bluuebunny/crossref_metadata_2025 huggingface dataset:
Word learning and the cerebral hemispheres: from serial to parallel processing of written words
Authors: Ellis Andrew W. , Ferreira Roberto , Cathles-Hagan Polly , Holt Kathryn , Jarvis Lisa , Barca Laura
Published: November 2009

Reading familiar words differs from reading unfamiliar non-words in two ways. First, word reading is faster and more accurate than reading of unfamiliar non-words. Second, effects of letter length are reduced for words, particularly when they are presented in the right visual field in familiar formats. Two experiments are reported in which right-handed participants read aloud non-words presented briefly in their left and right visual fields before and after training on those items. The non-words were interleaved with familiar words in the naming tests. Before training, naming was slow and error prone, with marked effects of length in both visual fields. After training, fewer errors were made, naming was faster, and the effect of length was much reduced in the right visual field compared with the left. We propose that word learning creates orthographic word forms in the mid-fusiform gyrus of the left cerebral hemisphere. Those word forms allow words to access their phonological and semantic representations on a lexical basis. But orthographic word forms also interact with more posterior letter recognition systems in the middle/inferior occipital gyri, inducing more parallel processing of right visual field words than is possible for any left visual field stimulus, or for unfamiliar non-words presented in the right visual field.
Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex
Authors: Tan-Wong Sue Mei , Wijayatilake Hashanthi D. , Proudfoot Nick J.
Published: November 2009

Inducible genes in yeast retain a “memory” of recent transcriptional activity during periods of short-term repression, allowing them to be reactivated faster when reinduced. This confers a rapid and versatile gene expression response to the environment. We demonstrate that this memory mechanism is associated with gene loop interactions between the promoter and 3′ end of the responsive genes HXK1 and GAL1∷FMP27. The maintenance of these memory gene loops (MGLs) during intervening periods of transcriptional repression is required for faster RNA polymerase II (Pol II) recruitment to the genes upon reinduction, thereby facilitating faster mRNA accumulation. Notably, a sua7-1 mutant or the endogenous INO1 gene that lacks this MGL does not display such faster reinduction. Furthermore, these MGLs interact with the nuclear pore complex through association with myosin-like protein 1 (Mlp1). An mlp1Δ strain does not maintain MGLs, and concomitantly loses transcriptional memory. We predict that gene loop conformations enhance gene expression by facilitating rapid transcriptional response to changing environmental conditions.
A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)
Authors: Lee Yong Sun , Shibata Yoshiyuki , Malhotra Ankit , Dutta Anindya
Published: November 2009

New types of small RNAs distinct from microRNAs (miRNAs) are progressively being discovered in various organisms. In order to discover such novel small RNAs, a library of 17- to 26-base-long RNAs was created from prostate cancer cell lines and sequenced by ultra-high-throughput sequencing. A significant number of the sequences are derived from precise processing at the 5′ or 3′ end of mature or precursor tRNAs to form three series of tRFs (tRNA-derived RNA fragments): the tRF-5, tRF-3, and tRF-1 series. These sequences constitute a class of short RNAs that are second most abundant to miRNAs. Northern hybridization, quantitative RT–PCR, and splinted ligation assays independently measured the levels of at least 17 tRFs. To demonstrate the biological importance of tRFs, we further investigated tRF-1001, derived from the 3′ end of a Ser-TGA tRNA precursor transcript that is not retained in the mature tRNA. tRF-1001 is expressed highly in a wide range of cancer cell lines but much less in tissues, and its expression in cell lines was tightly correlated with cell proliferation. siRNA-mediated knockdown of tRF-1001 impaired cell proliferation with the specific accumulation of cells in G2, phenotypes that were reversed specifically by cointroducing a synthetic 2′-O-methyl tRF-1001 oligoribonucleotide resistant to the siRNA. tRF-1001 is generated in the cytoplasm by tRNA 3′-endonuclease ELAC2, a prostate cancer susceptibility gene. Our data suggest that tRFs are not random by-products of tRNA degradation or biogenesis, but an abundant and novel class of short RNAs with precise sequence structure that have specific expression patterns and specific biological roles.
TNFα shedding and epidermal inflammation are controlled by Jun proteins
Authors: Guinea-Viniegra Juan , Zenz Rainer , Scheuch Harald , Hnisz Denes , Holcmann Martin , Bakiri Latifa , Schonthaler Helia B. , Sibilia Maria , Wagner Erwin F.
Published: November 2009

Inducible epidermal deletion ofJunBandc-Junin adult mice causes a psoriasis-like inflammatory skin disease. Increased levels of the proinflammatory cytokine TNFα play a major role in this phenotype. Here we define the underlying molecular mechanism using genetic mouse models. We show that Jun proteins control TNFα shedding in the epidermis by direct transcriptional activation of tissue inhibitor of metalloproteinase-3 (TIMP-3), an inhibitor of the TNFα-converting enzyme (TACE). TIMP-3 is down-regulated and TACE activity is specifically increased, leading to massive, cell-autonomous TNFα shedding upon loss of both JunB and c-Jun. Consequently, a prominent TNFα-dependent cytokine cascade is initiated in the epidermis, inducing severe skin inflammation and perinatal death of newborns from exhaustion of energy reservoirs such as glycogen and lipids. Importantly, this metabolic “cachectic” phenotype can be genetically rescued in a TNFR1-deficient background or by epidermis-specific re-expression of TIMP-3. These findings reveal that Jun proteins are essential physiological regulators of TNFα shedding by controlling the TIMP-3/TACE pathway. This novel mechanism describing how Jun proteins control skin inflammation offers potential targets for the treatment of skin pathologies associated with increased TNFα levels.
Nonallelic transvection of multiple imprinted loci is organized by the H19 imprinting control region during germline development
Authors: Sandhu Kuljeet Singh , Shi Chengxi , Sjölinder Mikael , Zhao Zhihu , Göndör Anita , Liu Liang , Tiwari Vijay K. , Guibert Sylvain , Emilsson Lina , Imreh Marta P. , Ohlsson Rolf
Published: November 2009

