Showing papers by "University of New Mexico published in 2005"

A transmembrane intracellular estrogen receptor mediates rapid cell signaling.

Abstract: The steroid hormone estrogen regulates many functionally unrelated processes in numerous tissues. Although it is traditionally thought to control transcriptional activation through the classical nuclear estrogen receptors, it also initiates many rapid nongenomic signaling events. We found that of all G protein-coupled receptors characterized to date, GPR30 is uniquely localized to the endoplasmic reticulum, where it specifically binds estrogen and fluorescent estrogen derivatives. Activating GPR30 by estrogen resulted in intracellular calcium mobilization and synthesis of phosphatidylinositol 3,4,5-trisphosphate in the nucleus. Thus, GPR30 represents an intracellular transmembrane estrogen receptor that may contribute to normal estrogen physiology as well as pathophysiology.

Regional vegetation die-off in response to global-change-type drought

Abstract: Future drought is projected to occur under warmer temperature conditions as climate change progresses, referred to here as global-change-type drought, yet quantitative assessments of the triggers and potential extent of drought-induced vegetation die-off remain pivotal uncertainties in assessing climate-change impacts. Of particular concern is regional-scale mortality of overstory trees, which rapidly alters ecosystem type, associated ecosystem properties, and land surface conditions for decades. Here, we quantify regional-scale vegetation die-off across southwestern North American woodlands in 2002-2003 in response to drought and associated bark beetle infestations. At an intensively studied site within the region, we quantified that after 15 months of depleted soil water content, >90% of the dominant, overstory tree species (Pinus edulis, a pinon) died. The die-off was reflected in changes in a remotely sensed index of vegetation greenness (Normalized Difference Vegetation Index), not only at the intensively studied site but also across the region, extending over 12,000 km2 or more; aerial and field surveys confirmed the general extent of the die-off. Notably, the recent drought was warmer than the previous subcontinental drought of the 1950s. The limited, available observations suggest that die-off from the recent drought was more extensive than that from the previous drought, extending into wetter sites within the tree species' distribution. Our results quantify a trigger leading to rapid, drought-induced die-off of overstory woody plants at subcontinental scale and highlight the potential for such die-off to be more severe and extensive for future global-change-type drought under warmer conditions.

Synthesizing U.S. river restoration efforts

Abstract: The authors of this Policy Forum developed a comprehensive database of >37,000 river restoration projects across the United States. Such projects have increased exponentially over the past decade with more than a billion dollars spent annually since 1990. Most are intended to enhance water quality, manage riparian zones, improve in-stream habitat, allow fish passage, and stabilize stream banks. Only 10% of project records document any form of project monitoring, and little if any of this information is either appropriate or available for assessing the ecological effectiveness of restoration activities.

Prophylactic quadrivalent human papillomavirus (types 6, 11, 16, and 18) L1 virus-like particle vaccine in young women: a randomised double-blind placebo-controlled multicentre phase II efficacy trial

Abstract: Summary Background A randomised double-blind placebo-controlled phase II study was done to assess the efficacy of a prophylactic quadrivalent vaccine targeting the human papillomavirus (HPV) types associated with 70% of cervical cancers (types 16 and 18) and with 90% of genital warts (types 6 and 11). Methods 277 young women (mean age 20·2 years [SD 1·7]) were randomly assigned to quadrivalent HPV (20 μg type 6, 40 μg type 11, 40 μg type 16, and 20 μg type 18) L1 virus-like-particle (VLP) vaccine and 275 (mean age 20·0 years [1·7]) to one of two placebo preparations at day 1, month 2, and month 6. For 36 months, participants underwent regular gynaecological examinations, cervicovaginal sampling for HPV DNA, testing for serum antibodies to HPV, and Pap testing. The primary endpoint was the combined incidence of infection with HPV 6, 11, 16, or 18, or cervical or external genital disease (ie, persistent HPV infection, HPV detection at the last recorded visit, cervical intraepithelial neoplasia, cervical cancer, or external genital lesions caused by the HPV types in the vaccine). Main analyses were done per protocol. Findings Combined incidence of persistent infection or disease with HPV 6, 11, 16, or 18 fell by 90% (95% CI 71–97, p Interpretation A vaccine targeting HPV types 6, 11, 16, 18 could substantially reduce the acquisition of infection and clinical disease caused by common HPV types. Published online April 7, 2005 DOI 10.1016/S1470-2045(05)70101-7

