bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient estimation of pairwise distances between genomes
Authors: Domazet-Lošo Mirjana , Haubold Bernhard
Published: October 2009

Motivation: Genome comparison is central to contemporary genomics and typically relies on sequence alignment. However, genome-wide alignments are difficult to compute. We have, therefore, recently developed an accurate alignment-free estimator of the number of substitutions per site based on the lengths of exact matches between pairs of sequences. The previous implementation of this measure requires n(n−1) suffix tree constructions and traversals, where n is the number of sequences analyzed. This does not scale well for large n.

Results: We present an algorithm to extract pairwise distances in a single traversal of a single suffix tree containing n sequences. As a result, the run time of the suffix tree construction phase of our algorithm is reduced from O(n2L) to O(nL), where L is the length of each sequence. We implement this algorithm in the program kr version 2 and apply it to 825 HIV genomes, 13 genomes of enterobacteria and the complete genomes of 12 Drosophila species. We show that, depending on the input dataset, the new program is at least 10 times faster than its predecessor.

Availability: Version 2 of kr can be tested via a web interface at http://guanine.evolbio.mpg.de/kr2/. It is written in standard C and its source code is available under the GNU General Public License from the same web site.

Contact:  haubold@evolbio.mpg.de

Supplementary informations: Supplementary data are available at Bioinformatics online.
CYP76M7 Is an ent-Cassadiene C11α-Hydroxylase Defining a Second Multifunctional Diterpenoid Biosynthetic Gene Cluster in Rice
Authors: Swaminathan Sivakumar , Morrone Dana , Wang Qiang , Fulton D. Bruce , Peters Reuben J.
Published: October 2009

Biosynthetic gene clusters are common in microbial organisms, but rare in plants, raising questions regarding the evolutionary forces that drive their assembly in multicellular eukaryotes. Here, we characterize the biochemical function of a rice (Oryza sativa) cytochrome P450 monooxygenase, CYP76M7, which seems to act in the production of antifungal phytocassanes and defines a second diterpenoid biosynthetic gene cluster in rice. This cluster is uniquely multifunctional, containing enzymatic genes involved in the production of two distinct sets of phytoalexins, the antifungal phytocassanes and antibacterial oryzalides/oryzadiones, with the corresponding genes being subject to distinct transcriptional regulation. The lack of uniform coregulation of the genes within this multifunctional cluster suggests that this was not a primary driving force in its assembly. However, the cluster is dedicated to specialized metabolism, as all genes in the cluster are involved in phytoalexin metabolism. We hypothesize that this dedication to specialized metabolism led to the assembly of the corresponding biosynthetic gene cluster. Consistent with this hypothesis, molecular phylogenetic comparison demonstrates that the two rice diterpenoid biosynthetic gene clusters have undergone independent elaboration to their present-day forms, indicating continued evolutionary pressure for coclustering of enzymatic genes encoding components of related biosynthetic pathways.
A robotic arm as a simple sample changer for a diffractometer with very low component costs
Authors: Lian D. , Swainson I. P. , Cranswick L. M. D. , Donaberger R.
Published: October 2009

Inexpensive model robots are a viable option for automation of simple, repetitive tasks and can be solutions when space restriction and funding are issues, both factors that may eliminate more advanced robots from consideration. A simple-to-program, inexpensive robotic arm has been integrated in a sample changer for room-temperature experiments on a neutron powder diffractometer. In spite of the limited precision inherent in a model, servo-controlled robot, a very reproducible overall system can be made. Simple `tricks' such as incorporating self-centering mechanisms,e.g.mechanically self-centering designs and magnets, can produce central forces that eliminate the need for high precision from the robot arm.
Simulation of the powder diffraction pattern of randomly restacked Ca2Nb3O10nanosheets
Authors: Onoda Mitsuko , Ebina Yasuo , Sasaki Takayoshi
Published: October 2009

From X-ray powder diffraction pattern features, layered KCa2Nb3O10·nH2O synthesized through flocculation of delaminated Ca2Nb3O10nanosheets with K ions appeared to be composed of randomly stacked nanosheets. Powder pattern simulation was conducted based on the matrix method using a random stacking model. When seven sheets were used as the coherent thickness, agreement in pattern fitting between the experimental and calculated intensities was satisfactory, and information about textures and atomic positions was obtained.
Scherrer grain-size analysis adapted to grazing-incidence scattering with area detectors
Authors: Smilgies Detlef-M.
Published: October 2009

Ever since its formulation, the Scherrer formula has been the workhorse for quantifying finite size effects in X-ray scattering. Various aspects of Scherrer-type grain-size analysis are discussed with regard to the characterization of thin films with grazing-incidence scattering methods utilizing area detectors. After a brief review of the basic features of Scherrer analysis, a description of resolution-limiting factors in grazing-incidence scattering geometry is provided. As an application, the CHESS D1 beamline is characterized for typical scattering modes covering length scales from the molecular scale to the nanoscale.
The phylogenetic relationships of the charismatic poster frogs, Phyllomedusinae (Anura, Hylidae)
Authors: Faivovich Julián , Haddad Célio F. B. , Baêta Délio , Jungfer Karl‐Heinz , Álvares Guilherme F. R. , Brandão Reuber A. , Sheil Christopher , Barrientos Lucas S. , Barrio‐Amorós César L. , Cruz Carlos A. G. , Wheeler Ward C.
Published: October 2009

