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ABSTRACT We report here the draft genome sequences of three isolates of Rhodovulum sulfidophilum from a single population that will serve as a model system for understanding genomic traits that underlie metabolic variation within closely related marine purple nonsulfur bacteria in natural microbial communities.
The candidate phyla radiation (CPR) comprises a large monophyletic group of bacterial lineages known almost exclusively based on genomes obtained using cultivation-independent methods. Within the CPR, Gracilibacteria (BD1-5) are particularly poorly understood due to undersampling and the inherent fragmented nature of available genomes. Here, we report the first closed, curated genome of a gracilibacterium from an enrichment experiment inoculated from the Gulf of Mexico and designed to investigate hydrocarbon degradation. The gracilibacterium rose in abundance after the community switched to dominance by Colwellia . Notably, we predict that this gracilibacterium completely lacks glycolysis, the pentose phosphate and Entner-Doudoroff pathways. It appears to acquire pyruvate, acetyl coenzyme A (acetyl-CoA), and oxaloacetate via degradation of externally derived citrate, malate, and amino acids and may use compound interconversion and oxidoreductases to generate and recycle reductive power. The initial genome assembly was fragmented in an unusual gene that is hypervariable within a repeat region. Such extreme local variation is rare but characteristic of genes that confer traits under pressure to diversify within a population. Notably, the four major repeated 9-mer nucleotide sequences all generate a proline-threonine-aspartic acid (PTD) repeat. The genome of an abundant Colwellia psychrerythraea population has a large extracellular protein that also contains the repeated PTD motif. Although we do not know the host for the BD1-5 cell, the high relative abundance of the C. psychrerythraea population and the shared surface protein repeat may indicate an association between these bacteria. CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved an unusual repeat region that would be invisible without genome curation. The nucleotide sequence is apparently under strong diversifying selection, but the amino acid sequence is under stabilizing selection. Finally, the amino acid repeat also occurs in a surface protein of a coexisting bacterium, suggesting colocation and possibly interdependence.
Abstract Background Zymomonas mobilis is an aerotolerant α-proteobacterium, which has been genetically engineered for industrial purposes for decades. However, a comprehensive comparison of existing strains on the genomic level in conjunction with phenotype analysis has yet to be carried out. We here performed whole-genome comparison of 17 strains including nine that were sequenced in this study. We then compared 15 available Zymomonas strains for their natural abilities to perform under conditions relevant to biofuel synthesis. We tested their growth in anaerobic rich media, as well as growth, ethanol production and xylose utilization in lignocellulosic hydrolysate. We additionally compared their tolerance to isobutanol, flocculation characteristics, and ability to uptake foreign DNA by electroporation and conjugation. Results Using clustering based on 99% average nucleotide identity (ANI), we classified 12 strains into four clusters based on sequence similarity, while five strains did not cluster with any other strain. Strains belonging to the same 99% ANI cluster showed similar performance while significant variation was observed between the clusters. Overall, conjugation and electroporation efficiencies were poor across all strains, which was consistent with our finding of coding potential for several DNA defense mechanisms, such as CRISPR and restriction–modification systems, across all genomes. We found that strain ATCC31821 (ZM4) had a more diverse plasmid profile than other strains, possibly leading to the unique phenotypes observed for this strain. ZM4 also showed the highest growth of any strain in both laboratory media and lignocellulosic hydrolysate and was among the top 3 strains for isobutanol tolerance and electroporation and conjugation efficiency. Conclusions Our findings suggest that strain ZM4 has a unique combination of genetic and phenotypic traits that are beneficial for biofuel production and propose investing future efforts in further engineering of ZM4 for industrial purposes rather than exploring new Zymomonas isolates.
Results of a detailed analysis of solar activity in 1957-1965 are compared with the data on solar activity with variations of cosmic ray activity, and geomagnetic, ionospheric and terrestrial currents. Cosmic ray variations are investigated with reference to the asymmetry of solar hemispheres. All storms in the IGY are classified and a symbolic diagram of the time sequence is drawn up.
