Evaluating Cumulative Ecosystem Response to Restoration Projects in the Lower Columbia River and Estuary, 2009

This is the sixth annual report of a seven-year project (2004 through 2010) to evaluate the cumulative effects of habitat restoration actions in the lower Columbia River and estuary (LCRE). The project, called the Cumulative Effects Study, is being conducted for the U.S. Army Corps of Engineers Portland District (USACE) by the Marine Sciences Laboratory of the Pacific Northwest National Laboratory (PNNL), the Pt. Adams Biological Field Station of the National Marine Fisheries Service (NMFS), the Columbia River Estuary Study Taskforce (CREST), and the University of Washington. The goal of the Cumulative Effects Study is to develop a methodology to evaluate the cumulative effects of multiple habitat restoration projects intended to benefit ecosystems supporting juvenile salmonids in the 235-km-long LCRE. Literature review in 2004 revealed no existing methods for such an evaluation and suggested that cumulative effects could be additive or synergistic. From 2005 through 2009, annual field research involved intensive, comparative studies paired by habitat type (tidal swamp versus marsh), trajectory (restoration versus reference site), and restoration action (tidegate replacement vs. culvert replacement vs. dike breach)

Evaluating Cumulative Ecosystem Response to Restoration Projects in the Columbia River Estuary, Annual Report 2007

The goal of this multi-year study (2004-2010) is to develop a methodology to evaluate the cumulative effects of multiple habitat restoration projects intended to benefit ecosystems supporting juvenile salmonids in the lower Columbia River and estuary. Literature review in 2004 revealed no existing methods for such an evaluation and suggested that cumulative effects could be additive or synergistic. Field research in 2005, 2006, and 2007 involved intensive, comparative studies paired by habitat type (tidal swamp vs. marsh), trajectory (restoration vs. reference site), and restoration action (tide gate vs. culvert vs. dike breach). The field work established two kinds of monitoring indicators for eventual cumulative effects analysis: core and higher-order indicators. Management implications of limitations and applications of site-specific effectiveness monitoring and cumulative effects analysis were identified

Mapping Connectivity Damage in the Case of Phineas Gage

White matter (WM) mapping of the human brain using neuroimaging techniques has gained considerable interest in the neuroscience community. Using diffusion weighted (DWI) and magnetic resonance imaging (MRI), WM fiber pathways between brain regions may be systematically assessed to make inferences concerning their role in normal brain function, influence on behavior, as well as concerning the consequences of network-level brain damage. In this paper, we investigate the detailed connectomics in a noted example of severe traumatic brain injury (TBI) which has proved important to and controversial in the history of neuroscience. We model the WM damage in the notable case of Phineas P. Gage, in whom a “tamping iron” was accidentally shot through his skull and brain, resulting in profound behavioral changes. The specific effects of this injury on Mr. Gage's WM connectivity have not previously been considered in detail. Using computed tomography (CT) image data of the Gage skull in conjunction with modern anatomical MRI and diffusion imaging data obtained in contemporary right handed male subjects (aged 25–36), we computationally simulate the passage of the iron through the skull on the basis of reported and observed skull fiducial landmarks and assess the extent of cortical gray matter (GM) and WM damage. Specifically, we find that while considerable damage was, indeed, localized to the left frontal cortex, the impact on measures of network connectedness between directly affected and other brain areas was profound, widespread, and a probable contributor to both the reported acute as well as long-term behavioral changes. Yet, while significantly affecting several likely network hubs, damage to Mr. Gage's WM network may not have been more severe than expected from that of a similarly sized “average” brain lesion. These results provide new insight into the remarkable brain injury experienced by this noteworthy patient

