Convergent Microbial Community Formation in Replicate Anaerobic Reactors Inoculated from Different Sources and Treating Ersatz Crew Waste
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Lisa M. Steinberg↗
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Results for “Replication”
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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Development of a Toolkit for Waveform Generator-Based Beam Signal Replication
This is an essay about the project that I worked on this summer. It was a program that was able to control a signal generator using scpi commands.
Manzo, D'Angelo↗
FRF error mitigation methods for time waveform replication
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Coletti, Keaton Patrick [Sandia National Laborator↗
Validation of A Sensorimotor Disorientation Ground Analog
INTRODUCTION Simulating the sensorimotor disorientation effects of gravity transitions after prolonged stays in microgravity is exceedingly challenging on Earth. In a previous study [1], a Sensorimotor Disorientation Analog (SDA) was developed based on subjective feedback from previously flown astronauts. The purpose of this study was to validate this SDA by comparing performance in movement tasks that have a wealth of spaceflight data against task performance while using the SDA. METHODS Thirty healthy non-astronaut subjects (17 males, 13 females; Mean ± SD, Age: 33.5 ± 7.2 years, Height: 68.0 ± 3.4 in, Weight: 164 ± 26 lbs.) volunteered to participate in this study. Subjects performed three movement tasks: computerized dynamic posturography (CDP), obstacle walk, and tandem walk. For CDP, subjects maintained an upright stance for 20s with eyes closed on an unstable pitch sway-referenced platform with head erect (sensory organization test (SOT)-5) and with head pitch ±20° to an auditory cue(SOT-5M). The obstacle walk involved a sit-to-stand with 10s of quiet stance followed by walking to and around a cone placed 4m away while navigating a 30cm obstacle to the cone and back. The tandem walk involved walking heel-to-toe for approximately 10-12 steps with eyes open and eyes closed. Subjects performed the three movement tasks under three levels of the SDA replicating different time points of recovery: none (preflight), low (Return (R)+24- 48hours), and high (R+0- 24hours). The SDA included galvanic vestibular stimulation (GVS) to disorient the vestibular system and a weighted suit (trunk, wrists, and ankles) to alter proprioceptive feedback and replicate subjective heaviness. RESULTS As the SDA magnitude increased, overall performance outcomes decreased. However, the ability of the SDA to replicate the range of astronaut postflight performance was task dependent. CDP SOT-5 performance across SDA levels closely replicated astronaut performance at all time points. SOT-5M, however, had minimal performance changes across SDA levels and was unable to replicate astronaut performance. The obstacle walk showed performance changes across SDA levels and matched astronaut performance preflight and at R+24-48hrs (low). Obstacle walk performance at the high SDA level was reduced in comparison to the low level; however, it was not replicative of astronaut performance immediately after landing. Last, tandem walk had distinct groupings of performance across SDA levels and was able to elicit a high level of disorientation consistent with R+0-24 hours (high) postflight performance for eyes open and eyes closed. The low SDA level for both eyes open and eyes closed was more disruptive than previous crewmember performance at the R+24-48 hours timepoint. CONCLUSION The SDA was developed to replicate postflight sensorimotor disruptions. However, it is well-known that immediately post-landing, astronauts can experience motion sickness, dehydration, fatigue, orthostatic intolerance, illusory sensations, lumbar pain, etc. This multi-system response to return to 1G varies widely across astronauts and, as such, it was not unexpected that the extreme ends of responses in the R+0-24hrs time period were the most difficult to replicate. These results suggest that the SDA levels are able to elicit distinct performance groupings and, although not able to perfectly replicate R+0-24hrs, the SDA did replicate a large range of performance after return to Earth.
