bluuebunny/crossref_metadata_2025 huggingface dataset:
Kierkegaard on Music
Authors: Croxall T.H.
Published: January 2007

The Essay by Sören Kierkegaard the Dane (1813-55) on music is, to my mind, a notable piece of work. Mr. Turner shows irritation at it, but he clearly has not understood it. Kierkegaard writes in Danish, which few read; he is translated badly into German; and far from excellently, as regards this Essay, into American; and his philosophy is cast in the Hegelian mode, one of the most difficult in the world. He is fluent, even prolix; and musical interpretation, as Professor Dent says, is a dangerous amusement to a fluent pen. Yet Kierkegaard avoids all pitfalls, and if we approach him sympathetically he can teach us much. He is seeking in Either/Or, to portray the æsthetic life so he impersonates an “æsthete” (the pseudonym “A”) and purposely makes him extravagantly exuberant. We must allow for this, or we may be put off.
Morley's Consort Lessons of 1599
Authors: Dart R. Thurston
Published: January 2007

A certain amount, though by no means enough, has been written on Morley the composer and teacher. The work I want to discuss to-day illustrates two other aspects of his wide genius which so far have been little studied—Morley as editor and arranger, and Morley as innovator.
The Recorder and its Music
Authors: Hunt Edgar
Published: January 2007

When I speak of the recorder as a musical instrument, I do so knowing that you cannot fail to have heard the instrument at some time, as it is now once again an integral part of our musical life.
Orphans and Ladies: The Venetian Conservatoires (1680–1790)
Authors: Arnold Denis
Published: January 2007

The Peacefulness and longevity of the Venetian Republic prove that it had solved one of its greatest problems—that of poverty. Not that it was rid of its poor even in times of prosperity: but at least they were cared for by a wealth of charitable organisations, and that desperation which leads to civil insurrection never gained a hold. The chronically sick, the girls having no dowry, the orphans and the beggars were each helped by various confraternities which were supported by the more fortunate. Some of these were specifically for members of a trade who had fallen on difficult times, like that founded in 1340 by a German cobbler called Henry, who left money to help infirm and needy shoemakers. Others, looked after ‘widows without male issue’; and old people attracted a great deal of money to provide homes for them.
The Concertos of Johann Adolf Hasse
Authors: Drummond Pippa
Published: January 2007

The name of Hasse is customarily associated with vocal rather than instrumental music. Rightly so, for the operas and sacred vocal works stand at the centre of his activity as a composer. It was the vocal music that established Hasse's international reputation and elicited such admiration from eighteenth-century critics. The same bias prevails in modern literature. Of the various studies devoted to Hasse since 1900 only one deals at length with any aspect of the instrumental music—and, significantly, it treats the overtures to dramatic works. The instrumental music proper remains largely unexplored. One might assume that instrumental music was of little importance for Hasse. But this is not the case. He wrote, for example, at least 60 concertos, a fair number even by the prodigious standards of the eighteenth century.
Estimation across Data Sets: Two-Stage Auxiliary Instrumental Variables Estimation (2SAIV)
Authors: Franklin Charles H.
Published: January 2007

Theories demand much of data, often more than a single data collection can provide. For example, many important research questions are set in the past and must rely on data collected at that time and for other purposes. As a result, we often find that the data lack crucial variables. Another common problem arises when we wish to estimate the relationship between variables that are measured in different data sets. A variation of this occurs with a split half sample design in which one or more important variables appear on the “wrong” half. Finally, we may need panel data but have only cross sections available. In each of these cases our ability to estimate the theoretically determined equation is limited by the data that are available.
Estimation of Models with Variable Coefficients
Authors: Jackson John E.
Published: January 2007

The ordinary least squares (OLS) estimator gives biased coefficient estimates if coefficients are not constant for all cases but vary systematically with the explanatory variables. This article discusses several different ways to estimate models with systematically and randomly varying coefficients using estimated generalized least squares and maximum likelihood procedures. A Monte Carlo simulation of the different methods is presented to illustrate their use and to contrast their results to the biased results obtained with ordinary least squares. Several applications of the methods are discussed and one is presented in detail. The conclusion is that, in situations with variables coefficients, these methods offer relatively easy means for overcoming the problems.
The Methodology of Cointegration
Authors: Beck Nathaniel
Published: January 2007

It is hardly surprising that I applaud the fine work of both Durr and Ostrom and Smith. I am on record in favor of the utility of the error correction model (e.g., Beck 1985) and it is impossible to obtain a visa to visit the economics department at UCSD without swearing an oath of loyalty to the methodology of cointegration. The two works here are notable for their methodological sophistication, their exposition of a relatively unknown and highly technical area, and, most important, their substantive contributions. Both articles show that political attitudes (approval and policy mood) adjust, in the long run, to changes in objective and subjective economic circumstance. Both articles are good examples of the synergy of methods and theory, since it is the methodology of cointegration that leads to this type of theorizing, and this type of theorizing can most easily be tested in the context of cointegration or error correction.
Error Correction, Attractors, and Cointegration: Substantive and Methodological Issues
Authors: Smith Renée M.
Published: January 2007

