ALBERT

Description: Focal adhesions mediate force transfer between ECM-integrin complexes and the cytoskeleton. Although vinculin has been implicated in force transmission, few direct measurements have been made, and there is little mechanistic insight. Using vinculin-null cells expressing vinculin mutants, we demonstrate that vinculin is not required for transmission of adhesive and traction...

Description: 〈span〉〈div〉ABSTRACT〈/div〉We have developed a novel approach to image vertical structures using multiply scattered waves. This method requires only a smooth seismic velocity model and data recorded at the surface. Previous methods to image near-vertical interfaces or faults using migration methods all require prior information about small-scale details in the seismic velocity model to infer the locations of multiple-scattering wave interactions. We used waves that had their last scattering interaction with near-vertical interfaces, while their other scattering points might be anywhere in the earth, including at the free surface. Our algorithm then images the final scattering point using a time-reversed mirror-style imaging condition, so we refer to the method as time-reversed mirror imaging. Artifacts in the images produced have clear causes and can be filtered out by stacking over shots and including contributions from multiples. Our numerical examples demonstrate the successful application of the method for staircase structures and a section of the Marmousi model. They also reveal a new way to diagnose errors in the smooth or reference velocity model used. In addition, our method can be used to image point scatterers in active seismic surveys or for event location in passive surveys.〈/span〉

Description: Century-old forests in the U.S. upper Midwest and Northeast power much of North America's terrestrial carbon (C) sink, but these forests' production and C sequestration capacity are expected to soon decline as fast-growing early successional species die and are replaced by slower growing late successional species. But will this really happen? Here we marshal empirical data and ecological theory to argue that substantial declines in net ecosystem production (NEP) owing to reduced forest growth, or net primary production (NPP), are not imminent in regrown temperate deciduous forests over the next several decades. Forest age and production data for temperate deciduous forests, synthesized from published literature, suggest slight declines in NEP and increasing or stable NPP during middle successional stages. We revisit long-held hypotheses by EP Odum and others that suggest low-severity, high-frequency disturbances occurring in the region's aging forests will, against intuition, maintain NEP at higher-than-expected rates by increasing ecosystem complexity, sustaining or enhancing NPP to a level that largely offsets rising C losses as heterotrophic respiration increases. This theoretical model is also supported by biological evidence and observations from the Forest Accelerated Succession Experiment in Michigan, USA. Ecosystems that experience high-severity disturbances that simplify ecosystem complexity can exhibit substantial declines in production during middle stages of succession. However, observations from these ecosystems have exerted a disproportionate influence on assumptions regarding the trajectory and magnitude of age-related declines in forest production. We conclude that there is a wide ecological space for forests to maintain NPP and, in doing so, lessens the declines in NEP, with significant implications for the future of the North American carbon sink. Our intellectual frameworks for understanding forest C cycle dynamics and resilience need to catch up to our more complex and nuanced understanding of ecological succession.

Description: Natural and anthropogenic disturbances influence ecological succession and impact the carbon cycle. Understanding disturbance effects and ecosystem recovery is essential to carbon modeling. We hypothesized that: (1) species-specific disturbances impact the carbon cycle differently from non-specific disturbances. In particular, disturbances that target early-successional species will lead to higher carbon uptake by the post-recovery, mid- and late-successional community; and (2) disturbances that affect the mid-successional deciduous species have more intense and long-lasting impacts on carbon uptake than disturbances of similar intensity that only affect the early-successional species. To test these hypotheses, we employed a series of simulations conducted with the Ecosystem Demography model version 2 to evaluate the sensitivity of a temperate mixed-deciduous forest to disturbance intensity and type. Our simulation scenarios included a control (undisturbed) case, a uniform disturbance case where we removed 30% of all trees regardless of their successional status, five cases where only early-successional deciduous trees were removed with increasing disturbance intensity (30%, 70%, 85%, and 100%), and four cases of mid-successional disturbances with increasing intensity (70%, 85%, and 100%). Our results indicate that disturbances affecting the mid-successional deciduous trees led to larger decreases in carbon uptake as well as longer recovery times when compared to disturbances that exclusively targeted the early-successional deciduous trees at comparable intensities. Moreover, disturbances affecting 30% to 100% of early-successional deciduous trees resulted in an increased carbon uptake, beginning 6 years after the disturbance and sustained through the end of the 100-year simulation.