S C Moudy↗
AI-Assisted Conceptual Development of a Pre-Geometric Cosmological Model - An Exercise in AI-Assisted Conceptual Framework Generation, Paper II: Local Geometry and Metric Structure
This paper develops the geometric sector of the replication-driven cosmogenesis framework introduced in Paper I. Starting from a pre-geometric spectral substrate and a minimal set of replication axioms, we show how coherent self-replicating units generate a spatial adjacency graph whose continuum limit acquires an effective Riemannian structure. The replication dynamics determines a characteristic correlation length that seeds the local metric, while overlap relations among coherent units produce an isotropic neighborhood geometry with an emergent dimensionality $d_{\rm eff}\simeq 3$ across a broad range of replication factors. As replication slows and causal order stabilizes, a limiting signal speed $c_\ast$ appears, providing the basis for the Lorentzian structure of spacetime without assuming a pre-existing light cone. We derive conditions under which the adjacency graph converges to a smooth three-dimensional manifold, describe the transition from Euclidean to Lorentzian propagation, and identify geometric invariants controlled by the replication parameters. This work establishes the geometric and causal layer of the replication cosmogenesis program, bridging the spectral axioms of Paper I to the cosmological dynamics explored in Paper III.
79 ASTRONOMY AND ASTROPHYSICS↗
Unnatural selection in chemical systems
The theory of evolution through natural selection was proposed by Darwin and Wallace to explain how the characteristics of populations of animals change with time. An examination of their assumptions shows that the theory has much broader application than they originally envisaged. We now know that in appropriate environments RNA molecules or computer viruses, for example, can evolve. The adventure with which we are concerned is the quest for chemical systems that undergo processes analogous to Darwinian selection in the test tube. The search is not restricted to systems that are closely related to nucleic acids, although most of the available experimental evidence concerns such systems. A population of molecules satisfies all the requirements of the theory is there are different kinds of molecules in the population and if each individual molecule can direct the formation of copies of itself, then a population of molecules will adapt to a varying environment by changing its composition so as to maintain as high as possible a rate of replication. Sol Spiegelman is the inventor of 'unnatural selection'. He showed clearly that populations of RNA molecules evolve when replicated repeatedly by Q beta RNA polymerase under a chosen set of adverse reaction conditions. In the systems that he studied, the initial population was fairly homogeneous and much of the variation was created during the course of the experiment by mutation, that is, error of replication. The term 'unnatural selection' will be used loosely to describe evolution of nucleic acids or other replicatable polymers in vitro. The term 'Natural Selection' will be reserved for the evolution of living organisms and their viruses. Natural Section usually involves the coevolution of nucleic acids and proteins, while 'unnatural selection', as practiced so far, allows replicating nucleic acids to evolve but hold constant the enzymes that catalyze replication. It is widely believed that biology based on DNA, RNA, and proteins was preceded by the biology of an 'RNA world' in which enzymes were composed of RNA alone. The origin of RNA replication is thus the central puzzle of the origins of life. Consequently, RNA-catalyzed RNA replication is presently one of the main goals of experimental work on unnatural selection. However, there is also a more distant goal, namely, to achieve replication and selection in systems unrelated to RNA. These different systems are discussed in this article.
Orgel, Leslie E.↗
Microscopic Observation of Self-Propagation of Calcifying Nanoparticles (Nanobacteria)
Biologists typically define living organisms as carbon and water-based cellular forms with :self-replication" as the fundamental trait of the life process. However, this standard dictionary definition of life does not help scientists to categorize self-replicators like viruses, prions, proteons and artificial life. CNP also named nanobacteria were discovered in early 1990s as about 100 nanometer-sized bacteria-like particles with unique apatite mineral-shells around them, and found to be associated with pathological-calcification related diseases. Although CNP have been isolated and cultured from mammalian blood and diseased calcified tissues, and their biomineralizing properties well established, their biological nature and self-replicating capability have always been severely challenged. The terms "self-replication", "self-assembly" or "self-propagation" have been widely used for all systems including nanomachines, crystals, computer viruses and memes. In a simple taxonomy, all biological and non-biological "self replicators", have been classified into "living" or "nonliving" based on the properties of the systems and the amount of support they require to self-replicate. To enhance our understanding about self-replicating nature of CNP, we have investigated their growth in specific culture conditions using conventional inverted light microscope and BioStation IM, Nikon s latest time-lapse imaging system. Their morphological structure was examined using scanning (SEM) and transmission (TEM) electron microscopy. This present study, in conjunction with previous findings of metabolic activity, antibiotic sensitivity, antibody specificity, morphological aspects and infectivity, all concomitantly validate CNP as living self-replicators.