I am pleased to participate in this symposium because I agree that mutual criticism of our theories and of the methods used to test them helps to make social science objective and rational (Popper 1976). Space limitations preclude me from responding to all of the comments and suggestions of Beck and Williams (in this volume), but my interpretation of their key points is as follows: (1) estimating multiequation error correction models (ECMs) is unnecessary either because many theories provide us with exogeneity restrictions that imply single equation ECMs (Beck) or because statistical inference is unaffected by integration and cointegration in vector autoregressive systems (Williams); (2) using OLS in one step to estimate a single equation ECM is statistically superior to using the Engle-Granger two-step estimator (Beck); (3) commonly used classical hypothesis tests for nonstationarity favor the null hypothesis of a unit root, and therefore cannot be believed, but Bayesian inference with a flat prior solves this and other problems of inference (Williams); and (4) presidential approval is neither statistically nor conceptually an integrated random walk, but is either long memoried (Beck) or stationary (Williams). These are thought-provoking comments, and to one of them I will reply mea culpa. However, some of them need to be qualified, and others are incorrect. I begin by responding to comments (1) and (2) assuming that two or more time-series are integrated and cointegrated and then address comments (3) and (4), which question assumptions of and tests for integration and cointegration.
Dynamic Analysis with Latent Constructs
Authors: Kellstedt Paul , McAvoy Gregory E. , Stimson James A.
Published: January 2007

Political scientists generally derive their quantitative methodologies from two disparate traditions: econometric or psychometric. The psychometric tradition has made a lasting impact on political analysis through attention to issues of measurement. Measurement issues are particularly troublesome to political scientists because many interesting concepts are either latent or multidimensional. On the other hand, the econometric tradition has provided political scientists with a means of coping with macrolevel phenomena. In studying macrophenomena, the problem of few cases (there is only one American economy, for example) is handled by using longitudinal analysis. Econometrics provided tools for coping with challenges that longitudinal analysis posed for regression analysis.
Reproducing lizards modify sex allocation in response to operational sex ratios
Authors: Warner Daniel A , Shine Richard
Published: December 2006

Sex-allocation theory suggests that selection may favour maternal skewing of offspring sex ratios if the fitness return from producing a son differs from that for producing a daughter. The operational sex ratio (OSR) may provide information about this potential fitness differential. Previous studies have reached conflicting conclusions about whether or not OSR influences sex allocation in viviparous lizards. Our experimental trials with oviparous lizards (
Amphibolurus muricatus
) showed that OSR influenced offspring sex ratios, but in a direction opposite to that predicted by theory: females kept in male-biased enclosures overproduced sons rather than daughters (i.e. overproduced the more abundant sex). This response may enhance fitness if local OSRs predict survival probabilities of offspring of each sex, rather than the intensity of sexual competition.
Life extension of self-healing polymers with rapidly growing fatigue cracks
Authors: Jones A.S , Rule J.D , Moore J.S , Sottos N.R , White S.R
Published: December 2006

Self-healing polymers, based on microencapsulated dicyclopentadiene and Grubbs' catalyst embedded in the polymer matrix, are capable of responding to propagating fatigue cracks by autonomic processes that lead to higher endurance limits and life extension, or even the complete arrest of the crack growth. The amount of fatigue-life extension depends on the relative magnitude of the mechanical kinetics of crack propagation and the chemical kinetics of healing. As the healing kinetics are accelerated, greater fatigue life extension is achieved. The use of wax-protected, recrystallized Grubbs' catalyst leads to a fourfold increase in the rate of polymerization of bulk dicyclopentadiene and extends the fatigue life of a polymer specimen over 30 times longer than a comparable non-healing specimen. The fatigue life of polymers under extremely fast fatigue crack growth can be extended through the incorporation of periodic rest periods, effectively training the self-healing polymeric material to achieve higher endurance limits.
Perturbation of eigenvalues due to gaps in two-dimensional boundaries
Authors: Davis Anthony M.J , Llewellyn Smith Stefan G
Published: December 2006

Motivated by problems involving diffusion through small gaps, we revisit two-dimensional eigenvalue problems with localized perturbations to Neumann boundary conditions. We recover the known result that the gravest eigenvalue is
O
(|ln 
ϵ
|
−1
), where
ϵ
is the ratio of the size of the hole to the length-scale of the domain, and provide a simple and constructive approach for summing the inverse logarithm terms and obtaining further corrections. Comparisons with numerical solutions obtained for special geometries, both for the Dirichlet ‘patch problem’ where the perturbation to the boundary consists of a different boundary condition and for the gap problem, confirm that this approach is a simple way of obtaining an accurate value for the gravest eigenvalue and hence the long-term outcome of the underlying diffusion problem.
What is the best control strategy for multiple infectious disease outbreaks?
Authors: Handel Andreas , Longini Ira M , Antia Rustom
Published: December 2006

