bluuebunny/crossref_metadata_2025 huggingface dataset:
Transition to chaos in a driven dusty plasma
Authors: Sheridan T. E. , Theisen W. L.
Published: January 2010

Dynamical chaos has previously been observed experimentally in a driven dusty plasma with three particles [T. E. Sheridan, Phys. Plasmas 12, 080701 (2005)]. In the present work, the transition to chaos in this system is studied as a function of the amplitude of a periodic driving force for two different driving frequencies fd. It is found that the system follows a quasiperiodic route to chaos. The dusty plasma’s center-of-mass modes are driven by the first harmonic of fd and lock to the driving force for small driving amplitudes. The breathing mode is driven by the second harmonic of fd and shows asymmetric spectral features indicating quasiperiodic dynamics for intermediate driving amplitudes. For large driving forces both the center-of-mass and breathing modes are entrained and a region of low-dimensional chaotic dynamics due to a resonance overlap is observed. In the chaotic regime the correlation dimension and Lyapunov exponent are found to increase with the driving force.
Dynamical heterogeneity in lattice glass models
Authors: Darst Richard K. , Reichman David R. , Biroli Giulio
Published: January 2010

In this paper, we consider in detail the properties of dynamical heterogeneity in lattice glass models (LGMs). LGMs are lattice models whose dynamical rules are based on thermodynamic, as opposed to purely kinetic, considerations. We devise a LGM that is not prone to crystallization and displays properties of a fragile glass-forming liquid. Particle motion in this model tends to be locally anisotropic on intermediate time scales even though the rules governing the model are isotropic. The model demonstrates violations of the Stokes–Einstein relation and the growth of various length scales associated with dynamical heterogeneity. We discuss future avenues of research comparing the predictions of LGMs and kinetically constrained models to atomistic systems.
Wave propagation downstream of a high power helicon in a dipolelike magnetic field
Authors: Prager James , Ziemba Timothy , Winglee Robert , Roberson B. Race
Published: January 2010

The wave propagating downstream of a high power helicon source in a diverging magnetic field was investigated experimentally. The magnetic field of the wave has been measured both axially and radially. The three-dimensional structure of the propagating wave is observed and its wavelength and phase velocity are determined. The measurements are compared to predictions from helicon theory and that of a freely propagating whistler wave. The implications of this work on the helicon as a thruster are also discussed.
Communications: Survival of the fittest: Accelerating convergence in full configuration-interaction quantum Monte Carlo
Authors: Cleland Deidre , Booth George H. , Alavi Ali
Published: January 2010

We provide a very simple adaptation of our recently published quantum Monte Carlo algorithm in full configuration-interaction (Slater determinant) spaces which dramatically reduces the number of walkers required to achieve convergence. A survival criterion is imposed for newly spawned walkers. We define a set of initiator determinants such that progeny of walkers spawned from such determinants onto unoccupied determinants are able to survive, while the progeny of walkers not in this set can survive only if they are spawned onto determinants which are already occupied. The set of initiators is originally defined to be all determinants constructable from a subset of orbitals, in analogy with complete-active spaces. This set is dynamically updated so that if a noninitiator determinant reaches an occupation larger than a preset limit, it becomes an initiator. The new algorithm allows sign-coherent sampling of the FCI space to be achieved with relatively few walkers. Using the N2 molecule as an illustration, we show that rather small initiator spaces and numbers of walkers can converge with submilliHartree accuracy to the known full configuration-interaction (FCI) energy (in the cc-pVDZ basis), in both the equilibrium geometry and the multiconfigurational stretched case. We use the same method to compute the energy with cc-pVTZ and cc-pVQZ basis sets, the latter having an FCI space of over 1015 with very modest computational resources.
Induced allostery in the directed evolution of an enantioselective Baeyer–Villiger monooxygenase
Authors: Wu Sheng , Acevedo Juan Pablo , Reetz Manfred T.
Published: January 2010

The molecular basis of allosteric effects, known to be caused by an effector docking to an enzyme at a site distal from the binding pocket, has been studied recently by applying directed evolution. Here, we utilize laboratory evolution in a different way, namely to induce allostery by introducing appropriate distal mutations that cause domain movements with concomitant reshaping of the binding pocket in the absence of an effector. To test this concept, the thermostable Baeyer–Villiger monooxygenase, phenylacetone monooxygenase (PAMO), was chosen as the enzyme to be employed in asymmetric Baeyer–Villiger reactions of substrates that are not accepted by the wild type. By using the known X-ray structure of PAMO, a decision was made regarding an appropriate site at which saturation mutagenesis is most likely to generate mutants capable of inducing allostery without any effector compound being present. After screening only 400 transformants, a double mutant was discovered that catalyzes the asymmetric oxidative kinetic resolution of a set of structurally different 2-substituted cyclohexanone derivatives as well as the desymmetrization of three different 4-substituted cyclohexanones, all with high enantioselectivity. Molecular dynamics (MD) simulations and covariance maps unveiled the origin of increased substrate scope as being due to allostery. Large domain movements occur that expose and reshape the binding pocket. This type of focused library production, aimed at inducing significant allosteric effects, is a viable alternative to traditional approaches to “designed” directed evolution that address the binding site directly.
Evidence for a recent increase in forest growth
Authors: McMahon Sean M. , Parker Geoffrey G. , Miller Dawn R.
Published: February 2010