Recent observations highlight that the mammalian genome extensively communicates with itself via long-range chromatin interactions. The causal link between such chromatin cross-talk and epigenetic states is, however, poorly understood. We identify here a network of physically juxtaposed regions from the entire genome with the common denominator of being genomically imprinted. Moreover, CTCF-binding sites within the H19 imprinting control region (ICR) not only determine the physical proximity among imprinted domains, but also transvect allele-specific epigenetic states, identified by replication timing patterns, to interacting, nonallelic imprinted regions during germline development. We conclude that one locus can directly or indirectly pleiotropically influence epigenetic states of multiple regions on other chromosomes with which it interacts.
Development of a shutterless continuous rotation method using an X-ray CMOS detector for protein crystallography
Authors: Hasegawa Kazuya , Hirata Kunio , Shimizu Tetsuya , Shimizu Nobutaka , Hikima Takaaki , Baba Seiki , Kumasaka Takashi , Yamamoto Masaki
Published: November 2009

A new shutterless continuous rotation method using an X-ray complementary metal-oxide semiconductor (CMOS) detector has been developed for high-speed, precise data collection in protein crystallography. The principle of operation and the basic performance of the X-ray CMOS detector (Hamamatsu Photonics KK C10158DK) have been shown to be appropriate to the shutterless continuous rotation method. The data quality of the continuous rotation method is comparable to that of the conventional oscillation method using a CCD detector and, furthermore, the combination with fine φ slicing improves the data accuracy without increasing the data-collection time. The new method is more sensitive to diffraction intensity because of the narrow dynamic range of the CMOS detector. However, the strong diffraction spots were found to be precisely measured by recording them on successive multiple images by selecting an adequate rotation step. The new method has been used to successfully determine three protein structures by multi- and single-wavelength anomalous diffraction phasing and has thereby been proved applicable in protein crystallography. The apparatus and method may become a powerful tool at synchrotron protein crystallography beamlines with important potential across a wide range of X-ray wavelengths.
Neutron powder diffraction in materials with incoherent scattering: an illustration of Rietveld refinement quality from nondeuterated gypsum
Authors: Henry Paul F. , Weller Mark T. , Wilson Chick C.
Published: November 2009

The power of the state-of-the-art neutron powder diffractometer suite at the Institut Laue–Langevin for investigating the structure of nondeuterated materials is presented using gypsum, CaSO4·2H2O, as a reference material. It is shown that flexible modern neutron powder diffraction instruments at reactor-based sources can yield data with sufficient counting statistics above the incoherent scattering contribution to perform unconstrained refinements in relatively short time periods (from minutes to a few hours, depending on the sample size and the instrument choice), without the requirement for significant changes to the standard operational modes of the instruments. The results are critically compared with previous literature from single-crystal and powder X-ray and neutron measurements on deuterated and nondeuterated gypsum.
Isomorphism in monomeric 1:3 complexes of silver(I) salts with tri-p-tolylphosphine
Authors: Omondi Bernard , Venter Gertruida J. S. , Roodt Andreas , Meijboom Reinout
Published: November 2009

Reaction of silver(I) salts with three equivalents of tri-p-tolylphosphine in CH3CN resulted in a series of isomorphous complexes [AgX{P(4-MeC6H4)3}3] (X = Br, SCN, ClO4). These complexes all crystallize in the orthorhombic space group Pna21. The complexes with X = Br, SCN are distorted tetrahedral around the silver(I) atom, whereas the ClO4
− complex is distorted trigonal planar around the silver. The new complexes are compared with each other using r.m.s. overlay calculations as well as half-normal probability plot analysis and with the previously reported isomorphous chloride, bromide as well as the non-isomorphous iodide complexes.
Cluster analyses of metal-organic fragments using the dSNAP software
Authors: Collins Anna , Wilson Chick C. , Gilmore Christopher J.
Published: November 2009

The dSNAP computer program has been used to classify searches of the Cambridge Structural Database for two ligands: —O—CH2—CH2—O— and N(CH2CH2O—)3 commonly found in metal-organic systems. The clustering method used is based on total geometries (i.e. all the lengths and angles involving all the atoms in the search fragment, whether bonded or not) and proved capable of distinguishing in a wholly automatic, objective way between different types of metal complex purely on the basis of the geometry of the ligand and the relative positions of the O atoms to the metals.
Growth and single-crystal refinement of phase-III potassium nitrate, KNO3
Authors: Freney Evelyn J. , Garvie Laurence A. J. , Groy Thomas L. , Buseck Peter R.
Published: November 2009

