Results for “collection 2.0” — Page 8

NASA NTRS1987

Tracking 3-D body motion for docking and robot control

An advanced method of tracking three-dimensional motion of bodies has been developed. This system has the potential to dynamically characterize machine and other structural motion, even in the presence of structural flexibility, thus facilitating closed loop structural motion control. The system's operation is based on the concept that the intersection of three planes defines a point. Three rotating planes of laser light, fixed and moving photovoltaic diode targets, and a pipe-lined architecture of analog and digital electronics are used to locate multiple targets whose number is only limited by available computer memory. Data collection rates are a function of the laser scan rotation speed and are currently selectable up to 480 Hz. The tested performance on a preliminary prototype designed for 0.1 in accuracy (for tracking human motion) at a 480 Hz data rate includes a worst case resolution of 0.8 mm (0.03 inches), a repeatability of plus or minus 0.635 mm (plus or minus 0.025 inches), and an absolute accuracy of plus or minus 2.0 mm (plus or minus 0.08 inches) within an eight cubic meter volume with all results applicable at the 95 percent level of confidence along each coordinate region. The full six degrees of freedom of a body can be computed by attaching three or more target detectors to the body of interest.

Donath, M.↗

NASA NTRS1989

Estimating laser transit anemometry noise performance capabilities

A Monte Carlo based LTA (laser transit anemometry) simulation system has been used to perform a detailed evaluation of a set of processing algorithms proposed by Mayo and Smart (1984) for the extraction of two-dimensional flow parameters from LTA data sets collected in a plane normal to the optical axis of the system. The present evaluation includes data ensembles containing 0.0, 5.0, 10.0, and 20.0 percent background noise levels in the constituent correlograms. The results of these evaluations indicate that for turbulence levels of up to 10.0 percent the processing system is able to extract the necessary flow parameters accurately from the LTA data sets. Mean velocity magnitude and flow angle are measurable to within 2.0 percent for turbulence intensity levels of up to 14.0 percent. Standard deviations are measureable to within 10.0 percent over a turbulence range of 3.0-10.0 percent at the same noise levels. These results indicate that the algorithms described have applications in fluid flow surveys.

Humphreys, William M., Jr.↗

DOE OSTI2023

Observation of electroweak W + W – pair production in association with two jets in proton-proton collisions at √s = 13 TeV

An observation is reported of the electroweak production of a W + W – pair in association with two jets, with both W bosons decaying leptonically. The data sample corresponds to an integrated luminosity of 138 fb –1 of proton-proton collisions at √s = 13 TeV, collected by the CMS detector at the CERN LHC. Events are selected by requiring exactly two opposite-sign leptons (electrons or muons) and two jets with large pseudorapidity separation and high dijet invariant mass. Events are categorized based on the flavor of the final-state leptons. A signal is observed with a significance of 5.6 standard deviations (5.2 expected) with respect to the background-only hypothesis. The measured fiducial cross section is 10.2 ± 2.0 fb and this value is consistent with the standard model prediction of 9.1 ± 0.6 fb.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Crystallographic structure of wild-type SARS-CoV-2 main protease acyl-enzyme intermediate with physiological C-terminal autoprocessing site

Abstract Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the pathogen that causes the disease COVID-19, produces replicase polyproteins 1a and 1ab that contain, respectively, 11 or 16 nonstructural proteins (nsp). Nsp5 is the main protease (M pro ) responsible for cleavage at eleven positions along these polyproteins, including at its own N- and C-terminal boundaries, representing essential processing events for subsequent viral assembly and maturation. We have determined X-ray crystallographic structures of this cysteine protease in its wild-type free active site state at 1.8 Å resolution, in its acyl-enzyme intermediate state with the native C-terminal autocleavage sequence at 1.95 Å resolution and in its product bound state at 2.0 Å resolution by employing an active site mutation (C145A). We characterize the stereochemical features of the acyl-enzyme intermediate including critical hydrogen bonding distances underlying catalysis in the Cys/His dyad and oxyanion hole. We also identify a highly ordered water molecule in a position compatible for a role as the deacylating nucleophile in the catalytic mechanism and characterize the binding groove conformational changes and dimerization interface that occur upon formation of the acyl-enzyme. Collectively, these crystallographic snapshots provide valuable mechanistic and structural insights for future antiviral therapeutic development including revised molecular docking strategies based on M pro inhibition.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS2022