The leaf or monkey frogs of the hylid subfamily Phyllomedusinae are a unique group of charismatic anurans. We present a molecular phylogenetic analysis that includes 45 of the 60 species of phyllomedusines using up to 12 genes and intervening tRNAs. The aims were to gain a better understanding of the phylogenetic position ofPhrynomedusa, test the monophyly and explore the relationships among several putative lineages (Hylomantis, theH. buckleyiGroup,Phasmahyla, the four species groups ofPhyllomedusa, and the species ofPhyllomedusathat remain unassigned to any group), and to examine the implications of our phylogeny for the evolution of several characters in phyllomedusines. The analyses resulted in a well‐supported phylogenetic hypothesis that provides a historical framework for a discussion of the evolution of characters associated with reproductive biology, gliding behaviour, the physiology of waterproofing, and bioactive peptides. Implications include an earlier origin for eggless capsules than for leaf‐folding behaviour during amplexus, two independent origins of gliding, and an earlier origin of reduction in evaporative water loss than uricotelism, which is a result that originally was predicted on the basis of physiology alone. Furthermore, our results support the prediction that bioactive peptides from different peptide families are to be expected in all species of Phyllomedusinae.Hylomantis(as recently redefined) is shown to be paraphyletic and the synonymy ofAgalychnisis revised to remedy this problem by including bothHylomantisandPachymedusa.

 © The Willi Hennig Society 2009.
Solubilities of Magnesia, Titania, and Magnesium Titanate in Aluminum Oxide
Authors: ROY SALIL K. , COBLE ROBERT L.
Published: October 2009

On heat treatment in air the solubility of MgO or TiO2, in Al23 is too small to detect by lattice parameter shifts. The solubility of MgTiO3 in Al2O3 in air increased to the measured values, expressed as atomic fractions Mg:A1or Ti:A1of0.82 × lo‐2, 1.43 × 10‐2, and 1.75 × 10‐2 at 1250°, 1650°, and 1850°C, respectively. In 1 atm hydrogen the TiO2 solubility expressed as the atomic fraction Ti:A1 is 0.55 × lo‐2, 0.75 × 10W2, 1.15 × 10‐2, and 1.50 × 10p2 at 1400°, 1500°, 1600°, and 1700°C, respectively. The increased solubility in H2 was attributed to reduction of the titanium ion. The solubility of MgO in A12O3 in vacuum (0.3μ)expressed as the atomic fraction Mg:A1 was measured as 1.10 × loW4, 3.00 × 10”4, 6.80 × 10–4, and 1.40 × 10‐3 at 1530°, 1630°, 1730°, and 183O°C, respectively. These contents did not cause an observable change in lattice parameter, but a slight change was observed when MgO was dissolved in A12O3 in a hydrogen atmosphere.
Effect of Alkali Oxides on the Diffusion of Helium in a Simple Borosilicate Glass
Authors: ALTEMOSE V. O.
Published: October 2009

Helium permeation rates, diffusivities, and solubilities in a simple borosilicate glass containing alkali oxides were measured. The major effect of increasing Na2O content from 2 to 13 mol% is a systematic decrease in permeation rate and diffusivity, indicating that the Na+ ion is essentially filling space in the glass network. At 7 mol% alkali oxide, as the alkali‐ion size is increased, the changes in diffusivity and activation energy indicate that from Li+ to Na+ to K+, the larger ion more effectively plugs the network interstices. The size distribution of interstices in the base‐glass network is such that ions larger than K+ are too large to simply fill the network and consequently tend to spread the network as well.
Survey of laxative use by adults with self‐defined constipation in South America and Asia: a comparison of six countries
Authors: WALD A. , Mueller‐LISSNER S. , KAMM M. A. , HINKEL U. , RICHTER E. , SCHUIJT C. , MANDEL K. G.
Published: October 2009

Background  In contrast to the US and Europe, prevalence and laxative use for self‐defined constipation among adults was previously reported to be unassociated with age among adults in South Korea and Brazil.

Aim  To determine whether observations in South Korea and Brazil are reflective of other Asian and South American countries.

Methods  A total of 8100 adults from Argentina, Colombia, Indonesia and China completed a questionnaire identical to that previously used in South Korea and Brazil.

Results  Prevalence of constipation was similar to that reported for Brazil and South Korea and was 2.17‐fold (95% CI: 1.71–2.64) higher amongst women than amongst men. Prevalence increased with age amongst all adults in Argentina and China and only among men in Colombia and Brazil. With the exception of Indonesia, the majority of those with constipation had symptoms at least once weekly, and for ≤3 years. Less than one‐third of adults reported using laxatives to treat constipation. Laxative use was not associated with gender and increased with age in Argentina and Colombia.

Conclusions  No clear geographical or cultural tendencies were observed in the prevalence of constipation and laxative use among the South American and Asian countries studied in this survey.