Oriented single crystals of the high-temperature phase of KNO3 (phase III), a ferroelectric compound that may also occur as an atmospheric aerosol particle, were grown at room temperature and pressure by atomizing a solution of KNO3 in water and allowing droplets to dry on a glass substrate. The crystals are up to 1 mm across and are stable unless mechanically disturbed. There is no evidence of the spontaneous transformation of phase III to the room-temperature stable phase (phase II), even after several months. Single-crystal structure determinations of phase III were obtained at 295 and 123 K. The unit cell regained its room-temperature dimensions after warming from 123 K. The phase-III KNO3 structure can be viewed as the stacking parallel to the c axis of alternating K atoms and planar NO3 groups. The NO3 groups connect the planes of K atoms, where each O is fourfold coordinated to one N and three K. Each K atom has nine O nearest neighbors, with three bonds at 2.813 and six at 2.9092 Å. The interatomic K—N—K distance alternates from 5.051 to 3.941 along the c axis. The N—O distances increase from 1.245 (2) Å at 295 K to 1.2533 (15) Å at 123 K. The nitrate group has a slight non-planarity, with the N atoms 0.011 Å above the O plane and directed toward the more distant K of the K—N—K chain.
[Ru(py)4Cl(NO)](PF6)2·0.5H2O: a model system for structural determination and ab initio calculations of photo-induced linkage NO isomers. Erratum
Authors: Cormary Benoît , Malfant Isabelle , Valade Lydie , Buron-Le Cointe Marylise , Toupet Loïc , Todorova Teodora , Delley Bernard , Schaniel Dominik , Mockus Nicholas , Woike Theo , Fejfarová Karla , Petříček Václav , Dušek Michal
Published: November 2009

In the paper by Cormary et al. [Acta Cryst. (2009), B65, 612–623] two authors were inadvertently omitted from the author list and one name was given incorrectly.
How to easily replace the independent atom model – the example of bergenin, a potential anti-HIV agent of traditional Asian medicine
Authors: Dittrich Birger , Weber Manuela , Kalinowski Roman , Grabowsky Simon , Hübschle Christian B. , Luger Peter
Published: November 2009

Bergenin, which has been isolated from a variety of tropical plants, has several pharmacological applications in traditional Asian medicine. Its electron-density distribution was obtained from a room-temperature low-resolution X-ray data set measured with point detection making use of multipole populations from the invariom library. Two refinement models were considered. In a first step, positional parameters and ADPs were refined with fixed library multipoles (model E1). This model was suitable to be input into a second refinement of multipoles (model E2), which converged smoothly although based on Cu Kα room-temperature data. Quantitative results of a topological analysis of the electron density from both models were compared with Hartree–Fock and density-functional calculations. With respect to the independent atom model (IAM) more information can be extracted from invariom modelling, including the electrostatic potential and hydrogen-bond energies, which are highly useful, especially for biologically active compounds. The reliability of the applied invariom formalism was assessed by a comparison of bond-topological properties of sucrose, for which high-resolution multipole and invariom densities were available. Since a conventional X-ray diffraction experiment using basic equipment was combined with the easy-to-use invariom formalism, the procedure described here for bergenin illustrates how it can be routinely applied in pharmacological research.
A multilocus approach to harvestman (Arachnida: Opiliones) phylogeny with emphasis on biogeography and the systematics of Laniatores
Authors: Giribet Gonzalo , Vogt Lars , González Abel Pérez , Sharma Prashant , Kury Adriano B.
Published: November 2009

The internal phylogeny of the arachnid order Opiliones is investigated by including molecular data from five molecular markers forca.140 species totalling 43 families of Opiliones. The phylogenetic analyses consisted of a direct optimization (DO) approach using POY v. 4 and sophisticated tree search algorithms as well as a static alignment analysed under maximum likelihood. The four Opiliones suborders were well‐supported clades, but subordinal relationships did not receive support in the DO analysis, with the exception of the monophyly of Palpatores (=Eupnoi + Dyspnoi). Maximum‐likelihood analysis strongly supported the traditional relationship of Phalangida and Palpatores: (Cyphophthalmi ((Eupnoi + Dyspnoi) Laniatores)). Relationships within each suborder are well resolved and largely congruent between direct optimization and maximum‐likelihood approaches. Age estimates for the main Opiliones lineages suggest a Carboniferous diversification of Cyphophthalmi, while its sister group, Phalangida, diversified in the Early Devonian. Diversification of all suborders predates the Triassic, and most major lineages predate the Cretaceous. The following taxonomic changes are proposed. Dyspnoi:Hesperonemastomais transferred to Sabaconidae. Insidiatores: Sclerobunidae stat. nov. is erected as a family forZuma acuta.

 © The Willi Hennig Society 2009.
Identification of quantitative trait loci for shank length and growth at different development stages in chicken
Authors: Gao Y. , Du Z.‐Q. , Feng C.‐G. , Deng X.‐M. , Li N. , Da Y. , Hu X.‐X.
Published: November 2009

