Leaf-level gas-exchange uniformity and photosynthetic capacity among loblolly pine (Pinus taeda L.) genotypes of contrasting inherent genetic variation.

Variation in leaf-level gas exchange among widely planted genetically improved loblolly pine (Pinus taeda L.) genotypes could impact stand-level water use, carbon assimilation, biomass production, C allocation, ecosystem sustainability and biogeochemical cycling under changing environmental conditions. We examined uniformity in leaf-level light-saturated photosynthesis (A(sat)), stomatal conductance (g(s)), and intrinsic water-use efficiency (A(sat)/g(s) or δ) among nine loblolly pine genotypes (selected individuals): three clones, three full-sib families and three half-sib families, during the early years of stand development (first 3 years), with each genetic group possessing varying amounts of inherent genetic variation.

Solvent-hindered intramolecular vibrational redistribution.

Ultrafast two-dimensional infrared spectroscopy and molecular dynamics simulations of Mn(2)(CO)(10) in a series of linear alcohols reveal that the rate of intramolecular vibrational redistribution among the terminal carbonyl stretches is dictated by the average number of hydrogen bonds formed between the solute and solvent. The presence of hydrogen bonds was found to hinder vibrational redistribution between eigenstates, while leaving the overall T(1) relaxation rate unchanged.

A systems biology approach to investigate the effect of pH-induced gene regulation on solvent production by Clostridium acetobutylicum in continuous culture.

Background: Clostridium acetobutylicum is an anaerobic bacterium which is known for its solvent-producing capabilities, namely regarding the bulk chemicals acetone and butanol, the latter being a highly efficient biofuel. For butanol production by C. acetobutylicum to be optimized and exploited on an industrial scale, the effect of pH-induced gene regulation on solvent production by C.

A critical review of neuroimaging applications in sports concussion.

While abnormalities related to concussion are typically not identified on traditional clinical neuroimaging (i.e., computed tomography [CT] or magnetic resonance imaging [MRI]), more sophisticated neuroimaging techniques have the potential to reveal the complex neurometabolic processes related to concussion and its recovery.

Individual-based modelling of angiogenesis inside three-dimensional porous biomaterials.

This paper presents a simulation modelling framework to study the growth of blood vessels and cells through a porous tissue engineering scaffold. The model simulates the migration of capillaries and the formation of a vascular network through a single pore of a tissue engineering scaffold when it is embedded in living tissue. The model also describes how the flow of blood through the network changes as growth proceeds.

Growth of the chorioallantoic membrane into a rapid-prototyped model pore system: experiments and mathematical model.

This paper presents a mathematical model to describe the growth of tissue into a rapid-prototyped porous scaffold when it is implanted onto the chorioallantoic membrane (CAM). The scaffold was designed to study the effects of the size and shape of pores on tissue growth into conventional tissue engineering scaffolds, and consists of an array of pores each having a pre-specified shape. The experimental observations revealed that the CAM grows through each pore as an intact layer of tissue, provided the width of the pore exceeds a threshold value.

Interconnectivity analysis of supercritical CO₂-foamed scaffolds.

This paper describes a computer algorithm for the determination of the interconnectivity of the pore space inside scaffolds used for tissue engineering. To validate the algorithm and its computer implementation, the algorithm was applied to a computer-generated scaffold consisting of a set of overlapping spherical pores, for which the interconnectivity was calculated exactly. The algorithm was then applied to micro-computed X-ray tomography images of supercritical CO(2)-foamed scaffolds made from poly(lactic-co-glycolic acid) (PLGA), whereby the effect of using different weight average molecular weight polymer on the interconnectivity was investigated.

Solvent-dependent spectral diffusion in a hydrogen bonded "vibrational aggregate".

Two-dimensional infrared spectroscopy (2DIR) is used to measure the viscosity-dependent spectral diffusion of a model vibrational probe, Mn(2)(CO)(10) (dimanganese decacarbonyl, DMDC), in a series of alcohols with time scales ranging from 2.67 ps in methanol to 5.33 ps in 1-hexanol.

Auxin carriers localization drives auxin accumulation in plant cells infected by Frankia in Casuarina glauca actinorhizal nodules.

Actinorhizal symbioses are mutualistic interactions between plants and the soil bacteria Frankia that lead to the formation of nitrogen-fixing root nodules. Little is known about the signaling mechanisms controlling the different steps of the establishment of the symbiosis. The plant hormone auxin has been suggested to play a role.

Establishing the boundaries: the hippocampal contribution to imagining scenes.

When we visualize scenes, either from our own past or invented, we impose a viewpoint for our "mind's eye" and we experience the resulting image as spatially coherent from that viewpoint. The hippocampus has been implicated in this process, but its precise contribution is unknown. We tested a specific hypothesis based on the spatial firing properties of neurons in the hippocampal formation of rats, that this region supports the construction of spatially coherent mental images by representing the locations of the environmental boundaries surrounding our viewpoint.

Radiocarbon dating of individual lignin phenols: a new approach for establishing chronology of late quaternary lake sediments.

The reliability of chronology is a prerequisite for meaningful paleoclimate reconstructions from sedimentary archives. The conventional approach of radiocarbon dating bulk organic carbon in lake sediments is often hampered by the old carbon effect, i.e.

Orientation determination of interfacial beta-sheet structures in situ.

Structural information such as orientations of interfacial proteins and peptides is important for understanding properties and functions of such biological molecules, which play crucial roles in biological applications and processes such as antimicrobial selectivity, membrane protein activity, biocompatibility, and biosensing performance. The alpha-helical and beta-sheet structures are the most widely encountered secondary structures in peptides and proteins. In this paper, for the first time, a method to quantify the orientation of the interfacial beta-sheet structure using a combined attenuated total reflectance Fourier transformation infrared spectroscopic (ATR-FTIR) and sum frequency generation (SFG) vibrational spectroscopic study was developed.

