The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration

Sulfide: quinone oxidoreductase (SQR) is a flavoprotein with homologues in all domains of life except plants. It plays a physiological role both in sulfide detoxification and in energy transduction. We isolated the protein from native membranes of the hyperthermophilic bacterium Aquifex aeolicus, and we determined its X-ray structure in the "as-purified,'' substrate-bound, and inhibitor-bound forms at resolutions of 2.3, 2.0, and 2.9 angstrom, respectively. The structure is composed of 2 Rossmann domains and 1 attachment domain, with an overall monomeric architecture typical of disulfide oxidoreductase flavoproteins. A. aeolicus SQR is a surprisingly trimeric, periplasmic integral monotopic membrane protein that inserts about 12 angstrom into the lipidic bilayer through an amphipathic helix-turn-helix tripodal motif. The quinone is located in a channel that extends from the si side of the FAD to the membrane. The quinone ring is sandwiched between the conserved amino acids Phe-385 and Ile-346, and it is possibly protonated upon reduction via Glu-318 and/or neighboring water molecules. Sulfide polymerization occurs on the re side of FAD, where the invariant Cys-156 and Cys-347 appear to be covalently bound to polysulfur fragments. The structure suggests that FAD is covalently linked to the polypeptide in an unusual way, via a disulfide bridge between the 8-methyl group and Cys-124. The applicability of this disulfide bridge for transferring electrons from sulfide to FAD, 2 mechanisms for sulfide polymerization and channeling of the substrate, S2-, and of the product, S-n, in and out of the active site are discussed.

Feeding and respiration rates of a planktonic copepod (Calanus sinicus) oversummering in Yellow Sea Cold Bottom Waters

The distribution, feeding and oxygen consumption of Calanus sinicus were studied in August 2001 on a transect across Yellow Sea Cold Bottom Waters (YSCBW) and two additional transects nearby. The distribution of C. sinicus adults and copepodites stage CV appeared to be well correlated with water temperature. They tended to concentrate in the YSCBW (>10,000 ind. m(-2)) to avoid high surface temperature. Gut pigment contents varied from 0.44 to 2.53 ng chlorophyll a equivalents (chl a equiv.) ind.(-1) for adults, and from 0.24 to 2.24 ng chl a equiv. ind.(-1) for CV copepodites. We found no relationship between gut pigment contents and the ambient chl a concentrations. Although the gut evacuation rate constants are consistent with those measured for other copepods, their low gut pigment contents meant an estimated daily herbivorous ingestion of <3% of body carbon in the YSCBW and <10% outside the YSCBW. However, based on estimates of clearance rates, C. sinicus feeds actively whether in the YSCBW or not, so the low ingestion rates probably reflect shortage of food. Oxygen consumption rates of C. sinicus ranged from 0.21 to 0.84 mul O-2 ind.(-1) h(-1), with high rates often associated with high temperature. From the oxygen consumption rates, daily loss of body carbon was estimated to be 4.0-13.7%, which exceeds our estimates of their carbon ingestion rates. C. sinicus was probably not in diapause, either within or outside the YSCBW, but this cold-water layer provides C. sinicus with a refuge to live through the hot, low-food summer.

Grazing intensity alters soil respiration in an alpine meadow on the Tibetan plateau

Grazing intensity may alter the soil respiration rate in grassland ecosystems. The objectives of our study were to (1) determine the influence of grazing intensity on temporal variations in soil respiration of an alpine meadow on the northeastern Tibetan Plateau; and (2) characterise, the temperature response of soil respiration under different grazing intensities. Diurnal and seasonal soil respiration rates were measured for two alpine meadow sites with different grazing intensities. The light grazing (LG) meadow site had a grazing intensity of 2.55 sheep ha(-1), while the grazing intensity of the heavy grazing (HG) meadow site, 5.35 sheep ha(-1), was approximately twice that of the LG site. Soil respiration measurements - showed that CO2 efflux was almost twice as great at the LG site as at the HG site during the growing season, but the diurnal and seasonal patterns of soil respiration rate were similar for the two sites. Both exhibited the highest annual soil respiration rate in mid-August and the lowest in January. Soil respiration rate was highly dependent on soil temperature. The Q(10) value for annual soil respiration was lower for the HG site (2.75) than for the LG site (3.22). Estimates of net ecosystem CO2 exchange from monthly measurements of biomass and soil respiration revealed that during the period from May 1998 to April 1999, the LG site released 2040 g CO2 m(-2) y(-1) to the atmosphere, which was about one third more than the 1530g CO2 m(-2) y(-1) released at the HG site. The results suggest that (1) grazing intensity alters not only soil respiration rate, but also the temperature dependence of soil CO2 efflux; and (2) soil temperature is the major environmental factor controlling the temporal variation of soil respiration rate in the alpine meadow ecosystem. (C) 2003 Elsevier Ltd. All fights reserved.

New phosphorescence based probes and techniques for the analysis of cellular oxygen and respiration

Real time monitoring of oxygenation and respiration is on the cutting edge of bioanalysis, including studies of cell metabolism, bioenergetics, mitochondrial function and drug toxicity. This thesis presents the development and evaluation of new luminescent probes and techniques for intracellular O2 sensing and imaging. A new oxygen consumption rate (OCR) platform based on the commercial microfluidic perfusion channel μ-slides compatible with extra- and intracellular O2 sensitive probes, different cell lines and measurement conditions was developed. The design of semi-closed channels allowed cell treatments, multiplexing with other assays and two-fold higher sensitivity to compare with microtiter plate. We compared three common OCR platforms: hermetically sealed quartz cuvettes for absolute OCRs, partially sealed with mineral oil 96-WPs for relative OCRs, and open 96-WPs for local cell oxygenation. Both 96-WP platforms were calibrated against absolute OCR platform with MEF cell line, phosphorescent O2 probe MitoXpress-Intra and time-resolved fluorescence reader. Found correlations allow tracing of cell respiration over time in a high throughput format with the possibility of cell stimulation and of changing measurement conditions. A new multimodal intracellular O2 probe, based on the phosphorescent reporter dye PtTFPP, fluorescent FRET donor and two-photon antennae PFO and cationic nanoparticles RL-100 was described. This probe, called MM2, possesses high brightness, photo- and chemical stability, low toxicity, efficient cell staining and high-resolution intracellular O2 imaging with 2D and 3D cell cultures in intensity, ratiometric and lifetime-based modalities with luminescence readers and FLIM microscopes. Extended range of O2 sensitive probes was designed and studied in order to optimize their spectral characteristics and intracellular targeting, using different NPs materials, delivery vectors, ratiometric pairs and IR dyes. The presented improvements provide useful tool for high sensitive monitoring and imaging of intracellular O2 in different measurement formats with wide range of physiological applications.

Human respiration rate estimation using ultra-wideband distributed cognitive radar system

It has been shown that remote monitoring of pulmonary activity can be achieved using ultra-wideband (UWB) systems, which shows promise in home healthcare, rescue, and security applications. In this paper, we first present a multi-ray propagation model for UWB signal, which is traveling through the human thorax and is reflected on the air/dry-skin/fat/muscle interfaces. A geometry-based statistical channel model is then developed for simulating the reception of UWB signals in the indoor propagation environment. This model enables replication of time-varying multipath profiles due to the displacement of a human chest. Subsequently, a UWB distributed cognitive radar system (UWB-DCRS) is developed for the robust detection of chest cavity motion and the accurate estimation of respiration rate. The analytical framework can serve as a basis in the planning and evaluation of future measurement programs. We also provide a case study on how the antenna beamwidth affects the estimation of respiration rate based on the proposed propagation models and system architecture