A Dual Read-Out Assay to Evaluate the Potency of Compounds Active against Mycobacterium tuberculosis

PMCID: PMC3617142This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

An Optimal Algorithm for Tiling the Plane with a Translated Polyomino

We give a $O(n)$-time algorithm for determining whether translations of a polyomino with $n$ edges can tile the plane. The algorithm is also a $O(n)$-time algorithm for enumerating all such tilings that are also regular, and we prove that at most $\Theta(n)$ such tilings exist.Comment: In proceedings of ISAAC 201

The soil and plant biogeochemistry sampling design for The National Ecological Observatory Network

Human impacts on biogeochemical cycles are evident around the world, from changes to forest structure and function due to atmospheric deposition, to eutrophication of surface waters from agricultural effluent, and increasing concentrations of carbon dioxide (CO2) in the atmosphere. The National Ecological Observatory Network (NEON) will contribute to understanding human effects on biogeochemical cycles from local to continental scales. The broad NEON biogeochemistry measurement design focuses on measuring atmospheric deposition of reactive mineral compounds and CO2 fluxes, ecosystem carbon (C) and nutrient stocks, and surface water chemistry across 20 eco‐climatic domains within the United States for 30 yr. Herein, we present the rationale and plan for the ground‐based measurements of C and nutrients in soils and plants based on overarching or “high‐level” requirements agreed upon by the National Science Foundation and NEON. The resulting design incorporates early recommendations by expert review teams, as well as recent input from the larger natural sciences community that went into the formation and interpretation of the requirements, respectively. NEON\u27s efforts will focus on a suite of data streams that will enable end‐users to study and predict changes to biogeochemical cycling and transfers within and across air, land, and water systems at regional to continental scales. At each NEON site, there will be an initial, one‐time effort to survey soil properties to 1 m (including soil texture, bulk density, pH, baseline chemistry) and vegetation community structure and diversity. A sampling program will follow, focused on capturing long‐term trends in soil C, nitrogen (N), and sulfur stocks, isotopic composition (of C and N), soil N transformation rates, phosphorus pools, and plant tissue chemistry and isotopic composition (of C and N). To this end, NEON will conduct extensive measurements of soils and plants within stratified random plots distributed across each site. The resulting data will be a new resource for members of the scientific community interested in addressing questions about long‐term changes in continental‐scale biogeochemical cycles, and is predicted to inspire further process‐based research

Soil respiration in a northeastern US temperate forest: a 22‐year synthesis

To better understand how forest management, phenology, vegetation type, and actual and simulated climatic change affect seasonal and inter‐annual variations in soil respiration (Rs), we analyzed more than 100,000 individual measurements of soil respiration from 23 studies conducted over 22 years at the Harvard Forest in Petersham, Massachusetts, USA. We also used 24 site‐years of eddy‐covariance measurements from two Harvard Forest sites to examine the relationship between soil and ecosystem respiration (Re). Rs was highly variable at all spatial (respiration collar to forest stand) and temporal (minutes to years) scales of measurement. The response of Rs to experimental manipulations mimicking aspects of global change or aimed at partitioning Rs into component fluxes ranged from −70% to +52%. The response appears to arise from variations in substrate availability induced by changes in the size of soil C pools and of belowground C fluxes or in environmental conditions. In some cases (e.g., logging, warming), the effect of experimental manipulations on Rs was transient, but in other cases the time series were not long enough to rule out long‐term changes in respiration rates. Inter‐annual variations in weather and phenology induced variation among annual Rs estimates of a magnitude similar to that of other drivers of global change (i.e., invasive insects, forest management practices, N deposition). At both eddy‐covariance sites, aboveground respiration dominated Re early in the growing season, whereas belowground respiration dominated later. Unusual aboveground respiration patterns—high apparent rates of respiration during winter and very low rates in mid‐to‐late summer—at the Environmental Measurement Site suggest either bias in Rs and Re estimates caused by differences in the spatial scale of processes influencing fluxes, or that additional research on the hard‐to‐measure fluxes (e.g., wintertime Rs, unaccounted losses of CO2 from eddy covariance sites), daytime and nighttime canopy respiration and its impacts on estimates of Re, and independent measurements of flux partitioning (e.g., aboveground plant respiration, isotopic partitioning) may yield insight into the unusually high and low fluxes. Overall, however, this data‐rich analysis identifies important seasonal and experimental variations in Rs and Re and in the partitioning of Re above‐ vs. belowground