Forests and their soils contain the majority of the earth’s terrestrial carbon stocks. Changes in patterns of tree growth can have a huge impact on atmospheric cycles, biogeochemical cycles, climate change, and biodiversity. Recent studies have shown increases in biomass across many forest types. This increase has been attributed to climate change. However, without knowing the disturbance history of a forest, growth could also be caused by normal recovery from unknown disturbances. Using a unique dataset of tree biomass collected over the past 22 years from 55 temperate forest plots with known land-use histories and stand ages ranging from 5 to 250 years, we found that recent biomass accumulation greatly exceeded the expected growth caused by natural recovery. We have also collected over 100 years of local weather measurements and 17 years of on-site atmospheric CO
2
measurements that show consistent increases in line with globally observed climate-change patterns. Combined, these observations show that changes in temperature and CO
2
that have been observed worldwide can fundamentally alter the rate of critical natural processes, which is predicted by biogeochemical models. Identifying this rate change is important to research on the current state of carbon stocks and the fluxes that influence how carbon moves between storage and the atmosphere. These results signal a pressing need to better understand the changes in growth rates in forest systems, which influence current and future states of the atmosphere and biosphere.
Encoding properties of haltere neurons enable motion feature detection in a biological gyroscope
Authors: Fox Jessica L. , Fairhall Adrienne L. , Daniel Thomas L.
Published: February 2010

The halteres of dipteran insects are essential sensory organs for flight control. They are believed to detect Coriolis and other inertial forces associated with body rotation during flight. Flies use this information for rapid flight control. We show that the primary afferent neurons of the haltere’s mechanoreceptors respond selectively with high temporal precision to multiple stimulus features. Although we are able to identify many stimulus features contributing to the response using principal component analysis, predictive models using only two features, common across the cell population, capture most of the cells’ encoding activity. However, different sensitivity to these two features permits each cell to respond to sinusoidal stimuli with a different preferred phase. This feature similarity, combined with diverse phase encoding, allows the haltere to transmit information at a high rate about numerous inertial forces, including Coriolis forces.
STAT5-glucocorticoid receptor interaction and MTF-1 regulate the expression of ZnT2 (Slc30a2) in pancreatic acinar cells
Authors: Guo Liang , Lichten Louis A. , Ryu Moon-Suhn , Liuzzi Juan P. , Wang Fudi , Cousins Robert J.
Published: January 2010

The exocrine pancreas plays an important role in endogenous zinc loss by regulating excretion into the intestinal tract and hence influences the dietary zinc requirement. The present experiments show that the zinc transporter ZnT2 (Slc30a2) is localized to the zymogen granules and that dietary zinc restriction in mice decreased the zinc concentration of zymogen granules and ZnT2 expression. Excess zinc given orally increased ZnT2 expression and was associated with increased pancreatic zinc accumulation. Rat AR42J acinar cells when induced into a secretory phenotype, using the glucocorticoid analog dexamethasone (DEX), exhibited increased ZnT2 expression and labile zinc as measured with a fluorophore. DEX administrated to mice also induced ZnT2 expression that accompanied a reduction of the pancreatic zinc content. ZnT2 promoter analyses identified elements required for responsiveness to zinc and DEX. Zinc regulation was traced to a MRE located downstream from the ZnT2 transcription start site. Responsiveness to DEX is produced by two upstream STAT5 binding sites that require the glucocorticoid receptor for activation. ZnT2 knockdown in the AR42J cells using siRNA resulted in increased cytoplasmic zinc and decreased zymogen granule zinc that further demonstrated that ZnT2 may mediate the sequestration of zinc into zymogen granules. We conclude, based upon experiments with intact mice and pancreatic acinar cells in culture, that ZnT2 participates in zinc transport into pancreatic zymogen granules through a glucocorticoid pathway requiring glucocorticoid receptor and STAT5, and zinc-regulated signaling pathways requiring MTF-1. The ZnT2 transporter appears to function in a physiologically responsive manner involving entero-pancreatic zinc trafficking.
Functional organization of motor cortex of adult macaque monkeys is altered by sensory loss in infancy
Authors: Qi Hui-Xin , Jain Neeraj , Collins Christine E. , Lyon David C. , Kaas Jon H.
Published: January 2010

When somatosensory cortex (S1) is deprived of some of its inputs after section of ascending afferents in the dorsal columns of the spinal cord, it reorganizes to overrepresent the surviving inputs. As somatosensory cortex provides guiding sensory information to motor cortex, such sensory loss and representational reorganization could affect the development of the motor map in primary motor cortex (M1), especially if the sensory loss occurs early in development. To address this possibility, the dorsal columns of the spinal cord were sectioned between cervical levels (C3–5) 3–12 days after birth in five macaque monkeys. After 3–5 years of maturation (young adults), we determined how movements were represented in M1 contralateral to the lesion by using microelectrodes to electrically stimulate sites in M1 to evoke movements. Although the details of the motor maps in these five monkeys varied, the forelimb motor maps were abnormal. The representations of digit movements were reduced and abnormally arranged. Current levels for evoking movements from the forelimb region of M1 were in the normal range, but the lowest mean stimulation thresholds were for wrist or elbow instead of digit movements. Incomplete lesions and bilateral lesions produced fewer abnormalities. The results suggest that the development of normal motor cortex maps in M1 depends on sensory feedback from somatosensory maps.
Postvocalic (r) in urban Indian English
Authors: Chand Vineeta
Published: January 2010

