The analysis of ring-recovery data using random effects

We show how random terms, describing both yearly variation and overdispersion, can easily be incorporated into models for mark-recovery data, through the use of Bayesian methods. For recovery data on lapwings, we show that the incorporation of the random terms greatly improves the goodness of fit. Omitting the random terms can lead to overestimation of the significance of weather on survival, and overoptimistic prediction intervals in simulations of future population behavior. Random effects models provide a natural way of modeling overdispersion-which is more satisfactory than the standard classical approach of scaling up all standard errors by a uniform inflation factor. We compare models by means of Bayesian p-values and the deviance information criterion (DIC).     

Quantification of exocytosis kinetics by DIC image analysis of cortical lawns

Cortical lawns prepared from sea urchin eggs have offered a robust in vitro system for study of regulated exocytosis and membrane fusion events since their introduction by Vacquier almost 40 years ago (Vacquier in Dev Biol 43:62–74, 1975). Lawns have been imaged by phase contrast, darkfield, differential interference contrast, and electron microscopy. Quantification of exocytosis kinetics has been achieved primarily by light scattering assays. We present simple differential interference contrast image analysis procedures for quantifying the kinetics and extent of exocytosis in cortical lawns using an open vessel that allows rapid solvent equilibration and modification. These preparations maintain the architecture of the original cortices, allow for cytological and immunocytochemical analyses, and permit quantification of variation within and between lawns. When combined, these methods can shed light on factors controlling the rate of secretion in a spatially relevant cellular context. We additionally provide a subroutine for IGOR Pro® that converts raw data from line scans of cortical lawns into kinetic profiles of exocytosis. Rapid image acquisition reveals spatial variations in time of initiation of individual granule fusion events with the plasma membrane not previously reported.     

Dissolved Inorganic Carbon Inventory and CO2Sequestration in Ureolytic Biocalcification Process with Bacillus Pasteurii

The generation and depletion of dissolved inorganic carbon (DIC) in a close-environment ureolytic biocalcification process by Bacillus pasteurii was evaluated. Three experimental sets, each containing 50 mM urea, were amended with either 50 mM Ca²⁺ before incubation (set–I) or 100 mM Ca²⁺ after 24-h incubation (set-II) or no Ca²⁺ addition (urea control).

Extent of ureolysis was maximum in urea control set (88%), followed by set–II (66.4%) and set–I (35.2%). Out of total DIC generated from microbial metabolism and ureolysis in set–I (277.6 mg/l) and set–II (464.9 mg/l), only about 54.1 mg/l and 180.1 mg/l was precipitated as CaCO₃, whereas 189.3 mg/l and 231.3 mg/l DIC escaped into headspace, respectively. Increased time separation between ureolysis and calcification steps in set–II and higher dosage of Ca²⁺ resulted in synergistic improvement in DIC capture. In a reusability test, the spent supernatant from set–II could precipitate additional amount CaCO₃from CO₂saturated water_,which was twice as much as that of the fresh media control.     

Bivalent SIRT1 inhibitors

In the current study, bivalent compounds 1–17 constructed by covalently linking the ?-amino group of lysine in a tripeptidic scaffold to a functionality via a linker were prepared and examined for their inhibitory potencies against SIRT1, a prototypical member of the β-nicotinamide adenine dinucleotide (β-NAD⁺)-dependent sirtuin family of protein N^ε-acyl-lysine deacylases. A few of them were found to be stronger SIRT1 inhibitors than the N^?-acetyl-lysine-containing monovalent counterparts 18 and 19. As exemplified with compounds 6 and 18, a bivalent SIRT1 inhibitor could exhibit a greater degree of inhibitory selectivity among SIRT1/2/3 than the corresponding monovalent counterpart. This study has laid a foundation for the future development of superior bivalent inhibitors against the (patho)physiologically and therapeutically important sirtuin family of deacylase enzymes.     

Measurement of Factor V Activity in Human Plasma Using a Microplate Coagulation Assay

In response to injury, blood coagulation is activated and results in generation of the clotting protease, thrombin. Thrombin cleaves fibrinogen to fibrin which forms an insoluble clot that stops hemorrhage. Factor V (FV) in its activated form, FVa, is a critical cofactor for the protease FXa and accelerator of thrombin generation during fibrin clot formation as part of prothrombinase ^{1, 2}. Manual FV assays have been described ^{3, 4}, but they are time consuming and subjective. Automated FV assays have been reported ^5-7, but the analyzer and reagents are expensive and generally provide only the clot time, not the rate and extent of fibrin formation. The microplate platform is preferred for measuring enzyme-catalyzed events because of convenience, time, cost, small volume, continuous monitoring, and high-throughput ^{8, 9}. Microplate assays have been reported for clot lysis ¹⁰, platelet aggregation ¹¹, and coagulation Factors ¹², but not for FV activity in human plasma. The goal of the method was to develop a microplate assay that measures FV activity during fibrin formation in human plasma.This novel microplate method outlines a simple, inexpensive, and rapid assay of FV activity in human plasma. The assay utilizes a kinetic microplate reader to monitor the absorbance change at 405nm during fibrin formation in human plasma (Figure 1) ¹³. The assay accurately measures the time, initial rate, and extent of fibrin clot formation. It requires only μl quantities of plasma, is complete in 6 min, has high-throughput, is sensitive to 24-80pM FV, and measures the amount of unintentionally activated (1-stage activity) and thrombin-activated FV (2-stage activity) to obtain a complete assessment of its total functional activity (2-stage activity - 1-stage activity).Disseminated intravascular coagulation (DIC) is an acquired coagulopathy that most often develops from pre-existing infections ¹⁴. DIC is associated with a poor prognosis and increases mortality above the pre-existing pathology ¹⁵. The assay was used to show that in 9 patients with DIC, the FV 1-stage, 2-stage, and total activities were decreased, on average, by 54%, 44%, and 42%, respectively, compared with normal pooled human reference plasma (NHP).The FV microplate assay is easily adaptable to measure the activity of any coagulation factor. This assay will increase our understanding of FV biochemistry through a more accurate and complete measurement of its activity in research and clinical settings. This information will positively impact healthcare environments through earlier diagnosis and development of more effective treatments for coagulation disorders, such as DIC.     

Quantitative analysis of shape and volume changes in activated thrombocytes in real time by single‐shot spatial light modulator‐based differential interference contrast imaging

We suggest to use a combination of optical tweezers and single‐image quantitative differential interference contrast (DIC) emulated by a spatial light modulator (SLM) to study physiological shape changes in thrombocytes after activation and demonstrate the effectiveness of this system for the given task. A specially designed phase mask displayed at the SLM enables quantitative phase calculation from only a single recording. The optical tweezers stabilize trapped thrombocytes for long‐time monitoring of changes in the optical thickness profile of thrombocytes during activation by adenosine diphosphate (ADP). (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)