Some parameters affecting respiratory control in Azotobacter vinelandii membranes

AbstractRCI :respiratory control index (state 3/state 4 rate of oxygen uptake)m-C1 CCP: carbonylcyanide m-chlorophenyl hydrazoneHQNO : 2-n-heptyl-4-hydroxyquinoline-N-oxidePIPES: piperazine-N,N′-bis 2-ethane sulphonic aci

Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiome

The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism's 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities

Satellites to Seafloor: Toward Fully Autonomous Ocean Sampling

Future ocean observing systems will rely heavily on autonomous vehicles to achieve the persistent and heterogeneous measurements needed to understand the ocean’s impact on the climate system. The day-to-day maintenance of these arrays will become increasingly challenging if significant human resources, such as manual piloting, are required. For this reason, techniques need to be developed that permit autonomous determination of sampling directives based on science goals and responses to in situ, remote-sensing, and model-derived information. Techniques that can accommodate large arrays of assets and permit sustained observations of rapidly evolving ocean properties are especially needed for capturing interactions between physical circulation and biogeochemical cycling. Here we document the first field program of the Satellites to Seafloor project, designed to enable a closed loop of numerical model prediction, vehicle path-planning, in situ path implementation, data collection, and data assimilation for future model predictions. We present results from the first of two field programs carried out in Monterey Bay, California, over a period of three months in 2016. While relatively modest in scope, this approach provides a step toward an observing array that makes use of multiple information streams to update and improve sampling strategies without human intervention

BCMA Is Essential for the Survival of Long-lived Bone Marrow Plasma Cells

Long-lived humoral immunity is manifested by the ability of bone marrow plasma cells (PCs) to survive for extended periods of time. Recent studies have underscored the importance of BLyS and APRIL as factors that can support the survival of B lineage lymphocytes. We show that BLyS can sustain PC survival in vitro, and this survival can be further enhanced by interleukin 6. Selective up-regulation of Mcl-1 in PCs by BLyS suggests that this α-apoptotic gene product may play an important role in PC survival. Blockade of BLyS, via transmembrane activator and cyclophilin ligand interactor–immunoglobulin treatment, inhibited PC survival in vitro and in vivo. Heightened expression of B cell maturation antigen (BCMA), and lowered expression of transmembrane activator and cyclophilin ligand interactor and BAFF receptor in PCs relative to resting B cells suggests a vital role of BCMA in PC survival. Affirmation of the importance of BCMA in PC survival was provided by studies in BCMA−/− mice in which the survival of long-lived bone marrow PCs was impaired compared with wild-type controls. These findings offer new insights into the molecular basis for the long-term survival of PCs

Satellites to seafloor : toward fully autonomous ocean sampling

Author Posting. © The Oceanography Society, 2017. This article is posted here by permission of The Oceanography Society for personal use, not for redistribution. The definitive version was published in Oceanography 30, no. 2 (2017): 160–168, doi:10.5670/oceanog.2017.238.Future ocean observing systems will rely heavily on autonomous vehicles to achieve the persistent and heterogeneous measurements needed to understand the ocean’s impact on the climate system. The day-to-day maintenance of these arrays will become increasingly challenging if significant human resources, such as manual piloting, are required. For this reason, techniques need to be developed that permit autonomous determination of sampling directives based on science goals and responses to in situ, remote-sensing, and model-derived information. Techniques that can accommodate large arrays of assets and permit sustained observations of rapidly evolving ocean properties are especially needed for capturing interactions between physical circulation and biogeochemical cycling. Here we document the first field program of the Satellites to Seafloor project, designed to enable a closed loop of numerical model prediction, vehicle path-planning, in situ path implementation, data collection, and data assimilation for future model predictions. We present results from the first of two field programs carried out in Monterey Bay, California, over a period of three months in 2016. While relatively modest in scope, this approach provides a step toward an observing array that makes use of multiple information streams to update and improve sampling strategies without human intervention.This work is funded by the Keck Institute for Space Studies (generously supported by the W.M. Keck Foundation) through the project “Science-driven Autonomous and Heterogeneous Robotic Networks: A Vision for Future Ocean Observation

Evaluating Multiplexed Quantitative Phosphopeptide Analysis on a Hybrid Quadrupole Mass Filter/Linear Ion Trap/Orbitrap Mass Spectrometer