The H2o Content of the Ureilite Parent Body

The fate of highly volatile elements (H, C, F, Cl and S) during planetary accretion and differentiation is debated. Recent analyses of water in non-carbonaceous chondrites (RC, OC, EC) and achondrites (angrites, eucrites) have been used to argue that inner solar system parent bodies accreted and retained their highly volatile element budgets from their primary feedstock without substantial loss during accretion, metamorphism and differentiation. An alternative model posits that differentiated inner solar system parent bodies (e.g., the angrite parent body, 4 Vesta, Earth) derived the majority of their water from a carbonaceous chondrite-like source, delivered during the final stages of accretion. In order to add new constraints to this debate, we have measured water in nominally anhydrous minerals, melt inclusions, and interstitial glass in ureilites, the largest group of primitive achondrites in the terrestrial meteorite collection. Primitive achondrites did not experience global melting and homogenization. Therefore, these meteorites capture part of the transition from chondritic to achondritic parent bodies, allowing us to constrain the fate of water during the earliest stages of differentiation. Our nano-scale secondary ion mass spectrometry (nanoSIMS) analyses allow us to assess the viability of ureilite-like material as a potential source of terrestrial water. Analyses of pigeonite in main group ureilites yield a range of 2.0 – 6.0 µg/g H2O, and analyses of high-Ca pyroxene and glass (glassy melt inclusions and interstitial glass) in the Almahata Sitta ureilitic trachyandesite yield ranges of 13 – 19 µg/g H2O and 44 – 216 µg/g H2O, respectively. Mass balance, incremental melting, and batch melting calculations yield a preferred ureilite parent body H2O content of 2 – 20 µg/g, similar to previous estimates of water in the eucrite parent body (4 Vesta), but lower than estimates of Earth’s water budget. With these data, we demonstrate that 1) the ureilite parent body is H2O-depleted relative to the Earth; 2) ureilite-like material is unlikely to be a primary source of H2O to the Earth; 3) C and H are not necessarily coupled elements during planetary accretion and thermal processing; and 4) accretion, heating, partial melting, and degassing of rocky planetesimals likely results in significant depletion of H2O.

Primitive achondrites↗

DOE OSTI2025

Search for the production of a Higgs boson in association with a single top quark in pp collisions at $\sqrt{s}=13$ TeV with the ATLAS detector

A search for the production of a Higgs boson in association with a single top quark, tH, is presented. The analysis uses proton-proton collision data corresponding to an integrated luminosity of 140 fb −1 at a centre-of-mass energy of 13 TeV, collected by the ATLAS detector at the LHC. The search targets Higgs-boson decays into $b\bar{b}$, WW * , ZZ * , and ττ, accompanied by an isolated lepton (electron or muon) from the top-quark decay. Multivariate techniques are employed to enhance the separation between signal and background processes. The observed signal strength, μ tH , defined as the ratio between the measured cross-section and the predicted Standard Model value, is μ tH = 8.1 ± 2.6 (stat.) ± 2.0 (syst.). The significance of the observed (expected) signal above the background-only expectation is 2.8 (0.4) standard deviations. The corresponding observed (expected) upper limit at the 95% confidence level on the tH cross-section is found to be 13.9 (6.1) times the value predicted by the Standard Model. An interpretation with an inverted sign of the top-quark Yukawa coupling is performed, and the signal strength and corresponding limit are reported.

Hadron-Hadron Scattering↗

NASA NTRS2008

Near-Infrared Spectroscopic Measurements of Calf Muscle during Walking at Simulated Reduced Gravity - Preliminary Results