Shank length affects chicken leg health and longer shanks are a source of leg problems in heavy‐bodied chickens. Identification of quantitative trait loci (QTL) affecting shank length traits may be of value to genetic improvement of these traits in chickens. A genome scan was conducted on 238 F2 chickens from a reciprocal cross between the Silky Fowl and the White Plymouth Rock breeds using 125 microsatellite markers to detect static and developmental QTL affecting weekly shank length and growth (from 1 to 12 weeks) in chickens. Static QTL affected shank length from birth to time t, while developmental QTL affected shank growth from time t−1 to time t. Seven static QTL on six chromosomes (GGA2, GGA3, GGA4, GGA7, GGA9 and GGA23) were detected at ages of 2, 3, 4, 5, 6, 7, 9 and 12 weeks, and six developmental QTL on five chromosomes (GGA1, GGA2, GGA4, GGA5 and GGA23) were detected for five shank growth periods, weeks 2–3, 4–5, 5–6, 10–11 and 11–12. A static QTL and a developmental QTL (SQSL1 and DQSL2) were identified at GGA2 (between ADL0190 and ADL0152). SQSL1 explained 2.87–5.30% of the phenotypic variation in shank length from 3 to 7 weeks. DQSL2 explained 2.70% of the phenotypic variance of shank growth between 2 and 3 weeks. Two static and two developmental QTL were involved chromosome 4 and chromosome 23. Two chromosomes (GGA7 and GGA9) had static QTL but no developmental QTL and another two chromosomes (GGA1 and GGA5) had developmental QTL but no static QTL. The results of this study show that shank length and shank growth at different developmental stages involve different QTL.
QTL mapping for two commercial traits in farmed saltwater crocodiles (Crocodylus porosus)
Authors: Miles L. G. , Isberg S. R. , Thomson P. C. , Glenn T. C. , Lance S. L. , Dalzell P. , Moran C.
Published: November 2009

The recent generation of a genetic linkage map for the saltwater crocodile (Crocodylus porosus) has now made it possible to carry out the systematic searches necessary for the identification of quantitative trait loci (QTL) affecting traits of economic, as well as evolutionary, importance in crocodilians. In this study, we conducted genome‐wide scans for two commercially important traits, inventory head length (which is highly correlated with growth rate) and number of scale rows (SR, a skin quality trait), for the existence of QTL in a commercial population of saltwater crocodiles at Darwin Crocodile Farm, Northern Territory, Australia. To account for the uncommonly large difference in sex‐specific recombination rates apparent in the saltwater crocodile, a duel mapping strategy was employed. This strategy employed a sib‐pair analysis to take advantage of our full‐sib pedigree structure, together with a half‐sib analysis to account for, and take advantage of, the large difference in sex‐specific recombination frequencies. Using these approaches, two putative QTL regions were identified for SR on linkage group 1 (LG1) at 36 cM, and on LG12 at 0 cM. The QTL identified in this investigation represent the first for a crocodilian and indeed for any non‐avian member of the Class Reptilia. Mapping of QTL is an important first step towards the identification of genes and causal mutations for commercially important traits and the development of selection tools for implementation in crocodile breeding programmes for the industry.
A linkage map of common carp (Cyprinus carpio) based on AFLP and microsatellite markers
Authors: Cheng L. , Liu L. , Yu X. , Wang D. , Tong J.
Published: November 2009

Common carp (Cyprinus carpio) is an important fish for aquaculture, but genomics of this species is still in its infancy. In this study, a linkage map of common carp based on Amplified Fragment Length Polymorphism (AFLP) and microsatellite (SSR) markers has been generated using gynogenetic haploids. Of 926 markers genotyped, 151 (149 AFLPs, two SSRs) were distorted and eliminated from the linkage analyses. A total of 699 AFLP and 20 microsatellite (SSR) markers were assigned to the map, which comprised 64 linkage groups and covered 5506.9 cM Kosambi, with an average interval distance of 7.66 cM Kosambi. The normality tests on interval map distances showed a non‐normal marker distribution. Visual inspection of the map distance distribution histogram showed a cluster of interval map distances on the left side of the chart, which suggested the occurrence of AFLP marker clusters. On the other hand, the lack of an obvious cluster on the right side showed that there were a few big gaps which need more markers to bridge. The correlation analysis showed a highly significant relatedness between the length of linkage group and the number of markers, indicating that the AFLP markers in this map were randomly distributed among different linkage groups. This study is helpful for research into the common carp genome and for further studies of genetics and marker‐assisted breeding in this species.
A shared 336 kb haplotype associated with the belt pattern in three divergent cattle breeds
Authors: Drögemüller C. , Demmel S. , Engensteiner M. , Rieder S. , Leeb T.
Published: November 2009

We recently mapped the belt mutation in Brown Swiss cattle to a 922 kb interval on BTA3. In this study, we analysed two additional cattle breeds with the belted phenotype: Galloway and Dutch Belted (Lakenvelder). By genotyping microsatellites in solid‐coloured and belted Galloways, we confirmed that the belt mutation in Galloways is strongly associated with the same chromosomal locus as in Brown Swiss cattle. Subsequently, we analysed 36 SNPs in the belt interval in three breeds. We identified a single belt‐associated haplotype for each of the analysed breeds. The three breed‐specific belt haplotypes share alleles in four blocks. Three of these blocks comprise only one single or two consecutive markers, while the largest shared haplotype block encompasses nine consecutive SNPs in a 336 kb interval. The large shared haplotype across divergent breeds suggests a common mutation for the belt phenotype in all three breeds. We identified a potential candidate gene within this interval coding for the developmental transcription factor HES6. We re‐sequenced the complete HES6 coding sequence in belted and solid‐coloured cattle but did not find belt‐associated polymorphisms. In conclusion, our data provide strong evidence in favour of a common founder for the belt phenotype in different cattle breeds and have resulted in an improved fine‐mapping of the causative mutation.
Y‐specific microsatellites reveal an African subfamily in taurine (Bos taurus) cattle
Authors: Pérez‐Pardal L. , Royo L. J. , Beja‐Pereira A. , Curik I. , Traoré A. , Fernández I. , Sölkner J. , Alonso J. , Álvarez I. , Bozzi R. , Chen S. , Ponce de León F. A. , Goyache F.
Published: November 2009