As a driver for many biological processes, phosphorylation remains an area of intense research interest. Advances in multiplexed quantitation utilizing isobaric tags (e.g., TMT and iTRAQ) have the potential to create a new paradigm in quantitative proteomics. New instrumentation and software are propelling these multiplexed workflows forward, which results in more accurate, sensitive, and reproducible quantitation across tens of thousands of phosphopeptides. This study assesses the performance of multiplexed quantitative phosphoproteomics on the Orbitrap Fusion mass spectrometer. Utilizing a two-phosphoproteome model of precursor ion interference, we assessed the accuracy of phosphopeptide quantitation across a variety of experimental approaches. These methods included the use of synchronous precursor selection (SPS) to enhance TMT reporter ion intensity and accuracy. We found that (i) ratio distortion remained a problem for phosphopeptide analysis in multiplexed quantitative workflows, (ii) ratio distortion can be overcome by the use of an SPS-MS3 scan, (iii) interfering ions generally possessed a different charge state than the target precursor, and (iv) selecting only the phosphate neutral loss peak (single notch) for the MS3 scan still provided accurate ratio measurements. Remarkably, these data suggest that the underlying cause of interference may not be due to coeluting and cofragmented peptides but instead from consistent, low level background fragmentation. Finally, as a proof-of-concept 10-plex experiment, we compared phosphopeptide levels from five murine brains to five livers. In total, the SPS-MS3 method quantified 38 247 phosphopeptides, corresponding to 11 000 phosphorylation sites. With 10 measurements recorded for each phosphopeptide, this equates to more than 628 000 binary comparisons collected in less than 48 h

The On-Orbit Performance of the Galaxy Evolution Explorer

We report the first year on-orbit performance results for the Galaxy Evolution Explorer (GALEX), a NASA Small Explorer that is performing a survey of the sky in two ultraviolet bands. The instrument comprises a 50 cm diameter modified Ritchey-Chretien telescope with a 1.25 degree field of view, selectable imaging and objective grism spectroscopic modes, and an innovative optical system with a thin-film multilayer dichroic beam splitter that enables simultaneous imaging by a pair of photon counting, microchannel plate, delay line readout detectors. Initial measurements demonstrate that GALEX is performing well, meeting its requirements for resolution, efficiency, astrometry, bandpass definition and survey sensitivity.Comment: This paper will be published as part of the Galaxy Evolution Explorer (GALEX) Astrophysical Journal Letters Special Issu

Was Dinosaurian Physiology Inherited by Birds? Reconciling Slow Growth in Archaeopteryx

Archaeopteryx is the oldest and most primitive known bird (Avialae). It is believed that the growth and energetic physiology of basalmost birds such as Archaeopteryx were inherited in their entirety from non-avialan dinosaurs. This hypothesis predicts that the long bones in these birds formed using rapidly growing, well-vascularized woven tissue typical of non-avialan dinosaurs. We report that Archaeopteryx long bones are composed of nearly avascular parallel-fibered bone. This is among the slowest growing osseous tissues and is common in ectothermic reptiles. These findings dispute the hypothesis that non-avialan dinosaur growth and physiology were inherited in totality by the first birds. Examining these findings in a phylogenetic context required intensive sampling of outgroup dinosaurs and basalmost birds. Our results demonstrate the presence of a scale-dependent maniraptoran histological continuum that Archaeopteryx and other basalmost birds follow. Growth analysis for Archaeopteryx suggests that these animals showed exponential growth rates like non-avialan dinosaurs, three times slower than living precocial birds, but still within the lowermost range for all endothermic vertebrates. The unexpected histology of Archaeopteryx and other basalmost birds is actually consistent with retention of the phylogenetically earlier paravian dinosaur condition when size is considered. The first birds were simply feathered dinosaurs with respect to growth and energetic physiology. The evolution of the novel pattern in modern forms occurred later in the group's history

Radiometer Calibration Using Colocated GPS Radio Occultation Measurements

We present a new high-fidelity method of calibrating a cross-track scanning microwave radiometer using Global Positioning System (GPS) radio occultation (GPSRO) measurements. The radiometer and GPSRO receiver periodically observe the same volume of atmosphere near the Earth's limb, and these overlapping measurements are used to calibrate the radiometer. Performance analyses show that absolute calibration accuracy better than 0.25 K is achievable for temperature sounding channels in the 50-60-GHz band for a total-power radiometer using a weakly coupled noise diode for frequent calibration and proximal GPSRO measurements for infrequent (approximately daily) calibration. The method requires GPSRO penetration depth only down to the stratosphere, thus permitting the use of a relatively small GPS antenna. Furthermore, only coarse spacecraft angular knowledge (approximately one degree rms) is required for the technique, as more precise angular knowledge can be retrieved directly from the combined radiometer and GPSRO data, assuming that the radiometer angular sampling is uniform. These features make the technique particularly well suited for implementation on a low-cost CubeSat hosting both radiometer and GPSRO receiver systems on the same spacecraft. We describe a validation platform for this calibration method, the Microwave Radiometer Technology Acceleration (MiRaTA) CubeSat, currently in development for the National Aeronautics and Space Administration (NASA) Earth Science Technology Office. MiRaTA will fly a multiband radiometer and the Compact TEC/Atmosphere GPS Sensor in 2015.United States. Dept. of Defense. Assistant Secretary of Defense for Research & Engineering (United States. Air Force Contract FA8721-05-C-0002