Parameter identification of the calvin photosynthesis cycle

Summary This article is concerned with the determination of kinetic parameters of the Calvin photosynthesis cycle which is described by seventeen nonlinear ordinary differential equations. It is shown that the task requires dynamic data for several sets of initial conditions. The numerical technique is based upon an algorithm for non-linear optimization and Gear's numerical integration scheme for stiff systems of differential equations. The sensitivity of the parameters to noise in the data is tested with a method adapted from Rosenbrook and Storey. A preliminary set of parameters has been obtained from a preliminary set of experimental data. The numerical methods are then tested with synthetic data derived from these parameters. The mathematical model and the results obtained in the simulation are used as an aid in designing new experiments.     

Value of the "gastric chamber", new technic performed ex vivo, for the study of the gastric mucosa of the rat]

The "gastric chamber" technique, performed in the anaesthetised rat, enables the study of gastric mucosal fragility induced by doses of phenylbutazone, which do not themselves cause ulceration or exulceration. The perfusion of buffered solution at pH 2-8 into the gastric chamber shows that prior oral administration of phenylbutazone 50 mg/kg increases the fragility of the mucosa. The optimal delay separating this administration from the time of experimentation is 6 hours. The effects seen are essentially vascular disorders.     

Oxidative refolding of lysozyme assisted by DsbA, DsbC and the GroEL apical domain immobilized in cellulose

Expression of recombinant proteins in Escherichia coli often leads to formation of inclusion bodies (IB). If a recombinant protein contains one or more disulfide bonds, protein refolding and thiol oxidation reactions are required to recover its biological activity. Previous studies have demonstrated that molecular chaperones and foldases assist with the in vitro protein refolding. However, their use has been limited by the stoichiometric amount required for the refolding reaction. In search of alternatives to facilitate the use of these folding biocatalysts in this study, DsbA, DsbC, and the apical domain of GroEL (AD) were fused to the carbohydrate-binding module CBD_Cex of Cellulomonas fimi. The recombinant proteins were purified and immobilized in cellulose and used to assist the oxidative refolding of denatured and reduced lysozyme. The assisted refolding yields obtained with immobilized folding biocatalysts were at least twice of those obtained in the spontaneous refolding, suggesting that the AD, DsbA, and DsbC immobilized in cellulose might be useful for the oxidative refolding of recombinant proteins that are expressed as inclusion bodies. In addition, the spontaneous or assisted refolding kinetics data fitted well (r² > 0.9) to a previously reported lysozyme refolding model. The estimated refolding (k _N) and aggregation (k _A) constants were consistent with the hypothesis that foldases assisted the oxidative refolding of lysozyme by decreasing protein aggregation rather than increasing the refolding rate.     

Combined anaerobic ammonium and methane oxidation for nitrogen and methane removal

Anammox (anaerobic ammonium oxidation) is an environment-friendly and cost-efficient nitrogen-removal process currently applied to high-ammonium-loaded wastewaters such as anaerobic digester effluents. In these wastewaters, dissolved methane is also present and should be removed to prevent greenhouse gas emissions into the environment. Potentially, another recently discovered microbial pathway, n-damo (nitrite-dependent anaerobic methane oxidation) could be used for this purpose. In the present paper, we explore the feasibility of simultaneously removing methane and ammonium anaerobically, starting with granules from a full-scale anammox bioreactor. We describe the development of a co-culture of anammox and n-damo bacteria using a medium containing methane, ammonium and nitrite. The results are discussed in the context of other recent studies on the application of anaerobic methane- and ammonia-oxidizing bacteria for wastewater treatment.     

Density and distribution of water boatmen and brine shrimp at a major shorebird wintering area in Puerto Rico

