primary productivity, and carbon export. However, phytoplankton communities are complex adaptive systems with immense diversity that could render them at least partially resilient to global changes. This can be illustrated by the biology of the Prochlorococcus “collective.” Adaptations to counter stress, use of alternative nutrient sources, and frugal resource allocation can allow Prochlorococcus to buffer climate-driven changes in nutrient availability. In contrast, cell physiology is more sensitive to temperature changes. We argue that biogeochemical models need to consider the adaptive potential of diverse phytoplankton communities. However, a full understanding of phytoplankton resilience to future ocean changes is hampered by a lack of global biogeographic observations to test theories. We propose that the resilience may in fact be greater in oligotrophic waters than currently considered with implications for future predictions of phytoplankton biomass, primary productivity, and carbon export.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS2022

Adaptation to environmental extremes structures functional traits in biological soil crust and hypolithic microbial communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semi-translucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities waging war using the Type VI Secretion System (T6SS) and hypoliths favoring diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems.

Biological soil crusts↗
DOE OSTI2022

Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities

Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Advanced silicone materials for soft actuator applications

Soft actuators are at the forefront of the innovation tide in medicine, manufacturing, and aerospace because they are able to mimic the behavior of biological tissue and adapt to complex, unstructured environments. Of all the materials used, silicone-based elastomers have drawn enormous attention since they offer a superb combination of mechanical flexibility, biocompatibility, thermal stability, and long-term durability. In the past few years, there has also been a rapid pace of material evolution, additive manufacturing, and biointegration that has enhanced the performance and applications of silicone-based soft actuators. However, there is no focused and timely review compiling these advances. This review seeks to address that need by critically discussing recent advancements in advanced silicone materials, exploring new fabrication methodologies, and discussing emerging applications that range from wearable devices to implantable robotics. We also present suggestions for directions and the problems which must be addressed in order to further develop the performance and potential of silicone-based soft actuators, justifying the relevance and urgency of this effort.

biocompatibility↗
DOE OSTI2024

Mechanically activated and deactivated ion transport across nanopores with heterogeneous surface charge distributions

To mimic the intricate and adaptive functionalities of biological ion channels, electrohydrodynamic ion transport has been studied extensively, albeit mostly, across uniformly charged nanochannels. Here, we analyze the ion transport under coupled electric field and pressure across heterogeneously charged nanopores with oppositely charged sections on their lateral surface. We only consider such pores with symmetric hourglass-like and cylindrical shapes to focus on the effects of the non-uniform surface charge distribution. Finite-element simulations of a continuum model demonstrate that a pressure applied in either direction of the pore-axis equally suppresses or amplifies the ionic conductance, depending on the electric field polarity, by distorting the quasi-static distribution of ions in the pore. The resulting anomalous mechanical deactivation and activation of ionic current under opposite voltage biases exhibit the functional modularity of our setup, while their intensities are highly tunable, substantially greater than those of analogous behaviors in other nanochannels, and fundamentally correlated to ionic current rectification (ICR) in our pores. A detailed study of ICR subsequently reveals its counterintuitive non-monotonous variations, in the pores, with the magnitude of applied voltage and the pore length, that can help optimize their diode-like behavior. We further illustrate that while the hourglass-shaped nanopores yield the more efficient mechanical suppressors of ion transport, their cylindrical analogs are the superior rectifiers and mechanical amplifiers of ion conduction. Therefore, this article provides a blueprint for the strategic design of nanofluidic circuits to attain a robust, modular, and tunable control of ion transport under external electrical and mechanical stimuli.

Physics↗
DOE OSTI2023

Elastomeric vitrimers from designer polyhydroxyalkanoates with recyclability and biodegradability

Cross-linked elastomers are stretchable materials that typically are not recyclable or biodegradable. Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) are soft and ductile, making these bio-based polymers good candidates for biodegradable elastomers. Elasticity is commonly imparted by a cross-linked network structure, and covalent adaptable networks have emerged as a solution to prepare recyclable thermosets via triggered rearrangement of dynamic covalent bonds. Here, we develop biodegradable and recyclable elastomers by chemically installing the covalent adaptable network within biologically produced mcl-PHAs. Specifically, an engineered strain of Pseudomonas putida was used to produce mcl-PHAs containing pendent terminal alkenes as chemical handles for postfunctionalization. Thiol-ene chemistry was used to incorporate boronic ester (BE) cross-links, resulting in PHA-based vitrimers. mcl-PHAs cross-linked with BE at low density (<6 mole %) affords a soft, elastomeric material that demonstrates thermal reprocessability, biodegradability, and denetworking at end of life. The mechanical properties show potential for applications including adhesives and soft, biodegradable robotics and electronics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1985