Aliment Pharmacol Ther 31, 274–284
Effects of irrigation pumps on riverine fish
Authors: BAUMGARTNER L. J. , REYNOLDSON N. K. , CAMERON L. , STANGER J. G.
Published: October 2009

Abstract  The total number and condition of fish extracted via high and low flow irrigation pumps was assessed over a 2‐year period in the Namoi River, Australia. A combination of boat electric fishing and fyke netting was used for 10 weeks during the peak irrigation period to determine species and size classes susceptible to entrainment during water abstraction. Over 2300 fish passed through the pump outlets over the study period, with many individuals (7.5% of total) both killed and injured. The maximum number of fish entrained in a single day was 232. Mortality was significantly higher from the high volume pump site, but only large (>200 mm long) or small (<50 mm long) fish were killed. Medium‐sized fish (50–200 mm long) largely survived the abstraction process; although 70 were injured (3% of total), only one was killed (0.07%). The Electric fishing surveys showed that only four species were present in storage dams, suggesting that survival through the pump systems may be size and species specific. Fish that survived the water abstraction process had no opportunities to return to the main river system and were effectively classified as lost from the main river population. The development of suitable mitigation measures, including operational changes and screening, are suggested as mechanisms to prevent extraction and minimise any adverse impacts arising from irrigation development.
Interaction effect among maternal environment, maternal investment and progeny genotype on life history traits inCallosobruchus chinensis
Authors: Yanagi Shin‐ichi , Tuda Midori
Published: October 2009

1. Transgenerational effects, genetic or non‐genetic, affect population dynamics and the evolution of life‐history traits. Besides genetic components, the size of gametes (eggs and seeds), simultaneously a parental and progeny character, can mediate environmental condition experienced by a parent. In both animals and arthropods, mothers are known to reduce their egg mass depending on their malcondition.

2. Progeny may also modify their life history traits to increase their own fitness when constrained by maternal investment, which may eventually nullify transgenerational effects on population dynamics and evolution. Such fitness modification by the progeny under new environmental conditions requires phenotypic plasticity interacting with egg mass. We hypothesize that different selective environments should produce inter‐population genetic diversification of the response to maternal investment on each egg, which would be detected as a paternal genotype × environment × previous (i.e. maternal) environment (G × E × preE) interaction in progeny fitness.

3. To evaluate the contribution of maternal non‐genetic resource and the genetic component separately, we used an inbred‐isofemale‐line approach to eliminate the influence of the genetic correlation between egg mass and other life history traits, in the adzuki bean beetle,Callosobruchus chinensis. The females were reared at either high or low densities to generate variability in egg resources. To test the additive or interactive effect of genotype, non‐genetic egg resources, and maternal environment on the life history traits of the progeny, they were crossed with males from laboratory and wild strains that had been subjected to different levels of population density.

4. The G × E × preE interaction effect was detected on the correlation structure between egg mass and development time: In the offspring of mothers reared at low density, the negative correlation between egg mass and development time was higher with lab strain fathers, whereas in the offspring of mothers reared at high density, the negative correlation was higher with the wild strain fathers.

5. Our results indicate a genetic difference in the response of development time but not of adult mass to environmental variation in egg mass. Such density‐dependent enhancement of maternal effects may destabilize population dynamics and accelerate evolution.
Avifauna response to hurricanes: regional changes in community similarity
Authors: RITTENHOUSE CHADWICK D. , PIDGEON ANNA M. , ALBRIGHT THOMAS P. , CULBERT PATRICK D. , CLAYTON MURRAY K. , FLATHER CURTIS H. , HUANG CHENGQUAN , MASEK JEFFREY G. , RADELOFF VOLKER C.
Published: October 2009

Global climate models predict increases in the frequency and intensity of extreme climatic events such as hurricanes, which may abruptly alter ecological processes in forests and thus affect avian diversity. Developing appropriate conservation measures necessitates identifying patterns of avifauna response to hurricanes. We sought to answer two questions: (1) does avian diversity, measured as community similarity, abundance, and species richness, change in areas affected by hurricane compared with unaffected areas, and (2) what factors are associated with the change(s) in avian diversity? We used North American Breeding Bird Survey data, hurricane track information, and a time series of Landsat images in a repeated measures framework to answer these questions. Our results show a decrease in community similarity in the first posthurricane breeding season for all species as a group, and for species that nest in the midstory and canopy. We also found significant effects of hurricanes on abundance for species that breed in urban and woodland habitats, but not on the richness of any guild. In total, hurricanes produced regional changes in community similarity largely without significant loss of richness or overall avian abundance. We identified several potential mechanisms for these changes in avian diversity, including hurricane‐induced changes in forest habitat and the use of refugia by birds displaced from hurricane‐damaged forests. The prospect of increasing frequency and intensity of hurricanes is not likely to invoke a conservation crisis for birds provided we maintain sufficient forest habitat so that avifauna can respond to hurricanes by shifting to areas of suitable habitat.
Soil organic carbon stock change due to land use activity along the agricultural frontier of the southwestern Amazon, Brazil, between 1970 and 2002
Authors: MAIA STOÉCIO M. F. , OGLE STEPHEN M. , CERRI CARLOS E. P. , CERRI CARLOS C.
Published: October 2009