Consideration for lunar and planetary exploration space suit design can be enhanced by investigating the physiologic responses of individual muscles during locomotion in reduced gravity. Near-infrared spectroscopy (NIRS) provides a non-invasive method to study the physiology of individual muscles in ambulatory subjects during reduced gravity simulations. PURPOSE: To investigate calf muscle oxygen saturation (SmO2) and pH during reduced gravity walking at varying treadmill inclines and added mass conditions using NIRS. METHODS: Four male subjects aged 42.3 +/- 1.7 years (mean +/- SE) and weighing 77.9 +/- 2.4 kg walked at a moderate speed (3.2 +/- 0.2 km/h) on a treadmill at inclines of 0, 10, 20, and 30%. Unsuited subjects were attached to a partial gravity simulator which unloaded the subject to simulate body weight plus the additional weight of a space suit (121 kg) in lunar gravity (0.17G). Masses of 0, 11, 23, and 34 kg were added to the subject and then unloaded to maintain constant weight. Spectra were collected from the lateral gastrocnemius (LG), and SmO2 and pH were calculated using previously published methods (Yang et al. 2007 Optics Express ; Soller et al. 2008 J Appl Physiol). The effects of incline and added mass on SmO2 and pH were analyzed through repeated measures ANOVA. RESULTS: SmO2 and pH were both unchanged by added mass (p>0.05), so data from trials at the same incline were averaged. LG SmO2 decreased significantly with increasing incline (p=0.003) from 61.1 +/- 2.0% at 0% incline to 48.7 +/- 2.6% at 30% incline, while pH was unchanged by incline (p=0.12). CONCLUSION: Increasing the incline (and thus work performed) during walking causes the LG to extract more oxygen from the blood supply, presumably to support the increased metabolic cost of uphill walking. The lack of an effect of incline on pH may indicate that, while the intensity of exercise has increased, the LG has not reached a level of work above the anaerobic threshold. In these preliminary studies, 30% incline walking at reduced gravity may not require anaerobic LG activity due to the low exercise intensity (42.8 +/- 1.6% of VO(sub 2max)). It is also possible that at reduced gravity additional work is being done by muscle groups other than the calf.

Ellerby, Gwenn E. C.↗

NASA NTRS1978

Modulation of centimetric waves by long gravity waves - Progress report on field and laboratory results

Results are presented from laboratory and field experiments on the modulation of short waves by long waves. The field study employed a wave follower capable of tracking ocean waves with frequencies less than 1.0 Hz and heights less than 2.0 m. A high-response laser-optical system was used to detect upwind-downwind and cross-wind slopes of short waves. The laboratory study was conducted with wind over periodic long waves. The laboratory findings are discussed and compared with laboratory radar measurements and also short wave measurements obtained in the field. It is found that long waves significantly modulate the short wave dispersion by their orbital velocity, and that demodulation is necessary if the data collected by remote sensors are to be compared to surface penetrating devices. The modulation level is weak for wavelengths in the range 2.76-3.30 cm. Other relevant results are also presented.

Shemdin, O. H.↗

DOE OSTI2020

Characterization of an architecture for front-end pixel binning in an integrating pixel array detector

Optimization of an area detector involves compromises between various parameters like frame rate, read noise, dynamic range and pixel size. We have implemented and tested a novel front-end binning design in a photon-integrating hybrid pixel array detector using the MM-PAD- 2.0 pixel architecture. In this architecture, the pixels can be optionally binned in a 2 x 2 pixel configuration using a network of switches to selectively direct the output of 4 sensor pixels to a single amplifier input. Doing this allows a trade-off between frame rate and spatial resolution. Tests show that the binned pixels perform well, but with some degradation on performance as compared to an un-binned pixel. The increased parasitic input capacitance does reduce the signal collected per x-ray as well as increases the noise of the pixel. Here, the increase in noise is, however, less than the factor of 2 increase one would observe for binning in post-processing. Spatial scans across the binned pixels show that no measured signal intensity is lost at the inner binning unit boundaries. In the high flux regime, at a 2 x 2 pixel wide beam spot (FWHM) size, binned mode responds linearly up to a photon flux of 10 7 x-rays/s, and performs comparably with un-binned mode up to a photon flux of 10 8 x-rays/s. While this study demonstrates a proof of concept for front-end binning in integrating detectors, we also identify changes to this early-stage prototype which can further improve the performance of binning pixel structures.