Effects of muscle atrophy on motor control

As a biological tissue, muscle adapts to the demands of usage. One traditional way of assessing the extent of this adaptation has been to examine the effects of an altered-activity protocol on the physiological properties of muscles. However, in order to accurately interpret the changes associated with an activity pattern, it is necessary to employ an appropriate control model. A substantial literature exists which reports altered-use effects by comparing experimental observations with those from animals raised in small laboratory cages. Some evidence suggests that small-cage-reared animals actually represent a model of reduced use. For example, laboratory animals subjected to limited physical activity have shown resistance to insulin-induced glucose uptake which can be altered by exercise training. This project concerned itself with the basic mechanisms underlying muscle atrophy. Specifically, the project addressed the issue of the appropriateness of rats raised in conventional-sized cages as experimental models to examine this phenomenon. The project hypothesis was that rats raised in small cages are inappropriate models for the study of muscle atrophy. The experimental protocol involved: 1) raising two populations of rats, one group in conventional (small)-sized cages and the other group in a much larger (133x) cage, from weanling age (21 days) through to young adulthood (125 days); 2) comparison of size- and force-related characteristics of selected test muscles in an acute terminal paradigm.

Stuart, D. G.↗
NASA NTRS2001

How Does C. elegans Respond to Altered Gravity?

All organisms on Earth have evolved at unit gravity (1xG), and thus are probably adapted to function optimally at 1xG. However, with the advent of space exploration, it has been shown that organisms are capable of surviving at much less than 1xG, as well as at greater than 1xG. Organisms subjected to increased G levels exhibit alterations in physiological processes that compensate for novel environmental stresses, such as increased weight and density-driven sedimentation. These physiological adaptations illustrate the plasticity of organisms when presented with environmental conditions in which they could not possibly have evolved. Investigating the mechanism(s) behind these adaptations may uncover biological pathways that have not previously been identified. An easily-cultured and well-studied organism, such as C. elegans, would be a desirable model system for these studies. Additional information is contained in the original extended abstract.

Catharine A Conley↗
NASA NTRSDate not supplied

Sample Processor for Life on Icy Worlds (SPLIce): Monolithic Manifold-Based System to Recover, Prepare, and Deliver Samples and Standards to Instrumentation Suites for Ocean World Life-Search Missions

A claim of life detection on one of the solar system’s icy ocean worlds would necessitate extraordinarily convincing evidence. Limited energy availability in the oceans of such bodies as Europa and Enceladus argues for microbes as most probable among possible life forms, but evidence of their existence in the surface layers of an icy moon or in a frozen plume ejected into space could take various forms, pointing to instrumentation suites as a preferred means to detect diverse molecular and morphological life indicators. Multiple disparate categories of positive detections could provide truly convincing evidence from samples that may be only a few micro-liters. SPLIce’s Foundation. Teams led by NASA’s Ames Research Center have developed and operated numerous small, live-biology and astrobiology science payloads in space over two decades. Since 2016, we have adapted and augmented their biological sample-handling systems to create compact, robust search-for-life fluidic processors designed to function after a decade or more in transit, in environments with very little gravity and lots of radiation: up to 100’s of kilorads.

Instrumentation suite↗
NASA NTRS2010

A Powerful Toolkit for Synthetic Biology: Over 3.8 Billion Years of Evolution

The combination of evolutionary with engineering principles will enhance synthetic biology. Conversely, synthetic biology has the potential to enrich evolutionary biology by explaining why some adaptive space is empty, on Earth or elsewhere. Synthetic biology, the design and construction of artificial biological systems, substitutes bio-engineering for evolution, which is seen as an obstacle. But because evolution has produced the complexity and diversity of life, it provides a proven toolkit of genetic materials and principles available to synthetic biology. Evolution operates on the population level, with the populations composed of unique individuals that are historical entities. The source of genetic novelty includes mutation, gene regulation, sex, symbiosis, and interspecies gene transfer. At a phenotypic level, variation derives from regulatory control, replication and diversification of components, compartmentalization, sexual selection and speciation, among others. Variation is limited by physical constraints such as diffusion, and chemical constraints such as reaction rates and membrane fluidity. While some of these tools of evolution are currently in use in synthetic biology, all ought to be examined for utility. A hybrid approach of synthetic biology coupled with fine-tuning through evolution is suggested