“Economic man” in cross-cultural perspective: Behavioral experiments in 15 small-scale societies

Abstract: Researchers from across the social sciences have found consistent deviations from the predictions of the canonical model of self-interest in hundreds of experiments from around the world. This research, however, cannot determine whether the uniformity re- sults from universal patterns of human behavior or from the limited cultural variation available among the university students used in virtually all prior experimental work. To address this, we undertook a cross-cultural study of behavior in ultimatum, public goods, and dictator games in a range of small-scale societies exhibiting a wide variety of economic and cultural conditions. We found, first, that the canonical model - based on self-interest - fails in all of the societies studied. Second, our data reveal substantially more behavioral vari- ability across social groups than has been found in previous research. Third, group-level differences in economic organization and the structure of social interactions explain a substantial portion of the behavioral variation across societies: the higher the degree of market integration and the higher the payoffs to cooperation in everyday life, the greater the level of prosociality expressed in experimental games. Fourth, the available individual-level economic and demographic variables do not consistently explain game behavior, either within or across groups. Fifth, in many cases experimental play appears to reflect the common interactional patterns of everyday life.

Standards for ecologically successful river restoration

Abstract: Summary 1. Increasingly, river managers are turning from hard engineering solutions to ecologically based restoration activities in order to improve degraded waterways. River restoration projects aim to maintain or increase ecosystem goods and services while protecting downstream and coastal ecosystems. There is growing interest in applying river restoration techniques to solve environmental problems, yet little agreement exists on what constitutes a successful river restoration effort. 2. We propose five criteria for measuring success, with emphasis on an ecological perspective. First, the design of an ecological river restoration project should be based on a specified guiding image of a more dynamic, healthy river that could exist at the site. Secondly, the river’s ecological condition must be measurably improved. Thirdly, the river system must be more self-sustaining and resilient to external perturbations so that only minimal follow-up maintenance is needed. Fourthly, during the construction phase, no lasting harm should be inflicted on the ecosystem. Fifthly, both pre- and postassessment must be completed and data made publicly available. 3. Determining if these five criteria have been met for a particular project requires development of an assessment protocol. We suggest standards of evaluation for each of the five criteria and provide examples of suitable indicators. 4. Synthesis and applications . Billions of dollars are currently spent restoring streams and rivers, yet to date there are no agreed upon standards for what constitutes ecologically beneficial stream and river restoration. We propose five criteria that must be met for a river restoration project to be considered ecologically successful. It is critical that the broad restoration community, including funding agencies, practitioners and citizen restoration groups, adopt criteria for defining and assessing ecological success in restoration. Standards are needed because progress in the science and practice of river restoration has been hampered by the lack of agreed upon criteria for judging ecological success. Without well-accepted criteria that are ultimately supported by funding and implementing agencies, there is little incentive for practitioners to assess and report restoration outcomes. Improving methods and weighing the ecological benefits of various restoration approaches require organized national-level reporting systems.

Experimental Demonstration of Near-Infrared Negative-Index Metamaterials

Abstract: Metal-based negative refractive-index materials have been extensively studied in the microwave region. However, negative-index metamaterials have not been realized at near-IR or visible frequencies due to difficulties of fabrication and to the generally poor optical properties of metals at these wavelengths. In this Letter, we report the first fabrication and experimental verification of a transversely structured metal-dielectricmetal multilayer exhibiting a negative refractive index around 2 mu m. Both the amplitude and the phase of the transmission and reflection were measured experimentally, and are in good agreement with a rigorous coupled wave analysis.

Measurement of neutrino oscillation with KamLAND: evidence of spectral distortion.

