A balanced psychology and a full life

Psychology since World War II has been largely devoted to repairing weakness and understanding suffering. Towards that end, we have made considerable gains. We have a classification of mental illness that allows international collaboration, and through this collaboration we have developed effective psychotherapeutic or pharmacological treatments for 14 major mental disorders. However, while building a strong science and practice of treating mental illness, we largely forgot about everyday well-being. Is the absence of mental illness and suffering sufficient to let individuals and communities flourish? Were all disabling conditions to disappear, what would make life worth living? Those committed to a science of positive psychology can draw on the effective research methods developed to understand and treat mental illness. Results from a new randomized, placebo-controlled study demonstrate that people are happier and less depressed three months after completing exercises targeting positive emotion. The ultimate goal of positive psychology is to make people happier by understanding and building positive emotion, gratification and meaning. Towards this end, we must supplement what we know about treating illness and repairing damage with knowledge about nurturing well-being in individuals and communities.     

Iron-sulfur proteins: ancient structures, still full of surprises

This article is a survey of the properties and functions of Fe-S proteins under the following headings: sulfur and iron; iron-sulfur clusters; evolution of cofactor use; early observations; complex and extended clusters; sulfur exchange and core interconversions; synthesis and biosynthesis of Fe-S clusters; functions of Fe-S clusters: electron transfer, electron delocalization, spin states and magnetism, covalency of sulfur bonds; non-electron transfer functions of Fe-S clusters: substrate binding and catalysis, regulatory and sensing functions.     

Base excision repair activities required for yeast to attain a full chronological life span

The chronological life span of yeast, the survival of stationary (G0) cells over time, provides a model for investigating certain of the factors that may influence the aging of non-dividing cells and tissues in higher organisms. This study measured the effects of defined defects in the base excision repair (BER) system for DNA repair on this life span. Stationary yeast survives longer when it is pre-grown on respiratory, as compared to fermentative (glucose), media. It is also less susceptible to viability loss as the result of defects in DNA glycosylase/AP lyases (Ogg1p, Ntg1p, Ntg2p), apurinic/apyrimidinic (AP) endonucleases (Apn1p, Apn2p) and monofunctional DNA glycosylase (Mag1p). Whereas single BER glycosylase/AP lyase defects exerted little influence over such optimized G0 survival, this survival was severely shortened with the loss of two or more such enzymes. Equally, the apn1delta and apn2delta single gene deletes survived as well as the wild type, whereas a apn1delta apn2delta double mutant totally lacking in any AP endonuclease activity survived poorly. Both this shortened G0 survival and the enhanced mutagenicity of apn1delta apn2delta cells were however rescued by the over-expression of either Apn1p or Apn2p. The results highlight the vital importance of BER in the prevention of mutation accumulation and the attainment of the full yeast chronological life span. They also reveal an appreciable overlap in the G0 maintenance functions of the different BER DNA glycosylases and AP endonucleases.     

"SNP Snappy": a strategy for fast genome-wide association studies fitting a full mixed model

A strategy to reduce computational demands of genome-wide association studies fitting a mixed model is presented. Improvements are achieved by utilizing a large proportion of calculations that remain constant across the multiple analyses for individual markers involved, with estimates obtained without inverting large matrices.     

"Feeding time" for the brain: a matter of clocks.

