bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microsatellite DNA analyses of a highly disjunct New Zealand tree reveal strong differentiation and imply a formerly more continuous distribution
Authors: SHEPHERD LARA D. , PERRIE LEON R. 
Published: February 2011

AbstractAlthough New Zealand is a biodiversity hotspot, there has been little genetic investigation of why so many of its threatened and uncommon plants have naturally disjunct distributions. We investigated the small tree Pseudopanax ferox (Araliaceae), which has a widespread but highly disjunct lowland distribution within New Zealand. Genotyping of nuclear microsatellites and a chloroplast locus revealed pronounced genetic differentiation and four principal genetic clusters. Our results indicate that the disjunct distribution is a product of vicariance rather than long‐distance dispersal. This highlights the need to preserve multiple populations when disjunct distributions are the result of vicariance, rather than focusing conservation efforts on a core area, in order to retain as much as possible of a species’ evolutionary legacy and potential. Additionally, based on our genetic findings and the ecology of P. ferox, we hypothesize that it was more continuously distributed during the drier (but not maximally colder) interstadials of glacial periods and/or on the fertile soils available immediately postglacial. We further hypothesize that P. ferox belongs to a suite of species of drought‐prone and/or fertile habitats whose distributions are actually restricted during warmer and wetter interglacial periods, despite being principally of the lowlands. Our genetic data for P. ferox are also the first consistent with the survival during the Last Glacial Maxima of a lowland tree at high latitudes in the south‐eastern South Island.
Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest
Authors: CALLENS TOM , GALBUSERA PETER , MATTHYSEN ERIK , DURAND ERIC Y. , GITHIRU MWANGI , HUYGHE JEROEN R. , LENS LUC 
Published: February 2011

AbstractHabitat fragmentation can restrict geneflow, reduce neighbourhood effective population size, and increase genetic drift and inbreeding in small, isolated habitat remnants. The extent to which habitat fragmentation leads to population fragmentation, however, differs among landscapes and taxa. Commonly, researchers use information on the current status of a species to predict population effects of habitat fragmentation. Such methods, however, do not convey information on species‐specific responses to fragmentation. Here, we compare levels of past population differentiation, estimated from microsatellite genotypes, with contemporary dispersal rates, estimated from multi‐strata capture–recapture models, to infer changes in mobility over time in seven sympatric, forest‐dependent bird species of a Kenyan cloud forest archipelago. Overall, populations of sedentary species were more strongly differentiated and clustered compared to those of vagile ones, while geographical patterning suggested an important role of landscape structure in shaping genetic variation. However, five of seven species with broadly similar levels of genetic differentiation nevertheless differed substantially in their current dispersal rates. We conclude that post‐fragmentation levels of vagility, without reference to past population connectivity, may not be the best predictor of how forest fragmentation affects the life history of forest‐dependent species. As effective conservation strategies often hinge on accurate prediction of shifts in ecological and genetic relationships among populations, conservation practices based solely upon current population abundances or movements may, in the long term, prove to be inadequate.
aprABC: a Mycobacterium tuberculosis complex‐specific locus that modulates pH‐driven adaptation to the macrophage phagosome
Authors: Abramovitch Robert B. , Rohde Kyle H. , Hsu Fong‐Fu , Russell David G. 
Published: February 2011

SummaryFollowing phagocytosis by macrophages, Mycobacterium tuberculosis (Mtb) senses the intracellular environment and remodels its gene expression for growth in the phagosome. We have identified an acid and phagosome regulated (aprABC) locus that is unique to the Mtb complex and whose gene expression is induced during growth in acidic environments in vitro and in macrophages. Using the aprA promoter, we generated a strain that exhibits high levels of inducible fluorescence in response to growth in acidic medium in vitro and in macrophages. aprABC expression is dependent on the two‐component regulator phoPR, linking phoPR signalling to pH sensing. Deletion of the aprABC locus causes defects in gene expression that impact aggregation, intracellular growth, and the relative levels of storage and cell wall lipids. We propose a model where phoPR senses the acidic pH of the phagosome and induces aprABC expression to fine‐tune processes unique for intracellular adaptation of Mtb complex bacteria.
Mechanism of adhesion maintenance by methionine sulphoxide reductase in Streptococcus gordonii
Authors: Lei Y. , Zhang Y. , Guenther B. D. , Kreth J. , Herzberg M. C. 
Published: February 2011