Durability and long-term performance are among the primary concerns for the use of advanced polymer matrix composites (PMCs) in modern aerospace structural applications. For a PMC subJected to long-term exposure at elevated temperatures. the viscoelastic nature of the polymer matrix will contribute to macroscopic changes in composite stiffness, strength and fatigue life. Over time. changes in the polymer due to physical aging will have profound effects on tile viscoelastic compliance of the material, hence affecting its long-term durability. Thus, the ability to predict material performance using intrinsic properties, such as crosslink density and molecular weight, would greatly enhance the efficiency of design and development of PMCs. The objective of this paper is to discuss and present the results of an experimental study that considers the effects of crosslink density, molecular weight and temperature on the viscoelastic behavior including physical aging of an advanced polymer. Five distinct variations in crosslink density were used to evaluate the differences in mechanical performance of an advanced polyimide. The physical aging behavior was isolated by conducting sequenced, short-term isothermal creep compliance tests in tension. These tests were performed over a range of sub-glass transition temperatures. The material constants, material master curves and physical aging-related parameters were evaluated as a function of temperature crosslink density and molecular weight using time-temperature and time-aging time superposition techniques.
Small meteorological rockets released inflatable falling spheres during the MaCWAVE Campaign. The Mountain and Convective Waves Ascending Vertically Experiment (MaCWAVE) was carried out in two parts, a summer sequence from Andoya Rocket Range (69N) during July 2002 to examine convective initiation of gravity waves and a winter sequence from ESRANGE (68N) during January 2003 to examine mountain-terrain initiated gravity waves. The sphere-tracked data provided significant information about the variation of temperature and wind from 70 km and above. The changes observed may be considered akin to tidal motion; unfortunately the launch activity was restricted to 12-hour periods, thus the observation of a full diurnal cycle was not possible. During summer, temperature variation was smaller than that observed during winter when peak to null differences reached 15-20 K at 80-85 km. Variation in the zonal winds varied up to 100+mps in summer and winter. Examination of the times of peak wind vs altitude showed that the peak zonal wind occurred approximately two hours ahead of the peak meridional wind. We provide details about the measurements and observed variations.
The photometric signature of a debris object can be useful in determining what the physical characteristics of a piece of debris are. We report on optical observations in multiple filters of debris at geosynchronous Earth orbit (GEO). Our sample is taken from GEO objects discovered in a survey with the University of Michigan's 0.6-m aperture Schmidt telescope MODEST (for Michigan Orbital DEbris Survey Telescope), and then followed up in real-time with the SMARTS (Small and Medium Aperture Research Telescope System) 0.9-m at CTIO for orbits and photometry. Our goal is to determine 6 parameter orbits and measure colors for all objects fainter than R = 15 th magnitude that are discovered in the MODEST survey. At this magnitude the distribution of observed angular rates changes significantly from that of brighter objects. There are two objectives: 1. Estimate the orbital distribution of objects selected on the basis of two observational criteria: brightness (magnitude) and angular rates. 2. Obtain magnitudes and colors in standard astronomical filters (BVRI) for comparison with reflectance spectra of likely spacecraft materials. What is the faint debris likely to be? In this paper we report on the photometric results. For a sample of 50 objects, more than 90 calibrated sequences of R-B-V-I-R magnitudes have been obtained with the CTIO 0.9-m. For objects that do not show large brightness variations, the colors are largely redder than solar in both B-R and R-I. The width of the color distribution may be intrinsic to the nature of the surfaces, but also could be that we are seeing irregularly shaped objects and measuring the colors at different times with just one telescope. For a smaller sample of objects we have observed with synchronized CCD cameras on the two telescopes. The CTIO 0.9-m observes in B, and MODEST in R. The CCD cameras are electronically linked together so that the start time and duration of observations are the same to better than 50 milliseconds. Thus the B-R color is a true measure of the surface of the debris piece facing the telescopes for that observation. Any change in color reflects a real change in the debris surface.
