Summer Colloquium in Theoretical Biology
Theoretical cell biology including self-reproductive systems - conferences
Danielli, J. F.↗
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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.
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Analysis of the Innovation Trend in Cell-Free Synthetic Biology
Cell-free synthetic biology is a maturing field that aims to assemble biomolecular reactions outside cells for compelling applications in drug discovery, metabolic engineering, biomanufacturing, diagnostics, and education. Cell-free systems have several key features. They circumvent mechanisms that have evolved to facilitate species survival, bypass limitations on molecular transport across the cell wall, enable high-yielding and rapid synthesis of proteins without creating recombinant cells, and provide high tolerance towards toxic substrates or products. Here, we analyze ~750 published patents and ~2000 peer-reviewed manuscripts in the field of cell-free systems. Three hallmarks emerged. First, we found that both patent filings and manuscript publications per year are significantly increasing (five-fold and 1.5-fold over the last decade, respectively). Second, we observed that the innovation landscape has changed. Patent applications were dominated by Japan in the early 2000s before shifting to China and the USA in recent years. Finally, we discovered an increasing prevalence of biotechnology companies using cell-free systems. Our analysis has broad implications on the future development of cell-free synthetic biology for commercial and industrial applications.
60 APPLIED LIFE SCIENCES↗
Co-assembly of liposomes, Dendrimersomes, and Polymersomes with amphiphilic Janus dendrimers conjugated to Mono- and Tris-Nitrilotriacetic Acid (NTA, TrisNTA) enhances protein recruitment
Metal-chelating ligands such as nitrilotriacetic acid (NTA) bind to polyhistidine-tagged (His-tagged) proteins. Lipids conjugated to NTA are widely used to decorate the surface of liposomes with proteins in cell biology applications. Multivalent NTA ligands such as tris-nitrilotriacetic acid (TrisNTA) display higher affinities than the monovalent NTA when co-assembled with phospholipids and cholesterol in liposomes. However, there is a limited number of available lipids conjugated to NTA and only few are commercially available. Additionally, their activity diminishes during storage or upon exposure to air. Here we report a library of five amphiphilic Janus dendrimers conjugated to NTA (JD-NTA) and three to TrisNTA (JD-TrisNTA). Both JD-NTA and JD-TrisNTA are indefinitely stable at room temperature in air and preliminary results demonstrate that they co-assemble with phospholipids and cholesterol into liposomes, with Janus dendrimers into dendrimersomes, and with block copolymers into polymersomes. The resulting hybrid liposomes co-assembled with JD-NTA display up to thirty-fold higher activity towards His-tagged fluorescent proteins when compared to lipid-NTAs. Hybrid liposomes co-assembled with JD-TrisNTA exhibit even higher binding affinity to His-tagged proteins and can function at much lower ligand concentration in hybrid liposomes than those containing JD-NTA. These preliminary results demonstrate the power of modular synthesis of JD-NTA or JD-TrisNTA to provide highly efficient new tools for biological reconstitution and synthetic cell biology as well as for nanomedicine.
36 MATERIALS SCIENCE↗
NASA-Ames Life Sciences Flight Experiments program - 1980 status report
The paper deals with the ESA's Spacelab LSFE (Life Sciences Flight Experiments) program which, once operational, will provide new and unique opportunities to conduct research into the effects of spaceflight and weightlessness on living organisms under conditions approximating ground-based laboratories. Spacelab missions, launched at 18-month intervals, will enable scientists to test hypotheses from such disciplines as vestibular physiology, developmental biology, biochemistry, cell biology, plant physiology, and similar life sciences.
Berry, W. E.↗
Life sciences flight experiments program - Overview
The considered LSFE program focuses on Spacelab life sciences missions planned for the 1984-1985 time frame. Life Sciences Spacelab payloads, launched at approximately 18-months intervals, will enable scientists to test hypotheses from such disciplines as vestibular physiology, developmental biology, biochemistry, cell biology, plant physiology, and a variety of other life sciences. An overview is presented of the LSFE program that will take advantage of the unique opportunities for biological experimentation possible on Spacelab. Program structure, schedules, and status are considered along with questions of program selection, and the science investigator working groups. A description is presented of the life sciences laboratory equipment program, taking into account the general purpose work station, the research animal holding facility, and the plant growth unit.
Berry, W. E.↗
Bioprocessing in Space
Proceedings are presented of the 1976 NASA Colloquium on bioprocessing in space. The program included general sessions and formal presentations on the following topics: NASA's Space Shuttle, Spacelab, and space-processing programs; the known unusual behavior of materials in space; space-processing experiment results; cell biology, gravity sensors in cells, space electrophoresis of living cells, new approaches to biosynthesis of biologicals from cell culture in space, and zero-g fermentation concepts; and upcoming flight opportunities and industrial application planning studies already underway.