Mathew, Grace↗
Exploiting bacterial effector proteins to uncover evolutionarily conserved antiviral host machinery
Arboviruses are a diverse group of insect-transmitted pathogens that pose global public health challenges. Identifying evolutionarily conserved host factors that combat arbovirus replication in disparate eukaryotic hosts is important as they may tip the balance between productive and abortive viral replication, and thus determine virus host range. Here, we exploit naturally abortive arbovirus infections that we identified in lepidopteran cells and use bacterial effector proteins to uncover host factors restricting arbovirus replication. Bacterial effectors are proteins secreted by pathogenic bacteria into eukaryotic hosts cells that can inhibit antimicrobial defenses. Since bacteria and viruses can encounter common host defenses, we hypothesized that some bacterial effectors may inhibit host factors that restrict arbovirus replication in lepidopteran cells. Thus, we used bacterial effectors as molecular tools to identify host factors that restrict four distinct arboviruses in lepidopteran cells. By screening 210 effectors encoded by seven different bacterial pathogens, we identify several effectors that individually rescue the replication of all four arboviruses. We show that these effectors encode diverse enzymatic activities that are required to break arbovirus restriction. We further characterize Shigella flexneri-encoded IpaH4 as an E3 ubiquitin ligase that directly ubiquitinates two evolutionarily conserved proteins, SHOC2 and PSMC1, promoting their degradation in insect and human cells. We show that depletion of either SHOC2 or PSMC1 in insect or human cells promotes arbovirus replication, indicating that these are ancient virus restriction factors conserved across invertebrate and vertebrate hosts. Collectively, our study reveals a novel pathogen-guided approach to identify conserved antimicrobial machinery, new effector functions, and conserved roles for SHOC2 and PSMC1 in virus restriction.
59 BASIC BIOLOGICAL SCIENCES↗
Mars, clays and the origins of life
To detect life in the Martian soil, tests were designed to look for respiration and photosynthesis. Both tests (labeled release, LR, and pyrolytic release, PR) for life in the Martian soils were positive. However, when the measurement for organic molecules in the soil of Mars was made, none were found. The interpretation given is that the inorganic constituents of the soil of Mars were responsible for these observations. The inorganic analysis of the soil was best fitted by a mixture of minerals: 60 to 80 percent clay, iron oxide, quartz, and soluble salts such as halite (NaCl). The minerals most successful in simulating the PR and LR experiments are iron-rich clays. There is a theory that considers clays as the first organisms capable of replication, mutation, and catalysis, and hence of evolving. Clays are formed when liquid water causes the weathering of rocks. The distribution of ions such as aluminum, magnesium, and iron play the role of bases in the DNA. The information was stored in the distribution of ions in the octahedral and tetrahedral molecules, but that they could, like RNA and DNA, replicate. When the clays replicated, each sheet of clay would be a template for a new sheet. The ion substitutions in one clay sheet would give rise to a complementary or similar pattern on the clay synthesized on its surface. It was theorized that it was on the surface of replicating iron-rich clays that carbon dioxide would be fixed in the light into organic acids such as formic or oxalic acid. If Mars had liquid water during a warm period in its past, clay formation would have been abundant. These clays would have replicated and evolved until the liquid water was removed due to cooling of Mars. It is entirely possible that the Viking mission detected life on Mars, but it was clay life that awaits the return of water to continue its evolution into life based on organic molecules.