After the Columbus Moderate Temperature Loop (MTL) InterFace Heat eXchanger (IFHX) low temperature event of GMT 345-2013, NASA investigated relevant transient scenarios involving IFHX rupture after water freezing and subsequent thawing. NASA recommended development of a Fault Detection Isolation and Recovery (FDIR) plan that would, in the event of a heat exchanger freeze event, close the Water On/Off Valves (WOOVs) to isolate the heat exchanger and prevent ammonia from the external flow loops from spreading into the cabin. NASA performed a preliminary simplified analysis for the reference case of IFHX rupture, but for a deeper understanding TAS developed detailed SINDA-FLUINT models of the Columbus ITCS that were built and run through the SINAPS GUI. This allowed simulation of the ammonia leakage physics including the variation of environmental parameters, thus providing more accurate and specific input to the FDIR under development. The result was finalization of the IFHX WOOVs closure sequence and wait times to contain the ammonia propagation to Columbus and allow identification of the leaking IFHX. In addition, the analysis results provided reference pressure profiles to be used on console and by the Engineering as support for the telemetry data assessment in case of failure.This paper gives an overview on the issue and focuses on the analytical aspects of the multiphase fluid dynamics involved.
Two-phase thermal management systems are far superior to their single-phase counterparts because of their ability to capitalize on the coolant’s both sensible and latent heats, thereby yielding orders of magnitude higher heat transfer coefficients and smaller system footprints. A vital knowledge necessary for their implementation in future space systems is performance in microgravity. Long-duration microgravity experiments are necessary to obtain reliable databases, which would then be used to build reliable predictive tools. To achieve this goal, investigators at the Purdue University Boiling and Two-Phase Flow Laboratory (PU-BTPFL) and the NASA Glenn Research Center (NASA-GRC) have been collaborating towards the development of the Flow Boiling and Condensation Experiment (FBCE) and eventual execution onboard the International Space Station (ISS). FBCE has now matured to a point where it is ready for transport to the ISS, where first tests will be conducted using the Flow Boiling Module (FBM). In preparation for the ISS tests, a series of pre-launch Mission Sequence Tests (MSTs) was performed at GRC in Earth gravity with FBM mounted in a vertical upflow orientation using n-perfluorohexane as working fluid. The pre-launch tests included variations of flow rate, surface heat flux, inlet conditions, and both single-sided and double-sided wall heating. This presentation will summarize experimental results from these tests as well as both analytic and theoretical tools for prediction of two-phase heat transfer coefficient and critical heat flux (CHF). Also discussed will be an assessment of predictive accuracy of these tools against the experimental data.
Various manifestations of solar activity cause disturbances known as space weather effects in the interplanetary space, near-Earth environment, and all the Earth's "spheres. Longterm variations in the frequency, intensity and relative importance of the manifestations of solar activity are due to the slow changes in the output of the solar dynamo, and they define space climate. Space climate governs long-term variations in geomagnetic activity and is the primary natural driver of terrestrial climate. To understand how the variable solar activity affects the Earth's environment, geomagnetic activity and climate on both short and long time scales, we need to understand the origins of solar activity itself and its different manifestations, as well as the sequence of coupling processes linking various parts of the system. This session provides a forum to discuss the chain of processes and relations from the Sun to the Earth's surface: the origin and long-term and short-term evolution of solar activity, initiation and temporal variations in solar flares, CMEs, coronal holes, the solar wind and its interaction with the terrestrial magnetosphere, the ionosphere and its connection to the neutral dominated regions below and the plasma dominated regions above, the stratosphere, its variations due to the changing solar activity and its interactions with the underlying troposphere, and the mechanisms of solar influences on the lower atmosphere on different time-scales. Particularly welcome are papers highlighting the coupling processes between the different domains in this complex system.
Recent studies suggest that the microbiome has an impact on gestational health and outcome. However, characterization of the pregnancy-associated microbiome has largely relied on 16S rRNA gene amplicon-based surveys. Here, we describe an assembly-driven, metagenomics-based, longitudinal study of the vaginal, gut, and oral microbiomes in 292 samples from 10 subjects sampled every three weeks throughout pregnancy. Nonhuman sequences in the amount of 1.53 Gb were assembled into scaffolds, and functional genes were predicted for gene- and pathway-based analyses. Vaginal assemblies were binned into 97 draft quality genomes. Redundancy analysis (RDA) of microbial community composition at all three body sites revealed gestational age to be a significant source of variation in patterns of gene abundance. In addition, health complications were associated with variation in community functional gene composition in the mouth and gut. The diversity of Lactobacillus iners-dominated communities in the vagina, unlike most other vaginal community types, significantly increased with gestational age. The genomes of co-occurring Gardnerella vaginalis strains with predicted distinct functions were recovered in samples from two subjects. In seven subjects, gut samples contained strains of the same Lactobacillus species that dominated the vaginal community of that same subject and not other Lactobacillus species; however, these within-host strains were divergent. CRISPR spacer analysis suggested shared phage and plasmid populations across body sites and individuals. This work underscores the dynamic behavior of the microbiome during pregnancy and suggests the potential importance of understanding the sources of this behavior for fetal development and gestational outcome.