Soil respiration in a northeastern US temperate forest: a 22‐year synthesis

To better understand how forest management, phenology, vegetation type, and actual and simulated climatic change affect seasonal and inter‐annual variations in soil respiration (Rs), we analyzed more than 100,000 individual measurements of soil respiration from 23 studies conducted over 22 years at the Harvard Forest in Petersham, Massachusetts, USA. We also used 24 site‐years of eddy‐covariance measurements from two Harvard Forest sites to examine the relationship between soil and ecosystem respiration (Re). Rs was highly variable at all spatial (respiration collar to forest stand) and temporal (minutes to years) scales of measurement. The response of Rs to experimental manipulations mimicking aspects of global change or aimed at partitioning Rs into component fluxes ranged from −70% to +52%. The response appears to arise from variations in substrate availability induced by changes in the size of soil C pools and of belowground C fluxes or in environmental conditions. In some cases (e.g., logging, warming), the effect of experimental manipulations on Rs was transient, but in other cases the time series were not long enough to rule out long‐term changes in respiration rates. Inter‐annual variations in weather and phenology induced variation among annual Rs estimates of a magnitude similar to that of other drivers of global change (i.e., invasive insects, forest management practices, N deposition). At both eddy‐covariance sites, aboveground respiration dominated Re early in the growing season, whereas belowground respiration dominated later. Unusual aboveground respiration patterns—high apparent rates of respiration during winter and very low rates in mid‐to‐late summer—at the Environmental Measurement Site suggest either bias in Rs and Re estimates caused by differences in the spatial scale of processes influencing fluxes, or that additional research on the hard‐to‐measure fluxes (e.g., wintertime Rs, unaccounted losses of CO2 from eddy covariance sites), daytime and nighttime canopy respiration and its impacts on estimates of Re, and independent measurements of flux partitioning (e.g., aboveground plant respiration, isotopic partitioning) may yield insight into the unusually high and low fluxes. Overall, however, this data‐rich analysis identifies important seasonal and experimental variations in Rs and Re and in the partitioning of Re above‐ vs. belowground

Mycobacterium tuberculosis ClpP Proteases Are Co-transcribed but Exhibit Different Substrate Specificities

PMCID: PMC3613350This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Importance of carbon-nitrogen interactions and ozone on ecosystem hydrology during the 21st century

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 114 (2009): G01020, doi:10.1029/2008JG000826.There is evidence that increasing CO2 concentrations have reduced evapotranspiration and increased runoff through reductions in stomatal conductance during the twentieth century. While this process will continue to counteract increased evapotranspiration associated with future warming, it is highly dependent upon concurrent changes in photosynthesis, especially due to CO2 fertilization, nitrogen limitation, and ozone exposure. A new version of the Terrestrial Ecosystem Model (TEM-Hydro) was developed to examine the effects of carbon and nitrogen on the water cycle. We used two climate models (NCAR CCSM3 and DOE PCM) and two emissions scenarios (SRES B1 and A2) to examine the effects of climate, elevated CO2, nitrogen limitation, and ozone exposure on the hydrological cycle in the eastern United States. While the direction of future runoff changes is largely dependent upon predicted precipitation changes, the effects of elevated CO2 on ecosystem function (stomatal closure and CO2 fertilization) increase runoff by 3–7%, as compared to the effects of climate alone. Consideration of nitrogen limitation and ozone damage on photosynthesis increases runoff by a further 6–11%. Failure to consider the effects of the interactions among nitrogen, ozone, and elevated CO2 may lead to significant regional underestimates of future runoff.This study was funded by the Interdisciplinary Science Program of the U.S. National Aeronautics and Space Administration (NNG04GJ80G, NNG04GM39G), the Dynamic Global Economic Modeling of Greenhouse Gas Emissions and Mitigation from Land-Use Activities of the U.S. Environmental Protection Agency (XA-83240101), and the Nonlinear Response to Global Change in Linked Aquatic and Terrestrial Ecosystems of the U.S. EPA (XA-83326101)

Field Emission of ITO-Coated Vertically Aligned Nanowire Array

An indium tin oxide (ITO)-coated vertically aligned nanowire array is fabricated, and the field emission characteristics of the nanowire array are investigated. An array of vertically aligned nanowires is considered an ideal structure for a field emitter because of its parallel orientation to the applied electric field. In this letter, a vertically aligned nanowire array is fabricated by modified conventional UV lithography and coated with 0.1-μm-thick ITO. The turn-on electric field intensity is about 2.0 V/μm, and the field enhancement factor, β, is approximately 3,078 when the gap for field emission is 0.6 μm, as measured with a nanomanipulator in a scanning electron microscope

Universal Rights and Wrongs

This paper argues for the important role of customers as a source of competitive advantage and firm growth, an issue which has been largely neglected in the resource-based view of the firm. It conceptualizes Penrose’s (1959) notion of an ‘inside track’ and illustrates how in-depth knowledge about established customers combines with joint problem-solving activities and the rapid assimilation of new and previously unexploited skills and resources. It is suggested that the inside track represents a distinct and perhaps underestimated way of generating rents and securing long-term growth. This also implies that the sources of sustainable competitive advantage in important respects can be sought in idiosyncratic interfirm relationships rather than within the firm itself