The Cabo Rojo salt flats are an important wintering area for migratory shorebirds. Their quality is intimately related to prey availability, as prey are needed to meet energetic requirements. Understanding prey dynamics is, therefore, a key element of shorebird conservation plans. To this end, we monitored the density and distribution of water-boatmen (Trichocorixa spp.) and brine shrimp (Artemia spp.) in relation to water salinity from September to November of 1994 and 1995. Salinity ranged from 4 to 292 ppt, and gradients were related to hydrological alterations (e.g., salt extraction) and connection to the ocean. Brine shrimp were restricted to areas of highest salinity ( 106 ppt), whereas water-boatmen to areas of lowest salinity (< 65 ppt). We used aquaria experiments to discern potential mechanisms influencing density and distribution of water boatmen. We focused on this species because its caloric value is similar to the brine shrimp's, but it occurs in areas of lower salinity where shorebirds are less prone to hyperosmotic stress. We hypothesized that areas devoid of water boatmen exceeded their tolerance limit, and that these limits could hamper survival as individuals move among areas. Experiments showed that an increase of 8.5 ± 2.1 ppt, when the base salinity was 40 ppt, induced a 50% mortality rate. From a base salinity of 55 ppt, median survival time decreased curvilinearly across salinity concentrations of 65 to 195 ppt. Median survival was lowest > 100 ppt. Lowering water salinity did not result in osmolal related mortality. Results underscored the sensitivity of water boatmen to high salinity, particularly when the difference in salinity between the source and destination localities widened. Water boatmen density increased in one lagoon as salinity decreased from 65 to 47 ppt. On the basis of our experiments, local adult survivorship improved and immigration and subsequent survival of adults, if any, was not hindered. The density of nymphs also suggested that hatching occurred concurrently. The foraging value of the salt flats can be enhanced by maintaining salinity at < 65 ppt in selected management units and minimizing differences in salinity concentrations among them.     

The Psychedelic State Induced by Ayahuasca Modulates the Activity and Connectivity of the Default Mode Network

The experiences induced by psychedelics share a wide variety of subjective features, related to the complex changes in perception and cognition induced by this class of drugs. A remarkable increase in introspection is at the core of these altered states of consciousness. Self-oriented mental activity has been consistently linked to the Default Mode Network (DMN), a set of brain regions more active during rest than during the execution of a goal-directed task. Here we used fMRI technique to inspect the DMN during the psychedelic state induced by Ayahuasca in ten experienced subjects. Ayahuasca is a potion traditionally used by Amazonian Amerindians composed by a mixture of compounds that increase monoaminergic transmission. In particular, we examined whether Ayahuasca changes the activity and connectivity of the DMN and the connection between the DMN and the task-positive network (TPN). Ayahuasca caused a significant decrease in activity through most parts of the DMN, including its most consistent hubs: the Posterior Cingulate Cortex (PCC)/Precuneus and the medial Prefrontal Cortex (mPFC). Functional connectivity within the PCC/Precuneus decreased after Ayahuasca intake. No significant change was observed in the DMN-TPN orthogonality. Altogether, our results support the notion that the altered state of consciousness induced by Ayahuasca, like those induced by psilocybin (another serotonergic psychedelic), meditation and sleep, is linked to the modulation of the activity and the connectivity of the DMN.     

The Southern Megalopolis: Using the Past to Predict the Future of Urban Sprawl in the Southeast U.S

The future health of ecosystems is arguably as dependent on urban sprawl as it is on human-caused climatic warming. Urban sprawl strongly impacts the urban ecosystems it creates and the natural and agro-ecosystems that it displaces and fragments. Here, we project urban sprawl changes for the next 50 years for the fast-growing Southeast U.S. Previous studies have focused on modeling population density, but the urban extent is arguably as important as population density per se in terms of its ecological and conservation impacts. We develop simulations using the SLEUTH urban growth model that complement population-driven models but focus on spatial pattern and extent. To better capture the reach of low-density suburban development, we extend the capabilities of SLEUTH by incorporating street-network information. Our simulations point to a future in which the extent of urbanization in the Southeast is projected to increase by 101% to 192%. Our results highlight areas where ecosystem fragmentation is likely, and serve as a benchmark to explore the challenging tradeoffs between ecosystem health, economic growth and cultural desires.     