Abstract: We present results of a study of neutrino oscillation based on a 766 ton/year exposure of KamLAND to reactor antineutrinos. We observe 258 [overline nu ]e candidate events with energies above 3.4 MeV compared to 365.2±23.7 events expected in the absence of neutrino oscillation. Accounting for 17.8±7.3 expected background events, the statistical significance for reactor [overline nu ]e disappearance is 99.998%. The observed energy spectrum disagrees with the expected spectral shape in the absence of neutrino oscillation at 99.6% significance and prefers the distortion expected from [overline nu ]e oscillation effects. A two-neutrino oscillation analysis of the KamLAND data gives Deltam2=7.9 -0.5 +0.6 ×10-5 eV2. A global analysis of data from KamLAND and solar-neutrino experiments yields Deltam2=7.9 -0.5 +0.6 ×10-5 eV2 and tan2theta=0.40 -0.07 +0.10 , the most precise determination to date.

A practical clinical approach to diagnosis of fetal alcohol spectrum disorders: clarification of the 1996 institute of medicine criteria.

Abstract: Background. The adverse effects of alcohol on the developing human represent a spectrum of structural anomalies and behavioral and neurocognitive disabilities, most accurately termed fetal alcohol spectrum disorders (FASD). The first descriptions in the modern medical literature of a distinctly recognizable pattern of malformations associated with maternal alcohol abuse were reported in 1968 and 1973. Since that time, substantial progress has been made in developing specific criteria for defining and diagnosing this condition. Two sets of diagnostic criteria are now used most widely for evaluation of children with potential diagnoses in the FASD continuum, ie, the 1996 Institute of Medicine (IOM) criteria and the Washington criteria. Although both approaches have improved the clinical delineation of FASD, both suffer from significant drawbacks in their practical application in pediatric practice. Objective. The purpose of this report is to present specific clarifications of the 1996 IOM criteria for the diagnosis of FASD, to facilitate their practical application in clinical pediatric practice. Methods. A large cohort of children who were prenatally exposed to alcohol were identified, through active case-ascertainment methods, in 6 Native American communities in the United States and 1 community in the Western Cape Province of South Africa. The children and their families underwent standardized multidisciplinary evaluations, including a dysmorphology examination, developmental and neuropsychologic testing, and a structured maternal interview, which gathered data about prenatal drinking practices and other demographic and family information. Data for these subjects were analyzed, and revisions and clarifications of the existing IOM FASD diagnostic categories were formulated on the basis of the results. Results. The revised IOM method defined accurately and completely the spectrum of disabilities among the children in our study. On the basis of this experience, we propose specific diagnostic criteria for fetal alcohol syndrome and partial fetal alcohol syndrome. We also define alcohol-related birth defects and alcohol-related neurodevelopmental disorder from a practical standpoint. Conclusions. The 1996 IOM criteria remain the most appropriate diagnostic approach for children prenatally exposed to alcohol. The proposed revisions presented here make these criteria applicable in clinical pediatric practice. Pediatrics 2005;115:39–47; fetal alcohol syndrome, fetal alcohol spectrum disorders, diagnostic criteria, mental retardation, developmental disabilities.

Functional- and abundance-based mechanisms explain diversity loss due to N fertilization.

Abstract: Human activities have increased N availability dramatically in terrestrial and aquatic ecosystems. Extensive research demonstrates that local plant species diversity generally declines in response to nutrient enrichment, yet the mechanisms for this decline remain unclear. Based on an analysis of >900 species responses from 34 N-fertilization experiments across nine terrestrial ecosystems in North America, we show that both trait-neutral and trait-based mechanisms operate simultaneously to influence diversity loss as production increases. Rare species were often lost because of soil fertilization, randomly with respect to traits. The risk of species loss due to fertilization ranged from >60% for the rarest species to 10% for the most abundant species. Perennials, species with N-fixing symbionts, and those of native origin also experienced increased risk of local extinction after fertilization, regardless of their initial abundance. Whereas abundance was consistently important across all systems, functional mechanisms were often system-dependent. As N availability continues to increase globally, management that focuses on locally susceptible functional groups and generally susceptible rare species will be essential to maintain biodiversity.

Finding local community structure in networks.