Morrison, D. R.↗
Microfluidics microFACS for Life Detection
A prototype micro-scale Fluorescent Activated Cell Sorter (microFACS) for life detection has been built and is undergoing testing. A functional miniature microfluidics instrument with the ability to remotely distinguish live or dead bacterial cells from abiotic particulates in ice or permafrost of icy bodies of the solar system would be of fundamental value to NASA. The use of molecular probes to obtain the bio-signature of living or dead cells could answer the most fundamental question of Astrobiology: Does life exist beyond Earth? The live-dead fluorescent stains to be used in the microFACS instrument function only with biological cell walls. The detection of the cell membranes of living or dead bacteria (unlike PAH's and many other Biomarkers) would provide convincing evidence of present or past life. This miniature device rapidly examine large numbers of particulates from a polar ice or permafrost sample and distinguish living from dead bacteria cells and biological cells from mineral grains and abiotic particulates and sort the cells and particulates based on a staining system. Any sample found to exhibit fluorescence consistent with living cells could then be used in conjunction with a chiral labeled release experiment or video microscopy system to seek addition evidence for cellular metabolism or motility. Results of preliminary testing and calibration of the microFACS prototype instrument system with pure cultures and enrichment assemblages of microbial extremophiles will be reported.
Platt, Donald W.↗
Theories and models on the biological of cells in space
A wide variety of observations on cells in space, admittedly made under constraining and unnatural conditions in may cases, have led to experimental results that were surprising or unexpected. Reproducibility, freedom from artifacts, and plausibility must be considered in all cases, even when results are not surprising. The papers in symposium on 'Theories and Models on the Biology of Cells in Space' are dedicated to the subject of the plausibility of cellular responses to gravity -- inertial accelerations between 0 and 9.8 m/sq s and higher. The mechanical phenomena inside the cell, the gravitactic locomotion of single eukaryotic and prokaryotic cells, and the effects of inertial unloading on cellular physiology are addressed in theoretical and experimental studies.
Todd, P.↗
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↗
Modular cell-free expression plasmids to accelerate biological design in cells
Industrial biotechnology aims to produce high-value products from renewable resources. This can be challenging because model microorganisms—organisms that are easy to use like Escherichia coli—often lack the machinery required to utilize desired feedstocks like lignocellulosic biomass or syngas. Non-model organisms, such as Clostridium, are industrially proven and have desirable metabolic features but have several hurdles to mainstream use. Namely, these species grow more slowly than conventional laboratory microbes, and genetic tools for engineering them are far less prevalent. To address these hurdles for accelerating cellular design, cell-free synthetic biology has matured as an approach for characterizing non-model organisms and rapidly testing metabolic pathways in vitro. Unfortunately, cell-free systems can require specialized DNA architectures with minimal regulation that are not compatible with cellular expression. In this work, we develop a modular vector system that allows for T7 expression of desired enzymes for cell-free expression and direct Golden Gate assembly into Clostridium expression vectors. Utilizing the Joint Genome Institute’s DNA Synthesis Community Science Program, we designed and synthesized these plasmids and genes required for our projects allowing us to shuttle DNA easily between our in vitro and in vivo experiments. We next validated that these vectors were sufficient for cell-free expression of functional enzymes, performing on par with the previous state-of-the-art. Lastly, we demonstrated automated six-part DNA assemblies for Clostridium autoethanogenum expression with efficiencies ranging from 68% to 90%. We anticipate this system of plasmids will enable a framework for facile testing of biosynthetic pathways in vitro and in vivo by shortening development cycles.
59 BASIC BIOLOGICAL SCIENCES↗
Illustrations of cell fine structure
Electron micrography to illustrate biological cell structure
MICROGRAPHY↗
Physical bioenergetics: Energy fluxes, budgets, and constraints in cells
Cells are the basic units of all living matter which harness the flow of energy to drive the processes of life. While the biochemical networks involved in energy transduction are well-characterized, the energetic costs and constraints for specific cellular processes remain largely unknown. In particular, what are the energy budgets of cells? What are the constraints and limits energy flows impose on cellular processes? Do cells operate near these limits, and if so how do energetic constraints impact cellular functions? Physics has provided many tools to study nonequilibrium systems and to define physical limits, but applying these tools to cell biology remains a challenge. Physical bioenergetics, which resides at the interface of nonequilibrium physics, energy metabolism, and cell biology, seeks to understand how much energy cells are using, how they partition this energy between different cellular processes, and the associated energetic constraints. In this work, we review recent advances and discuss open questions and challenges in physical bioenergetics.
59 BASIC BIOLOGICAL SCIENCES↗
The Biotechnology Facility for International Space Station
The primary mission of the Cellular Biotechnology Program is to advance microgravity as a tool in basic and applied cell biology. The microgravity environment can be used to study fundamental principles of cell biology and to achieve specific applications such as tissue engineering. The Biotechnology Facility (BTF) will provide a state-of-the-art facility to perform cellular biotechnology research onboard the International Space Station (ISS). The BTF will support continuous operation, which will allow performance of long-duration experiments and will significantly increase the on-orbit science throughput.