SummaryMethionine sulphoxide reductase maintains adhesin function during oxidative stress. Using Streptococcus gordonii as a model, we now show the mechanistic basis of adhesin maintenance provided by MsrA. In biofilms, S. gordonii selectively expresses the msrA gene. When the wild‐type strain was grown with exogenous hydrogen peroxide (H2O2), msrA‐specific mRNA expression significantly increased, while acid production was unaffected. In the presence of H2O2, a msrA‐deletion mutant (ΔMsrA) showed a 6 h delay in lag phase growth, a 30% lower yield of H2O2, significantly greater inhibition by H2O2 on agar plates (reversed by complementation), 30% less adhesion to saliva‐coated hydroxyapatite, 87% less biofilm formation and an altered electrophoretic pattern of SspAB protein adhesins. Using mass spectrometry, methionine residues in the Met‐rich central region of SspB were shown to be oxidized by H2O2 and reduced by MsrA. In intact wild‐type cells, MsrA colocalized with a cell wall‐staining dye, and MsrA was detected in both cell wall and cytosolic fractions. To maintain normal adhesion and biofilm function of S. gordonii in response to exogenous oxidants therefore msrA is upregulated, methionine oxidation of adhesins and perhaps other proteins is reversed, and adhesion and biofilm formation is maintained.
Fission yeast Ubr1 ubiquitin ligase influences the oxidative stress response via degradation of active Pap1 bZIP transcription factor in the nucleus
Authors: Kitamura Kenji , Taki Masumi , Tanaka Nobukazu , Yamashita Ichiro 
Published: February 2011

SummaryCells adapt to oxidative stress by transcriptional activation of genes encoding antioxidants and proteins of other protective roles. A bZIP transcription factor, Pap1, plays a critical role in this process and overexpression of Pap1 confers resistance to various oxidants and drugs in fission yeast. Pap1 temporarily enters the nucleus upon oxidative stress but returns to the cytoplasm once cells adapt to the stress, suggesting that cellular localization regulates Pap1 function. We report here an additional regulatory mechanism that Ubr1 ubiquitin ligase‐dependent degradation lowered the Pap1 protein levels. ubr1 cells were causally resistant to hydrogen peroxide because of the increment of Pap1 levels. Pap1 was preferentially degraded in the nucleus where Ubr1 was consistently enriched. Proteolysis was critical to downregulate Pap1 especially when its activation persisted, as constitutively nuclear Pap1 severely inhibited growth in ubr1 mutants. Inactive mutations in the bZIP DNA binding domain stabilized Pap1 but rescued the lethality caused by constitutively active Pap1 in ubr1 mutants. These findings indicate that either nuclear export or Ubr1‐mediated proteolysis must be operative to prevent uncontrolled Pap1 function. Coincidental dysfunction in both inhibitory pathways causes lethality because of prolonged activation of Pap1. Ubr1 is a critical regulator for the homeostasis of oxidative stress response.
Escherichia coli YaeJ protein mediates a novel ribosome‐rescue pathway distinct from SsrA‐ and ArfA‐mediated pathways
Authors: Chadani Yuhei , Ono Katsuhiko , Kutsukake Kazuhiro , Abo Tatsuhiko 
Published: February 2011

SummaryAccumulation of stalled ribosomes at the 3′ end of mRNA without a stop codon (non‐stop mRNA) is supposed to be toxic to bacterial cells. Escherichia coli has at least two distinct systems to rescue such stalled ribosomes: SsrA‐dependent trans‐translation and ArfA‐dependent ribosome rescue. Combination of the ssrA and arfA mutations is synthetically lethal, suggesting the significance of ribosome rescue. In this study, we identified the E. coli yaeJ gene, encoding a peptide‐release factor homologue with GGQ motif, as a multicopy suppressor of the lethal phenotype of ssrA arfA double mutant. The YaeJ protein was shown to bind to ribosomes. Both in vivo and in vitro, YaeJ showed the ribosome‐rescue activity and promoted the hydrolysis of peptidyl‐tRNA residing in the stalled ribosome. Missense mutation in the GGQ motif or deletion of the C‐terminal unstructured tail abolished both the suppressor activity for ssrA arfA synthetic lethality and the ribosome‐rescue activity, suggesting the importance of these structural features. On the basis of these observations, we propose that YaeJ acts as a stop codon‐independent peptidyl‐tRNA hydrolysing factor through binding to ribosomes stalled at the 3′ end of non‐stop mRNAs. It was also suggested that ArfA and YaeJ rescue the stalled ribosomes by distinct mechanisms.
Short pulse gastric electrical stimulation for cisplatin‐induced emesis in dogs
Authors: Song J. , Zhong D.‐X. , Qian W. , Hou X.‐H. , Chen J. D. Z. 
Published: February 2011