Five cattle Y‐specific microsatellites, totalling six loci, were selected from a set of 44 markers and genotyped on 608 Bos taurus males belonging to 45 cattle populations from Europe and Africa. A total of 38 haplotypes were identified. Haplogroups (Y1 and Y2) previously defined using single nucleotide polymorphisms did not share haplotypes. Nine of the 27 Y2‐haplotypes were only present in African cattle. Network and correspondence analyses showed that this African‐specific subfamily clustered separately from the main Y2‐subfamily and the Y1 haplotypes. Within‐breed genetic variability was generally low, with most breeds (78%) showing haplotypes belonging to a single haplogroup. amova analysis showed that partitioning of genetic variation among breeds can be mainly explained by their geographical and haplogroup assignment. Between‐breed genetic variability summarized via Principal Component Analysis allowed the identification of three principal components explaining 94.2% of the available information. Projection of principal components on geographical maps illustrated that cattle populations located in mainland Europe, the three European Peninsulas and Mediterranean Africa presented similar genetic variation, whereas those breeds from Atlantic Europe and British Islands (mainly carrying Y1 haplotypes) and those from Sub‐Saharan Africa (belonging to Y2‐haplogroup) showed genetic variation of a different origin. Our study confirmed the existence of two large Y‐chromosome lineages (Y1 and Y2) in taurine cattle. However, Y‐specific microsatellites increased analytical resolution and allowed at least two different Y2‐haplotypic subfamilies to be distinguished, one of them restricted to the African continent.
Autoantibody-mediated regulation of B cell responses by functional anti-CD22 autoantibodies in patients with systemic sclerosis
Authors: Odaka M , Hasegawa M , Hamaguchi Y , Ishiura N , Kumada S , Matsushita T , Komura K , Sato S , Takehara K , Fujimoto M
Published: November 2009

Studies have demonstrated that B cells play important roles in systemic sclerosis (SSc), especially through the CD19/CD22 autoimmune loop. CD22 is a B cell-specific inhibitory receptor that dampens B cell antigen receptor (BCR) signalling via tyrosine phosphorylation-dependent mechanism. In this study, we examined the presence and functional property of circulating autoantibodies reacting with CD22 in systemic sclerosis. Serum samples from 10 tight skin (TSK/+) mice and 50 SSc patients were assessed for anti-CD22 autoantibodies by enzyme-linked immunosorbent assays using recombinant mouse or human CD22. The association between anti-CD22 antibodies and clinical features was also investigated in SSc patients. Furthermore, the influence of SSc serum including anti-CD22 autoantibodies for CD22 tyrosine phosphorylation was examined by Western blotting using phosphotyrosine-specific antibodies reacting with four major tyrosine motifs of CD22 cytoplasmic domain. Anti-CD22 autoantibodies were positive in 80% of TSK/+ mice and in 22% of SSc patients. Patients positive for anti-CD22 antibodies showed significantly higher modified Rodnan skin thickness score compared with patients negative for anti-CD22 antibodies. Furthermore, anti-CD22 antibodies from patients' sera were capable of reducing phosphorylation of all four CD22 tyrosine motifs, while sera negative for anti-CD22 antibodies did not affect CD22 phosphorylation. Thus, a subset of SSc patients possessed autoantibodies reacting with a major inhibitory B cell response regulator, CD22. Because these antibodies can interfere CD22-mediated suppression onto B cell activation in vitro, SSc B cells produce functional autoantibodies that can enhance their own activation. This unique regulation may contribute to the autoimmune aspect of SSc.
Effects of land use on aquatic macrophyte diversity and water quality of ponds
Authors: AKASAKA MUNEMITSU , TAKAMURA NORIKO , MITSUHASHI HIROMUNE , KADONO YASURO
Published: November 2009

1. Aquatic macrophyte diversity and water quality of 55 ponds in western Japan were related to land use and morphometric variables to identify the environmental factors that sustain biodiversity and the spatial extent at which these factors operate.

2. The relevant spatial extent for floating‐leaved macrophyte richness (500 m from pond edge) was larger than that for submerged macrophyte occurrence (10, 75 and 100 m), whereas emergent macrophyte richness was best explained at much larger extents (1000 m). Total macrophyte richness was explained at the extent of 500, 750 and 1000 m. The extents relevant for explaining the physicochemical condition of pond water (100 and 250 m) were similar to those for submerged and floating‐leaved macrophytes, suggesting that these two growth forms are more sensitive to water quality compared to emergent macrophytes.

3. Diversity of all three growth forms and that of total macrophytes collectively were inversely related to turbidity and nutrient concentration; among the three growth forms, submerged macrophytes were most affected by water quality.

4. Negative relationships were found between the proportion of urban area and the diversity of the three growth forms and that of total macrophytes and water quality. Species richness of emergent, floating‐leaved and total macrophytes decreased with depth and increased with surface area up to about 5000 m2, above which it declined.

5. Urbanisation and enlargement of ponds were the two main factors that decreased aquatic macrophyte diversity in irrigation ponds. To alleviate the adverse effects of urban areas on aquatic macrophyte diversity, our results suggest that management efforts should focus on the creation of buffer zones within the relevant spatial extent from the pond edge.
Fish species richness in spring‐fed ponds: effects of habitat size versus isolation in temporally variable environments
Authors: UCHIDA YUKI , INOUE MIKIO
Published: November 2009

1. Species richness in a habitat patch is determined by immigration (regional) and extinction (local) processes, and understanding their relative importance is crucial for conservation of biodiversity. In this study, we applied the Island Biogeography concept to spring ponds connected to a river in southwestern Japan to examine how immigration and extinction processes interact to determine fish species richness in temporally variable environments.

