Excluded-Volume Effects in Tethered-Particle Experiments: Bead Size Matters

The tethered-particle method is a single-molecule technique that has been used to explore the dynamics of a variety of macromolecules of biological interest. We give a theoretical analysis of the particle motions in such experiments. Our analysis reveals that the proximity of the tethered bead to a nearby surface (the microscope slide) gives rise to a volume-exclusion effect, resulting in an entropic force on the molecule. This force stretches the molecule, changing its statistical properties. In particular, the proximity of bead and surface brings about intriguing scaling relations between key observables (statistical moments of the bead) and parameters such as the bead size and contour length of the molecule. We present both approximate analytic solutions and numerical results for these effects in both flexible and semiflexible tethers. Finally, our results give a precise, experimentally-testable prediction for the probability distribution of the distance between the polymer attachment point and the center of the mobile bead.Comment: 4 pages, 3 figure

A generalized theory of semiflexible polymers

DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a renewed interest in the polymer mechanics relevant for describing the conformational free energy of DNA bending induced by protein-DNA complexes. Recent experimental results from DNA cyclization studies have cast doubt on the applicability of the canonical semiflexible polymer theory, the wormlike chain (WLC) model, to DNA bending on biological length scales. This paper develops a theory of the chain statistics of a class of generalized semiflexible polymer models. Our focus is on the theoretical development of these models and the calculation of experimental observables. To illustrate our methods, we focus on a specific toy model of DNA bending. We show that the WLC model generically describes the long-length-scale chain statistics of semiflexible polymers, as predicted by the Renormalization Group. In particular, we show that either the WLC or our new model adequate describes force-extension, solution scattering, and long-contour-length cyclization experiments, regardless of the details of DNA bend elasticity. In contrast, experiments sensitive to short-length-scale chain behavior can in principle reveal dramatic departures from the linear elastic behavior assumed in the WLC model. We demonstrate this explicitly by showing that our toy model can reproduce the anomalously large short-contour-length cyclization J factors observed by Cloutier and Widom. Finally, we discuss the applicability of these models to DNA chain statistics in the context of future experiments

Model for Gravitational Interaction between Dark Matter and Baryons

We propose a phenomenological model where the gravitational interaction between dark matter and baryons is suppressed on small, subgalactic scales. We describe the gravitational force by adding a Yukawa contribution to the standard Newtonian potential and show that this interaction scheme is effectively suggested by the available observations of the inner rotation curves of small mass galaxies. Besides helping in interpreting the cuspy profile of dark matter halos observed in N-body simulations, this potential regulates the quantity of baryons within halos of different masses.Comment: 4 pages, 2 figures, final versio

Maternal behaviour and welfare of the domestic and wild rabbit doe and its litter

El conejo europeo (Oryctolagus cuniculus), además de tener importancia faunística en el Mediterráneo occidental, es una especie ganadera relevante que es la base de un subsector pecuario industrializado orientado a la producción de carne en varios países, sobre todo europeos, mientras que en algunos pa- íses en vías de desarrollo se explota bajo sistemas alternativos orientados a la integración de renta y a la seguridad alimentaria. A la orientación cárnica se suman otras aptitudes productivas heterogéneas que configuran una gran diversidad de sistemas de producción cunícola. Este trabajo revisa el comportamiento materno de la coneja y de su camada, incluyendo su regulación endocrina, tanto en el animal silvestre como en la producción cunícola comercial y alternativa, y se relaciona con los factores de manejo, con la productividad en granja y con el bienestar de la especie. Se analizan también las implicaciones que las normativas sobre bienestar animal comportan respecto al alojamiento, manejo y satisfacción de las necesidades etológicas de las conejas reproductoras y de los gazapos durante la cría, caracterizadas, fundamentalmente, porque en algunos países tienden a proporcionar más espacio y enriquecimiento ambiental en las jaulas.The European rabbit (Oryctolagus cuniculus), in addition to its faunal interest in the western Mediterranean, is a relevant species which in several European countries is the basis of a meat-oriented, industrial livestock subsector, while in many developing countries rabbits are raised under alternative systems aimed at income integration and food security. In addition to meat production, other productive orientations exist that generate a variety of rabbit production systems. This paper reviews the ethology of maternal behaviour of the breeding doe and her litter, including its endocrine regulation, both in wild animal and in industrial and alternative farming systems, and its relation to management factors, productivity and performance as well as the welfare of the species. It also discusses the implications of the regulations concerning animal welfare on housing, management and satisfaction of behavioural needs of breeding does and their litters, which in some countries tend to provide more space and environmental enrichment in cage

Does elevated CO2 alter silica uptake in trees?