Effective control of infectious disease outbreaks is an important public health goal. In a number of recent studies, it has been shown how different intervention measures like travel restrictions, school closures, treatment and prophylaxis might allow us to control outbreaks of diseases, such as SARS, pandemic influenza and others. In these studies, control of a single outbreak is considered. It is, however, not clear how one should handle a situation where multiple outbreaks are likely to occur. Here, we identify the best control strategy for such a situation. We further discuss ways in which such a strategy can be implemented to achieve additional public health objectives.
Future directions in behavioural syndromes research
Authors: Bell Alison M
Published: December 2006

A behavioural syndrome occurs when individuals behave in a consistent way through time or across contexts and is analogous to ‘personality’ or ‘temperament’. Interest is accumulating in behavioural syndromes owing to their important ecological and evolutionary consequences. There are plenty of opportunities in this burgeoning young field to integrate proximate and functional approaches to studying behaviour, but there are few guidelines about where to start or how to design a study on behavioural syndromes. After summarizing what we do and do not know, this brief review aims to act as a general guide for studying behavioural syndromes. Although the array of possible behavioural combinations can seem overwhelming, there are at least four different strategies that can be used to choose which behaviours or contexts to study in a behavioural syndromes view. I describe the strengths and weaknesses of these non-exclusive strategies, and then discuss the methodological and statistical issues raised by such studies.
Partner choice creates competitive altruism in humans
Authors: Barclay Pat , Willer Robb
Published: December 2006

Reciprocal altruism has been the backbone of research on the evolution of altruistic behaviour towards non-kin, but recent research has begun to apply costly signalling theory to this problem. In addition to signalling resources or abilities, public generosity could function as a costly signal of cooperative intent, benefiting altruists in terms of (i) better access to cooperative relationships and (ii) greater cooperation within those relationships. When future interaction partners can choose with whom they wish to interact, this could lead to competition to be more generous than others. Little empirical work has tested for the possible existence of this ‘competitive altruism’. Using a cooperative monetary game with and without opportunities for partner choice and signalling cooperative intent, we show here that people actively compete to be more generous than others when they can benefit from being chosen for cooperative partnerships, and the most generous people are correspondingly chosen more often as cooperative partners. We also found evidence for increased scepticism of altruistic signals when the potential reputational benefits for dishonest signalling were high. Thus, this work supports the hypothesis that public generosity can be a signal of cooperative intent, which people sometimes ‘fake’ when conditions permit it.
No gastric mill in sauropod dinosaurs: new evidence from analysis of gastrolith mass and function in ostriches
Authors: Wings Oliver , Sander P. Martin
Published: December 2006

Polished pebbles occasionally found within skeletons of giant herbivorous sauropod dinosaurs are very likely to be gastroliths (stomach stones). Here, we show that based on feeding experiments with ostriches and comparative data for relative gastrolith mass in birds, sauropod gastroliths do not represent the remains of an avian-style gastric mill. Feeding experiments with farm ostriches showed that bird gastroliths experience fast abrasion in the gizzard and do not develop a polish. Relative gastrolith mass in sauropods (gastrolith mass much less than 0.1% of body mass) is at least an order of magnitude less than that in ostriches and other herbivorous birds (gastrolith mass approximates 1% of body mass), also arguing against the presence of a gastric mill in sauropods. Sauropod dinosaurs possibly compensated for their limited oral processing and gastric trituration capabilities by greatly increasing food retention time in the digestive system. Gastrolith clusters of some derived theropod dinosaurs (oviraptorosaurs and ornithomimosaurs) compare well with those of birds, suggesting that the gastric mill evolved in the avian stem lineage.
Testosterone and oxidative stress: the oxidation handicap hypothesis
Authors: Alonso-Alvarez Carlos , Bertrand Sophie , Faivre Bruno , Chastel Olivier , Sorci Gabriele
Published: December 2006

Secondary sexual traits (SST) are usually thought to have evolved as honest signals of individual quality during mate choice. Honesty of SST is guaranteed by the cost of producing/maintaining them. In males, the expression of many SST is testosterone-dependent. The immunocompetence handicap hypothesis has been proposed as a possible mechanism ensuring honesty of SST on the basis that testosterone, in addition to its effect on sexual signals, also has an immunosuppressive effect. The immunocompetence handicap hypothesis has received mixed support. However, the cost of testosterone-based signalling is not limited to immunosuppression and might involve other physiological functions such as the antioxidant machinery. Here, we tested the hypothesis that testosterone depresses resistance to oxidative stress in a species with a testosterone-dependent sexual signal, the zebra finch. Male zebra finches received subcutaneous implants filled with flutamide (an anti-androgen) or testosterone, or kept empty (control). In agreement with the prediction, we found that red blood cell resistance to a free radical attack was the highest in males implanted with flutamide and the lowest in males implanted with testosterone. We also found that cell-mediated immune response was depressed in testosterone-treated birds, supporting the immunocompetence handicap hypothesis. The recent finding that red blood cell resistance to free radicals is negatively associated with mortality in this species suggests that benefits of sexual signalling might trade against the costs derived from oxidation.
Culture or climate? The relative influences of past processes on the composition of the lowland Congo rainforest
Authors: Brncic Terry M , Willis Katherine J , Harris David J , Washington Richard
Published: December 2006