Abstract: Although the inference of global community structure in networks has recently become a topic of great interest in the physics community, all such algorithms require that the graph be completely known. Here, we define both a measure of local community structure and an algorithm that infers the hierarchy of communities that enclose a given vertex by exploring the graph one vertex at a time. This algorithm runs in time O(k2d) for general graphs when d is the mean degree and k is the number of vertices to be explored. For graphs where exploring a new vertex is time consuming, the running time is linear, O(k). We show that on computer-generated graphs the average behavior of this technique approximates that of algorithms that require global knowledge. As an application, we use this algorithm to extract meaningful local clustering information in the large recommender network of an online retailer.

Some Precambrian banded iron-formations (BIFs) from around the world: Their age, geologic setting, mineralogy, metamorphism, geochemistry, and origins

Abstract: Banded iron-formations (BIFs) occur in the Precambrian geologic record over a wide time span. Beginning at 3.8 Ga (Isua, West Greenland), they are part of Archean cratons and range in age from about 3.5 until 2.5 Ga. Their overall volume reaches a maximum at about 2.5 Ga (iron-formations in the Hamersley Basin of Western Australia) and they disappear from the geologic record at about 1.8 Ga, only to reappear between 0.8 and 0.6 Ga. The stratigraphic sequences in which BIFs occur are highly variable. Most Archean iron-formations are part of greenstone belts that have been deformed, metamorphosed, and dismembered. This makes reconstruction of the basinal setting of such BIFs very difficult. The general lack of metamorphism and deformation of extensive BIFs of the Hamersley Range of Western Australia and the Transvaal Supergroup of South Africa allow for much better evaluations of original basinal settings. Most Archean iron-formations show fine laminations and/or microbanding. Such microbanding is especially well developed in the Brockman Iron Formation of Western Australia, where it has been interpreted as chemical varves, or annual layers of sedimentation. BIFs ranging in age from 2.2 Ga to about 1.8 Ga (e.g., those of the Lake Superior region, U.S.A., Labrador Trough, Canada, and the Nabberu Basin of Western Australia) commonly exhibit granular textures and lack microbanding. The mineralogy of the least metamorphosed BIFs consists of combinations of the following minerals: chert, magnetite, hematite, carbonates (most commonly siderite and members of the dolomite-ankerite series), greenalite, stilpnomelane, and riebeckite, and locally pyrite. Minnesotaite is a common, very low-grade metamorphic reaction product. The Eh-pH stability fields of the above minerals (and/or their precursors) indicate anoxic conditions for the original depositional environment. The average bulk chemistry of BIFs, from 3.8 through 1.8 Ga in age, is very similar. They are rich in total Fe (ranging from about 20 to 40 wt%) and SiO2 (ranging from 43 to 56 wt%). CaO and MgO contents range from 1.75 to 9.0 and from 1.20 to 6.7 wt%, respectively. Al2O3 contents are very low, ranging from 0.09 to 1.8 wt%. These chemical values show that they are clean chemical sediments devoid of detrital input. Only the Neoproterozoic iron-formations (of 0.8 to 0.6 Ga in age) have very different mineralogical and chemical make-ups. They consist mainly of chert and hematite, with minor carbonates. The rare-earth element profiles of almost all BIFs,with generally pronounced positive Eu anomalies, indicate that the source of Fe and Si was the result of deep ocean hydrothermal activity admixed with sea water. The prograde metamorphism of iron-formations produces sequentially Fe-amphiboles, then Fe-pyroxenes, and finally (at highest grade) Fe-olivine-containing assemblages. Such metamorphic reactions are isochemical except for decarbonation and dehydration. The common fine lamination (and/or microbanding) as well as the lack of detrital components in most BIFs suggest that such are the result of deposition, below wave base, in the deeper parts of ocean basins. Those with granular textures are regarded as the result of deposition in shallow water, platformal areas. Carbon isotope data suggest that for a long period of time (from Archean to Early Proterozoic) the ocean basins were stratified with respect to δ13C (in carbonates) as well as organic carbon content. In Middle Proterozoic time (when granular BIFs appear) this stratification diminishes and is lost. The Neoproterozoic BIFs occur in stratigraphic sequences with glaciomarine deposits. These BIFs are the result of anoxic conditions that resulted from the stagnation in the oceans beneath a near-global ice cover, referred to as “Snowball Earth.” All of the most “primary” mineral assemblages appear to be the result of chemical precipitation under anoxic conditions. There are, as yet, no data to support that BIF precipitation was linked directly to microbial activity. The relative abundance of BIF throughout the Precambrian record is correlated with a possible curve for the evolution of the O2 content in the Precambrian atmosphere.