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Plant Science 5 (2015): 793, doi:10.3389/fpls.2014.00793.Human activities have greatly altered global carbon (C) and Nitrogen (N) cycling. In fact, atmospheric concentrations of carbon dioxide (CO2) have increased 40% over the last century and the amount of N cycling in the biosphere has more than doubled. In an effort to understand how plants will respond to continued global CO2 fertilization, long-term free-air CO2 enrichment experiments have been conducted at sites around the globe. Here we examine how atmospheric CO2 enrichment and N fertilization affects the uptake of silicon (Si) in the Duke Forest, North Carolina, a stand dominated by Pinus taeda (loblolly pine), and five hardwood species. Specifically, we measured foliar biogenic silica concentrations in five deciduous and one coniferous species across three treatments: CO2 enrichment, N enrichment, and N and CO2 enrichment. We found no consistent trends in foliar Si concentration under elevated CO2, N fertilization, or combined elevated CO2 and N fertilization. However, two-thirds of the tree species studied here have Si foliar concentrations greater than well-known Si accumulators, such as grasses. Based on net primary production values and aboveground Si concentrations in these trees, we calculated forest Si uptake rates under control and elevated CO2 concentrations. Due largely to increased primary production, elevated CO2 enhanced the magnitude of Si uptake between 20 and 26%, likely intensifying the terrestrial silica pump. This uptake of Si by forests has important implications for Si export from terrestrial systems, with the potential to impact C sequestration and higher trophic levels in downstream ecosystems.This research was supported in part by the Sloan Foundation in a fellowship to Robinson W. Fulweiler. The Duke Forest FACE was supported by his study was supported by the US Department of Energy (Grant No. DE-FG02-95ER62083) through the Office of Biological and Environmental Research (BER) and its National Institute for Global Environmental Change (NIGEC), Southeast Regional Center (SERC) at the University of Alabama, and by the US Forest Service through both the Southern Global Climate Change Program and the Southern Research Station. Adrien C. Finzi acknowledges ancillary support from the US NSF (DEB0236356)

Effect of short range order on electronic and magnetic properties of disordered Co based alloys

We here study electronic structure and magnetic properties of disordered CoPd and CoPt alloys using Augmented Space Recursion technique coupled with the tight-binding linearized muffin tin orbital (TB-LMTO) method. Effect of short range ordering present in disordered phase of alloys on electronic and magnetic properties has been discussed. We present results for magnetic moments, Curie temperatures and electronic band energies with varying degrees of short range order for different concentrations of Co and try to understand and compare the magnetic properties and ordering phenomena in these systems.Comment: 15 pages,17 postscript figures,uses own style file

Research frontiers in the analysis of coupled biogeochemical cycles

Author Posting. © Ecological Society of America, 2011. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Frontiers in Ecology and the Environment 9 (2011): 74–80, doi:10.1890/100137.The analysis of coupled biogeochemical cycles (CBCs) addresses the scientific basis for some of today's major environmental problems. Drawing from information presented at a series of sessions on CBCs held at the 2009 Annual Meeting of the Ecological Society of America and from the research community's expertise, we identify several principal research themes that justify action and investment. Critical areas for research include: coupling of major element cycles to less studied yet equally important trace element cycles; analyzing CBCs across ecosystem boundaries; integrating experimental results into regional- and global-scale models; and expanding the analysis of human interactions with CBCs arising from human population growth, urbanization, and geoengineering. To advance the current understanding of CBCs and to address the environmental challenges of the 21st century, scientists must maintain and synthesize data from existing observational and experimental networks, develop new instrumentation networks, and adopt emerging technologies.We thank the National Science Foundation (NSF) and the Ecological Society of America (ESA) for their financial and logistical support of the Coupled Biogeochemical Cycles sessions held at the 2009 ESA Annual Meeting, and the publication of this special feature issue of Frontiers. ACF was supported by the NSF (DEB- 0743564) and the US Department of Energy’s (DOE’s) Office of Biological and Environmental Research (10- DOE-1053). SCD was supported by the Center for Microbial Oceanography, Research and Education (NSF EF-0424599). RBJ was supported by the NSF (DEB #0717191) and by the DOE’s National Institute for Climate Change 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

Dark matter and non-Newtonian gravity from General Relativity coupled to a fluid of strings

An exact solution of Einstein's field equations for a point mass surrounded by a static, spherically symmetric fluid of strings is presented. The solution is singular at the origin. Near the string cloud limit there is a $1/r$ correction to Newton's force law. It is noted that at large distances and small accelerations, this law coincides with the phenomenological force law invented by Milgrom in order to explain the flat rotation curves of galaxies without introducing dark matter. When interpreted in the context of a cosmological model with a string fluid, the new solution naturally explains why the critical acceleration of Milgrom is of the same order of magnitude as the Hubble parameter.Comment: 12 pages, REVTeX, no figure