2. Fish censuses were conducted 15 times in 13 study ponds at 1–4 month intervals from August 1998 through October 2000. Effects of habitat size (pond area), isolation (distance from the river) and temporal environmental variability (water level fluctuation) on (i) species richness, (ii) immigration and extinction rates and (iii) population size and persistence of each fish species were assessed.

3. The results revealed predominant effects of distance on species richness, immigration/extinction rates and population size and persistence. Species richness decreased with increasing distance but was not related to either pond area or water level fluctuation. A negative effect of distance on immigration rate was detected, while neither pond area nor water level fluctuation had significant effects on extinction rate. Further, population size and persistence of four species increased with decreasing distance, suggesting that, in ponds close to the river, immigrants from the river reduce the probability of extinction (i.e. provide a rescue effect), contributing to the maintenance of high species richness.

4. Overall results emphasise the importance of immigration processes, rather than extinction, in shaping patterns of species richness in our system. The predominant importance of immigration was probably because of (i) high temporal variability that negates habitat‐size effects and (ii) continuous immigration that easily compensates for local extinctions. Our results suggest that consideration of regional factors (e.g. connectivity, locations of source populations and barriers to colonisation) is crucial for conservation and restoration of local habitats.
Expression of cyclin D1 and retinoblastoma protein in Paget’s disease of the vulva and breast: an immunohistochemical study of 108 cases
Authors: Ellis Patricia E , MacLean Allan B , Crow Julie C , Wong Te Fong L F , Rolfe Kerstin J , Perrett Christopher W
Published: November 2009

Aims:  Loss of retinoblastoma protein expression and overexpression of cyclin D1 have been implicated in the development and progression of some cancers. Paget’s disease of the vulva (PDV) and Paget’s disease of the breast (PDB) are uncommon conditions and the pathogenesis of these diseases is still unclear. The aim was to examine the expression of the retinoblastoma and cyclin D1 proteins in PDV and PDB and to correlate any differences between PDV and PDB, and in the presence or absence of an underlying carcinoma.

Methods and results:  Seventy‐two archival cases of PDV including 10 with invasive disease and 36 cases of PDB were evaluated immunohistochemically for the expression of cyclin D1 and retinoblastoma protein. Forty‐four percent (32/72) of cases of PDV showed loss of expression of the retinoblastoma protein, compared with 67% (24/36) of PDB cases. Fifty‐nine percent (41/69) of PDV overexpressed cyclin D1. In PDB, 8% (3/34) overexpressed cyclin D1. There were no significant differences in the expression of retinoblastoma and cyclin D1 in PDV cases with or without underlying invasive disease. There were significant differences between the expression of retinoblastoma (P = 0.03) and cyclin D1 (P < 0.001) in PDV compared with PDB.

Conclusions:  The differences in the expression of cyclin D1 and retinoblastoma may indicate the differences in the pathogenesis of PDV and PDB.
Ketamine cystitis as a mimic of carcinoma in situ
Authors: Oxley Jon D , Cottrell Angela M , Adams Susan , Gillatt David
Published: November 2009

Aims:  To describe the histopathological features of a series of patients with ketamine‐related cystitis.

Methods and results:  Seventeen patients with ketamine‐related cystitis, who had undergone biopsy, were identified and reviewed. Twelve showed ulceration with significant urothelial atypia. In 10 of these, immunohistochemistry was performed; 9/10 had high p53 immunoreactivity and 7/10 had moderate to high levels of Ki67 reactivity, but all were negative for cytokeratin 20.

Conclusions:  Ketamine can lead to reactive urothelial changes that can mimic carcinoma in situ, but the long‐term cancer risk remains unknown.
Activation of ERK, AKT and JNK signalling pathways in human schwannomas in situ
Authors: Hilton David A , Ristic Natalia , Hanemann Clemens O
Published: November 2009

Aims:  Schwannomas are common tumours that may be multiple in neurofibromatosis type 2, when they may be difficult to treat without significant morbidity using surgery and radiosurgery. Previous in vitro work has suggested that merlin loss is associated with activation of the JNK/JUN, PI3K/AKT and MEK/ERK pathways and that these pathways may be susceptible to pharmacological inhibition. The aim was to investigate the expression of proteins involved in these pathways in human schwannomas in situ.

Methods and results:  Immunohistochemistry using antibodies to AKT, pAKT, MEK, pMEK, ERK, pERK, JUN and pJUN was applied to 16 schwannomas (sporadic and NF2), and the results were compared with those seen in traumatic neuromas. Increased expression of pMEK, pERK and pJUN was seen in the schwannomas samples and of pAKT in schwannomas and controls.