Nonhost status of Citrus sinensis cultivar valencia and C. paradisi cultivar ruby red to Mexican Anastrepha fraterculus (Diptera: Tephritidae)

Anastrepha fraterculus (Wiedemann) is recognized as a pest of citrus, apples, and blackberries in South America. In Mexico, it is mainly found in fruit of the family Myrtaceae and has never been reported infesting citrus. Here, we sought to determine whether females stemming from Mexican A. fraterculus populations (collected in the state of Veracruz) would lay eggs in 'Valencia' oranges and 'Ruby Red' grapefruit and, if so, whether larvae would hatch and develop. We worked under laboratory and seminatural conditions (i.e., gravid females released in fruit-bearing, bagged branches in a commercial citrus grove) and used Anastrepha ludens (Loew), a notorious pest of citrus, as a control species. Under laboratory conditions, A. ludens readily accepted both oranges and grapefruit as oviposition substrates, but A. fraterculus rarely oviposited in these fruit (but did so in guavas, a preferred host) and no larvae ever developed. Eggs were deposited in the toxic flavedo (A. fraterculus) and nontoxic albedo (A. ludens) regions. Field studies revealed that, as was the case in the laboratory, A. fraterculus rarely oviposited into oranges or grapefruit and that, when such was the case, either no larvae developed (oranges) or of the few (13) that developed and pupated (grapefruit), only two adults emerged that survived 1 and 3 d, respectively (5-17% of the time necessary to reach sexual maturity). In sharp contrast, grapefruit exposed to A. ludens yielded up to 937 pupae and adults survived for >6 mo. Therefore, the inability of Mexican A. fraterculus to successfully develop in citrus renders the status of Mexican A. fraterculus as a pest of citrus in Mexico as unsubstantiated.     

Terrestrial carbon balance in a drier world: the effects of water availability in southwestern North America

Global modeling efforts indicate semiarid regions dominate the increasing trend and interannual variation of net CO₂ exchange with the atmosphere, mainly driven by water availability. Many semiarid regions are expected to undergo climatic drying, but the impacts on net CO₂ exchange are poorly understood due to limited semiarid flux observations. Here we evaluated 121 site‐years of annual eddy covariance measurements of net and gross CO₂ exchange (photosynthesis and respiration), precipitation, and evapotranspiration (ET) in 21 semiarid North American ecosystems with an observed range of 100 – 1000 mm in annual precipitation and records of 4–9 years each. In addition to evaluating spatial relationships among CO₂ and water fluxes across sites, we separately quantified site‐level temporal relationships, representing sensitivity to interannual variation. Across the climatic and ecological gradient, photosynthesis showed a saturating spatial relationship to precipitation, whereas the photosynthesis–ET relationship was linear, suggesting ET was a better proxy for water available to drive CO₂ exchanges after hydrologic losses. Both photosynthesis and respiration showed similar site‐level sensitivity to interannual changes in ET among the 21 ecosystems. Furthermore, these temporal relationships were not different from the spatial relationships of long‐term mean CO₂ exchanges with climatic ET. Consequently, a hypothetical 100‐mm change in ET, whether short term or long term, was predicted to alter net ecosystem production (NEP) by 64 gCm^?2 yr^?1. Most of the unexplained NEP variability was related to persistent, site‐specific function, suggesting prioritization of research on slow‐changing controls. Common temporal and spatial sensitivity to water availability increases our confidence that site‐level responses to interannual weather can be extrapolated for prediction of CO₂ exchanges over decadal and longer timescales relevant to societal response to climate change.     

Molecular analysis of intestinal microbiota of rainbow trout (Oncorhynchus mykiss)

The aim of this study was to evaluate different molecular tools based on the 16S rRNA gene, internal transcribed spacer, and the rpo B gene to examine the bacterial populations present in juvenile rainbow trout intestines. DNA was extracted from both pooled intestinal samples and bacterial strains. Genes were PCR-amplified and analysed using both temporal temperature gradient gel electrophoresis (TTGE) and restriction fragment length polymorphism methods. Because of the high cultivability of the samples, representative bacterial strains were retrieved and we compared the profiles obtained from isolated bacteria with the profile of total bacteria from intestinal contents. Direct analysis based on rpo B-TTGE revealed a simple bacterial composition with two to four bands per sample, while the 16S rRNA gene-TTGE showed multiple bands and comigration for a few species. Sequencing of the 16S rRNA gene- and rpo B-TTGE bands revealed that the intestinal microbiota was dominated by Lactococcus lactis, Citrobacter gillenii, Kluyvera intermedia, Obesumbacterium proteus , and Shewanella marinus . In contrast to 16S rRNA gene-TTGE, rpo B-TTGE profiles derived from bacterial strains produced one band per species. Because the single-copy state of rpo B leads to a single band in TTGE, the rpo B gene is a promising molecular marker for investigating the bacterial community of the rainbow trout intestinal microbiota.