The southwestern portion of the Brazilian Amazon arguably represents the largest agricultural frontier in the world, and within this region the states of Rondônia and Mato Grosso have about 24% and 32% of their respective areas under agricultural management, which is almost half of the total area deforested in the Brazilian Amazon biome. Consequently, it is assumed that deforestation in this region has caused substantial loss of soil organic carbon (SOC). In this study, the changes in SOC stocks due to the land use change and management in the southwestern Amazon were estimated for two time periods from 1970–1985 and 1985–2002. An uncertainty analysis was also conducted using a Monte Carlo approach. The results showed that mineral soils converted to agricultural management lost a total of 5.37 and 3.74 Tg C yr−1 between 1970–1985 and 1985–2002, respectively, along the Brazilian Agricultural Frontier in the states of Mato Grosso and Rondônia. Uncertainties in these estimates were ±37.3% and ±38.6% during the first and second time periods, respectively. The largest sources of uncertainty were associated with reference carbon (C) stocks, expert knowledge surveys about grassland condition, and the management factors for nominal and degraded grasslands. These results showed that land use change and management created a net loss of C from soils, however, the change in SOC stocks decreased substantially from the first to the second time period due to the increase in land under no‐tillage.
Eutrophication and macroalgal blooms in temperate and tropical coastal waters: nutrient enrichment experiments with Ulva spp.
Authors: TEICHBERG MIRTA , FOX SOPHIA E. , OLSEN YLVA S. , VALIELA IVAN , MARTINETTO PAULINA , IRIBARNE OSCAR , MUTO ELIZABETI YURIKO , PETTI MONICA A. V. , CORBISIER THAÏS N. , SOTO‐JIMÉNEZ MARTÍN , PÁEZ‐OSUNA FEDERICO , CASTRO PAULA , FREITAS HELENA , ZITELLI ANDREINA , CARDINALETTI MASSIMO , TAGLIAPIETRA DAVIDE
Published: October 2009

Receiving coastal waters and estuaries are among the most nutrient‐enriched environments on earth, and one of the symptoms of the resulting eutrophication is the proliferation of opportunistic, fast‐growing marine seaweeds. Here, we used a widespread macroalga often involved in blooms, Ulva spp., to investigate how supply of nitrogen (N) and phosphorus (P), the two main potential growth‐limiting nutrients, influence macroalgal growth in temperate and tropical coastal waters ranging from low‐ to high‐nutrient supplies. We carried out N and P enrichment field experiments on Ulva spp. in seven coastal systems, with one of these systems represented by three different subestuaries, for a total of nine sites. We showed that rate of growth of Ulva spp. was directly correlated to annual dissolved inorganic nitrogen (DIN) concentrations, where growth increased with increasing DIN concentration. Internal N pools of macroalgal fronds were also linked to increased DIN supply, and algal growth rates were tightly coupled to these internal N pools. The increases in DIN appeared to be related to greater inputs of wastewater to these coastal waters as indicated by high δ15N signatures of the algae as DIN increased. N and P enrichment experiments showed that rate of macroalgal growth was controlled by supply of DIN where ambient DIN concentrations were low, and by P where DIN concentrations were higher, regardless of latitude or geographic setting. These results suggest that understanding the basis for macroalgal blooms, and management of these harmful phenomena, will require information as to nutrient sources, and actions to reduce supply of N and P in coastal waters concerned.
Paternally derived immune priming for offspring in the red flour beetle, Tribolium castaneum
Authors: Roth Olivia , Joop Gerrit , Eggert Hendrik , Hilbert Jonas , Daniel Jens , Schmid‐Hempel Paul , Kurtz Joachim
Published: October 2009

1. Parasitized females in mammals, fish and birds can enhance the immune defence of their offspring by transferring specific antibodies for the embryo. Likewise, social insect mothers transfer immunity despite the fact that invertebrates lack antibodies.

2. Female trans‐generational immune priming is consistent with parental investment theory, because mothers invest more into rearing their offspring than fathers. However, when immune priming is not directly linked to parental care, as is often the case in insects that abandon their eggs after oviposition, both sexes might benefit from protecting their offspring.

3. Using the red flour beetle, Tribolium castaneum, we show that after parental exposure to heat‐killed bacteria, trans‐generational immune priming occurs through fathers as well as mothers.

4. This novel finding challenges the traditional view that males provide only genes to their offspring in species without paternal care, and raises the possibility of a division of tasks with respect to immune protection between parents.
Are the Northern Andes a species pump for Neotropical birds? Phylogenetics and biogeography of a clade of Neotropical tanagers (Aves: Thraupini)
Authors: Sedano Raul E. , Burns Kevin J.
Published: October 2009

Aim  We used mitochondrial DNA sequence data to reconstruct the phylogeny of a large clade of tanagers (Aves: Thraupini). We used the phylogeny of this Neotropical bird group to identify areas of vicariance, reconstruct ancestral zoogeographical areas and elevational distributions, and to investigate the correspondence of geological events to speciation events.

Location  The species investigated are found in 18 of the 22 zoogeographical regions of South America, Central America and the Caribbean islands; therefore, we were able to use the phylogeny to address the biogeographical history of the entire region.

Methods  Molecular sequence data were gathered from two mitochondrial markers (cytochrome b and ND2) and analysed using Bayesian and maximum‐likelihood approaches. Dispersal–vicariance analysis (DIVA) was used to reconstruct zoogeographical areas and elevational distributions. A Bayesian framework was also used to address changes in elevation during the evolutionary history of the group.