This paper presents the results from a palaeoecological study to establish the impact of prehistoric human activity and climate change on the vegetation and soils of the Goualougo area of the Nouabalé-Ndoki National Park, in the Republic of Congo (Congo–Brazzaville). This is a region that is known from previous work (through evidence of pottery, furnaces and charcoal layers beneath the present day rainforest vegetation) to have had prehistoric settlement dating back to at least 2000 calibrated years before present. In addition, there is climatic evidence to suggest that significant variations in precipitation have occurred in central Africa over the last few millennia. Presently, the region is covered in uninhabited moist semi-evergreen rainforest. Key research questions addressed in this paper include the extent to which the present-day composition of rainforest in this region is as a result of processes of the past (climate change and/or human activity), and the resilience of the rainforest to these perturbations.

Statistical analyses of pollen, microscopic charcoal and geochemical data are used to determine the relationship over time between vegetation dynamics and climate change, anthropogenic burning and metal smelting. Significant changes in forest composition are linked to burning and climate change but not metallurgy. The strongest influence on the present day composition appears to be related to the increased anthropogenic burning that started approximately 1000 years ago. Results from this study are discussed in terms of their implications for the present and future management of this globally important forested region.
Late Quaternary vegetation, biodiversity and fire dynamics on the southern Brazilian highland and their implication for conservation and management of modernAraucariaforest and grassland ecosystems
Authors: Behling Hermann , Pillar Valério DePatta
Published: December 2006

Palaeoecological background information is needed for management and conservation of the highly diverse mosaic ofAraucariaforest and Campos (grassland) in southern Brazil. Questions on the origin ofAraucariaforest and grasslands; its development, dynamic and stability; its response to environmental change such as climate; and the role of human impact are essential. Further questions on its natural stage of vegetation or its alteration by pre- and post-Columbian anthropogenic activity are also important. To answer these questions, palaeoecological and palaeoenvironmental data based on pollen, charcoal and multivariate data analysis of radiocarbon dated sedimentary archives from southern Brazil are used to provide an insight into past vegetation changes, which allows us to improve our understanding of the modern vegetation and to develop conservation and management strategies for the strongly affected ecosystems in southern Brazil.
Tree-line changes along the Andes: implications of spatial patterns and dynamics
Authors: Young Kenneth R , León Blanca
Published: December 2006

The Andes provide an extensive latitudinal and topographical framework for studying the factors that control the spatial patterns of forests (timberlines) and their species components expressed through the presence of tree growth forms (tree lines). Despite consistent overall similarities in landscape patterns, many processes must be unique, given the dramatic differences in species richness and biophysical constraints along the Andes. In all cases evaluated to date, morphological plasticity is a common trait of plant species that dominate at tree lines. In fact, many changes observed can be related to species-specific traits. Physiological limitations on tree growth form only explain species limits, while disturbances and cyclical climate fluctuations interact to affect many landscape patterns. Over long periods of time, tree lines provide unique habitats and perhaps opportunities for speciation. Understanding the spatial organization of tree-line dynamics is one viable research approach for evaluating the likely past fluxes and possible future changes.
Long-term forest–savannah dynamics in the Bolivian Amazon: implications for conservation
Authors: Mayle Francis E , Langstroth Robert P , Fisher Rosie A , Meir Patrick
Published: December 2006

The aim of this paper is to evaluate the respective roles of past changes in climate, geomorphology and human activities in shaping the present-day forest–savannah mosaic of the Bolivian Amazon, and consider how this palaeoecological perspective may help inform conservation strategies for the future. To this end, we review a suite of palaeoecological and archaeological data from two distinct forest–savannah environments in lowland Bolivia: Noel Kempff Mercado National Park (NKMNP) on the Precambrian Shield and the ‘Llanos de Moxos’ in the Beni basin. We show that they contain markedly contrasting legacies of past climatic, geomorphic and anthropogenic influences between the last glacial period and the Spanish Conquest. In NKMNP, increasing precipitation caused evergreen rainforest expansion, at the expense of semi-deciduous dry forest and savannahs, over the last three millennia. In contrast, pre-Hispanic indigenous cultures were instrumental in facilitating recent forest expansion in the Llanos de Moxos by building a vast network of earthworks. Insights from Mid-Holocene palaeodata, together with ecological observations and modelling studies, suggest that there will be progressive replacement of rainforest by dry forest and savannah in NKMNP over the twenty-first century in response to the increased drought predicted by general circulation models. Protection of the latitudinal landscape corridors may be needed to facilitate these future species reassortments. However, devising appropriate conservation strategies for the Llanos de Moxos will be more difficult due to its complex legacy of Palaeo-Indian impact. Without fully understanding the degree to which its current biota has been influenced by past native cultures, the type and intensity of human land use appropriate for this landscape in the future will be difficult to ascertain.
Rapid and cost-effective polymorphism identification and genotyping using restriction site associated DNA (RAD) markers
Authors: Miller Michael R. , Dunham Joseph P. , Amores Angel , Cresko William A. , Johnson Eric A.
Published: December 2006