Native varieties of World Englishes can shed light on competing local and international language ideologies and alignments with different standards, while quantitative variationist methods permit dialect internal analysis of structural variation without direct reference to external standards, by focusing on internal linguistic and social constraints. Contributing to these endeavors, this study examines variation in postvocalic (r)-deletion in Indian English (IndE), uncovering rhotic patterns which are significantly influenced by, and illuminate, distinct urban Indian sociolinguistic alignments. The results also demonstrate that IndE is diverging from both its British colonially influenced past, and from modern internationally prestigious English varieties, through real and apparent time analysis. This analysis focuses on the larger sociolinguistic milieu of IndE emergence and evolution, offering a nuanced response to superficial and oftentimes categorical IndE grammars. Further, studying native speakers offers a counterpoint to L1 contact explanations for IndE stabilization and evolution in the postcolonial context.
Preterite be
Authors: Richards Hazel
Published: January 2010

In this paper I analyse variation in the use of past tense be in data from Morley, a suburb of Leeds, in the North of England, using both real-time and apparent-time data. Rather than concentrating on the traditional aspects of this variable, namely alternation between was and were, I identify four phonetic variants of the past tense be system. I propose that the community under consideration are adopting intermediate variants that, both in terms of perception and production, lie between the standard (British) realisations of was [wɒz] and were [wɜː]. A reallocation process has occurred between these two intermediate forms, along the lines of polarity. The inclusion of the intermediate forms of past tense be enables us to perceive previously unobserved patterns of variation with regard to this variable.
How much does parental language behaviour reflect their language beliefs in language maintenance?
Authors: Yu Shanjiang
Published: January 2010

It has been widely accepted that parental language beliefs play a crucial role in language maintenance. Studies show that Chinese immigrants are not exempted from language shift although they are frequently reported cherishing their language as an important part of their culture. This paper attempts to find out how parental language beliefs reflect their daily language behaviour. Eight recent Chinese migrant families had 60 minutes of conversation recorded each month for one calendar year. Their language use has been analyzed and compared with the information gathered from a home language use questionnaire. Results show that there is a substantial gap between parental language beliefs and their actual language behaviour. Although the parents state they strongly support mother tongue maintenance, within 28 months, the use of mother tongue had dropped significantly and there is very little evidence showing much effort from the parents to prevent this from happening. This could be either because they want their children to keep their first language but do not know how to do this, or, their language beliefs are different from their behaviour. This should raise methodological issues regarding how to interpret parental language beliefs properly in the research area.
Stimulant-Induced Trichotillomania
Authors: Hamalian Gareen , Citrome Leslie
Published: January 2010

A prior report described the presentation of cocaine-induced trichotillomania, which resolved with the cessation of cocaine use. Here the authors describe the case of stimulant-induced trichotillomania that resolved with the discontinuation of stimulants and initiation of olanzapine. To the authors’ knowledge this is the first reported adult case of stimulant-induced trichotillomania. The case is of a patient with a previous diagnosis of attention deficit hyperactivity disorder whose symptoms of trichotillomania coincide with abuse of amphetamine and with the resolution of symptoms in the absence of amphetamine use. Given the increase in exposure of prescription amphetamines among adults, further study into the association between stimulants and adverse events such as trichotillomania is needed.
Alcohol Consumption Patterns: Gay and Lesbian Urban Ethnic Minority Members
Authors: Chappin Sean R. , Tross Susan , Sanchez John-Paul , Dermatis Helen , Galanter Marc
Published: January 2010

The aim of this study was to assess patterns of alcohol consumption and alcohol related problems in a sample of lesbian and gay NYC residents. There were no differences between lesbian (n = 93) and gay (n = 90) subgroups with regard to alcohol use and health related variables. The average number of drinking days reported for the previous 30 day period was 6.87 (SD 7.0) and 16% of the sample reported consuming more than 4 drinks per drinking day. Age, educational level, and feelings of excessive restlessness were associated with alcohol use. Although there have been reports of increased rates of alcohol use and alcohol related problems in the lesbian and gay population, this is not reflected in this sample.
Par-4: A New Activator of Myosin Phosphatase
Authors: Vetterkind Susanne , Lee Eunhee , Sundberg Eric , Poythress Ransom H. , Tao Terence C. , Preuss Ute , Morgan Kathleen G.
Published: February 2010