The origin of allometric scaling laws in biology from genomes to ecosystems: towards a quantitative unifying theory of biological structure and organization

Abstract: Life is the most complex physical phenomenon in the Universe, manifesting an extraordinary diversity of form and function over an enormous scale from the largest animals and plants to the smallest microbes and subcellular units. Despite this many of its most fundamental and complex phenomena scale with size in a surprisingly simple fashion. For example, metabolic rate scales as the 3/4-power of mass over 27 orders of magnitude, from molecular and intracellular levels up to the largest organisms. Similarly, time-scales (such as lifespans and growth rates) and sizes (such as bacterial genome lengths, tree heights and mitochondrial densities) scale with exponents that are typically simple powers of 1/4. The universality and simplicity of these relationships suggest that fundamental universal principles underly much of the coarse-grained generic structure and organisation of living systems. We have proposed a set of principles based on the observation that almost all life is sustained by hierarchical branching networks, which we assume have invariant terminal units, are space-filling and are optimised by the process of natural selection. We show how these general constraints explain quarter power scaling and lead to a quantitative, predictive theory that captures many of the essential features of diverse biological systems. Examples considered include animal circulatory systems, plant vascular systems, growth, mitochondrial densities, and the concept of a universal molecular clock. Temperature considerations, dimensionality and the role of invariants are discussed. Criticisms and controversies associated with this approach are also addressed.

Ecohydrological implications of woody plant encroachment

Abstract: Increases in the abundance or density of woody plants in historically semiarid and arid grassland ecosystems have important ecological, hydrological, and socioeconomic implications. Using a simplified water-balance model, we propose a framework for con- ceptualizing how woody plant encroachment is likely to affect components of the water cycle within these ecosystems. We focus in particular on streamflow and the partitioning of evapotranspiration into evaporation and transpiration. On the basis of this framework, we suggest that streamflow and evaporation processes are affected by woody plant en- croachment in different ways, depending on the degree and seasonality of aridity and the availability of subsurface water. Differences in landscape physiography, climate, and runoff mechanisms mediate the influence of woody plants on hydrological processes. Streamflow is expected to decline as a result of woody plant encroachment in landscapes dominated by subsurface flow regimes. Similarly, encroachment of woody plants can be expected to produce an increase in the fractional contribution of bare soil evaporation to evapotrans- piration in semiarid ecosystems, whereas such shifts may be small or negligible in both subhumid and arid ecosystems. This framework for considering the effects of woody plant encroachment highlights important ecological and hydrological interactions that serve as a basis for predicting other ecological aspects of vegetation change—such as potential changes in carbon cycling within an ecosystem. In locations where woody plant encroach- ment results in increased plant transpiration and concurrently the availability of soil water is reduced, increased accumulation of carbon in soils emerges as one prediction. Thus, explicitly considering the ecohydrological linkages associated with vegetation change pro- vides needed information on the consequences of woody plant encroachment on water yield, carbon cycling, and other processes.

Ionic polymer–metal composites: IV. Industrial and medical applications

Abstract: This paper, the last in a series of four review papers to appear in this journal, presents some critical applications using ionic polymer?metal composites?(IPMCs). Industrial and biomedical applications of IPMCs are identified and presented along with brief illustration.