Results  Our phylogeny was similar to previous tanager phylogenies constructed using fewer species; however, we identified three genera that are not monophyletic and uncovered high levels of sequence divergence within some species. DIVA identified early diverging nodes as having a Northern Andean distribution, and the most recent common ancestor of the species included in this study occurred at high elevations. Most speciation events occurred either within highland areas or within lowland areas, with few exchanges occurring between the highlands and lowlands. The Northern Andes has been a source for lineages in other regions, with more dispersals out of this area relative to dispersals into this area. Most of the dispersals out of the Northern Andes were dispersals into the Central Andes; however, a few key dispersal events were identified out of the Andes and into other zoogeographical regions.

Main conclusions  The timing of diversification of these tanagers correlates well with the main uplift of the Northern Andes, with the highest rate of speciation occurring during this timeframe. Central American tanagers included in this study originated from South American lineages, and the timing of their dispersal into Central America coincides with or post‐dates the completion of the Panamanian isthmus.
Image‐based 3D reconstruction using helical nanobelts for localized rotations
Authors: KRATOCHVIL B.E. , DONG L.X. , ZHANG L. , NELSON B.J.
Published: October 2009

A variety of different methods exist for gathering three‐dimensional information for micro‐ and nanoscale objects. Tilting of samples in a scanning electron microscope provides a non‐destructive way of generating these data. Traditionally, the reconstruction of this image data is performed by stereo photogrammetric methods that compare features from two or three frames. We propose the application of techniques from the structure‐from‐motion community as being efficient, high‐precision alternatives to stereo methods, which allows for automated utilization of a large number of sampled images. We propose the use of nanobelts to generate localized rotational motions. Using this method alleviates the demand of high‐precision actuators, allows 360° rotations, and provides a useful tool for micro‐ and nanomanipulation.
Leptin: Back and Forward
Authors: Mercer Julian
Published: October 2009

The discovery of leptin resulted in a gear change in obesity research. Exploiting its therapeutic potential has proved to be a long game, although encouraging progress is now being made with leptin monotherapy in conditions of relative deficiency, and with combination therapy against common obesity. Leptin’s role in early brain development constitutes an exciting area for mechanistic study with potential therapeutic implications.
Photic and Nonphotic Seasonal Cues Differentially Engage Hypothalamic Kisspeptin and RFamide‐Related Peptide mRNA Expression in Siberian Hamsters
Authors: Paul M. J. , Pyter L. M. , Freeman D. A. , Galang J. , Prendergast B. J.
Published: October 2009

Seasonally breeding animals use a combination of photic (i.e. day length) and nonphotic (e.g. food availability, temperature) cues to regulate their reproduction. How these environmental cues are integrated is not understood. To assess the potential role of two candidate neuropeptides, kisspeptin and RFamide‐related peptide‐3 (RFRP), we monitored regional changes in their gene expression in a seasonally breeding mammal exposed to moderate changes in photoperiod and food availability. Adult male Siberian hamsters (Phodopus sungorus) were housed under a long (16 h light/day; 16 L) or intermediate (13.5 L) photoperiod and fed ad lib. or a progressive food restriction schedule (FR; reduced to 80% of ad lib.) for 11 weeks. Gonadal regression occurred only in FR hamsters housed under 13.5 L. Immunohistochemistry was used to identify diencephalic populations of kisspeptin‐ and RFRP‐immunoreactive cells, and quantitative PCR was used to measure gene expression in adjacent coronal brain sections. Photoperiod, but not food availability, altered RFRP mRNA expression in the dorsomedial sections, whereas food availability but not photoperiod altered Kiss1 expression in the arcuate sections; intermediate photoperiods elevated RFRP expression, and food restriction suppressed Kiss1 expression. Regional‐ and neuropeptide‐specific activity of RFamides may provide a mechanism for integration of multi‐modal environmental information in the seasonal control of reproduction.
Up against the edge: invasive species as testbeds for basic questions about evolution in heterogeneous environments
Authors: HOLT ROBERT D.
Published: October 2009

Yogi Berra is often credited* with having opined that ‘prediction is very difficult, especially about the future’. There is no discipline for which this statement holds with more force than invasion biology, where it has been historically very challenging to predict the fate of introduced species (Williamson 2006). Some species after introduction quickly go extinct. Other relatively similar species may persist, but with little spread from their initial beachheads. Yet others can become aggressive invaders, with devastating consequences for native communities and ecosystems. This lack of predictability may of course sometimes reflect a simple lack of knowledge, both about key features of a species’ basic biology, and about the environmental and community milieu in which invasion occurs (Williamson 2006). However, unpredictability may also arise from a fundamental fact about populations of living organisms – they almost always contain genetic variation, and so are not fixed entities responding to an environmental template, but instead labile in how they cope with the environment, over many spatial and temporal scales. Chance vicissitudes in the origination, maintenance and spatial organization of genetic variation could play a large role in generating the observed unpredictability in the fates of introduced species. The degree to which a particular introduced species becomes ‘invasive’– to the extent of coming to the attention of worried land managers, governmental officials and the public – may reflect in part its capacity for adaptive evolution across a wide range of environmental conditions.
Molybdenum and tungsten in Campylobacter jejuni: their physiological role and identification of separate transporters regulated by a single ModE‐like protein
Authors: Taveirne Michael E. , Sikes Michael L. , Olson Jonathan W.
Published: October 2009