The North American tree-ring fire-scar network

Fire regimes in North American forests are diverse and modern fire records are often too short to capture important patterns, trends, feedbacks, and drivers of variability. Tree-ring fire scars provide valuable perspectives on fire regimes, including centuries-long records of fire year, season, frequency, severity, and size. Here, we introduce the newly compiled North American tree-ring fire-scar network (NAFSN), which contains 2562 sites, >37,000 fire-scarred trees, and covers large parts of North America. We investigate the NAFSN in terms of geography, sample depth, vegetation, topography, climate, and human land use. Fire scars are found in most ecoregions, from boreal forests in northern Alaska and Canada to subtropical forests in southern Florida and Mexico. The network includes 91 tree species, but is dominated by gymnosperms in the genus Pinus. Fire scars are found from sea level to >4000-m elevation and across a range of topographic settings that vary by ecoregion. Multiple regions are densely sampled (e.g., >1000 fire-scarred trees), enabling new spatial analyses such as reconstructions of area burned. To demonstrate the potential of the network, we compared the climate space of the NAFSN to those of modern fires and forests; the NAFSN spans a climate space largely representative of the forested areas in North America, with notable gaps in warmer tropical climates. Modern fires are burning in similar climate spaces as historical fires, but disproportionately in warmer regions compared to the historical record, possibly related to under-sampling of warm subtropical forests or supporting observations of changing fire regimes. The historical influence of Indigenous and non-Indigenous human land use on fire regimes varies in space and time. A 20th century fire deficit associated with human activities is evident in many regions, yet fire regimes characterized by frequent surface fires are still active in some areas (e.g., Mexico and the southeastern United States). These analyses provide a foundation and framework for future studies using the hundreds of thousands of annually- to sub-annually-resolved tree-ring records of fire spanning centuries, which will further advance our understanding of the interactions among fire, climate, topography, vegetation, and humans across North America

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Perforin is detrimental to controlling [corrected] C. muridarum replication in vitro, but not in vivo.

CD4 T cells are critical for clearing experimental Chlamydia muridarum genital tract infections. Two independent in vitro CD4 T cell mechanisms have been identified for terminating Chlamydia replication in epithelial cells. One mechanism, requiring IFN-γ and T cell-epithelial cell contact, terminates infection by triggering epithelial production of nitric oxide to chlamydiacidal levels; the second is dependent on T cell degranulation. We recently demonstrated that there are two independent in vivo clearance mechanisms singly sufficient for clearing genital tract infections within six weeks; one dependent on iNOS, the other on Plac8. Redundant genital tract clearance mechanisms bring into question negative results in single-gene knockout mice. Two groups have shown that perforin-knockout mice were not compromised in their ability to clear C. muridarum genital tract infections. Because cell lysis would be detrimental to epithelial nitric oxide production we hypothesized that perforin was not critical for iNOS-dependent clearance, but posited that perforin could play a role in Plac8-dependent clearance. We tested whether the Plac8-dependent clearance was perforin-dependent by pharmacologically inhibiting iNOS in perforin-knockout mice. In vitro we found that perforin was detrimental to iNOS-dependent CD4 T cell termination of Chlamydia replication in epithelial cells. In vivo, unexpectedly, clearance in perforin knockout mice was delayed to the end of week 7 regardless of iNOS status. The discordant in vitro/in vivo results suggest that the perforin's contribution to bacterial clearance in vivo is not though enhancing CD4 T cell termination of Chlamydia replication in epithelial cells, but likely via a mechanism independent of T cell-epithelial cell interactions

NOₓ Emission of Equipment and Blasting Agents in Surface Coal Mining

Surface coal mining in the Appalachian region consumes a significant amount of energy in the form of diesel fuel and blasting agents. Emission of oxides of nitrogen (NOx) from these sources represents an environmental challenge to the mining industry. This paper presents the results of research work related to determination of NOx emission of mining equipment and blasting agents, which is part of a broader industrial project conducted by the Appalachian Research Initiative for Environmental Research (ARIES). Data for this project are collected from an operating surface coal mine in West Virginia. The research work presented here may be used by mining professionals to aid in quantifying NOx emission and determine strategies for reducing its overall environmental impact

Cytokine profile of immune splenocytes from each experimental group infigure 1 (20 independent splenocyte populations) activated with UV-inactivated <i>C. muridarum.</i>

<p>3×10⁶ splenocytes were activated with 7.5×10⁶ UV-inactivated <i>C. muridarum</i> (multiplicity of 2.5 IFU per splenocyte) or mock-activated with equivalent volume of SPG buffer (con = control) in triplicate wells. Supernatants were collected at 72 h and analyzed by ELISA. Data representing each mouse strain/treatment condition were aggregated and compared to the aggregated data for the untreated C57BL/6J mice. Comparisons were made for each cytokine. There were no statistically significant differences in cytokine polarization between wild type and perforin knockout mice with or without MLA treatment.</p