47 OTHER INSTRUMENTATION↗

DOE OSTI2026

Combination of searches for heavy vector boson resonances in proton-proton collisions at $\sqrt{s}=13$ TeV

A combined statistical analysis of searches for heavy vector boson resonances decaying into pairs of W, Z, or Higgs bosons, as well as into quark pairs $\left(\mathrm{q}\overline{\mathrm{q}},\mathrm{b}\overline{\mathrm{b}},\mathrm{t}\overline{\mathrm{t}},\mathrm{t}\overline{\mathrm{b}}\right)$ or lepton pairs ℓ + ℓ – , ℓ$\bar{v}$, with ℓ = e, μ, τ, is presented. The results are based on proton-proton collision data at a center-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 138 fb −1 , collected by the CMS experiment from 2016 to 2018. No significant deviation from the expectations of the standard model is observed. The results are interpreted in the simplified heavy vector triplet (HVT) framework, setting 95% confidence level upper limits on the production cross sections and on the coupling strengths of the HVT bosons to standard model particles. The results exclude HVT resonances with masses below 5.5 TeV in a weakly coupled scenario, below 4.8 TeV in a strongly coupled scenario, and up to 2.0 TeV in the case of production via vector boson fusion. The combination provides the most stringent constraints to date on new phenomena predicted by the HVT model.

beyond Standard Model↗

NASA NTRS1981

Global atmospheric distribution and trend of methylchloroform /CH3CCl3/

Results of global measurements of the concentration of atmospheric methylchloroform, a man-made gas with potentially harmful environmental consequences, performed over a two-year period are presented. Samples were collected weekly at Pt. Barrow and Poker Flats, Alaska, Cape Meares, Oregon, Cape Kumakahi, Hawaii, Samoa, and Cape Grim, Tasmania, and yearly at the South Pole, and methylchloroform concentrations were determined by electron capture-gas chromatographic techniques. A latitudinal profile of CH3CCl3 concentrations derived from the data exhibits a bump at high northern latitudes, where most of the sources are located. Average concentrations calculated for the Northern and Southern Hemispheres showed a rise in global concentrations at a rate of 6.7 + or - 2.0%/year for the period from January 1979 to January 1981, with concentrations rising more slowly in 1980 than in 1979. These yearly increases are also smaller than earlier rates of increase, explainable by a reduction in the rate of emission increase, and are consistent with an atmospheric lifetime of between 6 and 10 years.

Rasmussen, R. A.↗

DOE OSTI2021

Search for the doubly charmed baryon $ {\varXi}_{cc}^{+} $ in the $ {\varXi}_c^{+}{\pi}^{-}{\pi}^{+} $ final state

A search for the doubly charmed baryon $ {\varXi}_{cc}^{+} $ is performed in the $ {\varXi}_c^{+}{\pi}^{-}{\pi}^{+} $ invariant-mass spectrum, where the $ {\varXi}_c^{+} $ baryon is reconstructed in the pK - π + final state. The study uses proton-proton collision data collected with the LHCb detector at a centre- of-mass energy of 13 TeV, corresponding to a total integrated luminosity of 5.4 fb -1 . No significant signal is observed in the invariant-mass range of 3.4–3.8 GeV/ c 2 . Upper limits are set on the ratio of branching fractions multiplied by the production cross-section with respect to the $ {\varXi}_{cc}^{++} $ →( $ {\varXi}_c^{+} $ → pK - π + ) π + decay for different $ {\varXi}_{cc}^{+} $ mass and lifetime hypotheses in the rapidity range from 2.0 to 4.5 and the transverse momentum range from 2.5 to 25 GeV/ c . The results from this search are combined with a previously published search for the $ {\varXi}_{cc}^{+} $ → $ {\varLambda}_c^{+} $ K - π + decay mode, yielding a maximum local significance of 4.0 standard deviations around the mass of 3620 MeV/ c 2 , including systematic uncertainties. Taking into account the look-elsewhere effect in the 3.5–3.7 GeV/ c 2 mass window, the combined global significance is 2.9 standard deviations including systematic uncertainties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1987

Analysis of mid-tropospheric Space Shuttle exhausted aluminum oxide particles

Aluminum oxide particles from the exhaust of the Space Shuttle were collected immediately after the launch of the SEPEX mission and during the descent over the altitude interval of 7.6-4.6 km. The SEM examination revealed that the particles were spherical and ranged in diameter from about 0.1 micron to 10 microns. Results from the energy dispersive analysis (by an X-ray method) and of the particle chemistry (by electron spectroscopy) confirmed that the particles were predominantly composed of aluminum and oxygen. The particle size distribution of the Al2O3 was bimodal, with one observed peak centered near 2.0 microns; the other distribution mode centered at a diameter of less than 0.3 micron, but could not be accurately located. A mass median diameter was slightly less than 2 microns. Evaluation of ice nucleation activity revealed only a small fraction (about 1 ppm) of active ice nuclei among the Al2O3 particulates.