Restriction siteassociatedDNA (RAD) tags are a genome-wide representation of every site of a particular restriction enzyme by short DNA tags. Most organisms segregate large numbers of DNA sequence polymorphisms that disrupt restriction sites, which allows RAD tags to serve as genetic markers spread at a high density throughout the genome. Here, we demonstrate the applicability of RAD markers for both individual and bulk-segregant genotyping. First, we show that these markers can be identified and typed on pre-existing microarray formats. Second, we present a method that uses RAD marker DNA to rapidly produce a low-cost microarray genotyping resource that can be used to efficiently identify and type thousands of RAD markers. We demonstrate the utility of the former approach by using a tiling path array for the fruit fly to map a recombination breakpoint, and the latter approach by creating and using an enriched RAD marker array for the threespine stickleback. The high number of RAD markers enabled localization of a previously identified region, as well as a second region also associated with the lateral plate phenotype. Taken together, our results demonstrate that RAD markers, and the method to develop a RAD marker microarray resource, allow high-throughput, high-resolution genotyping in both model and nonmodel systems.
Transcriptional Profiling of the Arabidopsis Embryo
Authors: Spencer Matthew W.B. , Casson Stuart A. , Lindsey Keith
Published: December 2006

We have used laser-capture microdissection to isolate RNA from discrete tissues of globular, heart, and torpedo stage embryos of Arabidopsis (Arabidopsis thaliana). This was amplified and analyzed by DNA microarray using the Affymetrix ATH1 GeneChip, representing approximately 22,800 Arabidopsis genes. Cluster analysis showed that spatial differences in gene expression were less significant than temporal differences. Time course analysis reveals the dynamics and complexity of gene expression in both apical and basal domains of the developing embryo, with several classes of synexpressed genes identifiable. The transition from globular to heart stage is associated in particular with an up-regulation of genes involved in cell cycle control, transcriptional regulation, and energetics and metabolism. The transition from heart to torpedo stage is associated with a repression of cell cycle genes and an up-regulation of genes encoding storage proteins, and pathways of cell growth, energy, and metabolism. The torpedo stage embryo shows strong functional differentiation in the root and cotyledon, as inferred from the classes of genes expressed in these tissues. The time course of expression of the essential EMBRYO-DEFECTIVE genes shows that most are expressed at unchanging levels across all stages of embryogenesis. We show how identified genes can be used to generate cell type-specific markers and promoter activities for future application in cell biology.
Cross-Species Translocation of mRNA from Host Plants into the Parasitic Plant Dodder
Authors: Roney Jeannine K. , Khatibi Piyum A. , Westwood James H.
Published: December 2006

An intriguing new paradigm in plant biology is that systemically mobile mRNAs play a role in coordinating development. In this process, specific mRNAs are loaded into the phloem transport stream for translocation to distant tissues, where they may impact on developmental processes. However, despite its potential significance for plant growth regulation, mRNA trafficking remains poorly understood and challenging to study. Here, we show that phloem-mobile mRNAs can also traffic between widely divergent species from a host to the plant parasite lespedeza dodder (Cuscuta pentagona Engelm.). Reverse transcription-polymerase chain reaction and microarray analysis were used to detect specific tomato (Lycopersicon esculentum Mill.) transcripts in dodder grown on tomato that were not present in control dodder grown on other host species. Foreign transcripts included LeGAI, which has previously been shown to be translocated in the phloem, as well as nine other transcripts not reported to be mobile. Dodders are parasitic plants that obtain resources by drawing from the phloem of a host plant and have joint plasmodesmata with host cortical cells. Although viruses are known to move between dodder and its hosts, translocation of endogenous plant mRNA has not been reported. These results point to a potentially new level of interspecies communication, and raise questions about the ability of parasites to recognize, use, and respond to transcripts acquired from their hosts.
Diversity and Evolution of CYCLOIDEA-Like TCP Genes in Relation to Flower Development in Papaveraceae
Authors: Damerval Catherine , Guilloux Martine Le , Jager Muriel , Charon Céline
Published: December 2006