Linear array geometry synthesis with minimum sidelobe level and null control using particle swarm optimization

Abstract: This paper describes the synthesis method of linear array geometry with minimum sidelobe level and null control using the particle swarm optimization (PSO) algorithm. The PSO algorithm is a newly discovered, high-performance evolutionary algorithm capable of solving general N-dimensional, linear and nonlinear optimization problems. Compared to other evolutionary methods such as genetic algorithms and simulated annealing, the PSO algorithm is much easier to understand and implement and requires the least of mathematical preprocessing. The array geometry synthesis is first formulated as an optimization problem with the goal of sidelobe level (SLL) suppression and/or null placement in certain directions, and then solved by the PSO algorithm for the optimum element locations. Three design examples are presented that illustrate the use of the PSO algorithm, and the optimization goal in each example is easily achieved. The results of the PSO algorithm are validated by comparing with results obtained using the quadratic programming method (QPM).

A new tool to assess treatment fidelity and evaluation of treatment fidelity across 10 years of health behavior research

Abstract: A. Bellg, B. Borrelli, et al. (2004) previously developed a framework that consisted of strategies to enhance treatment fidelity of health behavior interventions. The present study used this framework to (a) develop a measure of treatment fidelity and (b) use the measure to evaluate treatment fidelity in articles published in 5 journals over 10 years. Three hundred forty-two articles met inclusion criteria; 22% reported strategies to maintain provider skills, 27% reported checking adherence to protocol, 35% reported using a treatment manual, 54% reported using none of these strategies, and 12% reported using all 3 strategies. The mean proportion adherence to treatment fidelity strategies was .55; 15.5% of articles achieved greater than or equal to .80. This tool may be useful for researchers, grant reviewers, and editors planning and evaluating trials.

Use of antimicrobial prophylaxis for major surgery: baseline results from the National Surgical Infection Prevention Project.

Abstract: Hypothesis Surgical site infections (SSIs) are a major contributor to patient injury, mortality, and health care costs. Despite evidence of effectiveness of antimicrobials to prevent SSIs, previous studies have demonstrated inappropriate timing, selection, and excess duration of administration of antimicrobial prophylaxis. We herein describe the use of antimicrobial prophylaxis for Medicare patients undergoing major surgery. Design National retrospective cohort study with medical record review. Setting Two thousand nine hundred sixty-five acute-care US hospitals. Patients A systematic random sample of 34 133 Medicare inpatients undergoing coronary artery bypass grafting; other open-chest cardiac surgery (excluding transplantation); vascular surgery, including aneurysm repair, thromboendarterectomy, and vein bypass operations; general abdominal colorectal surgery; hip and knee total joint arthroplasty (excluding revision surgery); and abdominal and vaginal hysterectomy from January 1 through November 30, 2001. Main Outcome Measures The proportion of patients who had parenteral antimicrobial prophylaxis initiated within 1 hour before the surgical incision; the proportion of patients who were given a prophylactic antimicrobial agent that was consistent with currently published guidelines; and the proportion of patients whose antimicrobial prophylaxis was discontinued within 24 hours after surgery. Results An antimicrobial dose was administered to 55.7% (95% confidence interval [CI], 54.8%-56.6%) of patients within 1 hour before incision. Antimicrobial agents consistent with published guidelines were administered to 92.6% (95% CI, 92.3%-92.8%) of the patients. Antimicrobial prophylaxis was discontinued within 24 hours of surgery end time for only 40.7% (95% CI, 40.2%-41.2%) of patients. Conclusion Substantial opportunities exist to improve the use of prophylactic antimicrobials for patients undergoing major surgery.

Examining the relationship between executive functions and restricted, repetitive symptoms of Autistic Disorder.

Abstract: The executive function theory was utilized to examine the relationship between cognitive process and the restricted, repetitive symptoms of Autistic Disorder (AD). Seventeen adults with AD were compared to 17 nonautistic controls on a new executive function battery (Delis-Kaplin Executive Function Scales). Restricted, repetitive symptoms were measured by a variety of instruments (i.e., the Autism Diagnostic Observation Schedule, Autism Diagnostic Interview-Revised, Gilliam Autism Rating Scale, and the Aberrant Behavior Checklist). The study replicated the executive function profile that has been reported in adults with AD. In addition to the replication findings, the study found several executive processes (i.e., cognitive flexibility, working memory, and response inhibition) were highly related to the restrictive, repetitive symptoms of AD; whereas, other executive process (i.e., planning and fluency) were not found to be significantly correlated with restricted, repetitive symptoms. Similarly, we found an executive function model consisting of relative strengths and deficits was the best predictor of restricted, repetitive symptoms of autism. The implications for the executive function theory and how the theory predicts core symptoms of autism are discussed.