Campylobacter jejuni is an important human pathogen that causes millions of cases of food‐borne enteritis each year. The C. jejuni respiratory chain is highly branched and contains at least four enzymes predicted to contain a metal binding pterin (MPT), with the metal being either molybdenum or tungsten. Also predicted are two separate transport systems, one for molybdenum encoded by modABC and a second for tungsten encoded by tupABC. Both transport systems were mutated and the activities of the four predicted MPT‐containing enzymes were assayed in the presence of molybdenum and tungsten in wild‐type and mod and tup backgrounds. Results indicate that mod is primarily a molybdenum transporter that can also transport tungsten, while tup is a tungsten‐specific transporter. The MPT‐containing enzymes nitrate reductase, sulphite oxidase, and SN oxide reductase are strict molybdoenzymes while formate dehydrogenase prefers tungsten. A ModE‐like protein regulates both transporters, repressing mod in the presence of both molybdenum and tungsten and tup only in the presence of tungsten. Like other ModE proteins, the C. jejuni ModE binds DNA through a helix–turn–helix DNA binding domain, but unlike other members of the ModE family it does not have a metal binding domain.
Genetic polymorphisms and haplotype structures of HSPA5 gene in the Han population of Southern China
Authors: Zhu X. , Cheng J. , Zhao J , Chen L. , Hou S. , Zhao G. , Lan F. , Wang W. , Kung H. , He M.
Published: October 2009

The heat shock 70 kDa protein 5 (HSPA5) gene is known to be involved in stress‐associated diseases. In this study, the promoter, exons, 3′ untranslated region (3′UTR), and subtotal introns of the HSPA5 gene were sequenced in a sub‐population of 161 healthy Han Chinese. Nine single‐nucleotide polymorphisms (SNPs) including a new one (‐86bp T > A from the estimated translation start site) were found and 15 haplotypes (frequencies > 1%) were inferred. Polymorphisms rs391957 and rs11355458 were completely linked in our population (r 2 = 1.00). Using this information, fellow scientists may be able to decrease the number of SNPs to be genotyped in future disease case‐control studies.
Fine mapping of the CELIAC2 locus on chromosome 5q31‐q33 in the Finnish and Hungarian populations
Authors: Koskinen L. L. E. , Einarsdottir E. , Korponay‐Szabo I. R. , Kurppa K. , Kaukinen K. , Sistonen P. , Pocsai Z. , Széles G. , Ádány R. , Mäki M. , Kere J. , Saavalainen P.
Published: October 2009

Celiac disease is a chronic inflammation of the small intestine, arising in genetically predisposed individuals as a result of ingestion of dietary gluten. The only confirmed and functionally characterised genetic risk factors for celiac disease are the DQ2 or DQ8 heterodimers at the major histocompatibility complex (MHC) class II locus (CELIAC1). These genes are necessary but alone not sufficient for disease onset. Genome‐wide linkage scans have suggested chromosome 5q31‐q33 (CELIAC2) as an important risk locus for celiac disease. This region has also been associated to other inflammatory disorders, although as yet, no clear gene associations have been found. In the current study, 11 celiac disease candidate loci were screened for genetic linkage in the Hungarian population. As the CELIAC2 locus showed the strongest evidence for linkage, this locus was selected for follow‐up. Seventeen candidate genes were selected from the CELIAC2 locus, and genotyped using 48 haplotype tagging single nucleotide polymorphisms (SNPs) in large Finnish and Hungarian family materials. A subset of these, 40 tagging SNPs in 15 genes, were genotyped in an independent set of Finnish and Hungarian cases and controls. We confirmed linkage of this region with celiac disease and report strong linkage in both the Finnish and Hungarian populations. The association analysis showed modest associations throughout the whole region. These association findings were not replicated in the case–control datasets. Our study strongly supports the role of the CELIAC2 locus in celiac disease, but it also highlights the need for a more powerful study design in the region, to locate the true disease risk variants.
Evaluation of duodenal hypersensitivity induced by duodenal acidification using transnasal endoscopy
Authors: Ishii Manabu , Kusunoki Hiroaki , Manabe Noriaki , Kamada Tomoari , Sato Motonori , Imamura Hiroshi , Shiotani Akiko , Hata Jiro , Haruma Ken
Published: October 2009

Background and Aim:  Although duodenal hypersensitivity has been suggested as one of the causes of functional dyspepsia (FD), a practical method to clarify this has not yet been established. The aim of this study was to evaluate whether patients with FD have duodenal hypersensitivity to acid, using transnasal endoscopy.

Methods:  In all, 44 patients with FD and 16 healthy volunteers were enrolled, and all the subjects received transnasal endoscopy in the morning after overnight fasting. After ordinary transnasal endoscopy, an infusion tube was introduced into the duodenal bulb by transnasal endoscopy and acid (20 mL, 0.1 N HCl, 20 mL/min, 36.5°C) was injected via the infusion tube. The severity of 12 symptoms was assessed by each subject using a 100‐mm visual analogue scale. The maximum severity scale was defined as the maximum score of the symptom severity scale. The total score was defined as the aggregate score of the maximum severity scale of the 12 symptoms. The maximum severity scales and the total scores between patients with FD and healthy volunteers were evaluated.

Results:  The maximum severity scales of nine symptoms increased significantly more after acid infusion in patients with FD than in healthy volunteers (P < 0.05). There were significant differences in the total scores (patients with FD vs healthy volunteers 233.8 ± 37.8 vs 63.9 ± 14.6, mean ± standard error of the mean, P < 0.001).

