In Situ Monitoring of Free-Phase Gas Accumulation and Release in Peatlands Using Ground Penetrating Radar (GPR)

We tested a set of surface common mid-point (CMP) ground penetrating radar (GPR) surveys combined with elevation rods ( to monitor surface deformation) and gas flux measurements to investigate in-situ biogenic gas dynamics and ebullition events in a northern peatland ( raised bog). The main findings are: ( 1) changes in the two-way travel time from the surface to prominent reflectors allow estimation of average gas contents and evolution of free-phase gas (FPG); ( 2) peat surface deformation and gas flux measurements are strongly consistent with GPR estimated changes in FPG content over time; ( 3) rapid decreases in atmospheric pressure are associated with increased gas flux; and ( 4) single ebullition events can induce releases of methane much larger ( up to 192 g/m(2)) than fluxes reported by others. These results indicate that GPR is a useful tool for assessing the spatial distribution, temporal variation, and volume of biogenic gas deposits in peatlands.

Seasonal Geophysical Monitoring of Biogenic Gases in a Northern Peatland: Implications for Temporal and Spatial Variability in Free Phase Gas Production Rates

A set of high resolution surface ground penetrating radar (GPR) surveys, combined with elevation rod ( to monitor surface deformation) and gas flux measurements, were used to investigate in situ biogenic gas dynamics within a northern peatland (Caribou Bog, Maine). Gas production rates were directly estimated from the time series of GPR measurements. Spatial variability in gas production was also investigated by comparing two sites with different geological and ecological attributes, showing differences and/or similarities depending on season. One site characterized by thick highly humified peat deposits (5-6 m), wooded heath vegetation and open pools showed large ebullition events during the summer season, with estimated emissions (based on an assumed range of CH(4) concentration) between 100 and 172 g CH(4) m(-2) during a single event. The other site characterized by thinner less humified peat deposits (2-3 m) and shrub vegetation showed much smaller ebullition events during the same season (between 13 and 23 g CH(4) m(-2)). A consistent period of free-phase gas (FPG) accumulation during the fall and winter, enhanced by the frozen surficial peat acting as a confining layer, was followed by a decrease in FPG after the snow/ice melt that released estimated fluxes between 100 and 200 g CH(4) m(-2) from both sites. Estimated FPG production rates during periods of biogenic gas accumulation ranged between 0.22 and 2.00 g CH(4) m(3) d(-1) and reflected strong seasonal and spatial variability associated with differences in temperature, peat soil properties, and/or depositional attributes (e. g., stratigraphy). Periods of decreased atmospheric pressure coincided with short-period increases in biogenic gas flux, including a very rapid decrease in FPG content associated with an ebullition event that released an estimated 39 and 67 g CH(4) m(-2) in less than 3.5 hours. These results provide insights into the spatial and seasonal variability in production and emission of biogenic gases from northern peatlands.

Dynamics of a Tularemia Outbreak in a Closely Monitored Free-Roaming Population of Wild House Mice.

Infectious disease outbreaks can be devastating because of their sudden occurrence, as well as the complexity of monitoring and controlling them. Outbreaks in wildlife are even more challenging to observe and describe, especially when small animals or secretive species are involved. Modeling such infectious disease events is relevant to investigating their dynamics and is critical for decision makers to accomplish outbreak management. Tularemia, caused by the bacterium Francisella tularensis, is a potentially lethal zoonosis. Of the few animal outbreaks that have been reported in the literature, only those affecting zoo animals have been closely monitored. Here, we report the first estimation of the basic reproduction number R0 of an outbreak in wildlife caused by F. tularensis using quantitative modeling based on a susceptible-infected-recovered framework. We applied that model to data collected during an extensive investigation of an outbreak of tularemia caused by F. tularensis subsp. holarctica (also designated as type B) in a closely monitored, free-roaming house mouse (Mus musculus domesticus) population in Switzerland. Based on our model and assumptions, the best estimated basic reproduction number R0 of the current outbreak is 1.33. Our results suggest that tularemia can cause severe outbreaks in small rodents. We also concluded that the outbreak self-exhausted in approximately three months without administrating antibiotics.