Circadian clocks are autonomous time-keeping mechanisms that allow living organisms to predict and adapt to environmental rhythms of light, temperature and food availability. At the molecular level, circadian clocks use clock and clock-controlled genes to generate rhythmicity and distribute temporal signals. In mammals, synchronization of the master circadian clock located in the suprachiasmatic nuclei of the hypothalamus is accomplished mainly by light stimuli. Meal time, that can be experimentally modulated by temporal restricted feeding, is a potent synchronizer for peripheral oscillators with no clear synchronizing influence on the suprachiasmatic clock. Furthermore, food-restricted animals are able to predict meal time, as revealed by anticipatory bouts of locomotor activity, body temperature and plasma corticosterone. These food anticipatory rhythms have long been thought to be under the control of a food-entrainable clock (FEC). Analysis of clock mutant mice has highlighted the relevance of some, but not all of the clock genes for food-entrainable clockwork. Mutations of Clock or Per1 do not impair expression of food anticipatory components, suggesting that these clock genes are not essential for food-entrainable oscillations. By contrast, mice mutant for Npas2 or deficient for Cry1 and Cry2 show more or less altered responses to restricted feeding conditions. Moreover, a lack of food anticipation is specifically associated with a mutation of Per2, demonstrating the critical involvement of this gene in the anticipation of meal time. The actual location of the FEC is not yet clearly defined. Nevertheless, current knowledge of the putative brain regions involved in food-entrainable oscillations is discussed. We also describe several neurochemical pathways, including orexinergic and noradrenergic, likely to participate in conveying inputs to and outputs from the FEC to control anticipatory processes.     

Arginine, scurvy and Cartier's "tree of life"

Hunting for wild animals is stimulated by the many different human uses of faunal resources, and these animals constitute important subsistence items in local communities in the Caatinga region. In order to gain access to these resources, hunters have developed a series of techniques and strategies that are described in the present work. The principal hunting techniques encountered were: waiting, especially directed towards hunting diurnal birds; calling ("arremedo"), a technique in which the hunters imitate the animal's call to attract it to close range; hunting with dogs, a technique mostly used for capturing mammals; tracking, a technique used by only a few hunters who can recognize and follow animal tracks; and "facheado", in which the hunters go out at night with lanterns to catch birds in their nests. Additionally, many animal species are captured using mechanical traps. The types of traps used by the interviewees were: dead-fall traps ("quixó"), iron-jaw snap traps ("arataca"), wooden cages with bait ("arapuca"), iron-cage traps ("gaiola'), "visgo", multi-compartment bird cages ("alçapão"), buried ground traps with pivoted tops ("fojo"), and nooses and cages for carnivorous. The choice of which technique to use depends on the habits of the species being hunted, indicating that the hunters possess a wide knowledge of the biology of these animals. From a conservation perspective, active hunting techniques (waiting, imitation, hunting with dogs, and "facheado") have the greatest impact on the local fauna. The use of firearm and dogs brought greater efficiency to hunting activities. Additional studies concerning these hunting activities will be useful to contribute to proposals for management plans regulating hunting in the region – with the objective of attaining sustainable use of faunal resources of great importance to the local human communities.     

Uptake or extrusion: crystal structures of full ABC transporters suggest a common mechanism

ATP-binding cassette (ABC) transporters are integral membrane proteins that move diverse substrates across cellular membranes. ABC importers catalyse the uptake of essential nutrients from the environment, whereas ABC exporters facilitate the extrusion of various compounds, including drugs and antibiotics, from the cytoplasm. How ABC transporters couple ATP hydrolysis to the transport reaction has long remained unclear. The recent crystal structures of four complete ABC transporters suggest that a key step of the molecular mechanism is conserved in importers and exporters. Whereas binding of ATP promotes an outward-facing conformation, the release of the hydrolysis products ADP and phosphate promotes an inward-facing conformation. This basic scheme can in principle explain ATP-driven drug export and binding protein-dependent nutrient uptake.     

FlyGEM, a full transcriptome array platform for the Drosophila community

We have constructed a DNA microarray to monitor expression of predicted genes in Drosophila. By using homotypic hybridizations, we show that the array performs reproducibly, that dye effects are minimal, and that array results agree with systematic northern blotting. The array gene list has been extensively annotated and linked-out to other databases. Incyte and the NIH have made the platform available to the community via academic microarray facilities selected by an NIH committee.     

Pentagon packing models for "all-pentamer" virus structures.

A connection is made between 1) the observed structures of virus capsids whose capsomers are all pentamers and 2) the mathematical problem of determination of the largest size of a given number of equal regular spherical pentagons that can be packed on the surface of the unit sphere without overlapping. It is found that papillomaviruses provide the conjectured solution to the spherical pentagon packing problem for 72 pentagons. Thus, a study of some virus structures has given additional insight into a mathematical problem. At the same time this mathematical problem enables prediction of an octahedral form of papillomavirus particles consisting of 24 pentamers. It is also found that the various tubular and spherical "all-pentamer" virus structures identified so far can be represented by closet-packing arrangements of equal morphological units composed of equal regular pentagons on a cylinder and on a sphere.     