In phenotype the mycoplasmas are very different from ordinary bacteria. However, genotypically (i.e., phylogenetically) they are not. On the basis of ribosomal RNA homologies the mycoplasmas belong with the clostridia, and indeed have specific clostridial relatives. Mycoplasmas are, however, unlike almost all other bacteria in the evolutionary characteristics of their ribosomal RNAs. These RNAs contain relatively few of the highly conserved oligonucleotide sequences characteristic of normal eubacterial ribosomal RNAs. This is interpreted to be a reflection of an elevated mutation rate in mycoplasma lines of descent. A general consequence of this would be that the variation associated with a mycoplasma population is augmented both in number and kind, which in turn would lead to an unusual evolutionary course, one unique in all respects. Mycoplasmas, then, are actually tachytelic bacteria. The unusual evolutionary characteristics of their ribosomal RNAs are the imprints of their rapid evolution.
Photolithographic patterning using extreme ultraviolet (EUV, 92.5 eV) light is a radiolytic process that initially forms electrons, radical cations, anions, and neutral radicals in the polymeric photoresist matrix. These species may participate in the chemical reactions that define the ultimate resolution of the printed image, and their concentrations and nanometer-scale stochastic variations in their formation influence printed image quality. Proposals have been made that polymer chain uniformity may be advantageous in reducing stochastics due to spatial inhomogeneities, and this aspect of radiolysis is examined in this work. We have simulated the initial subpicosecond stages of the imaging process for a series of photoresist films that are identical in composition but vary in their polymer chain structures. We use detailed, physically accurate stochastic reaction-diffusion calculations to evaluate the influence of defined sequence and random copolymer structures on radiolytic spur formation, i.e., a cluster of species formed by electron-polymer interactions that defines the initial spatial characteristic of the imaging process. Predictions of electron thermalization in the present work are shown to be consistent with the literature, indicating that our overall computational approach for ultrafast nanoscale processes is sound. The computational results show that the polymer sequence has no significant effect on the spur composition. This suggests that any potential imaging improvements to be gained by sequence control must originate from postimaging lithographic process steps.
The Limb Radiance Inversion Radiometer (LRIR) on the Nimbus 6 spacecraft obtained measurements of atmospheric infrared emission from which vertical profiles of temperature and ozone mixing ratio can be deduced. A three day sequence of data on either side of the evening terminator has been analyzed as a function of solar zenith angle (35 deg to 105 deg) and pressure level (2 mb to .1 mb). The response of the ozone field to solar flux extinction, temperature variability, and nighttime recombination are readily detected.
Abstract Purpose The land-lake interface is a unique zone where terrestrial and aquatic ecosystems meet, forming part of the Earth’s most geochemically and biologically active zones. The unique characteristics of this interface are yet to be properly understood due to the inherently high spatiotemporal variability of subsurface properties, which are difficult to capture with the traditional soil sampling methods. Geophysical methods offer non-invasive techniques to capture variabilities in soil properties at a high resolution across various spatiotemporal scales. Methods We combined electromagnetic induction (EMI), electrical resistivity tomography (ERT), and ground penetrating radar (GPR) with data from soil cores and in situ sensors to investigate hydrostratigraphic heterogeneities across land-lake interfaces along the western basin of Lake Erie. Results EMI revealed high spatial heterogeneities in ECa distribution across the land-lake interfaces, with higher values in the wetland and transition zones compared to the upland zone. Soil ECa maps matched soil maps from a public database with the hydric soil units delineated as high conductivity zones (ECa > 40 mS/m). ERT and GPR showed vertical variation in soil properties with clear stratigraphic boundaries, and correlation of ERT profiles with lithologs from piezometers revealed the stratigraphic units of silt–clay and till sequence down to 3.5 m depth which are consistent with the surficial geology of the study area. Conclusions These results validate the use of multiple geophysical methods for extrapolating soil properties and mapping stratigraphic structures at land-lake interfaces, thereby providing the missing information required to improve the earth system model (ESM) of coastal interfaces.