Cofer, Wesley R., III↗

NASA NTRS1981

Acoustic near field and local flow properties associated with broadband shock noise

Shock noise associated with unheated supersonic jets were investigated using a near field microphone array and a single sensor wedge shaped hot-film probe. Both over and underexpanded cases were investigated using Mach 1.5 and 2.0 convergent-divergent nozzles. Correlation measurements through each shock cell of a single underexpanded case with the Mach 1.5 nozzle were obtained between the hot-film probe and microphone array. The results show for the Mach number cases selected that the probe's response is primarily sensitive to velocity. The results of the hot-film near field microphone correlations show general agreement with certain theoretical models as to the location for shock noise production, although they demonstrate the existence of some large perhaps turbulent structure that collectively interacts and phases the motion of the downstream shocks. The near field microphone correlations demonstrate that downstream shocks dominate shock noise production, and suggests the existence of a Doppler effect in near field of the sources. In addition broadband shock noise is found to also propagate at small angles to the jet axis.

Seiner, J. M.↗

NASA NTRS2025

JWST Reveals Spectral Tracers of Recent Surface Modification on Europa

Europa has been modified by a variety of geologic processes, exposing internally-derived materials that are heavily irradiated by charged particles trapped in Jupiter’s magnetosphere. Prior spectral analysis of H2O ice on Europa relied on low signal-to-noise data at wavelengths >2.5 µm, limiting assessment of a 3.1 µm Fresnel peak that is diagnostic of exposed crystalline ice. We report new measurements of H2O ice spectral features using high signal-to-noise data collected by the NIRSpec spectrograph (1.48 – 5.35 µm) on the James Webb Space Telescope. These data reveal a narrow 3.1 µm crystalline H2O ice Fresnel peak, which is primarily located at southern latitudes in Tara and Powys Regiones. Our analysis indicates that crystalline ice exposed in these low-latitude regiones is likely sustained by ongoing thermal (re)crystallization outpacing charged particle amorphization of the top ∼10 µm of Europa’s regolith over short timescales (<15 days). We also measured H2O ice features centered near 1.5 µm, 1.65 µm, and 2.0 µm, and a broad 3.6 µm H2O continuum peak, which are all stronger at northern latitudes, in contrast to the 3.1 µm Fresnel peak identified at southern latitudes. These results support the hypothesis that H2O ice in Europa’s regolith is vertically stratified, with amorphous ice grains dominating its exposed surface, except in Tara and Powys Regiones. We also find that a previously detected 4.38 µm 13CO2 feature is present almost exclusively at southern latitudes in Tara and Powys Regiones, likely derived from an internal source of carbon-bearing material.

Surface processes (2116)↗

DOE OSTI2025

Measurement of the time-integrated 𝐶⁢𝑃 asymmetry in 𝐷 0 → 𝐾$^{0}_{S}$𝐾$^{0}_{S}$ decays using opposite-side flavor tagging at Belle and Belle II

We measure the time-integrated 𝐶⁢𝑃 asymmetry in 𝐷 0 → 𝐾$^{0}_{S}$𝐾$^{0}_{S}$ decays reconstructed in 𝑒 + ⁢𝑒 − → $c\bar{c}$ events collected by the Belle and Belle II experiments. The corresponding data samples have integrated luminosities of 980 and 428 fb −1 , respectively. To infer the flavor of the 𝐷 0 meson, we exploit the correlation between the flavor of the reconstructed decay and the electric charges of particles reconstructed in the rest of the 𝑒 + ⁢𝑒 − → $c\bar{c}$ event. This results in a sample which is independent from any other previously used at Belle or Belle II. The result, 𝐴 𝐶⁢𝑃 ⁡(𝐷 0 → 𝐾$^{0}_{S}$𝐾$^{0}_{S}$)=(1.3±2.0±0.2)%, where the first uncertainty is statistical and the second systematic, is consistent with previous determinations and with 𝐶⁢𝑃 symmetry.