Rothschild, Lynn J.↗
DOE OSTI2024

Enhancers in Plant Development, Adaptation and Evolution

Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene expression changes, governed by cis-regulatory modules (CRMs) including enhancers, are a major source of plant phenotypic variation. However, while genome-wide approaches have revealed thousands of putative enhancers in mammals, far fewer have been identified and functionally characterized in plants. This review provides an overview of how enhancers function to control gene regulation, methods to predict DNA sequences that may have enhancer activity, methods utilized to functionally validate enhancers and the current knowledge of enhancers in plants, including how they impact plant development, response to environment and evolutionary adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2016

Analysis of Cell Biomechanics Response to Gravity:A Fluids for Biology Study Utilizing NASA Glenns Zero Gravity Research Facility

It remains unclear how biological cells sense and respond to gravitational forces. Leading scientists state that a large gap exists in the understanding of physiological and molecular adaptation that occurs as biology enters the spaceflight realm. We are seeking a method to fully understand how cells sense microgravity/gravity and what triggers their response.

cells↗
NASA NTRS2022

Co-leveraging Scientific Advances in Space Biology and Astrobiology Towards Achieving NASA’s Life Science Objectives

Executive Summary: Distinct lines of scientific inquiry drives the separation of NASA’s fundamental life science research into Space Biology and Astrobiology. This division developed as a way to place life scientists alongside experts in the physical constraints that define the acclimation, adaptation and evolution of biology systems relevant to their respective subjects. For astrobiology, integration with disciplines such as geology, geochemistry, astronomy, planetary science, etc., enables a comprehensive assessment of the physical environment and its co-evolution with biological processes. Space Biology’s co-location with Physical Sciences places life science researchers adjacent to experts in the physical phenomena associated with microgravity and spaceflight, enabling an understanding of how the spaceflight environment affects biological systems. Despite this separation, aspects of both disciplines have converged on a similar, fundamental objective: to describe and understand the dynamics of complex living communities in the contexts of their physical environments. While the environmental systems and timescales are dramatically different, continuing to motivate the separation into distinct fields, similarities in the underlying objective present opportunities to find efficiencies, reduce overlap, and minimize duplication of effort. Space Biology and Astrobiology share a common need to understand microbial physiology in extreme environments – whether the ‘built’ spaceflight environment or the natural environments in which many astrobiology studies are conducted. In particular, open questions in each discipline require the development of quantitative frameworks, applicable at the ecosystem level, that support predictive capabilities for environments where observations are sparse. Additionally, both disciplines have a need to prepare, detect, and analyze the (potential) biological signal in complex samples-often in a completely autonomous fashion. The next decade will see NASA Space Biology moving to understand and describe the effects of the beyond low-earth orbit (BLEO) spaceflight environment on living systems. This new direction will dramatically reduce the opportunities for ground-based analysis of space-flown samples, driving space biology investigations towards fully autonomous experiments and missions. At the same time, astrobiology life detection missions aimed at detecting biosignatures on Mars and icy moons in the outer solar system could benefit from fully automated sample processing and analysis. There are opportunities to leverage instrument and method development between both disciplines within the context of these BLEO missions.