Description: Epigenetics is a change in gene expression that is heritable without a change in DNA sequence itself. This phenomenon is well studied in eukaryotes, particularly in humans for its role in cellular differentiation, X chromosome inactivation and diseases like cancer. However, comparatively little is known about epigenetic regulation in bacteria. Bacterial epigenetics is mainly present in the form of DNA methylation where DNA methyltransferases add methyl groups to nucleotides. This review focuses on two methyltransferases well characterized for their roles in gene regulation: Dam and CcrM. Dam methyltransferase in Escherichia coli is important for expression of certain genes such as the pap operon, as well as other cellular processes like DNA replication initiation and DNA repair. In Caulobacter crescentus and other Alphaproteobacteria, the methyltransferase CcrM is cell cycle regulated and is involved in the cell-cycle-dependent regulation of several genes. The diversity of regulatory targets as well as regulatory mechanisms suggests that gene regulation by methylation could be a widespread and potent method of regulation in bacteria.

Description: Accurately simulating gross primary productivity (GPP) in terrestrial ecosystem models is critical because errors in simulated GPP propagate through the model to introduce additional errors in simulated biomass and other fluxes. We evaluated simulated, daily average GPP from 26 models against estimated GPP at 39 eddy covariance flux tower sites across the United States and Canada. None of the models in this study match estimated GPP within observed uncertainty. On average, models overestimate GPP in winter, spring, and fall, and underestimate GPP in summer. Models overpredicted GPP under dry conditions and for temperatures below 0°C. Improvements in simulated soil moisture and ecosystem response to drought or humidity stress will improve simulated GPP under dry conditions. Adding a low-temperature response to shut down GPP for temperatures below 0°C will reduce the positive bias in winter, spring, and fall and improve simulated phenology. The negative bias in summer and poor overall performance resulted from mismatches between simulated and observed light use efficiency (LUE). Improving simulated GPP requires better leaf-to-canopy scaling and better values of model parameters that control the maximum potential GPP, such as εmax (LUE), Vcmax (unstressed Rubisco catalytic capacity) or Jmax (the maximum electron transport rate).

Description: Much of our biogeochemical understanding of forest disturbances comes from studies of severe or stand-replacing events, which may have different impacts on coupled carbon (C) and nitrogen (N) cycling than subtler disturbances affecting only a fraction of the canopy. We measured a suite of interdependent C and N cycling processes following an experimental disturbance that accelerated mortality of the early successional canopy dominants (39% of basal area) in an aging secondary forest, hypothesizing that this subtle, spatially diffuse disturbance would temporarily decouple C and N cycles by decreasing belowground C allocation and thereby alter N cycling rates and pathways. We postulated that a short-term decrease in ecosystem C uptake and an increase in N leaching would accompany this decoupling, but that concomitant increases in N availability and uptake by later successional species would promote rapid resilience of coupled C-N cycles along new, stable trajectories. Disturbance decreased belowground C allocation and soil respiration, accelerated root turnover, and decreased root mass. These perturbations increased forest floor NH4+ and NO3− availability and NO emission, and declining root function caused water stress and N deficiency in senescent trees. Foliar N and leaf area increased in later successional trees, suggesting that enhanced N uptake supported new leaf area production. Two years after disturbance, N leaching losses and the decline in net ecosystem CO2 exchange were small, suggesting that coupled C-N cycling was resilient to this subtle experimental disturbance. Therefore, compared with the severe disturbances reported in the literature, our subtle disturbance likely will have different effects on longer-term forest biogeochemical trajectories.