Monosymmetry evolved several times independently during flower evolution. In snapdragon (Antirrhinum majus), a key gene for monosymmetry is CYCLOIDEA (CYC), which belongs to the class II TCP gene family encoding transcriptional activators. We address the questions of the evolutionary history of this gene family and of possible recruitment of genes homologous to CYC in floral development and symmetry in the Papaveraceae. Two to three members of the class II TCP family were found in each species analyzed, two of which were CYC-like genes, on the basis of the presence of both the TCP and R conserved domains. The duplication that gave rise to these two paralogous lineages (named PAPACYL1 and PAPACYL2) probably predates the divergence of the two main clades within the Papaveraceae. Phylogenetic relationships among angiosperm class II TCP genes indicated that (1) PAPACYL genes were closest to Arabidopsis (Arabidopsis thaliana) AtTCP18, and a duplication at the base of the core eudicot would have given rise to two supplementary CYC-like lineages; and (2) at least three class II TCP genes were present in the ancestor of monocots and eudicots. Semiquantitative reverse transcription-polymerase chain reaction and in situ hybridization approaches in three species with different floral symmetry indicated that both PAPACYL paralogs were expressed during floral development. A pattern common to all three species was observed at organ junctions in inflorescences and flowers. Expression in the outer petals was specifically observed in the two species with nonactinomorphic flowers. Hypotheses concerning the ancestral pattern of expression and function of CYC-like genes and their possible role in floral development of Papaveraceae species leading to bisymmetric buds are discussed.
Purdue Ionomics Information Management System. An Integrated Functional Genomics Platform
Authors: Baxter Ivan , Ouzzani Mourad , Orcun Seza , Kennedy Brad , Jandhyala Shrinivas S. , Salt David E.
Published: December 2006

The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics.
Modulation of Ethylene Responses Affects Plant Salt-Stress Responses
Authors: Cao Wan-Hong , Liu Jun , He Xin-Jian , Mu Rui-Ling , Zhou Hua-Lin , Chen Shou-Yi , Zhang Jin-Song
Published: December 2006

Ethylene signaling plays important roles in multiple aspects of plant growth and development. Its functions in abiotic stress responses remain largely unknown. Here, we report that alteration of ethylene signaling affected plant salt-stress responses. A type II ethylene receptor homolog gene NTHK1 (Nicotiana tabacum histidine kinase 1) from tobacco (N. tabacum) conferred salt sensitivity in NTHK1-transgenic Arabidopsis (Arabidopsis thaliana) plants as judged from the phenotypic change, the relative electrolyte leakage, and the relative root growth under salt stress. Ethylene precursor 1-aminocyclopropane-1-carboxylic acid suppressed the salt-sensitive phenotype. Analysis of Arabidopsis ethylene receptor gain-of-function mutants further suggests that receptor function may lead to salt-sensitive responses. Mutation of EIN2, a central component in ethylene signaling, also results in salt sensitivity, suggesting that EIN2-mediated signaling is beneficial for plant salt tolerance. Overexpression of the NTHK1 gene or the receptor gain-of-function activated expression of salt-responsive genes AtERF4 and Cor6.6. In addition, the transgene NTHK1 mRNA was accumulated under salt stress, suggesting a posttranscriptional regulatory mechanism. These findings imply that ethylene signaling may be required for plant salt tolerance.
Somatic Cytokinesis and Pollen Maturation inArabidopsisDepend on TPLATE, Which Has Domains Similar to Coat Proteins
Authors: Van Damme Daniël , Coutuer Silvie , De Rycke Riet , Bouget Francois-Yves , Inzé Dirk , Geelen Danny
Published: December 2006

TPLATE was previously identified as a potential cytokinesis protein targeted to the cell plate. Disruption of TPLATE in Arabidopsis thaliana leads to the production of shriveled pollen unable to germinate. Vesicular compartmentalization of the mature pollen is dramatically altered, and large callose deposits accumulate near the intine cell wall layer. Green fluorescent protein (GFP)–tagged TPLATE expression under the control of the pollen promoter Lat52 complements the phenotype. Downregulation of TPLATE in Arabidopsis seedlings and tobacco (Nicotiana tabacum) BY-2 suspension cells results in crooked cell walls and cell plates that fail to insert into the mother wall. Besides accumulating at the cell plate, GFP-fused TPLATE is temporally targeted to a narrow zone at the cell cortex where the cell plate connects to the mother wall. TPLATE-GFP also localizes to subcellular structures that accumulate at the pollen tube exit site in germinating pollen. Ectopic callose depositions observed in mutant pollen also occur in RNA interference plants, suggesting that TPLATE is implicated in cell wall modification. TPLATE contains domains similar to adaptin and β-COP coat proteins. These data suggest that TPLATE functions in vesicle-trafficking events required for site-specific cell wall modifications during pollen germination and for anchoring of the cell plate to the mother wall at the correct cortical position.
The Plant-Specific ssDNA Binding Protein OSB1 Is Involved in the Stoichiometric Transmission of Mitochondrial DNA inArabidopsis
Authors: Zaegel Vincent , Guermann Benoît , Le Ret Monique , Andrés Charles , Meyer Denise , Erhardt Mathieu , Canaday Jean , Gualberto José M. , Imbault Patrice
Published: December 2006

