Modeling speciation effects on biodegradation in mixed metal/chelate systems

A new model, CCBATCH, comprehensively couples microbially catalyzed reactions to aqueous geochemistry. The effect of aqueous speciation on biodegradation reactions and the effect of biological reactions on the concentration of chemical species (e.g. H₂CO₃, NH ₄ ⁺ , O₂) are explicitly included in CCBATCH, allowing systematic investigation of kinetically controlled biological reactions. Bulk-phase chemical speciation reactions including acid/base and complexation are modeled as thermodynamically controlled, while biological reactions are modeled as kinetically controlled. A dual-Monod kinetic formulation for biological degradation reactions is coupled with stoichiometry for the degradation reaction to predict the rate of change of all biological and chemical species affected by the biological reactions. The capability of CCBATCH to capture pH and speciation effects on biological reactions is demonstrated by a series of modeling examples for the citrate/Fe(III) system. pH controls the concentration of potentially biologically available forms of citrate. When the percentage of the degradable substrate is low due to complexation or acid/base speciation, degradation rates may be slow despite high concentrations of substrate Complexation reactions that sequester substratein non-degradable forms may prevent degradation or stopdegradation reactions prior to complete substrate utilization. The capability of CCBATCH to couple aqueous speciation changes to biodegradation reaction kinetics and stoichiometry allows prediction of these key behaviors in mixed metal/chelate systems.     

Barred owl occupancy surveys within the range of the northern spotted owl

The range expansion by barred owls (Strix varia) into western North America has raised considerable concern regarding their potential effects on declining northern spotted owl (Strix occidentalis caurina) populations, yet most information on the occurrence of barred owls in the region is limited to incidental detections during surveys for spotted owls. To address this shortcoming we investigated response behavior, detection probabilities, and landscape occupancy patterns of barred owls in western Oregon, USA, during conspecific versus spotted owl call-broadcast surveys. Subtle differences in barred owl response behavior to conspecific versus spotted owl vocalizations combined with minor procedural differences between species-specific survey protocols led to a sizeable difference in estimated detection probabilities during conspecific (0.66, 95% CI = 0.61–0.71) versus spotted owl (0.48, 95% CI = 0.39–0.56) surveys. We identified 61 territorial pairs of barred owls during repeated surveys of a multi-ownership study area with the probability of occupancy being highest in the structurally diverse mixture of mature and old forests that occurred almost entirely on public lands. Our findings suggest that research and management strategies to address potential competitive interactions between spotted owls and barred owls will require carefully designed, species-specific survey methods that account for erratic response behaviors and imperfect detection of both species. Our sampling methods can be used by forest managers to determine the occurrence and distribution of barred owls with high confidence. © 2011 The Wildlife Society.     

Influence of feeding schedules on the chronobiology of renin activity,urinary electrolytes and blood pressure in dogs

The contribution of the renin–angiotensin–aldosterone system (RAAS) to the development of congestive heart failure (CHF) and hypertension (HT) has long been recognized. Medications that are commonly used in the course of CHF and HT are most often given with morning food for the sake of convenience and therapeutic compliance. However, biological rhythms and their responsiveness to environmental clues such as food intake may noticeably impact the effectiveness of drugs used in the management of cardiovascular disorders. Only sparse information about the effect of feeding schedules on the biology of the RAAS and blood pressure (BP) is presently available. Two studies were designed to explore the chronobiology of renin activity (RA), BP, renal sodium (U_Na,fe) and potassium (U_K,fe) handling in relation to meal timing in dogs. In a first experiment (Study a), blood and urinary samples for measurement of RA, U_Na,fe and U_K,fe were drawn from 18 healthy beagle dogs fed a normal-sodium diet at either 07:00, 13:00 or 19:00?h. In a second experiment (Study b), BP was recorded continuously from six healthy, telemetered beagle dogs fed a similar diet at 07:00, or 19:00?h. Data were collected throughout 24-h time periods, and analyzed by means of nonlinear mixed-effects models. Differences between the geometric means of early versus late time after feeding observations were further compared using parametric statistics. In agreement with our previous investigations, the results indicate that RA, U_Na,fe, U_K,fe, systolic, and diastolic BP oscillate with a circadian periodicity in dogs fed a regular diet at 07:00?h. A cosine model with a fixed 24-h period was found to fit the variations of RA, U_K,fe and BP well, whereas cyclic changes in U_Na,fe were best characterized by means of a combined cosine and surge model, reflecting a postprandial sodium excretion followed by a monotonous decay. Our data show that feeding time has a marked influence on the chronobiology of the renin cascade, urinary electrolytes, and BP. Introducing a 6- or 12-h delay in the dogs’ feeding schedule caused a shift of similar magnitude (05:06 and 12:32?h for Studies a and b, respectively) in the rhythm of these biomarkers. In all study groups, RA and BP exhibited a marked fall just after food intake. The drop in RA is consistent with sodium and water-induced body fluid expansion, while the reduction of BP could be related to the decreased activity of renin and the secretion of vasodilatory gut peptides. An approximately 1.5-fold (1.2–1.6-fold) change between the average early and late time after feeding observations was found for RA (p?<?0.0001), U_Na,fe (p?<?0.01) and U_K,fe (p?<?0.05). Postprandial variations in BP, albeit small (ca. 10?mmHg), were statistically significant (p?<?0.01) and supported by the model-based analysis.

In conclusion, the timing of food intake appears to be pivotal to the circadian organization of the renin cascade and BP. This synchronizing effect could be mediated by feeding-related signals, such as dietary sodium, capable of entraining circadian oscillators downstream of the master, light–dark-adjusted pacemaker in the suprachiasmatic nucleus.     