Myosin phosphatase (MP) is a key regulator of myosin light chain (LC20) phosphorylation, a process essential for motility, apoptosis, and smooth muscle contractility. Although MP inhibition is well studied, little is known about MP activation. We have recently demonstrated that prostate apoptosis response (Par)-4 modulates vascular smooth muscle contractility. Here, we test the hypothesis that Par-4 regulates MP activity directly. We show, by proximity ligation assays, surface plasmon resonance and coimmunoprecipitation, that Par-4 interacts with the targeting subunit of MP, MYPT1. Binding is mediated by the leucine zippers of MYPT1 and Par-4 and reduced by Par-4 phosphorylation. Overexpression of Par-4 leads to increased phosphatase activity of immunoprecipitated MP, whereas small interfering RNA knockdown of endogenous Par-4 significantly decreases MP activity and increases MYPT1 phosphorylation. LC20 phosphorylation assays demonstrate that overexpression of Par-4 reduces LC20 phosphorylation. In contrast, a phosphorylation site mutant, but not wild-type Par-4, interferes with zipper-interacting protein kinase (ZIPK)-mediated MP inhibition. We conclude from our results Par-4 operates through a “padlock” model in which binding of Par-4 to MYPT1 activates MP by blocking access to the inhibitory phosphorylation sites, and inhibitory phosphorylation of MYPT1 by ZIPK requires “unlocking” of Par-4 by phosphorylation and displacement of Par-4 from the MP complex.
The Na+/H+Exchanger NHE6 in the Endosomal Recycling System Is Involved in the Development of Apical Bile Canalicular Surface Domains in HepG2 Cells
Authors: Ohgaki Ryuichi , Matsushita Masafumi , Kanazawa Hiroshi , Ogihara Satoshi , Hoekstra Dick , van IJzendoorn Sven C.D.
Published: February 2010

Polarized epithelial cells develop and maintain distinct apical and basolateral surface domains despite a continuous flux of membranes between these domains. The Na+/H+exchanger NHE6 localizes to endosomes but its function is unknown. Here, we demonstrate that polarized hepatoma HepG2 cells express an NHE6.1 variant that localizes to recycling endosomes and colocalizes with transcytosing bulk membrane lipids. NHE6.1 knockdown or overexpression decreases or increases recycling endosome pH, respectively, and inhibits the maintenance of apical, bile canalicular plasma membranes and, concomitantly, apical lumens. NHE6.1 knockdown or overexpression has little effect on the de novo biogenesis of apical surface domains. NHE6.1 knockdown does not inhibit basolateral-to-apical transcytosis of bulk membrane lipids, but it does promote their progressive loss from the apical surface, leaving cells unable to efficiently retain bulk membrane and bile canalicular proteins at the apical surface. The data suggest that a limited range of endosome pH mediated by NHE6.1 is important for securing the polarized distribution of membrane lipids at the apical surface and maintenance of apical bile canaliculi in HepG2 cells and hence cell polarity. This study underscores the emerging role of the endosomal recycling system in apical surface development and identifies NHE6 as a novel regulatory protein in this process.
Easy retrieval of single amino-acid polymorphisms and phenotype information using SwissVar
Authors: Mottaz Anaïs , David Fabrice P.A. , Veuthey Anne-Lise , Yip Yum L.
Published: January 2010

Summary: The SwissVar portal provides access to a comprehensive collection of single amino acid polymorphisms and diseases in the UniProtKB/Swiss-Prot database via a unique search engine. In particular, it gives direct access to the newly improved Swiss-Prot variant pages. The key strength of this portal is that it provides a possibility to query for similar diseases, as well as the underlying protein products and the molecular details of each variant. In the context of the recently proposed molecular view on diseases, the SwissVar portal should be in a unique position to provide valuable information for researchers and to advance research in this area.

Availability: The SwissVar portal is available at www.expasy.org/swissvar

Contact:  anais.mottaz@isb-sib.ch; lina.yip@isb-sib.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
A Selection Model for Panel Data: The Prospects of Green Party Support
Authors: Spiess Martin , Kroh Martin
Published: January 2010

Although sample selection bias is a frequent problem of applied research, there has been no generalization of sample selection models with binary dependent variables of interest to data with temporal error correlations. We suggest a generalized estimating equation approach to panel data selection models, considering binary responses in both equations. We demonstrate the utility of this model by a simulation study and by analyzing highly unbalanced annual panel data taken from the German Socio-Economic Panel Study covering two decades of Green party support.
Landscape evolutionary genomics
Authors: Lowry David B.
Published: January 2010

Tremendous advances in genetic and genomic techniques have resulted in the capacity to identify genes involved in adaptive evolution across numerous biological systems. One of the next major steps in evolutionary biology will be to determine how landscape-level geographical and environmental features are involved in the distribution of this functional adaptive genetic variation. Here, I outline how an emerging synthesis of multiple disciplines has and will continue to facilitate a deeper understanding of the ways in which heterogeneity of the natural landscapes mould the genomes of organisms.
Sexual dimorphism for water balance mechanisms in montane populations ofDrosophila kikkawai
Authors: Parkash Ravi , Sharma Vineeta , Kalra Bhawna
Published: January 2010