Hydraulic redistribution of soil water by roots affects whole-stand evapotranspiration and net ecosystem carbon exchange.

*Hydraulic redistribution (HR) of water via roots from moist to drier portions of the soil occurs in many ecosystems, potentially influencing both water use and carbon assimilation. *By measuring soil water content, sap flow and eddy covariance, we investigated the temporal variability of HR in a loblolly pine (Pinus taeda) plantation during months of normal and below-normal precipitation, and examined its effects on tree transpiration, ecosystem water use and carbon exchange. *The occurrence of HR was explained by courses of reverse flow through roots.

Interleukin-28B polymorphism improves viral kinetics and is the strongest pretreatment predictor of sustained virologic response in genotype 1 hepatitis C virus.

Background & Aims: We recently identified a polymorphism upstream of interleukin (IL)-28B to be associated with a 2-fold difference in sustained virologic response (SVR) rates to pegylated interferon-alfa and ribavirin therapy in a large cohort of treatment-naive, adherent patients with chronic hepatitis C virus genotype 1 (HCV-1) infection. We sought to confirm the polymorphism's clinical relevance by intention-to-treat analysis evaluating on-treatment virologic response and SVR.

Methods: HCV-1 patients were genotyped as CC, CT, or TT at the polymorphic site, rs12979860.

Stochastic and deterministic multiscale models for systems biology: an auxin-transport case study.

Background: Stochastic and asymptotic methods are powerful tools in developing multiscale systems biology models; however, little has been done in this context to compare the efficacy of these methods. The majority of current systems biology modelling research, including that of auxin transport, uses numerical simulations to study the behaviour of large systems of deterministic ordinary differential equations, with little consideration of alternative modelling frameworks.

Results: In this case study, we solve an auxin-transport model using analytical methods, deterministic numerical simulations and stochastic numerical simulations.

Mathematical modelling of the sporulation-initiation network in Bacillus subtilis revealing the dual role of the putative quorum-sensing signal molecule PhrA.

Bacillus subtilis cells may opt to forgo normal cell division and instead form spores if subjected to certain environmental stimuli, for example nutrient deficiency or extreme temperature. The resulting spores are extremely resilient and can survive for extensive periods of time, importantly under particularly harsh conditions such as those mentioned above. The sporulation process is highly time and energy consuming and essentially irreversible.

A mathematical investigation of the effects of inhibitor therapy on three putative phosphorylation cascades governing the two-component system of the agr operon.

Two-component systems (TCSs) are widely employed by bacteria to sense specific external signals and conduct an appropriate response via a phosphorylation cascade within the cell. The TCS of the agr operon in the bacterium Staphylococcus aureus forms part of a regulatory process termed quorum sensing, a cell-to-cell communication mechanism used to assess population density. Since S.

Acute effects of alcohol on intrusive memory development and viewpoint dependence in spatial memory support a dual representation model.

Background: A dual representation model of intrusive memory proposes that personally experienced events give rise to two types of representation: an image-based, egocentric representation based on sensory-perceptual features; and a more abstract, allocentric representation that incorporates spatiotemporal context. The model proposes that intrusions reflect involuntary reactivation of egocentric representations in the absence of a corresponding allocentric representation. We tested the model by investigating the effect of alcohol on intrusive memories and, concurrently, on egocentric and allocentric spatial memory.

Resident assistant and college students' perceptions of alcohol use.

Resident assistants (RAs) are often involved in prevention efforts addressing the problem of college drinking. This project investigated the perceptions that 60 RAs and 662 college students have of each other's drinking and attitudes towards alcohol use. Students' self-reported frequency, quantity, and binge drinking levels were all significantly higher than their friends, students on campus, and RAs.

Marine habitat classification for ecosystem-based management: a proposed hierarchical framework.

Creating a habitat classification and mapping system for marine and coastal ecosystems is a daunting challenge due to the complex array of habitats that shift on various spatial and temporal scales. To meet this challenge, several countries have, or are developing, national classification systems and mapping protocols for marine habitats. To be effectively applied by scientists and managers it is essential that classification systems be comprehensive and incorporate pertinent physical, geological, biological, and anthropogenic habitat characteristics.

Data mining pathogen genomes using GeneOrder and CoreGenes and CGUG: gene order, synteny and in silico proteomes.

Sequence databases are growing exponentially due to 'next generation' DNA analysers and applications of these data. Databases include multiple sequences of previously sequenced organisms, particularly ones of consequence to human health. Applications are limited by tools available to mine them, particularly user-friendly tools that are useful for bench researchers.

Temporal trends of triclosan contamination in dated sediment cores from four urbanized estuaries: evidence of preservation and accumulation.

Triclosan is an antimicrobial agent added to a wide array of consumer goods and personal care products. Through its use, it is introduced into municipal sewer systems where it is only partially removed during wastewater treatment. In this study, triclosan was measured in dated sediment cores from four urbanized estuaries in order to reconstruct temporal and spatial trends of accumulation.

Challenges in elevated CO2 experiments on forests.

Current forest Free Air CO(2) Enrichment (FACE) experiments are reaching completion. Therefore, it is time to define the scientific goals and priorities of future experimental facilities. In this opinion article, we discuss the following three overarching issues (i) What are the most urgent scientific questions and how can they be addressed? (ii) What forest ecosystems should be investigated? (iii) Which other climate change factors should be coupled with elevated CO(2) concentrations in future experiments to better predict the effects of climate change? Plantations and natural forests can have conflicting purposes for high productivity and environmental protection.