Astrobiology↗
DOE OSTI2025

Knowledge Oriented Graph Unified Transformer (KOGUT) v0.1

KOGUT — Knowledge Oriented Graph Unified Transformer KOGUT implements the Relational Graph Transformer (RelGT) architecture for knowledge graph link prediction in biological domains, with a primary focus on microbial growth media prediction. While the original RelGT (arXiv:2505.10960) targets relational tables, time series, and multi-table databases, KOGUT adapts this architecture for heterogeneous biological knowledge graphs, providing first-in-class AI predictive models for microbial cultivation. Key Adaptations Beyond Original RelGT: - Knowledge Graph Focus: Applied to biological KGs with semantic node types (taxa, chemicals, media, phenotypes, environments) versus generic relational database tables, trained on the KG-Microbe knowledge graph (1.3M entities, 2.9M edges, 24 relation types). - Multimodal Node Encoding: Integrates node labels, categories, descriptions, and synonyms from KG metadata through learned embedding layers—adapting relational column features to graph node attributes with textual semantics. - Extended K-Hop Subgraph Strategy: Optimized neighborhood sampling (3-hop default, configurable up to 200 nodes) tuned for sparse biological networks, building on the original local-global attention framework with biological relation preservation. - Biolink Predicate Preservation: Type-specific transformations for 24 biological edge semantics (occurs_in, consumes, produces, has_phenotype, subclass_of) beyond standard relational foreign keys, enabling multi-relation link prediction. - Inductive Learning Support: Enables zero-shot predictions for novel taxa through feature-based embeddings (temperature, oxygen requirements, gram stain, cell shape), extending the original transductive relational benchmark scope to uncultured microorganisms. CheapSOTA Performance Optimizations (This Distribution): - VQ-EMA Centroid Attention: Vector quantization with exponential moving average for improved global context modeling (+5-10% MRR improvement). - HDF5 Precomputed Data Loading: One-time preprocessing of k-hop subgraphs to eliminate redundant graph traversals (2-5× training speedup). - Distributed Data Parallel Training: Multi-GPU support for scaling to larger knowledge graphs (tested on 4× NVIDIA A100 GPUs at NERSC Perlmutter). - Mixed Precision Training: Automatic mixed precision (AMP) for memory efficiency and faster training. Advantages Over Standard Knowledge Graph Embedding Models: Combines RelGT's proven multi-element tokenization (features, type, hop, structure) with graph-native biological representations, enabling interpretable link prediction across heterogeneous entities that standard embedding models (TransE, RotatE, ComplEx) and table-based transformers cannot directly model. Achieves near-perfect performance on microbial growth media prediction (MRR: 0.9966, Precision@1: 0.9932, Hit@10: 1.0000) while maintaining explainability through attention-based reasoning over biological pathways. Training Data: - KG-Microbe merged knowledge graph: 1,379,337 nodes, 2,960,472 edges - 24 biological relation types including taxonomic hierarchies, metabolic interactions, phenotype associations, and environmental relationships - Primary prediction task: Growth media suitability for microbial taxa (biolink:occurs_in, 50K edges) - Multi-relation capability: Predicts links for any of the 24 relation types, including chemical consumption/production, phenotype associations, and taxonomic classification Citation: Original RelGT Architecture: Dwivedi et al., "Relational Graph Transformer", arXiv:2505.10960, 2025 KOGUT Implementation: Knowledge Oriented Graph Unified Transformer for Microbial Growth Media Prediction Developed at Lawrence Berkeley National Laboratory (LBNL) Trained on NERSC Perlmutter supercomputer

Joachimiak, Marcin [Lawrence Berkeley National Lab↗
DOE OSTI2022

HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Abstract Background Pacific Biosciences HiFi read technology is currently the industry standard for high accuracy long-read sequencing that has been widely adopted by large sequencing and assembly initiatives for generation of de novo assemblies in non-model organisms. Though adapter contamination filtering is routine in traditional short-read analysis pipelines, it has not been widely adopted for HiFi workflows. Results Analysis of 55 publicly available HiFi datasets revealed that a read-sanitation step to remove sequence artifacts derived from PacBio library preparation from read pools is necessary as adapter sequences can be erroneously integrated into assemblies. Conclusions Here we describe the nature of adapter contaminated reads, their consequences in assembly, and present HiFiAdapterFilt, a simple and memory efficient solution for removing adapter contaminated reads prior to assembly.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1990

USSR Space Life Sciences Digest, issue 25

This is the twenty-fifth issue of NASA's Space Life Sciences Digest. It contains abstracts of 42 journal papers or book chapters published in Russian and of 3 Soviet monographs. Selected abstracts are illustrated with figures and tables from the original. The abstracts in this issue have been identified as relevant to 26 areas of space biology and medicine. These areas include: adaptation, body fluids, botany, cardiovascular and respiratory systems, developmental biology, endocrinology, enzymology, equipment and instrumentation, exobiology, gravitational biology, habitability and environmental effects, human performance, immunology, life support systems, man-machine systems, mathematical modeling, metabolism, microbiology, musculoskeletal system, neurophysiology, nutrition, operational medicine, psychology, radiobiology, reproductive system, and space biology and medicine.

Hooke, Lydia Razran↗