Description: We have developed an extension of the mixture-density neural network as a computationally efficient probabilistic method to solve nonlinear inverse problems. In this method, any postinversion (a posteriori) joint probability density function (PDF) over the model parameters is represented by a weighted sum of multivariate Gaussian PDFs. A mixture-density neural network estimates the weights, mean vector, and covariance matrix of the Gaussians given any measured data set. In one study, we have jointly inverted compressional- and shear-wave velocity for the joint PDF of porosity, clay content, and water saturation in a synthetic, fluid-saturated, dispersed sand-shale system. Results show that if the method is applied appropriately, the joint PDF estimated by the neural network is comparable to the Monte Carlo sampled a posteriori solution of the inverse problem. However, the computational cost of training and using the neural network is much lower than inversion by sampling (more than a factor of 104 in this case and potentially a much larger factor for 3D seismic inversion). To analyze the performance of the method on real exploration geophysical data, we have jointly inverted P-wave impedance and Poisson's ratio logs for the joint PDF of porosity and clay content. Results show that the posterior model PDF of porosity and clay content is a good estimate of actual porosity and clay-content log values. Although the results may vary from one field to another, this fast, probabilistic method of solving nonlinear inverse problems can be applied to invert well logs and large seismic data sets for petrophysical parameters in any field.

Description: A sizable fraction of colorectal cancer (CRC) is expected to be explained by heritable factors, with heritability estimates ranging from 12 to 35% twin and family studies. Genome-wide association studies (GWAS) have successfully identified a number of common single-nucleotide polymorphisms (SNPs) associated with CRC risk. Although it has been shown that these CRC susceptibility SNPs only explain a small proportion of the genetic risk, it is not clear how much of the heritability these SNPs explain and how much is left to be detected by other, yet to be identified, common SNPs. Therefore, we estimated the heritability of CRC under different scenarios using Genome-Wide Complex Trait Analysis in the Genetics and Epidemiology of Colorectal Cancer Consortium including 8025 cases and 10 814 controls. We estimated that the heritability explained by known common CRC SNPs identified in GWAS was 0.65% (95% CI:0.3–1%; P = 1.11 x 10–16), whereas the heritability explained by all common SNPs was at least 7.42% (95% CI: 4.71–10.12%; P = 8.13 x 10 –8 ), suggesting that many common variants associated with CRC risk remain to be detected. Comparing the heritability explained by the common variants with that from twin and family studies, a fraction of the heritability may be explained by other genetic variants, such as rare variants. In addition, our analysis showed that the gene x smoking interaction explained a significant proportion of the CRC variance ( P = 1.26 x 10 –2 ). In summary, our results suggest that known CRC SNPs only explain a small proportion of the heritability and more common SNPs have yet to be identified.

Description: Intermediate disturbances shape forest structure and composition, which may in turn alter carbon, nitrogen, and water cycling. We used a large-scale experiment in a forest in northern lower Michigan where we prescribed an intermediate disturbance by stem-girdling all canopy-dominant early successional trees to simulate an accelerated age-related senescence associated with natural succession. Using three years of eddy covariance and sap flux measurements in the disturbed area and an adjacent control plot, we analyzed disturbance induced changes to plot level and species-specific transpiration and stomatal conductance. We found transpiration to be ~15% lower in disturbed plots than in unmanipulated control plots. However, species-specific responses to changes in microclimate varied. While red oak and white pine showed increases in stomatal conductance during post-disturbance (62.5 and 132.2%, respectively), red maple reduced stomatal conductance by 36.8%. We used the hysteresis between sap flux and vapor pressure deficit to quantify diurnal hydraulic stress incurred by each species in both plots. Red oak, a ring porous anisohydric species, demonstrated the largest mean relative hysteresis, while red maple, bigtooth aspen, and paper birch, all diffuse porous isohydric species, had the lowest relative hysteresis. We employed the Penman-Monteith model for LE to demonstrate that these species-specific responses to disturbance are not well captured using current modeling strategies, and that accounting for changes to leaf area index ( LAI ) and plot microclimate are insufficient to fully describe the effects of disturbance on transpiration.