Mechanism of phagolysosome biogenesis block by viable Mycobacterium tuberculosis

Abstract: Live Mycobacterium tuberculosis persists in macrophage phagosomes by interfering with phagolysosome biogenesis. Here, using four-dimensional microscopy and in vitro assays, we report the principal difference between phagosomes containing live and dead mycobacteria. Phosphatidylinositol 3-phosphate (PI3P), a membrane trafficking regulatory lipid essential for phagosomal acquisition of lysosomal constituents, is retained on phagosomes harboring dead mycobacteria but is continuously eliminated from phagosomes with live bacilli. We show that the exclusion of PI3P from live mycobacterial phagosomes can be only transiently reversed by Ca2+ fluxes, and that live M. tuberculosis secretes a lipid phosphatase, SapM, that hydrolyzes PI3P, inhibits phagosome–late endosome fusion in vitro, and contributes to inhibition of phagosomal maturation.

Multiple processes in prospective memory retrieval: factors determining monitoring versus spontaneous retrieval.

Abstract: Theoretically, prospective memory retrieval can be accomplished either by controlled monitoring of the environment for a target event or by a more reflexive process that spontaneously responds to the presence of a target event. These views were evaluated in Experiments 1-4 by examining whether performing a prospective memory task produced costs on the speed of performing the ongoing task. In Experiment 5, the authors directly tested for the existence of spontaneous retrieval. The results supported the multiprocess theory (M. A. McDaniel & G. O. Einstein, 2000) predictions that (a) spontaneous retrieval can occur and can support good prospective memory and (b) depending on task demands and individual differences, people rely to different degrees on monitoring versus spontaneous retrieval for prospective remembering.

Linking the global carbon cycle to individual metabolism

Abstract: Summary 1. We present a model that yields ecosystem-level predictions of the flux, storage and turnover of carbon in three important pools (autotrophs, decomposers, labile soil C) based on the constraints of body size and temperature on individual metabolic rate. 2. The model predicts a 10 000-fold increase in C turnover rates moving from tree- to phytoplankton-dominated ecosystems due to the size dependence of photosynthetic rates. 3. The model predicts a 16-fold increase in rates controlled by respiration (e.g. decomposition, turnover of labile soil C and microbial biomass) over the temperature range 0‐30 °C due to the temperature dependence of ATP synthesis in respiratory complexes. 4. The model predicts only a fourfold increase in rates controlled by photosynthesis (e.g. net primary production, litter fall, fine root turnover) over the temperature range 0‐30 °C due to the temperature dependence of Rubisco carboxylation in chloroplasts. 5. The difference between the temperature dependence of respiration and photosynthesis yields quantitative predictions for distinct phenomena that include acclimation of plant respiration, geographic gradients in labile C storage, and differences between the short- and long-term temperature dependence of whole-ecosystem CO2 flux. 6. These four sets of model predictions were tested using global compilations of data on C flux, storage and turnover in ecosystems. 7. Results support the hypothesis that the combined effects of body size and temperature on individual metabolic rate impose important constraints on the global C cycle. The model thus provides a synthetic, mechanistic framework for linking global biogeochemical cycles to cellular-, individual- and community-level processes.