Conservation of water is critical to the ecological success ofDrosophilaspecies living in the drier montane localities of the Western Himalayas. We observed clinal variation in desiccation resistance for both sexes ofDrosophila kikkawaifrom an altitudinal transect (512–2226 m above sea level). Since more than 90 per cent of body water is lost through cuticular transpiration, the target of selection may be cuticular lipids or cuticular melanization. We tested whether melanic females and non-melanic males ofD. kikkawaihave similar mechanisms of desiccation resistance. There is clinal variation in the amount of cuticular lipids per fly in males, but not in females. By contrast, for females, elevational increase in melanization is positively correlated with desiccation resistance and negatively with cuticular water loss, but there is no variation in the amount of cuticular lipids. Thus, sexual dimorphism for the mechanism of desiccation resistance inD. kikkawaimatches the water proofing role of body melanization as well as cuticular lipids.
Gradients of strain and strain rate in the hollow muscular organs of soft-bodied animals
Authors: Thompson Joseph T. , Taylor Kari R. , Gentile Christopher
Published: January 2010

The cylindrical shape of soft-bodied invertebrates is well suited to functions in skeletal support and locomotion, but may result in a previously unrecognized cost—large non-uniformities in muscle strain and strain rate among the circular muscle fibres of the body wall. We investigated such gradients of strain and strain rate in the mantle of eight long-finned squidDoryteuthis pealeiiand two oval squidSepioteuthis lessoniana. Transmural gradients of circumferential strain were present during all jets (n= 312); i.e. for a given change in the circumference of the outer surface of the mantle, the inner surface experienced a greater proportional change. The magnitude of the difference increased with the amplitude of the mantle movement, with circular muscle fibres at the inner surface of the mantle experiencing a total range of strains up to 1.45 times greater than fibres at the outer surface during vigorous jets. Differences in strain rate between the circular fibres near the inner versus the outer surface of the mantle were also present in all jets, with the greatest differences occurring during vigorous jetting. The transmural gradients of circumferential strain and strain rate we describe probably apply not only to squids and other coleoid cephalopods, but also to diverse soft-bodied invertebrates with hollow cylindrical or conical bodies and muscular organs.
Spatially mismatched trophic dynamics: cyclically outbreaking geometrids and their larval parasitoids
Authors: Hagen Snorre B. , Jepsen Jane U. , Schott Tino , Ims Rolf A.
Published: January 2010

For trophic interactions to generate population cycles and complex spatio-temporal patterns, like travelling waves, the spatial dynamics must be matched across trophic levels. Here, we propose a spatial methodological approach for detecting such spatial match–mismatch and apply it to geometrid moths and their larval parasitoids in northern Norway, where outbreak cycles and travelling waves occur. We found clear evidence of spatial mismatch, suggesting that the spatially patterned moth cycles in this system are probably ruled by trophic interactions involving other agents than larval parasitoids.
Links between global taxonomic diversity, ecological diversity and the expansion of vertebrates on land
Authors: Sahney Sarda , Benton Michael J. , Ferry Paul A.
Published: January 2010

Tetrapod biodiversity today is great; over the past 400 Myr since vertebrates moved onto land, global tetrapod diversity has risen exponentially, punctuated by losses during major extinctions. There are links between the total global diversity of tetrapods and the diversity of their ecological roles, yet no one fully understands the interplay of these two aspects of biodiversity and a numerical analysis of this relationship has not so far been undertaken. Here we show that the global taxonomic and ecological diversity of tetrapods are closely linked. Throughout geological time, patterns of global diversity of tetrapod families show 97 per cent correlation with ecological modes. Global taxonomic and ecological diversity of this group correlates closely with the dominant classes of tetrapods (amphibians in the Palaeozoic, reptiles in the Mesozoic, birds and mammals in the Cenozoic). These groups have driven ecological diversity by expansion and contraction of occupied ecospace, rather than by direct competition within existing ecospace and each group has used ecospace at a greater rate than their predecessors.
Selective prefrontal cortex responses to joint attention in early infancy
Authors: Grossmann Tobias , Johnson Mark H.
Published: January 2010

The process by which two people share attention towards the same object or event is called joint attention. Joint attention and the underlying triadic representations between self, other person and object are thought to be unique to humans, supporting teaching, cooperation and language learning. Despite the progress that has been made in understanding the behavioural importance of joint attention during early social development, almost nothing is known about the brain substrate that supports joint attention in the developing infant. We examined responses in five-month-old infants' prefrontal cortex during triadic social interactions using near-infrared spectroscopy. The results demonstrate that, even by the age of five months, infants are sensitive to triadic interactions and, like adults, they recruit a specific brain region localized in left dorsal prefrontal cortex when engaged in joint attention with another person. This suggests that the human infant is neurobiologically prepared for sharing attention with other humans, which may provide the basis for a wide variety of uniquely human social and cultural learning processes.
Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian–Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates
Authors: Cox Murray P. , Karafet Tatiana M. , Lansing J. Stephen , Sudoyo Herawati , Hammer Michael F.
Published: January 2010