Conclusions:  Duodenal acidification using transnasal endoscopy enabled the evaluation of duodenal hypersensitivity to acid in healthy volunteers and patients with FD.
PSA at postoperative three months can predict biochemical recurrence in patients with pathological T3 prostate cancer following radical prostatectomy
Authors: Inagaki Takeshi , Kohjimoto Yasuo , Nishizawa Satoshi , Kuramoto Tomomi , Nanpo Yoshihito , Fujii Reona , Matsumura Nagahide , Shintani Yasuyo , Uekado Yasunari , Hara Isao
Published: October 2009

Objectives:  To identify the prognostic factors and determine which pT3 prostate cancer patients can be safely followed up after surgery without any adjuvant treatment.

Methods:  A retrospective review was carried out on 106 patients with pT3 prostate cancer. All preoperative and postoperative parameters, including the postoperative serum prostate‐specific antigen (PSA) level at 3 months after surgery, were assessed by univariate and multivariate analyses.

Results:  Mean follow‐up period was 18 months. The overall biochemical recurrence‐free rate was 53.7% and 34.1% at 12 and 36 months, respectively. On univariate analysis, all preoperative clinical factors were significantly correlated with biochemical progression. On multivariate analysis, pathological Gleason score, pathological stage and postoperative PSA were significant predictors. Among those with undetectable PSA after surgery, 38 patients (88.4% of 43) did not have disease progression during the follow‐up period. On the other hand, of the 27 patients with detectable PSA that was not defined as progressive (range 0.01–0.20), 22 (81.5%) had biochemical disease progression. The progression free probability was significantly different between these two groups (P‐value < 0.0001).

Conclusions:  pT3 prostate cancer patients showing low pathological Gleason score, without seminal vesicle invasion, and undetectable postoperative PSA values have low probability of PSA progression. Careful follow up including periodic PSA assessment and clinical observation represents an adequate strategy in the management of these patients.
Influence of photoperiod duration and light–dark transitions on entrainment of Per1 and Per2 gene and protein expression in subdivisions of the mouse suprachiasmatic nucleus
Authors: Sosniyenko Serhiy , Hut Roelof A. , Daan Serge , Sumová Alena
Published: October 2009

The circadian clock located within the suprachiasmatic nuclei (SCN) of the hypothalamus responds to changes in the duration of day length, i.e. photoperiod. Recently, changes in phase relationships among the SCN cell subpopulations, especially between the rostral and caudal region, were implicated in the SCN photoperiodic modulation. To date, the effect of abrupt, rectangular, light‐to‐dark transitions have been studied while in nature organisms experience gradual dawn and twilight transitions. The aim of this study was to compare the effect of a long (18 h of light) and a short (6 h of light) photoperiod with twilight relative to that with rectangular light‐to‐dark transition on the daily profiles of Per1 and Per2 mRNA (in situ hybridization) and PER1 and PER2 protein (immunohistochemistry) levels within the rostral, middle and caudal regions of the mouse SCN. Under the short but not under the long photoperiod, Per1, Per2 and PER1, PER2 profiles were significantly phase‐advanced under the twilight relative to rectangular light‐to‐dark transition in all SCN regions examined. Under the photoperiods with rectangular light‐to‐dark transition, Per1 and Per2 mRNA profiles in the caudal SCN were phase‐advanced as compared with those in the rostral SCN. The phase differences between the SCN regions were reduced under the long, or completely abolished under the short, photoperiods with twilight. The data indicate that the twilight photoperiod provides stronger synchronization among the individual SCN cell subpopulations than the rectangular one, and the effect is more pronounced under the short than under the long photoperiod.
Population coding of tone stimuli in auditory cortex: dynamic rate vector analysis
Authors: Bartho Peter , Curto Carina , Luczak Artur , Marguet Stephan L. , Harris Kenneth D.
Published: October 2009

Neural representations of even temporally unstructured stimuli can show complex temporal dynamics. In many systems, neuronal population codes show ‘progressive differentiation’, whereby population responses to different stimuli grow further apart during a stimulus presentation. Here we analysed the response of auditory cortical populations in rats to extended tones. At onset (up to 300 ms), tone responses involved strong excitation of a large number of neurons; during sustained responses (after 500 ms) overall firing rate decreased, but most cells still showed statistically significant rate modulation. Population vector trajectories evoked by different tone frequencies expanded rapidly along an initially similar trajectory in the first tens of milliseconds after tone onset, later diverging to smaller amplitude fixed points corresponding to sustained responses. The angular difference between onset and sustained responses to the same tone was greater than between different tones in the same stimulus epoch. No clear orthogonalization of responses was found with time, and predictability of the stimulus from population activity also decreased during this period compared with onset. The question of whether population activity grew more or less sparse with time depended on the precise mathematical sense given to this term. We conclude that auditory cortical population responses to tones differ from those reported in many other systems, with progressive differentiation not seen for sustained stimuli. Sustained acoustic stimuli are typically not behaviorally salient: we hypothesize that the dynamics we observe may instead allow an animal to maintain a representation of such sounds, at low energetic cost.
A critical role for dynamic changes in histone H3 methylation at the Bdnf promoter during postnatal thermotolerance acquisition
Authors: Kisliouk Tatiana , Meiri Noam
Published: October 2009