The rate of DNA evolution: Effects of body size and temperature on the molecular clock

Abstract: Observations that rates of molecular evolution vary widely within and among lineages have cast doubts on the existence of a single “molecular clock.” Differences in the timing of evolutionary events estimated from genetic and fossil evidence have raised further questions about the accuracy of molecular clocks. Here, we present a model of nucleotide substitution that combines theory on metabolic rate with the now-classic neutral theory of molecular evolution. The model quantitatively predicts rate heterogeneity and may reconcile differences in molecular- and fossil-estimated dates of evolutionary events. Model predictions are supported by extensive data from mitochondrial and nuclear genomes. By accounting for the effects of body size and temperature on metabolic rate, this model explains heterogeneity in rates of nucleotide substitution in different genes, taxa, and thermal environments. This model also suggests that there is indeed a single molecular clock, as originally proposed by Zuckerkandl and Pauling [Zuckerkandl, E. & Pauling, L. (1965) in Evolving Genes and Proteins, eds. Bryson, V. & Vogel, H. J. (Academic, New York), pp. 97–166], but that it “ticks” at a constant substitution rate per unit of mass-specific metabolic energy rather than per unit of time. This model therefore links energy flux and genetic change. More generally, the model suggests that body size and temperature combine to control the overall rate of evolution through their effects on metabolism.

Chromatin remodelling at a DNA double-strand break site in Saccharomyces cerevisiae

Abstract: The repair of DNA double-strand breaks (DSBs) is crucial for maintaining genome stability. Eukaryotic cells repair DSBs by both non-homologous end joining and homologous recombination. How chromatin structure is altered in response to DSBs and how such alterations influence DSB repair processes are important issues. In vertebrates, phosphorylation of the histone variant H2A.X occurs rapidly after DSB formation1, spreads over megabase chromatin domains, and is required for stable accumulation of repair proteins at damage foci2. In Saccharomyces cerevisiae, phosphorylation of the two principal H2A species is also signalled by DSB formation, which spreads ∼40 kb in either direction from the DSB3. Here we show that near a DSB phosphorylation of H2A is followed by loss of histones H2B and H3 and increased sensitivity of chromatin to digestion by micrococcal nuclease; however, phosphorylation of H2A and nucleosome loss occur independently. The DNA damage sensor MRX4 is required for histone loss, which also depends on INO80, a nucleosome remodelling complex5. The repair protein Rad51 (ref. 6) shows delayed recruitment to DSBs in the absence of histone loss, suggesting that MRX-dependent nucleosome remodelling regulates the accessibility of factors directly involved in DNA repair by homologous recombination. Thus, MRX may regulate two pathways of chromatin changes: nucleosome displacement for efficient recruitment of homologous recombination proteins; and phosphorylation of H2A, which modulates checkpoint responses to DNA damage2.

Diversity decreases invasion via both sampling and complementarity effects

Abstract: Complementarity and sampling effects may both contribute to increased invasion resistance at higher diversity We measured plant invader biomass across a long-term experimental plant diversity gradient Invader species biomass was inhibited in more diverse plots, largely because of the presence of strongly competitive C4 bunchgrasses, consistent with a sampling effect Invader biomass was negatively correlated with resident root biomass, and positively correlated with soil nitrate concentrations, suggesting that competition for nitrogen limited invader success Resident root biomass increased and soil nitrate concentrations decreased with the presence of C4 grasses and also across the diversity gradient, suggesting that diverse plots are more competitive because of the presence of C4 grasses In addition to this evidence for a sampling effect, we also found evidence for a complementarity effect Specifically, the percentage of plots that had lower invader biomass than did the best resident monoculture (ie that had invader underyielding) increased across the species richness gradient This pattern cannot be explained by a sampling effect and is a unique signature of complementarity effects Our results demonstrate the importance of multiple mechanisms by which diversity can increase invasion resistance

Energy Constraints on the Evolution of Gene Expression

Abstract: I here estimate the energy cost of changes in gene expression for several thousand genes in the yeast Saccharomyces cerevisiae. A doubling of gene expression, as it occurs in a gene duplication event, is significantly selected against for all genes for which expression data is available. It carries a median selective disadvantage of s > 10 - 5 , several times greater than the selection coefficient s = 1.47 × 10 - 7 below which genetic drift dominates a mutant's fate. When considered separately, increases in messenger RNA expression or protein expression by more than a factor 2 also have significant energy costs for most genes. This means that the evolution of transcription and translation rates is not an evolutionarily neutral process. They are under active selection opposing them. My estimates are based on genome-scale information of gene expression in the yeast S. cerevisiae as well as information on the energy cost of biosynthesizing amino acids and nucleotides.