Plant mitochondrial genomes exist in a natural state of heteroplasmy, in which substoichiometric levels of alternative mitochondrial DNA (mtDNA) molecules coexist with the main genome. These subgenomes either replicate autonomously or are created by infrequent recombination events. We found that Arabidopsis thaliana OSB1 (for Organellar Single-stranded DNA Binding protein1) is required for correct stoichiometric mtDNA transmission. OSB1 is part of a family of plant-specific DNA binding proteins that are characterized by a novel motif that is required for single-stranded DNA binding. The OSB1 protein is targeted to mitochondria, and promoter–β-glucuronidase fusion showed that the gene is expressed in budding lateral roots, mature pollen, and the embryo sac of unfertilized ovules. OSB1 T-DNA insertion mutants accumulate mtDNA homologous recombination products and develop phenotypes of leaf variegation and distortion. The mtDNA rearrangements occur in two steps: first, homozygous mutants accumulate subgenomic levels of homologous recombination products; second, in subsequent generations, one of the recombination products becomes predominant. After the second step, the process is no longer reversible by backcrossing. Thus, OSB1 participates in controlling the stoichiometry of alternative mtDNA forms generated by recombination. This regulation could take place in gametophytic tissues to ensure the transmission of a functional mitochondrial genome.
Prediction of structures of multidomain proteins from structures of the individual domains
Authors: Wollacott Andrew M. , Zanghellini Alexandre , Murphy Paul , Baker David
Published: December 2006

We describe the development of a method for assembling structures of multidomain proteins from structures of isolated domains. The method consists of an initial low‐resolution search in which the conformational space of the domain linker is explored using the Rosetta de novo structure prediction method, followed by a high‐resolution search in which all atoms are treated explicitly and backbone and side chain degrees of freedom are simultaneously optimized. The method recapitulates, often with very high accuracy, the structures of existing multidomain proteins.
Thermodynamic stability of a cold‐adapted protein, type III antifreeze protein, and energetic contribution of salt bridges
Authors: García‐Arribas Olga , Mateo Roberto , Tomczak Melanie M. , Davies Peter L. , Mateu Mauricio G.
Published: December 2006

A thermodynamic analysis of a cold‐adapted protein, type III anti‐freeze protein (AFP), was carried out. The results indicate that the folding equilibrium of type III AFP is a reversible, unimolecular, two‐state process with no populated intermediates. Compared to most mesophilic proteins whose folding is two‐state, the psychrophilic type III AFP has a much lower thermodynamic stability at 25°C, ∼3 kcal/mol, and presents a remarkably downshifted stability–temperature curve, reaching a maximum of 5 kcal/mol around 0°C. Type III AFPs contain few and non‐optimally distributed surface charges relative to their mesophilic homologs, the C‐terminal domains of sialic acid synthases. We used thermodynamic double mutant cycles to evaluate the energetic role of every surface salt bridge in type III AFP. Two isolated salt bridges provided no contribution to stability, while the Asp36–Arg39 salt bridge, involved in a salt bridge network with the C‐terminal carboxylate, had a substantial contribution (∼1 kcal/mol). However, this contribution was more than counteracted by the destabilizing effect of the Asp36 carboxylate itself, whose removal led to a net 30% increase in stability at 25°C. This study suggests that type III AFPs may have evolved for a minimally acceptable stability at the restricted, low temperature range (around 0°C) at which AFPs must function. In addition, it indicates that salt bridge networks are used in nature also for the stability of psychrophilic proteins, and has led to a type III AFP variant of increased stability that could be used for biotechnological purposes.
The transmembrane homotrimer of ADAM 1 in model lipid bilayers
Authors: Gan Siok Wan , Xin Lin , Torres Jaume
Published: December 2006

Fertilin is a transmembrane protein heterodimer formed by the two subunits fertilin α and fertilin β that plays an important role in sperm–egg fusion. Fertilin α and β are members of the ADAM family, and contain each one transmembrane α‐helix, and are termed ADAM 1 and ADAM 2, respectively. ADAM 1 is the subunit that contains a putative fusion peptide, and we have explored the possibility that the transmembrane α‐helical domain of ADAM 1 forms homotrimers, in common with other viral fusion proteins. Although this peptide was found to form various homooligomers in SDS, the infrared dichroic data obtained with the isotopically labeled peptide at specific positions is consistent with the presence of only one species in DMPC or POPC lipid bilayers. Comparison of the experimental orientational data with molecular dynamics simulations performed with sequence homologues of ADAM 1 show that the species present in lipid bilayers is only consistent with an evolutionarily conserved homotrimeric model for which we provide a backbone structure. These results support a model where ADAM 1 forms homotrimers as a step to create a fusion active intermediate.
Evaluation of features for catalytic residue prediction in novel folds
Authors: Youn Eunseog , Peters Brandon , Radivojac Predrag , Mooney Sean D.
Published: December 2006