The geographical region between mainland Asia and New Guinea is characterized by numerous small islands with isolated human populations. Phenotypically, groups in the west are similar to their neighbours in mainland Southeast Asia, eastern groups near New Guinea are similar to Melanesians, and intervening populations are intermediate in appearance. A long-standing question is whether this pattern primarily reflects mixing between groups with distinct origins or whether natural selection has shaped this range of variation by acting differentially on populations across the region. To address this question, we genotyped a set of 37 single nucleotide polymorphisms that are evolutionarily independent, putatively neutral and highly informative for Asian–Melanesian ancestry in 1430 individuals from 60 populations spanning mainland Asia to Melanesia. Admixture analysis reveals a sharp transition from Asian to Melanesian genetic variants over a narrow geographical region in eastern Indonesia. Interestingly, this admixture cline roughly corresponds to the human phenotypic boundary noted by Alfred Russell Wallace in 1869. We conclude that this phenotypic gradient probably reflects mixing of two long-separated ancestral source populations—one descended from the initial Melanesian-like inhabitants of the region, and the other related to Asian groups that immigrated during the Paleolithic and/or with the spread of agriculture. A higher frequency of Asian X-linked markers relative to autosomal markers throughout the transition zone suggests that the admixture process was sex-biased, either favouring a westward expansion of patrilocal Melanesian groups or an eastward expansion of matrilocal Asian immigrants. The matrilocal marriage practices that dominated early Austronesian societies may be one factor contributing to this observed sex bias in admixture rates.
The gastrointestinal tract as a nutrient-balancing organ
Authors: Clissold Fiona J. , Tedder Benjamin J. , Conigrave Arthur D. , Simpson Stephen J.
Published: February 2010

Failure to provision tissues with an appropriate balance of nutrients engenders fitness costs. Maintaining nutrient balance can be achieved by adjusting the selection and consumption of foods, but this may not be possible when the nutritional environment is limiting. Under such circumstances, rebalancing of an imbalanced nutrient intake requires post-ingestive mechanisms. The first stage at which such post-ingestive rebalancing might occur is within the gastrointestinal tract (GIT), by differential release of digestive enzymes—releasing less of those enzymes for nutrients present in excess while maintaining or boosting levels of enzymes for nutrients in deficit. Here, we use an insect herbivore, the locust, to show for the first time that such compensatory responses occur within the GIT. Furthermore, we show that differential release of proteases and carbohydrases in response to nutritional state translate into differential extraction of macronutrients from host plants. The prevailing view is that physiological and structural plasticity in the GIT serves to maximize the rate of nutrient gain in relation to costs of maintaining the GIT; our findings show that GIT plasticity is integral to the maintenance of nutrient balance.
Birds learn to use distastefulness as a signal of toxicity
Authors: Skelhorn John , Rowe Candy
Published: February 2010

Aposematic prey advertise their toxicity using conspicuous visual signals that predators quickly learn to avoid. However, it is advantageous for predators not to simply avoid toxic prey, but to learn about the amount of toxin that prey contain, and include them in their diets when the nutritional gains are high relative to the costs of ingesting the toxin. Therefore, when foraging on a defended prey population where individuals vary in their toxin concentration, predators should learn to use cues which distinguish prey with different levels of toxicity in order to include less defended individuals in their diets. In this experiment, we found that European starlings (
Sturnus vulgaris
) could learn to use a bitter taste to predict the amount of toxin that individual prey contained, and use that information to preferentially ingest less toxic prey to maximize their nutrient intake relative to the amount of toxin ingested. Our results suggest that bitter tastes could evolve as reliable signals of toxicity, and can help to explain why many toxins taste bitter. They also highlight the need to develop new mathematical simulations of the evolution of prey defences which incorporate the adaptive decision-making processes underlying nutrient and toxin management.
Origin of ultradian pulsatility in the hypothalamic–pituitary–adrenal axis
Authors: Walker Jamie J. , Terry John R. , Lightman Stafford L.
Published: February 2010

The hypothalamic–pituitary–adrenal (HPA) axis is a neuroendocrine system that regulates the circulating levels of vital glucocorticoid hormones. The activity of the HPA axis is characterized not only by a classic circadian rhythm, but also by an ultradian pattern of discrete pulsatile release of glucocorticoids. A number of psychiatric and metabolic diseases are associated with changes in glucocorticoid pulsatility, and it is now clear that glucocorticoid responsive genes respond to these rapid fluctuations in a biologically meaningful way. Theoretical modelling has enabled us to identify and explore potential mechanisms underlying the ultradian activity in this axis, which to date have not been identified successfully. We demonstrate that the combination of delay with feed-forward and feedback loops in the pituitary–adrenal system is sufficient to give rise to ultradian pulsatility in the absence of an ultradian source from a supra-pituitary site. Moreover, our model enables us to predict the different patterns of glucocorticoid release mediated by changes in hypophysial-portal corticotrophin-releasing hormone levels, with results that parallel our experimentalin vivodata.
Resolving phylogenetic incongruence to articulate homology and phenotypic evolution: a case study from Nematoda
Authors: Ragsdale Erik J. , Baldwin James G.
Published: January 2010