Process-oriented ecological modeling approach and scientific workflow system

A scientific workflow system is designed specifically to organize, manage and execute a series of research steps, or a workflow, in a given runtime environment. The vision for scientific workflow systems is that the scientists around the world can collaborate on designing global-scaled experiments, sharing the data sets, experimental processes, and results on an easy-to-use platform. Each scientist can create and execute their own workflows and view results in real-time, and then subsequently share and reuse workflows among other scientists. Two case studies, using the Kepler system and BioVeL, are introduced in this paper. Ecological niche modeling process, which is a specialized form of scientific workflow system included in both Kepler system and BioVeL, was used to describe and discuss the features, developmental trends, and problems of scientific workflows.     

MV-mimicking micelles loaded with PEG-serine-ACP nanoparticles to achieve biomimetic intra/extra fibrillar mineralization of collagen in vitro

Since their discovery, matrix vesicles (MVs) containing minerals have received considerable attention for their role in the mineralization of bone, dentin and calcified cartilage. Additionally, MVs' association with collagen fibrils, which serve as the scaffold for calcification in the organic matrix, has been repeatedly highlighted. The primary purpose of the present study was to establish a MVs–mimicking model (PEG-S-ACP/micelle) in vitro for studying the exact mechanism of MVs-mediated extra/intra fibrillar mineralization of collagen in vivo. In this study, high-concentration serine was used to stabilize the amorphous calcium phosphate (S-ACP), which was subsequently mixed with polyethylene glycol (PEG) to form PEG-S-ACP nanoparticles. The nanoparticles were loaded in the polysorbate 80 micelle through a micelle self-assembly process in an aqueous environment. This MVs–mimicking model is referred to as the PEG-S-ACP/micelle model. By adjusting the pH and surface tension of the PEG-S-ACP/micelle, two forms of minerals (crystalline mineral nodules and ACP nanoparticles) were released to achieve the extrafibrillar and intrafibrillar mineralization, respectively. This in vitro mineralization process reproduced the mineral nodules mediating in vivo extrafibrillar mineralization and provided key insights into a possible mechanism of biomineralization by which in vivo intrafibrillar mineralization could be induced by ACP nanoparticles released from MVs. Also, the PEG-S-ACP/micelle model provides a promising methodology to prepare mineralized collagen scaffolds for repairing bone defects in bone tissue engineering.     

Vesicle Shrinking and Enlargement Play Opposing Roles in the Release of Exocytotic Contents

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Effects of detergents on catalytic activity of human endometase/matrilysin 2, a putative cancer biomarker

Matrix metalloproteinases (MMPs) are a family of hydrolytic enzymes that play significant roles in development, morphogenesis, inflammation, and cancer invasion. Endometase (matrilysin 2 or MMP-26) is a putative early biomarker for human carcinomas. The effects of the ionic and nonionic detergents on catalytic activity of endometase were investigated. The hydrolytic activity of endometase was detergent concentration dependent, exhibiting a bell-shaped curve with its maximum activity near the critical micelle concentration (CMC) of nonionic detergents tested. The effect of Brij-35 on human gelatinase B (MMP-9), matrilysin (MMP-7), and membrane-type 1 MMP (MT1-MMP) was further explored. Their maximum catalysis was observed near the CMC of Brij-35 (∼ 90 μM). Their IC₅₀ values were above the CMC. The inhibition mechanism of MMP-7, MMP-9, and MT1-MMP by Brij-35 was a mixed type as determined by Dixon’s plot; however, the inhibition mechanism of endometase was noncompetitive with a K_i value of 240 μM. The catalytic activities of MMPs are influenced by detergents. Monomer of detergents may activate and stabilize MMPs to enhance catalysis, but micelle of detergents may sequester enzyme and block the substrate binding site to impede catalysis. Under physiological conditions, a lipid or membrane microenvironment may regulate enzymatic activity.     

Global Scenarios: Background Review for the Millennium Ecosystem Assessment

The long-range outlook for the world’s ecosystems depends on the course taken by global development in the coming decades. Current global trends and ecological dynamics are consistent with very different outcomes, defined by alternative assumptions about the technological, economic, demographic, geopolitical, and social aspects of development and the ways in which institutions, personal and public values, and natural systems may be expected to respond to historically novel stressors. Recent advances in scenario analysis have addressed the dual methodological challenge of exploring these uncertainties in an organized way and determining what would be needed to make the transition to sustainability. This paper reviews global scenario research, setting current efforts in a historical context. It focuses on seven recent studies that are comprehensive, regionally disaggregated, and narratively rich—and thus of greatest relevance to the Millennium Ecosystem Assessment (MA). It summarizes their social visions and the level of quantitative detail used in these exercises. Taken together, this suite of global scenario studies provides a useful platform for the MA by offering insight into the complex factors that drive ecosystem change, estimating the magnitude of regional pressures on ecosystems, sounding the alert on critical uncertainties that could undermine sustainable development, and understanding the importance of institutions and values. But these studies are only a point of departure. The integration of changing ecosystem conditions into global development scenarios, as both effects and causes, is at the cutting edge of scenario analysis. The paper concludes by identifying directions for this research program and suggesting ways that the MA can contribute to this effort.     

A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria

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Highlights

• •XL-MS reveals new PPIs in yeast mitochondria under glycerol and glucose condition.
• •Significant but limited results from quantitative XL-MS experiments.
• •Ndi1 participates in a CIII₂CIV₂ respiratory supercomplex.
• •Min8 promotes assembly of Cox12 into an intermediate complex IV.