CP violation↗

DOE OSTI2024

KBase Narrative - Porphyromonadaceae sp. W3.11 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗

DOE OSTI2024

KBase Narrative - Lachnospiraceae sp. C1.1 genome

Narratives for The phenotype and genotype of fermentative prokaryotes This is the Narrative for Porphyromonadaceae sp. W3.11. A complementary Narrative for Lachnospiraceae sp. C1.1 is available here. This is the Narrative for Lachnospiraceae sp. C1.1. A complementary Narrative for Porphyromonadaceae sp. W3.11 is available here. Background and Isolation This Narrative and its complementary Narrative contain assembly and annotation of two bacterial isolates that were isolated by our laboratory from the rumen of a Holstein heifer. All procedures with animals have been approved by University of California Davis’s Institutional Animal Care and Use Committee. Rumen contents were collected through a rumen fistula and strained through two layers of cheesecloth into a bottle. The bottle was sealed to exclude air and maintained at 39°C. Contents were brought to the laboratory and bubbled under O2-free CO2 within 15 min. At the laboratory, serial dilutions were made with anaerobic dilution solution for Lachnospiraceae sp. C1.1 and propionibacterium diluent for Porphyromonadaceae sp. W3.11 (table S2). Aliquots (0.1 ml) of each dilution were injected into anaerobic bottle plates (1) containing 9 ml of LH medium (table S2). After incubation at 37°C for 7 days, isolated colonies were picked. Lachnospiraceae sp. C1.1 was picked from a bottle inoculated with a 104 dilution of rumen contents, and Porphyromonadaceae sp. W3.11 was picked from a bottle inoculated with a 103 dilution. After initial isolation, these organisms were purified by growing on anaerobic roll tubes (2) and picking isolated colonies. We performed de novo sequencing of Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11. Aliquots of liquid culture (9 and 1.5 ml, respectively) were collected by syringe and centrifuged (21,000g for 10 min at 4°C). Cell pellets were submitted to Molecular Research LP for DNA extraction, library preparation, and sequencing. After resuspending pellets in 180 µl of ATL buffer (Qiagen), DNA was extracted using the MagAttract HMW DNA Kit (Qiagen). DNA was eluted in 100 µl of AE buffer (Qiagen) and then cleaned using the DNEasy PowerClean Pro Cleanup Kit (Qiagen). DNA was then sheared using the Covaris g-TUBE (Covaris). Sequencing libraries were prepared using the SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences) and 1500 ng of the sheared and purified DNA. The SMRTbell libraries were size-selected (>6 Kb) using a BluePippin instrument (Sage Science) and 0.75% agarose gel. Libraries were then sequenced using the PacBio Sequel II (Pacific Biosciences) platform and a 30-hour movie time. Narrative Summary In these Narratives, we filtered low-quality reads using Trimmomatic (v0.36), assembled filtered reads with SPAdes (v3.15.3), and then checked completeness and contamination of the assembled genomes with CheckM (v1.0.18). Statistics for sequencing and assembly are in table S3. Using the assembled contigs (genomes), we called genes and annotated them. Protein-coding genes were called using Prodigal (v2.6.3) (3) locally or using KBase via RASTtk (v1.073), with identical results. Genes were annotated with KO IDs using KAAS (4). They were further annotated with pfam and TIGRFAM IDs using KBase and the Annotate Domains in a Genome app. We classified putative genes for hydrogenases using HydDB. Genes for 16S ribosomal RNA (rRNA) were called using RASTtk (v1.073) in KBase. The contigs (genomes) were analyzed to determine whether they belonged to new species. Taxonomy was assigned using GTDB-Tk (v1.7.0) in KBase. The identity of 16S rRNA genes to other organisms was found using EzBioCloud (5). Values of digital DNA-DNA hybridization (dDDH) were found with Type (Strain) Genome Server (6). These analyses suggest that Lachnospiraceae sp. C1.1 and Porphyromonadaceae sp. W3.11 represent novel species or genera. GTDB-Tk assigned Lachnospiracae sp. C1.1 to family Lachnospiraceae and genus NK4A144, which contains no type strains. It assigned Porphyromonadaceae sp. W3.11 to Porphyromonadaceae and genus Porphyromonas_A. Values of 16S rRNA identity and dDDH with respect to type strains were low (table S4). Although more phenotypic data are needed, available evidence supports assignment of genomes to new species or genera. Related publication Hackmann TJ, Zhang B. The phenotype and genotype of fermentative prokaryotes. Sci Adv. 2023 Sep 29;9(39):eadg8687. doi: 10.1126/sciadv.adg8687. Epub 2023 Sep 27. PMID: 37756392; PMCID: PMC10530074.

Hackmann, Timothy↗