Conclusions:  These findings provide further direct evidence for activation of the JNK/JUN, PI3K/AKT and MEK/ERK signalling pathways in schwannomas and support the development of therapeutic agents directed against these pathways for the treatment of this group of tumours.
Soy, phyto‐oestrogens and male reproductive function: a review
Authors: Cederroth Christopher R. , Auger Jacques , Zimmermann Céline , Eustache Florence , Nef Serge
Published: November 2009

There is growing interest in the possible health threat posed by the effects of endocrine disruptors on reproduction. Soy and soy‐derived products contain isoflavones that mimic the actions of oestrogens and may exert adverse effects on male fertility. The purpose of this review was to examine the evidence regarding the potential detrimental effects of soy and phyto‐oestrogens on male reproductive function and fertility in humans and animals. Overall, there are some indications that phyto‐oestrogens, alone or in combination with other endocrine disruptors, may alter reproductive hormones, spermatogenesis, sperm capacitation and fertility. However, these results must be interpreted with care, as a result of the paucity of human studies and as numerous reports did not reveal any adverse effects on male reproductive physiology. Further investigation is needed before a firm conclusion can be drawn. In the meantime, caution would suggest that perinatal phyto‐oestrogen exposure, such as that found in infants feeding on soy‐based formula, should be avoided.
Differences in mouse models of diabetes mellitus in studies of male reproduction
Authors: O’Neill J. , Czerwiec A. , Agbaje I. , Glenn J. , Stitt A. , McClure N. , Mallidis C.
Published: November 2009

Diabetes Mellitus (DM) has been found to have subtle yet profound effects on the metabolic status of the testis, the expression of numerous spermatogenic genes and is associated with increased numbers of sperm with nuclear DNA damage. The precise mechanism causing these detrimental effects remains unknown. The presence of increased levels of the most prominent member (carboxymethyllysine – CML) of the advanced glycation end product adducts and their receptor (RAGE) in the reproductive tract of DM men has provided a new avenue for research. As there are suspicions that the antibiotic (streptozotocin – STZ) employed to induce DM is also capable of causing oxidative stress and DNA damage, we compared CML and RAGE levels in the reproductive tract and sperm nDNA status of STZ mice with the levels in the Ins2Akita mouse to determine which more closely mimics the situation described in the human diabetic. CML was observed in the testes, epididymes and sperm of all animals. Sperm from DM mice showed particularly strong CML immunolocalization in the acrosomal cap, the equatorial region and whenever present, cytoplasmic droplets. Although increased, the level of CML on the sperm of the STZ and Ins2Akita DM mice did not reach statistical significance. RAGE was present on the developing acrosome and epididymal sperm of all animals and in discrete regions of the epididymes of the DM models. Only the epididymal sperm of the Ins2Akita mice were found to have significantly increased (p < 0.0001) nDNA damage. The Ins2Akita mouse therefore appears to more accurately reflect the conditions found in the human and, as such, is a more representative model for the study of diabetes and glycation’s influence on male fertility.
Integrating species distribution models and interacting particle systems to predict the spread of an invasive alien plant
Authors: Smolik M.G. , Dullinger S. , Essl F. , Kleinbauer I. , Leitner M. , Peterseil J. , Stadler L.‐M. , Vogl G.
Published: November 2009

Aim  We demonstrate how to integrate two widely used tools for modelling the spread of invasive plants, and compare the performance of the combined model with that of its individual components using the recent range dynamics of the invasive annual weed Ambrosia artemisiifolia L.

Location  Austria.

Methods  Species distribution models, which deliver habitat‐based information on potential distributions, and interacting particle systems, which simulate spatio‐temporal range dynamics as dependent on neighbourhood configurations, were combined into a common framework. We then used the combined model to simulate the invasion of A. artemisiifolia in Austria between 1990 and 2005. For comparison, simulations were also performed with models that accounted only for habitat suitability or neighbourhood configurations. The fit of the three models to the data was assessed by likelihood ratio tests, and simulated invasion patterns were evaluated against observed ones in terms of predictive discrimination ability (area under the receiver operating characteristic curve, AUC) and spatial autocorrelation (Moran’s I).

Results  The combined model fitted the data significantly better than the single‐component alternatives. Simulations relying solely on parameterized spread kernels performed worst in terms of both AUC and spatial pattern formation. Simulations based only on habitat information correctly predicted infestation of susceptible areas but reproduced the autocorrelated patterns of A. artemisiifolia expansion less adequately than did the integrated model.

Main conclusions  Our integrated modelling approach offers a flexible tool for forecasts of spatio‐temporal invasion patterns from landscape to regional scales. As a further advantage, scenarios of environmental change can be incorporated consistently by appropriately updating habitat suitability layers. Given the susceptibility of many alien plants, including A. artemisiifolia, to both land use and climate changes, taking such scenarios into account will increasingly become relevant for the design of proactive management strategies.
Support for vicariant origins of the New Zealand Onychophora
Authors: Allwood Julia , Gleeson Dianne , Mayer Georg , Daniels Savel , Beggs Jacqueline R. , Buckley Thomas R.
Published: November 2009

Aim  The distribution of Onychophora across the southern continents has long been considered the result of vicariance events. However, it has recently been hypothesized that New Zealand was completely inundated during the late Oligocene (25–22 Ma) and therefore that the entire biota is the result of long‐distance dispersal. We tested this assumption using phylogenetic and molecular dating of DNA sequence data from Onychophora.

Location  New Zealand, Australia, South Africa, Chile (South America).

Methods  We obtained DNA sequence data from the nuclear genes 28S and 18S rRNA to reconstruct relationships among species of Peripatopsidae (Onychophora). We performed molecular dating under a Bayesian relaxed clock model with a range of prior distributions using the rifting of South America and South Africa as a calibration.