Hartman, Hyman↗
Software reliability report
There are many software reliability models which try to predict future performance of software based on data generated by the debugging process. Unfortunately, the models appear to be unable to account for the random nature of the data. If the same code is debugged multiple times and one of the models is used to make predictions, intolerable variance is observed in the resulting reliability predictions. It is believed that data replication can remove this variance in lab type situations and that it is less than scientific to talk about validating a software reliability model without considering replication. It is also believed that data replication may prove to be cost effective in the real world, thus the research centered on verification of the need for replication and on methodologies for generating replicated data in a cost effective manner. The context of the debugging graph was pursued by simulation and experimentation. Simulation was done for the Basic model and the Log-Poisson model. Reasonable values of the parameters were assigned and used to generate simulated data which is then processed by the models in order to determine limitations on their accuracy. These experiments exploit the existing software and program specimens which are in AIR-LAB to measure the performance of reliability models.
Wilson, Larry↗
Hard X-Ray and Wide Focusing Telescopes
Studies are being carried out to compare the performance of several different separation materials used in the replication process. This report presents the results obtained during the second year of a program which consists of replicating smooth, thin substrates, depositing multilayer coatings upon them, and evaluating their performance. Replication and multilayer coatings are both critically important to the development of focussing hard X-ray telescopes that function up to 100 keV. The activities of the current year include extending the comparison between sputtered amorphous carbon and evaporated gold to include sputtered as well as evaporated gold. The figure of merit being the smoothness of the replica which has a direct effect on the specular reflectivity. These results were obtained with epoxy replication, but they should be applicable to electroformed nickel, the process we expect to use for the ultimate replicated optics.
Gorenstein, Paul↗
Research with Large Area Imaging X-Ray Telescope Sounding Rocket Program
We are engaged in a program to develop focussing hard X-ray telescopes in a double conical or Wolter 1 geometry that function up to 100 keV by employing small graze angles and multilayer coatings. Directly polished substrates are not an option because they are too thick to be nested efficiently. The only alternative is to fabricate the very thin substrates by replication. Our objective is the production of integral cylindrical substrates because they should result in better angular resolution than segmented foil geometries. In addition, integral cylinders would be more resistant to possible stress from deep multilayer coatings than segmented ones. Both electroforming of nickel (method of SkX, JET-X, and XMM) and epoxy replication are under consideration. Both processes can utilize the same types of mandrels and separation agents- While electroforming can produce substrates that are thin, the high density of the nickel may result in high weight optics for some missions. For convenience, experimentation with replication and coating is being carried out initially on flats. Our replication studies include trials with gold and carbon separation agents. This paper reports on our efforts with epoxy replicated optics.
Gorenstein, Paul↗
DNA-directed mutations. Leading and lagging strand specificity
The fidelity of replication has evolved to reproduce B-form DNA accurately, while allowing a low frequency of mutation. The fidelity of replication can be compromised, however, by defined order sequence DNA (dosDNA) that can adopt unusual or non B-DNA conformations. These alternative DNA conformations, including hairpins, cruciforms, triplex DNAs, and slipped-strand structures, may affect enzyme-template interactions that potentially lead to mutations. To analyze the effect of dosDNA elements on spontaneous mutagenesis, various mutational inserts containing inverted repeats or direct repeats were cloned in a plasmid containing a unidirectional origin of replication and a selectable marker for the mutation. This system allows for analysis of mutational events that are specific for the leading or lagging strands during DNA replication in Escherichia coli. Deletions between direct repeats, involving misalignment stabilized by DNA secondary structure, occurred preferentially on the lagging strand. Intermolecular strand switch events, correcting quasipalindromes to perfect inverted repeats, occurred preferentially during replication of the leading strand.
NASA Discipline Radiation Health↗
Data entry and error embedding system
A data entry and error embedding system in which, first, a document is bitmapped and recorded in a first memory. Then, it is displayed, and portions of it to be replicated by data entry are underlayed by a window, into which window replicated data is entered in location and size such that it is juxtaposed just below that which is replicated, enhancing the accuracy of replication. Second, with this format in place, selected portions of the replicated data are altered by the insertion of character or word substitutions, thus the embedding of errors. Finally, a proofreader would endeavor to correct the error embedded data and a record of his or her changes recorded. In this manner, the skill level of the proofreader and accuracy of the data are computed.