Records of a lake's life in time: the sediments

The evidence from analysis of cores from lake sediments is used to identify the influences which, acting through time, have brought about changes in the lakes of the English Lake District. These are: i. climatic changes, recorded mainly in microfossil assemblages ii. soil dynamics on catchments — the natural soil development of an interglacial cycle and its effect on water composition, and iii. perturbations of input resulting from activities of man.The present position of each of 14 lakes in a series of increasing eutrophication is shown to be the result of two processes of modification by man. The first was a significant reduction in volume of the hypolimnion of the shallow lakes, consequent on the accelerated rate of sediment accumulation which followed deforestation and cultivation of catchments in all the lakes — this did not affect the biology of the deep lakes. The second has been the introduction of human and animal wastes into some of the lakes during the last 120 years, which imposed on affected lakes a process of more rapid change which was more intense in the shallow lakes.     

Seasonal time constraints shape life history,physiology and behaviour independently,and decouple a behavioural syndrome in a damselfly

The integration of traits into ‘syndromes' has been suggested as a useful framework to advance insights in trait responses to environmental stressors. Yet, how stressors shape the consistency (‘repeatability') of traits and their covariation at the individual level remains debated. We studied how seasonal time constraints shape trait repeatability and integration of life-history, behavioural and physiological traits along a fast–slow continuum, using the ‘pace-of-life syndrome' as a framework. We manipulated the photoperiod during the larval development of the damselfly Ischnura elegans, generating a time-relaxed early, a control, and a time-constrained late group. The photoperiod treatment did not seem to affect the voltinism of the larvae. As predicted, late-period larvae accelerated development and growth, yet this acceleration was no longer detectable for growth and metabolic rate during the final instar, possibly due to costs of the initial life-history acceleration. This warrants caution when inferring a species' pace-of-life based on a specific developmental stage. The late-period larvae were as predicted more active (only during the later stages of the final instar) and bolder than the control larvae, but not different from the early-period larvae. Most studies on time constraints only compared late and control animals, thereby potentially wrongly concluding adaptive responses to time constraints. Activity, boldness and body mass were repeatable, while growth and metabolic rates were not. Notably, repeatabilities did not change under time constraints. There was no support for an overall trait integration in a pace-of-life syndrome, yet activity and boldness covaried positively as expected. Importantly, this ‘behavioural syndrome' was decoupled in the late-period larvae, which might be adaptive to enhance energy acquisition to fuel the accelerated development rate. Our results suggest that besides the predicted plastic acceleration of life-history, plastic changes in behavioural trait integration may also be an important but overlooked adaptive aspect of responding to time constraints.     

Spatial structures in a reaction-diffusion system--detailed analysis of the "Brusselator"

Continuous dependence of spatially nonuniform concentration profiles for the 'Brussellator" reaction mechanims on the characteristic length of the system is given both for zero flux and fixed boundary conditions. Branches of solutions arising through primary bifurcation form closed curves. Secondary bifurcations giving rise to spatially asymmetric solutions exist for fixed boundary conditions. Results of a stability analysis of individual solutions are discussed. A method of composing complex spatial profiles for higher lengths from elementary solutions for smaller lenghts is suggested and tested in the case of zero flux boundary conditions. Emergence of subsequently more complex stable patterns in dependence on increasing length of the system suggests many similarities to gradual build up of complex morphogenetic patterns.     

Two-dimensional infrared spectroscopy: a promising new method for the time resolution of structures.

Recently, new methods for determining time-evolving structures using infrared analogs of NMR spectroscopy have been introduced that have outstanding potential in structural biology. Already, within the past two years, structures of dipeptides, tripeptides and pentapeptides have been determined on much faster timescales than the conformational dynamics. Also, two-dimensional infrared correlation spectra of some proteins and isotopically edited alanine-rich helices have been examined.