As with other sensory mechanisms, determination of the thermal‐control set point is refined during a critical period of development by alterations in cellular properties in the frontal hypothalamus. These alterations in hypothalamic plasticity are achieved by renewal of the protein repertoire via activation or silencing of gene transcription, both of which are regulated by histone modifications. This study demonstrates induction of global histone H3 lysine 27 (H3K27) dimethylation, with no changes in its trimethylation levels, in the frontal hypothalamus, as well as at the promoter of the brain‐derived neurotrophic factor (BDNF) gene during thermal‐control establishment. Furthermore, antisense ‘knockdown’ of the H3K27‐specific methyltransferase, enhancer of zeste 2, which was induced in correlation with the dimethylation of H3K27, inhibited Bdnf mRNA expression and disrupted the establishment of thermoregulation. This phenotypic effect was partially rescued by intracranial injection of BDNF. The presented findings highlight the specific epigenetic role of chromatin modifications in thermal‐control establishment.
Stochastic Growth and Factor Income Risk
Authors: Clemens Christiane
Published: October 2009

This paper examines the effects of aggregate factor income risk in a tractable version of the stochastic Romer endogenous growth model. Labor supply is endogenous. The presence of labor income risk unambiguously increases savings and growth due to precautionary motives. Households not only underaccumulate but also work less along the balanced growth path of the competitive economy when compared with the Pareto-efficient allocation. The paper also discusses distributive disturbances for the case of inelastic labor supply. Here, growth effects are negative for empirically plausible correlations of the underlying shocks.
The Augmented Solow Model with Mincerian Schooling and Externalities
Authors: Carstensen Kai , Hartmann Susanne , Gundlach Erich
Published: October 2009

We combine the augmented Solow model with the Mincer equation to derive a specification that identifies an education externality within a production function framework. The previous empirical literature has not reached a consensus about the size of the education externality, which is given by the difference between the microeconomic and the macroeconomic return to education. Relative to our benchmark value that is based on a parameterization of the derived specification, we find that the estimated education externality is too large when the empirical model is not properly restricted, and appears to be absent when all control variables of the empirical model are properly accounted for. We note that the absence of an education externality is difficult to reconcile with observed levels of education subsidies for efficiency reasons.
Pre‐hospital notification reduced the door‐to‐needle time for iv t‐PA in acute ischaemic stroke
Authors: Kim S. K. , Lee S. Y. , Bae H. J. , Lee Y. S. , Kim S. Y. , Kang M. J. , Cha J. K.
Published: October 2009

Background and purpose:  Intrahospital delay is the most serious obstacle in thrombolysis in acute ischaemic stroke (AIS). We implemented the pre‐hospital notification system from the emergency medical information system in our metropolitan area to reduce intrahospital delay.

Methods:  From October 2007, we implemented a 24‐h hotline system between our stroke center and the Korean Emergency Medical Information System in Busan. We compared processing times and clinical outcomes amongst patients after using intravenous tissue type plasminogen activator (iv t‐PA) with and without the hotline system.

Results:  After the pre‐hospital notification system was implemented, the rate of iv t‐PA use increased from 6.5% to 14.3%. Time of onset in patients with pre‐hospital notification was much longer than in patients without (121.5 ± 34.8 min vs. 74.7 ± 38.5 min, P < 0.01) notification but door‐to‐needle time was significantly reduced (28.9 ± 11.4 min vs. 47.7 ± 22.8 min, P < 0.01). However, there were no significant differences in 90‐day clinical outcomes between the two groups.

Conclusions:  The pre‐hospital notification system reduced intrahospital processing times which led to increased iv t‐PA use after AIS. However, the improvement of clinical outcomes in thrombolysis might require organization of not only intrahospital processes but of outside processes such as the early recognition and rapid dispatch of patients with suspected AIS.
Should the SCOPA‐COG be modified?: a Rasch analysis perspective
Authors: Forjaz M. J. , Frades‐Payo B. , Rodriguez‐Blazquez C. , Ayala A. , Martinez‐Martin P. ,   on behalf of the Longitudinal Parkinson’s Disease Patient Study (Estudio longitudinal de pacientes con enfermedad de Parkinson–ELEP) Group
Published: October 2009

Background and purpose: The SCales for Outcomes in PArkinson’s disease‐Cognition (SCOPA‐COG) is a specific measure of cognitive function for Parkinson’s disease (PD) patients. Previous studies, under the frame of the classic test theory, indicate satisfactory psychometric properties. The Rasch model, an item response theory approach, provides new information about the scale, as well as results in a linear scale. This study aims at analysing the SCOPA‐COG according to the Rasch model and, on the basis of results, suggesting modification to the SCOPA‐COG.

Method: Fit to the Rasch model was analysed using a sample of 384 PD patients.

Results: A good fit was obtained after rescoring for disordered thresholds. The person separation index, a reliability measure, was 0.83. Differential item functioning was observed by age for three items and by gender for one item.

Conclusions: The SCOPA‐COG is a unidimensional measure of global cognitive function in PD patients, with good scale targeting and no empirical evidence for use of the subscale scores. Its adequate reliability and internal construct validity were supported. The SCOPA‐COG, with the proposed scoring scheme, generates true linear interval scores.