NASA Center JSC↗
The Biotechnology Facility for International Space Station
The primary mission of the Cellular Biotechnology Program is to advance microgravity as a tool in basic and applied cell biology. The microgravity environment can be used to study fundamental principles of cell biology and to achieve specific applications such as tissue engineering. The Biotechnology Facility (BTF) will provide a state-of-the-art facility to perform cellular biotechnology research onboard the International Space Station (ISS). The BTF will support continuous operation, which will allow performance of long-duration experiments and will significantly increase the on-orbit science throughput. With the BTF, dedicated ground support, and a community of investigators, the goals of the Cellular Biotechnology Program at Johnson Space Center are to: Support approximately 400 typical investigator experiments during the nominal design life of BTF (10 years). Support a steady increase in investigations per year, starting with stationary bioreactor experiments and adding rotating bioreactor experiments at a later date. Support at least 80% of all new cellular biotechnology investigations selected through the NASA Research Announcement (NRA) process. Modular components - to allow sequential and continuous experiment operations without cross-contamination Increased cold storage capability (+4 C, -80 C, -180 C). Storage of frozen cell culture inoculum - to allow sequential investigations. Storage of post-experiment samples - for return of high quality samples. Increased number of cell cultures per investigation, with replicates - to provide sufficient number of samples for data analysis and publication of results in peer-reviewed scientific journals.
Goodwin, Thomas↗
Pattern formation in a coupled membrane-bulk reaction-diffusion model for intracellular polarization and oscillations
Reaction-diffusion systems have been widely used to study spatio-temporal phenomena in cell biology, such as cell polarization. Coupled bulk-surface models naturally include compartmentalization of cytosolic and membrane-bound polarity molecules. Here we study the distribution of the polarity protein Cdc42 in a mass-conserved membrane-bulk model, and explore the effects of diffusion and spatial dimensionality on spatio-temporal pattern formation. We first analyze a one-dimensional (1-D) model for Cdc42 oscillations in fission yeast, consisting of two diffusion equations in the bulk domain coupled to nonlinear ODEs for binding kinetics at each end of the cell. In 1-D, our analysis reveals the existence of symmetric and asymmetric steady states, as well as anti-phase relaxation oscillations typical of slow-fast systems. We then extend our analysis to a two-dimensional (2-D) model with circular bulk geometry, for which species can either diffuse inside the cell or become bound to the membrane and undergo a nonlinear reaction-diffusion process. We also consider a nonlocal system of PDEs approximating the dynamics of the 2-D membrane-bulk model in the limit of fast bulk diffusion. In all three model variants we find that mass conservation selects perturbations of spatial modes that simply redistribute mass. In 1-D, only anti-phase oscillations between the two ends of the cell can occur, and in-phase oscillations are excluded. In higher dimensions, no radially symmetric oscillations are observed. Instead, the only instabilities are symmetry-breaking, either corresponding to stationary Turing instabilities, leading to the formation of stationary patterns, or to oscillatory Turing instabilities, leading to traveling and standing waves. Codimension-two Bogdanov—Takens bifurcations occur when the two distinct instabilities coincide, causing traveling waves to slow down and to eventually become stationary patterns. Our work clarifies the effect of geometry and dimensionality on behaviors observed in ma.ss-conserved cell polarity models.
97 MATHEMATICS AND COMPUTING↗
Novel small molecule inhibitor of Kpnβ1 induces cell cycle arrest and apoptosis in cancer cells
Karyopherin beta 1 (Kpnβ1) is a major nuclear import receptor that mediates the import of cellular cargoes into the nucleus. Recently it has been shown that Kpnβ1 is highly expressed in several cancers, and its inhibition by siRNA induces apoptotic cancer cell death, while having little effect on non-cancer cells. This study investigated the effect of a novel small molecule, Inhibitor of Nuclear Import-60 (INI-60), on cancer cell biology, as well as nuclear import activities associated with Kpnβ1, and cancer progression in vivo using cervical and oesophageal cancer cell lines. INI-60 treatment resulted in the inhibition of cancer cell proliferation, colony formation, migration and invasion, and induced a G1/S cell cycle arrest, followed by cancer cell death via apoptosis. Non-cancer cells were minimally affected by INI-60 at concentrations that inhibited cancer cells. INI-60 treatment altered the localisation of Kpnβ1 and its cargoes, NFκB/p65, NFAT and AP-1, and the overexpression of Kpnβ1 reduced INI-60 cytotoxicity. INI-60 also inhibited KYSE 30 oesophageal cancer cell line growth in vivo. Taken together, these results show that INI-60 inhibits the nuclear import of Kpnβ1 cargoes and interferes with cancer cell biology. INI-60 presents as a potential therapeutic approach for cancers of different tissue origins and warrants further investigation as a novel anti-cancer agent.
60 APPLIED LIFE SCIENCES↗
Report on approved bioscience experiments for Apollo - Effects of weightlessness on isolated human cells
Biosatellite instrument package for motion picture photography of living biological cells during weightlessness
BIOLOGICAL CELL↗