Microtubule dynamics and glutathione metabolism in phagocytizing human polymorphonuclear leukocytes.

Glutathione oxidants such as tertiary butyl hydroperoxide were shown previously to prevent microtubule assembly and cause breakdown of preassembled cytoplasmic microtubules in human polymorphonuclear leukocytes. The objectives of the present study were to determine the temporal relationship between the attachment and ingestion of phagocytic particles and the assembly of microtubules, and simultaneously to quantify the levels of reduced glutathione and products of its oxidation as potential physiological regulators of assembly. Polymorphonuclear leukocytes from human peripheral blood were induced to phagocytize opsonized zymosan at 30 degrees C. Microtubule assembly was assessed in the electron microscope by direct counts of microtubules in thin sections through centrioles. Acid extracts were assayed for reduced glutathione (GSH) and oxidized glutathione (GSSG), by the sensitive enzymatic procedure of Tietze. Washed protein pellets were assayed for free sulfhydryl groups and for mixed protein disulfides with glutathione (protein-SSG) after borohydride splitting of the disulfide bond. Resting cells have few assembled microtubules. Phagocytosis induces a cycle of rapid assembly followed by disassembly. Assembly is initiated by particle contact and is maximal by 3 min of phagocytosis. Disassembly after 5-9 min of phagocytosis is preceded by a slow rise in GSSG and coincides with a rapid rise in protein-SSG. Protein-SSG also increases under conditions in which butyl hydroperoxide inhibits the assembly of microtubules that normally follows binding of concanavalin A to leukocyte cell surface receptors. No evidence for direct involvement of GSH in the induction of assembly was obtained. The formation of protein-SSG, however, emerges as a possible regulatory mechanism for the inhibition of microtubule assembly and induction of their disassembly.

Are free condoms associated with the frequent use of condoms among men who have sex with men?

Introduction. The National Behavioral HIV Surveillance (NHBS) is a self-reported cross-sectional survey that monitors the spread of human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS). The 2004 survey asked if the participant received a free condom, used it, and if receiving a free condom made him more likely to use a condom. The aim of this cross-sectional study is to examine the Houston MSA sub-dataset to determine if there was a self-expressed association between receiving a free condom and likelihood of using a condom at next intercourse, and to determine if the strength of that association varied by demographic subgroup.^ Methods. The Houston MSA 2004 NHBS had 502 participants who were men who have sex with men (MSM). The present analysis examined the answers to the questions: "In the past 12 months, have you received free condoms?" "Have you used any of the free condoms you received?" and "Did getting these free condoms make you more likely to use condoms during sex?".^ Results. Out of 502 participants, 500 answered the question about receiving free condoms, 406 (81.2%) answered all three questions, and 204 (50.2%) answered "yes" to all three questions. In the subgroup analyses, Hispanics were significantly less likely and men under 29 years of age were significantly more likely to report that their condom use behavior was influenced by receiving a free condom. ^ Conclusion. The effect of receipt of free condoms on likelihood of condom use varies by demographic subgroup, but these potentially important preliminary findings will require further investigation to validate them and further explicate the possible underlying dynamics.^

A simple torsion-free nonlinear beam element for multibody dynamics

We propose in this work a very simple torsion-free beam element capable of capturing geometrical nonlinearities. The simple formulation is objective and unconditionally con- vergent for geometrically nonlinear models with large displacements, in the traditional sense that guarantees more precise numerical solutions for finer discretizations. The formulation does not employ rotational degrees of freedom, can be applied to two and three-dimensional problems, and it is computationally very efficient.