Modern morphology-based systematics, including questions of incongruence with molecular data, emphasizes analysis over similarity criteria to assess homology. Yet detailed examination of a few key characters, using new tools and processes such as computerized, three-dimensional ultrastructural reconstruction of cell complexes, can resolve apparent incongruence by re-examining primary homologies. In nematodes of Tylenchomorpha, a parasitic feeding phenotype is thus reconciled with immediate free-living outgroups. Closer inspection of morphology reveals phenotypes congruent with molecular-based phylogeny and points to a new locus of homology in mouthparts. In nematode models, the study of individually homologous cells reveals a conserved modality of evolution among dissimilar feeding apparati adapted to divergent lifestyles. Conservatism of cellular components, consistent with that of other body systems, allows meaningful comparative morphology in difficult groups of microscopic organisms. The advent of phylogenomics is synergistic with morphology in systematics, providing an honest test of homology in the evolution of phenotype.
Reproductive compensation in broad-nosed pipefish females
Authors: Goncalves Ines Braga , Mobley Kenyon B. , Ahnesjö Ingrid , Sagebakken Gry , Jones Adam G. , Kvarnemo Charlotta
Published: January 2010

The differential allocation hypothesis assumes that animals should weigh costs and benefits of investing into reproduction with a current mate against the expected quality of future mates, and predicts that they should invest more into reproduction when pairing with a high-quality mate. In the broad-nosed pipefish (
Syngnathus typhle
), males care for the embryos in a brood pouch and females compete for access to male mating partners. Both sexes prefer mating with large partners. In the present study, we show that the same female provides both large and small mating partners with eggs of similar size, weight and lipid content when mated to two males in succession. Importantly, however, eggs provided to small males (less preferred) had higher egg protein content (11% more) than those provided to large males (preferred). Thus, contrary to the differential allocation hypothesis, eggs did not contain more resources when females mated with a larger male. Instead, the pattern observed in our results is consistent with a compensatory reproductive strategy.
Actin Reorganization Underlies Phototropin-Dependent Positioning of Nuclei in Arabidopsis Leaf Cells
Authors: Iwabuchi Kosei , Minamino Ryoko , Takagi Shingo
Published: January 2010

In epidermal and mesophyll cells of Arabidopsis (Arabidopsis thaliana) leaves, nuclei become relocated in response to strong blue light. We previously reported that nuclear positions both in darkness and in strong blue light are regulated by the blue light receptor phototropin2 in mesophyll cells. Here, we investigate the involvement of phototropin and the actin cytoskeleton in nuclear positioning in epidermal cells. Analysis of geometrical parameters revealed that, in darkness, nuclei were distributed near the center of the cell, adjacent to the inner periclinal wall, independent of cell shape. Dividing the anticlinal wall into concave, convex, and intermediate regions indicated that, in strong blue light, nuclei became relocated preferably to a concave region of the anticlinal wall, nearest the center of the cell. Mutant analyses verified that light-dependent nuclear positioning was regulated by phototropin2, while dark positioning of nuclei was independent of phototropin. Nuclear movement was inhibited by an actin-depolymerizing reagent, latrunculin B, but not by a microtubule-disrupting reagent, propyzamide. Imaging actin organization by immunofluorescence microscopy revealed that thick actin bundles, periclinally arranged parallel to the longest axis of the epidermal cell, were associated with the nucleus in darkness, whereas under strong blue light, the actin bundles, especially in the vicinity of the nucleus, became arranged close to the anticlinal walls. Light-dependent changes in the actin organization were clear in phot1 mutant but not in phot2 and phot1phot2 mutants. We propose that, in Arabidopsis, blue-light-dependent nuclear positioning is regulated by phototropin2-dependent reorganization of the actin cytoskeleton.
Characterization ofdrr1, an Alkamide-Resistant Mutant of Arabidopsis, Reveals an Important Role for Small Lipid Amides in Lateral Root Development and Plant Senescence
Authors: Morquecho-Contreras Alina , Méndez-Bravo Alfonso , Pelagio-Flores Ramón , Raya-GonzÁlez Javier , Ortíz-Castro Randy , López-Bucio José
Published: January 2010

Alkamides belong to a class of small lipid signals of wide distribution in plants, which are structurally related to the bacterial quorum-sensing signals N-acyl-l-homoserine lactones. Arabidopsis (Arabidopsis thaliana) seedlings display a number of root developmental responses to alkamides, including primary root growth inhibition and greater formation of lateral roots. To gain insight into the regulatory mechanisms by which these compounds alter plant development, we performed a mutant screen for identifying Arabidopsis mutants that fail to inhibit primary root growth when grown under a high concentration of N-isobutyl decanamide. A recessive N-isobutyl decanamide-resistant mutant (decanamide resistant root [drr1]) was isolated because of its continued primary root growth and reduced lateral root formation in response to this alkamide. Detailed characterization of lateral root primordia development in the wild type and drr1 mutants revealed that DRR1 is required at an early stage of pericycle cell activation to form lateral root primordia in response to both N-isobutyl decanamide and N-decanoyl-l-homoserine lactone, a highly active bacterial quorum-sensing signal. Exogenously supplied auxin similarly inhibited primary root growth and promoted lateral root formation in wild-type and drr1 seedlings, suggesting that alkamides and auxin act by different mechanisms to alter root system architecture. When grown both in vitro and in soil, drr1 mutants showed dramatically increased longevity and reduced hormone- and age-dependent senescence, which were related to reduced lateral root formation when exposed to stimulatory concentrations of jasmonic acid. Taken together, our results provide genetic evidence indicating that alkamides and N-acyl-l-homoserine lactones can be perceived by plants to modulate root architecture and senescence-related processes possibly by interacting with jasmonic acid signaling.
Stable‐isotope comparisons between embryos and mothers of a placentatrophic shark species
Authors: McMeans B. C. , Olin J. A. , Benz G. W.
Published: January 2010