Proteins are an essential part of essentially all biological processes, and there is enormous variation in protein forms and concentrations that is not reflected in DNA or RNA. Recently there have been rapid advances in the ability to measure protein sequence, modification and concentration, particularly with methods based in mass spectrometry. Global measures of proteins in tissues or in the circulation provide a broad assessment of the proteome that can be extremely useful for discovery, and targeted proteomic measures can yield specific and sensitive assessments of specific peptides and proteins. While most proteomic measures are directed at the detection of consensus peptide sequences, mass spectrometry based proteomic methods also allow a detailed examination of the peptide sequence differences that result from genetic variants and that may have important effects on protein function. In evaluating proteomic data, a number of analytical considerations are important, including an understanding of missing data, the challenge of multiple testing and replication, and the use of rapidly evolving methods in systems biology. While proteomics has not yet had a major impact in skeletal research, interesting recent research has used these approaches in the study of bone cell biology and the discovery of biomarkers of skeletal disorders. Proteomics can be expected to have an increasing influence in the study of bone biology and pathophysiology
Jordan is located on an important spot along the Mediterranean and Black Sea Flyway. Hundreds of migratory bird species have been identified stopping over in Jordan during spring and autumn migratory seasons. Compared to mammals and economically important birds, the microbiomes of wild bird species are severely understudied. Gut microbial composition is a valuable source of information that reflects food preferences, foraging behavior, and the risk of pathogen transmission to humans and other animals. In this study, we assessed the microbiome composition of three species of migrating passerines (willow warblers, lesser whitethroats, and common reed warblers) captured during the spring migration stopover in Jordan in 2023. A total of 59 fecal samples were selected evenly from the three species and subjected to 16S sequencing and microbiome analysis. Our objectives were to determine the diversity of bacteria in these three species, assess the amount of intra- and inter-specific variation, and detect pathogenic genera and species that could pose health risks to humans, domestic animals, and wildlife. Bacteria mainly belonged to the phyla Proteobacteria (62%), Actinobacteriota (18%), Firmicutes (13%), Cyanobacteria (5%), and Bacteroidota (1%). The results reveal that lesser whitethroats had the greatest variation in bacterial genus richness, Shannon diversity, and microbial composition compared to willow warblers and common reed warblers. The three bird species harbored several pathogenic genera and species, including Campylobacter, Enterococcus, Escherichia-Shigella, Mycoplasma, Rickettsia, Clostridium perfringens, and Vibrio cholerae. We suggest further investigation to understand the relationship between migratory behavior and their gut microbiome. We advocate for the use of advanced molecular techniques to characterize the pathogens found in migratory birds that might have public and environmental health impacts in addition to economic loss.
Accurate reconstruction of 2D and 3D isotope densities is a desired capability with great potential impact in applications such as evaluation and development of next-generation nuclear fuels. Neutron time-of-flight (TOF) resonance imaging offers a potential approach by exploiting the characteristic neutron absorption spectra of each isotope. However, it is a major challenge to compute quantitatively accurate images due to a variety of confounding effects such as severe Poisson noise, background scatter, beam non-uniformity, absorption non-linearity, and extended source pulse duration. We present the TRINIDI algorithm which is based on a two-step process in which we first estimate the neutron flux and background counts, and then reconstruct the areal densities of each isotope and pixel. Both components are based on the inversion of a forward model that accounts for the highly non-linear absorption, energy-dependent emission profile, and Poisson noise, while also modeling the substantial spatio-temporal variation of the background and flux. Further, to do this, we formulate the non-linear inverse problem as two optimization problems that are solved in sequence. We demonstrate on both synthetic and measured data that TRINIDI can reconstruct quantitatively accurate 2D views of isotopic areal density that can then be reconstructed into quantitatively accurate 3D volumes of isotopic volumetric density.