Brownian dynamics simulations of protein folding: Access to milliseconds time scale and beyond

Protein folding occurs on a time scale ranging from milliseconds to minutes for a majority of proteins. Computer simulation of protein folding, from a random configuration to the native structure, is nontrivial owing to the large disparity between the simulation and folding time scales. As an effort to overcome this limitation, simple models with idealized protein subdomains, e.g., the diffusion–collision model of Karplus and Weaver, have gained some popularity. We present here new results for the folding of a four-helix bundle within the framework of the diffusion–collision model. Even with such simplifying assumptions, a direct application of standard Brownian dynamics methods would consume 10,000 processor-years on current supercomputers. We circumvent this difficulty by invoking a special Brownian dynamics simulation. The method features the calculation of the mean passage time of an event from the flux overpopulation method and the sampling of events that lead to productive collisions even if their probability is extremely small (because of large free-energy barriers that separate them from the higher probability events). Using these developments, we demonstrate that a coarse-grained model of the four-helix bundle can be simulated in several days on current supercomputers. Furthermore, such simulations yield folding times that are in the range of time scales observed in experiments.

Dynamics of contacts between lamellae of fibroblasts: Essential role of the actin cytoskeleton

We investigated actin cytoskeletal and adhesion molecule dynamics during collisions of leading lamellae of nontransformed and oncogene-transformed fibroblasts. By using real-time video microscopy, it was found that during lamellar collision there was considerable overlapping of leading lamellae followed by subsequent retraction. Overlapping of nontransformed fibroblasts was accompanied by formation of β-catenin-positive contact structures organized into strands oriented parallel to the long axis of the cell that were associated with bundles of actin filaments. Maintenance of such cell–cell contact structures critically depended on the contractility of actin cytoskeleton, as inhibition of contractility with serum-free medium or 2,3-butanedione 2-monoxime (BDM) resulted in loss of strand formation. Strand formation was recovered when cells in serum-free medium were incubated with the microtubule inhibitor nocodazole, which is known to increase contractility. Oncogene-transformed fibroblasts reacted to collisions with responses similar to nontransformed fibroblasts but did not develop well-organized cell–cell contacts. A model is presented to describe how differences in the organization of the actin cytoskeleton could account for the structurally distinct responses to cell–cell contact by polarized fibroblastic cells versus nonpolarized epithelial cells.

A theory for controlling cell cycle dynamics using a reversibly binding inhibitor

We demonstrate, by using mathematical modeling of cell division cycle (CDC) dynamics, a potential mechanism for precisely controlling the frequency of cell division and regulating the size of a dividing cell. Control of the cell cycle is achieved by artificially expressing a protein that reversibly binds and inactivates any one of the CDC proteins. In the simplest case, such as the checkpoint-free situation encountered in early amphibian embryos, the frequency of CDC oscillations can be increased or decreased by regulating the rate of synthesis, the binding rate, or the equilibrium constant of the binding protein. In a more complex model of cell division, where size-control checkpoints are included, we show that the same reversible binding reaction can alter the mean cell mass in a continuously dividing cell. Because this control scheme is general and requires only the expression of a single protein, it provides a practical means for tuning the characteristics of the cell cycle in vivo.

Dynamics and folding of single two-stranded coiled-coil peptides studied by fluorescent energy transfer confocal microscopy

We report single-molecule measurements on the folding and unfolding conformational equilibrium distributions and dynamics of a disulfide crosslinked version of the two-stranded coiled coil from GCN4. The peptide has a fluorescent donor and acceptor at the N termini of its two chains and a Cys disulfide near its C terminus. Thus, folding brings the two N termini of the two chains close together, resulting in an enhancement of fluorescent resonant energy transfer. End-to-end distance distributions have thus been characterized under conditions where the peptide is nearly fully folded (0 M urea), unfolded (7.4 M urea), and in dynamic exchange between folded and unfolded states (3.0 M urea). The distributions have been compared for the peptide freely diffusing in solution and deposited onto aminopropyl silanized glass. As the urea concentration is increased, the mean end-to-end distance shifts to longer distances both in free solution and on the modified surface. The widths of these distributions indicate that the molecules are undergoing millisecond conformational fluctuations. Under all three conditions, these fluctuations gave nonexponential correlations on 1- to 100-ms time scale. A component of the correlation decay that was sensitive to the concentration of urea corresponded to that measured by bulk relaxation kinetics. The trajectories provided effective intramolecular diffusion coefficients as a function of the end-to-end distances for the folded and unfolded states. Single-molecule folding studies provide information concerning the distributions of conformational states in the folded, unfolded, and dynamically interconverting states.