Stable nitrogen (δ15N) and carbon (δ13C) isotopes of Atlantic sharpnose shark Rhizoprionodon terraenovae embryos and mothers were analysed. Embryos were generally enriched in 15N in all studied tissue relative to their mothers' tissue, with mean differences between mother and embryo δ15N (i.e. Δδ15N) being 1·4‰ for muscle, 1·7‰ for liver and 1·1‰ for cartilage. Embryo muscle and liver were enriched in 13C (both Δδ13C means = 1·5‰) and embryo cartilage was depleted (Δδ13C mean = −1·01‰) relative to corresponding maternal tissues. While differences in δ15N and δ13C between mothers and their embryos were significant, muscle δ15N values indicated embryos to be within the range of values expected if they occupied a similar trophic position as their respective mothers. Positive linear relationships existed between embryo total length (LT) and Δδ15N for muscle and liver and embryo LT and Δδ13C for muscle, with those associations possibly resulting from physiological differences between smaller and larger embryos or differences associated with the known embryonic nutrition shift (yolk feeding to placental feeding) that occurs during the gestation of this placentatrophic species. Together these results suggest that at birth, the δ15N and δ13C values of R. terraenovae are likely higher than somewhat older neonates whose postpartum feeding habits have restructured their isotope profiles to reflect their postembryonic diet.
Diet and reproduction in the Australian butterfly ray Gymnura australis from northern and north‐eastern Australia
Authors: Jacobsen I. P. , Johnson J. W. , Bennett M. B.
Published: January 2010

The diet of Gymnura australis was dominated by teleosts (99·8% index of relative importance). A wide‐ranging species, females matured at 446 mm disc width (WD), had a single functional ovary and two functional uteri. Males matured at 377 mm WD and had a single functional testis.
Food partitioning and spatial subsidy in shelter‐limited fishes inhabiting patchy reefs of Patagonia
Authors: Galván D. E. , Botto F. , Parma A. M. , Bandieri L. , Mohamed N. , Iribarne O. O.
Published: January 2010

The diets of the most conspicuous reef‐fish species from northern Patagonia, the carnivorous speciesPseudopercis semifasciata,Acanthistius patachonicus,Pinguipes brasilianusandSebastes oculatuswere studied.Pinguipes brasilianushad the narrowest diet and most specialized feeding strategy, preying mostly on reef‐dwelling organisms such as sea urchins, limpets, bivalves, crabs and polychaetes. The diet ofA. patachonicuswas characterized by the presence of reef and soft‐bottom benthic organisms, mainly polychaetes, crabs and fishes.Pseudopercis semifasciatashowed the broadest spectrum of prey items, preying upon reef, soft‐bottom and transient organism (mainly fishes, cephalopods and crabs). AllS. oculatusguts were empty, but stable‐isotope analyses suggested that this species consumed small fishes and crabs. In general,P. brasilianusdepended on local prey populations and ate different reef‐dwelling prey than the other species.Pseudopercis semifasciata,A. patachonicusand probablyS. oculatus, however, had overlapping trophic niches and consumed resources from adjacent environments. The latter probably reduces the importance of food as a limiting resource for these reef‐fish populations, facilitating their coexistence in spite of their high trophic overlap.
Older triploid fish retain impaired reproductive endocrinology in the European sea bass Dicentrarchus labrax
Authors: Felip A. , Carrillo M. , Zanuy S.
Published: January 2010

This paper reports on an evaluation of growth, gonadal development and reproductive endocrinology of older triploid (3n) European sea bass Dicentrarchus labrax in comparison with their diploid (2n) counterparts throughout their fifth and seventh annual cycle of life. While older triploids retained impaired reproductive endocrinology, a sexually related dimorphic growth was observed with 3n females attaining the largest sizes. Comparisons of some body indexes showed that 3n females had a significantly lower hepato‐somatic index (IH) than 2n females but a significantly higher viscero‐somatic index (IF). In contrast, both male and female triploids showed significantly lower gonado‐somatic index (IG) than diploids. Accordingly, diploids produced mature gametes but triploids did not, demonstrating that despite the longer time given to triploids for gonadal development, they could not reproduce. Furthermore, older triploids had lower levels of plasma sex steroids (testosterone, T; 11‐ketotestosterone, 11‐KT and oestradiol‐17β, E2) and luteinizing hormone (LH) than their 2n counterparts with 3n females showing drastic effects of triploidization on their reproductive endocrinology. Vitellogenin (VTG) was undetectable in 3n females. Gonadal content of steroid hormones and Sparus aurata‐type gonadotropin‐releasing hormone (sbGnRH) in the brain and pituitary were also lower in triploids compared with diploids. These results suggest that older 3n D. labrax retain functional sterility in both sexes, and 3n females might reach larger sizes than 3n males and their 2n counterparts in this species.