Results  Our phylogenetic trees revealed that the New Zealand genera Ooperipatellus and Peripatoides, together with selected Australian genera (Euperipatoides, Phallocephale and an undescribed genus from Tasmania), form a monophyletic group that is the sister group to genera from Chile (Metaperipatus) and South Africa (Peripatopsis and Opisthopatus). The relaxed clock dating analyses yielded mean divergence times from 71.3 to 78.9 Ma for the split of the New Zealand Peripatoides from their Australian sister taxa. The 0.95 Bayesian posterior intervals were very broad and ranged from 24.5 to 137.6 Ma depending on the prior assumptions. The mean divergence of the New Zealand species of Ooperipatellus from the Australian species Ooperipatellus insignis was estimated at between 39.9 and 46.2 Ma, with posterior intervals ranging from 9.5 to 91.6 Ma.

Main conclusions  The age of Peripatoides is consistent with long‐term survival in New Zealand and implies that New Zealand was not completely submerged during the Oligocene. Ooperipatellus is less informative on the question of continuous land in the New Zealand region because we cannot exclude a post‐Oligocene divergence. The great age of Peripatoides is consistent with a vicariant origin of this genus resulting from the rifting of New Zealand from the eastern margin of Gondwana and supports the assumptions of previous authors who considered the Onychophora to be a relict component of the New Zealand biota.
Abdominal decompression for intra‐abdominal hypertension after simultaneous pancreas–kidney transplantation
Authors: Decoster T. , Vermassen F.E.G. , Peeters P.C. , Hoste E.A.J. , De Waele J.J.
Published: November 2009

Decoster T, Vermassen FEG, Peeters PC, Hoste EAJ, De Waele JJ. Abdominal decompression for intra‐abdominal hypertension after simultaneous pancreas–kidney transplantation. Clin Transplant 2010: 24: 118–121. © 2009 John Wiley & Sons A/S.

Abstract:  Intra‐abdominal hypertension (IAH) is increasingly recognized in critically ill patients and can result in respiratory, hemodynamic or renal dysfunction. We report the case of a patient suffering from diabetic nephropathy who underwent simultaneous pancreas–kidney transplantation. Within 12 h after the operation, the patient developed IAH resulting in oliguria and a rise in serum creatinine. Surgical abdominal decompression was performed, resulting in immediate restoration of kidney graft function.
The role of reactive oxygen species in signalling from chloroplasts to the nucleus
Authors: Galvez‐Valdivieso Gregorio , Mullineaux Philip M.
Published: November 2009

The coordination of chloroplast function with the rest of cellular activity requires a continual stream of communication from this organelle to the nucleus. Chloroplasts are major sites of the production of reactive oxygen species (ROS) as either by‐products of the reduction of molecular oxygen (O2) or its excitation in the presence of highly energised pigments. Such ROS, while potentially damaging to the cell, are also important initiators or transducers of signals from these organelles to the nucleus in response to environmental cues. ROS can initiate such retrograde signalling pathways that trigger either programmed cell death or adjustment to changed conditions. Such different outcomes have implications for the way in which signal transduction by ROS is accomplished and is the subject of this review. In response to mild‐stress situations, and as a consequence of their reactivity or because of their containment by cellular antioxidant systems, it is proposed that ROS engage with or initiate signalling at or very near their site of production. In contrast, under more extreme conditions, ROS are proposed to diffuse away from their site of production and consequently elicit a different set of signalling events.
A randomized, double‐blind, placebo‐controlled study of maintenance treatment with adjunctive risperidone long‐acting therapy in patients with bipolar I disorder who relapse frequently
Authors: Macfadden Wayne , Alphs Larry , Haskins J Thomas , Turner Norris , Turkoz Ibrahim , Bossie Cynthia , Kujawa Mary , Mahmoud Ramy
Published: November 2009

Objective:  No large controlled trials have evaluated adjunctive maintenance treatment with long‐acting injectable antipsychotics in patients with bipolar disorder. This study assessed whether adjunctive maintenance treatment with risperidone long‐acting therapy (RLAT), added to treatment‐as‐usual (TAU) medications for bipolar disorder, delays relapse in patients with bipolar disorder type I.

Methods:  This study included patients with bipolar disorder type I with ≥ four mood episodes in the 12 months prior to study entry. Following a 16‐week, open‐label stabilization phase with RLAT plus TAU, remitted patients entered a 52‐week, double‐blind, placebo‐controlled, relapse‐prevention phase. Randomized patients continued treatment with adjunctive RLAT (25–50 mg every two weeks) plus TAU (n = 65) or switched to adjunctive placebo injection plus TAU (n = 59). The primary outcome measure was time to relapse to any mood episode.

Results:  Of 240 enrolled patients, 124 entered double‐blind treatment. Time to relapse was longer in patients receiving adjunctive RLAT (p = 0.010). Relapse rates were 23.1% (n = 15) with adjunctive RLAT versus 45.8% (n = 27) with adjunctive placebo; relative relapse risk was 2.3‐fold higher with adjunctive placebo (p = 0.011). Completion rates were: adjunctive RLAT, 60.0% (n = 39) and adjunctive placebo, 42.4% (n = 25; p = 0.050). Adverse event (AE)‐related discontinuations were 4.6% (n = 3) and 1.7% (n = 1), respectively. Common AEs (adjunctive RLAT versus adjunctive placebo) were: tremor (24.6% versus 10.2%), insomnia (20.0% versus 18.6%), muscle rigidity (12.3% versus 5.1%), weight increased (6.2% versus 1.7%), and hypokinesia (7.7% versus 0.0%).

Conclusions:  Adjunctive RLAT significantly delayed time to relapse in patients with bipolar disorder type I who relapse frequently. Safety and tolerability of RLAT were generally consistent with that previously observed.