Structural genomics projects are determining the three‐dimensional structure of proteins without full characterization of their function. A critical part of the annotation process involves appropriate knowledge representation and prediction of functionally important residue environments. We have developed a method to extract features from sequence, sequence alignments, three‐dimensional structure, and structural environment conservation, and used support vector machines to annotate homologous and nonhomologous residue positions based on a specific training set of residue functions. In order to evaluate this pipeline for automated protein annotation, we applied it to the challenging problem of prediction of catalytic residues in enzymes. We also ranked the features based on their ability to discriminate catalytic from noncatalytic residues. When applying our method to a well‐annotated set of protein structures, we found that top‐ranked features were a measure of sequence conservation, a measure of structural conservation, a degree of uniqueness of a residue's structural environment, solvent accessibility, and residue hydrophobicity. We also found that features based on structural conservation were complementary to those based on sequence conservation and that they were capable of increasing predictor performance. Using a family nonredundant version of the ASTRAL 40 v1.65 data set, we estimated that the true catalytic residues were correctly predicted in 57.0% of the cases, with a precision of 18.5%. When testing on proteins containing novel folds not used in training, the best features were highly correlated with the training on families, thus validating the approach to nonhomologous catalytic residue prediction in general. We then applied the method to 2781 coordinate files from the structural genomics target pipeline and identified both highly ranked and highly clustered groups of predicted catalytic residues.
Redesigning protein pKavalues
Authors: Tynan‐Connolly Barbara Mary , Nielsen Jens Erik
Published: December 2006

The ability to re‐engineer enzymatic pH‐activity profiles is of importance for industrial applications of enzymes. We theoretically explore the feasibility of re‐engineering enzymatic pH‐activity profiles by changing active site pKavalues using point mutations. We calculate the maximum achievable ΔpKavalues for 141 target titratable groups in seven enzymes by introducing conservative net‐charge altering point mutations. We examine the importance of the number of mutations introduced, their distance from the target titratable group, and the characteristics of the target group itself. The results show that multiple mutations at 10Å can change pKavalues up to two units, but that the introduction of a requirement to keep other pKavalues constant reduces the magnitude of the achievable ΔpKa. The algorithm presented shows a good correlation with existing experimental data and is available for download and via a web server athttp://enzyme.ucd.ie/pKD.
Atomic model of human Rcd‐1 reveals an armadillo‐like‐repeat protein with in vitro nucleic acid binding properties
Authors: Garces Robert G. , Gillon Wanda , Pai Emil F.
Published: December 2006

Rcd‐1, a protein highly conserved across eukaryotes, was initially identified as a factor essential for nitrogen starvation‐invoked differentiation in fission yeast, and its Saccharomyces cerevisiae homolog, CAF40, has been identified as part of the CCR4–NOT transcription complex, where it interacts with the NOT1 protein. Mammalian homologs are involved in various cellular differentiation processes including retinoic acid‐induced differentiation and hematopoetic cell development. Here, we present the 2.2 Å X‐ray structure of the highly conserved region of human Rcd‐1 and investigate possible functional abilities of this and the full‐length protein. The monomer is made up of six armadillo repeats forming a solvent‐accessible, positively‐charged cleft 21–22 Å wide that, in contrast to other armadillo proteins, stays fully exposed in the dimer. Prompted by this finding, we established that Rcd‐1 can bind to single‐ and double‐stranded oligonucleotides in vitro with the affinity of G/C/T ≫ A. Mutation of an arginine residue within the cleft strongly reduced or abolished oligonucleotide binding. Rcd‐1's ability to bind to nucleic acids, in addition to the previously reported protein–protein interaction with NOT1, suggests a new feature in Rcd‐1's role in regulation of overall cellular differentiation processes.
Modification of the Pad‐plate Method of Determining Chlortetracycline in Egg White
Authors: BOYD JOSEPHINE W. , WEISER H. H. , HAQUE RIAZ UL , WINTER A. R.
Published: December 2006

The sensitivity of the pad‐plate method for detecting chlortetracycline in egg white is increased by using pH 4.5 citrate buffer rather than pH 4.5 phosphate buffer as a diluent. It is also increased by allowing about four hours for diffusion of antibiotic prior to incubation of the assay plates. Under these conditions of assay, protein binding of the antibiotic was not an important factor.
Sensory Evaluation of Accessory Foods With and Without Carriersa
Authors: KROLL BEVERLEY J. , PILGRIM FRANCIS J.
Published: December 2006

Accessory foods like jelly or catsup can be evaluated by consumers for preference without an appropriate carrier, such as bread or hamburger, at least as effectively as with the carrier. Time and money are saved, and accuracy is increased.
Destruction of alpha‐Tocopherol by gamma‐Irradiationa
Authors: ROSE DYSON , LIPS H. J. , CYR R.
Published: December 2006

Irradiation (Cow source) of solutions of DL‐a‐tocopherol caused extensive destruction of this vitamin and gave rise to products similar to those obtained by autoxidation. Irradiation in saturated solvents (mineral oil, methyl myristate) destroyed more tocopherol than did irradiation in unsaturated solvents (methyl oleate, methyl linoleate). Destruction by 2.0 Mrad of irradiation increased with increasing tocopherol concentration, but the increase became negligible above 0.5% tocopherol in the saturated and 0.1% tocopherol in the unsaturated solvents.