Woo, Jr., John↗
Discrepancy Reporting Management System
Discrepancy Reporting Management System (DRMS) is a computer program designed for use in the stations of NASA's Deep Space Network (DSN) to help establish the operational history of equipment items; acquire data on the quality of service provided to DSN customers; enable measurement of service performance; provide early insight into the need to improve processes, procedures, and interfaces; and enable the tracing of a data outage to a change in software or hardware. DRMS is a Web-based software system designed to include a distributed database and replication feature to achieve location-specific autonomy while maintaining a consistent high quality of data. DRMS incorporates commercial Web and database software. DRMS collects, processes, replicates, communicates, and manages information on spacecraft data discrepancies, equipment resets, and physical equipment status, and maintains an internal station log. All discrepancy reports (DRs), Master discrepancy reports (MDRs), and Reset data are replicated to a master server at NASA's Jet Propulsion Laboratory; Master DR data are replicated to all the DSN sites; and Station Logs are internal to each of the DSN sites and are not replicated. Data are validated according to several logical mathematical criteria. Queries can be performed on any combination of data.
Cooper, Tonja M.↗
Toward the fabrication of a 5 μm resolution Wolter microscope for the National Ignition Facility
Advancements in computer-controlled polishing, metrology, and replication have led to a x-ray mirror fabrication process that is capable of producing high-resolution Wolter microscopes. The mirror is a nickel-cobalt replicated full-shell mirror that was electroformed from a finely figured and polished mandrel. This mandrel was designed and fabricated for a 8 m source-to-detector distance microscope, with 10× magnification. A computer controlled polishing process corrected the low-frequency mandrel figure to < 2.0 nm RMS error. The mandrel design was optimized to reduce shell distortions that occur mainly < 20 mm from the shell ends. This design, in combination with improved replication tooling design and refined bath parameters informed by a detailed COMSOL model, have led to reductions in replication errors in the mirror shell. X-ray tests performed on a pair of mirror shells replicated from the mandrel have demonstrated < 10 μm FWHM source plane imaging resolution. Here we discuss the development process, highlight results from metrology and x-ray testing, and define a path for achieving 5 μm FWHM resolution.
Grazing Incidence, Wolter Microscope, X-ray Optics↗
SARS-CoV-2 evolution balances conflicting roles of N protein phosphorylation
All lineages of SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, contain mutations between amino acids 199 and 205 in the nucleocapsid (N) protein that are associated with increased infectivity. The effects of these mutations have been difficult to determine because N protein contributes to both viral replication and viral particle assembly during infection. Here, we used single-cycle infection and virus-like particle assays to show that N protein phosphorylation has opposing effects on viral assembly and genome replication. Ancestral SARS-CoV-2 N protein is densely phosphorylated, leading to higher levels of genome replication but 10-fold lower particle assembly compared to evolved variants with low N protein phosphorylation, such as Delta (N:R203M), Iota (N:S202R), and B.1.2 (N:P199L). A new open reading frame encoding a truncated N protein called N*, which occurs in the B.1.1 lineage and subsequent lineages of the Alpha, Gamma, and Omicron variants, supports high levels of both assembly and replication. Our findings help explain the enhanced fitness of viral variants of concern and a potential avenue for continued viral selection.
Microbiology↗
DNA fusion product of phage P2 with plasmid pBR322 - A new phasmid
The chromosome of the temperate bacteriophage P2 and that of the plasmid pBR322 have been joined in vitro after treatment with restriction endonuclease EcoRI. The fusion product - a phasmid - can behave as a plasmid, as a phage and as a prophage. It can replicate its DNA under the control of either the specific replication mechanism of the parent phage in a polA mutant or that of the parent plasmid in a rep mutant. Several interesting interactions between the two replication modes are indicated. In particular, phage particles may be produced even when the phage mode of DNA replication is blocked, and this throws new light on the involvement of the early gene A in the regulation of late gene expression in phage P2.
Nicoletti, M.↗