AbstractBackground In a previous study, we investigated the ameliorating effect of gastric electrical stimulation (GES) with a single set of parameters on emesis and behaviors suggestive of nausea induced by cisplatin in dogs. The aim of this study was to investigate the effects of GES with different parameters on cisplatin‐induced emesis in dogs.Methods Seven dogs implanted with gastric serosal electrodes were studied in six randomized sessions: one control session with cisplatin (2 mg kg−1) and five sessions with cisplatin plus GES of different parameters: GES‐A: 14 Hz, 5 mA, 0.3 ms, 0.1 s on and 5 s off; GES‐B: increased frequency and on‐time; GES‐C: increased frequency; GES‐D: increased frequency and pulse width; and GES‐E: increased frequency and amplitude. Gastric slow waves and emetic responses were recorded in each session.Key Results (i) Cisplatin induced emetic responses and gastric dysrhythmia. The peak time of the emetic response was during the fourth hour after cisplatin. (ii) GES with appropriate parameters reduced cisplatin‐induced emesis. The number of vomiting times during the 6 h after cisplatin was 7.0 ± 1.4 in the control, 4.7 ± 1.2 with GES‐A (P = 0.179), 4.2 ± 1.2 with GES‐B (P = 0.109), 7.0 ± 0.8 with GES‐C (P = 0.928), 2.1 ± 0.3 with GES‐D (P = 0.005) and 4.7 ± 1.5 with GES‐E (P = 0.129). However, none of the GES parameters could improve gastric dysrhythmia.Conclusions & Inferences Gastric electrical stimulation with appropriate parameters reduces cisplatin‐induced emetic responses and behaviors suggestive of nausea in dogs. Among the tested parameters, GES with increased pulse width seems to produce better relief of cisplatin‐induced emesis.
Development and application of new molecular markers for analysis of genetic diversity in Verticillium dahliae populations
Authors: Berbegal M. , Garzón C. D. , Ortega A. , Armengol J. , Jiménez‐Díaz R. M. , Jiménez‐Gasco M. M. 
Published: February 2011

The aim of this study was to develop new polymorphic markers for analysis of genetic diversity in the fungal soilborne plant pathogen Verticillium dahliae. Twelve polymorphic markers (five microsatellites and seven polymorphic sequences) were developed from a genomic library enriched for microsatellites. Screening of polymorphic loci was done using a collection of 25 V. dahliae isolates of diverse geographic origins, host sources and vegetative compatibility groups (VCGs). Three methods were used to score alleles: polyacrylamide gel electrophoresis (PAGE), sequencing of PCR‐amplified loci, and capillary electrophoresis. The new markers were used to assess genetic differentiation between isolates associated with different host plants. Two collections of isolates were analysed, obtained from artichoke (30 isolates) and potato (20 isolates) from crops grown in rotation located in the same area in eastern‐central Spain. The resolution of genetic differentiation between these two collections using the new markers was compared to that provided by other often‐used markers (SCARs and VCGs). Sequence analysis of the alleles proved to be the most unambiguous technique for scoring microsatellite data. The relatively high genetic differentiation observed between isolates from different crops (genetic differentiation coefficient, GST = 0·24) and their high genotypic diversity suggest a divergence between V. dahliae from artichoke and potato. It is hypothesized that evolution of V. dahliae from the local resident population in association with the two host crops has occurred. The new markers are useful for resolving population structure within V. dahliae and may contribute to a better understanding of the population biology of this fungus.
Colorectal Cancer–Derived Foxp3+IL‐17+ T Cells Suppress Tumour‐Specific CD8+ T Cells
Authors: Ma C. , Dong X. 
Published: February 2011

AbstractThe pathogenesis of cancer is remained to be further understood. This study aims to investigate the role of tumour‐derived Foxhead box P3 (Foxp3)+interleukin (IL)‐17+ T cells on suppressing tumour‐specific CD8+ T cells. Colorectal cancer (CRC) tissue was collected from surgically removed cancer tissue of 22 patients with CRC. Foxp3+IL‐17+ T cells in cancer tissue were examined by flow cytometry. A set of cell markers and cytokines expressed by Foxp3+IL‐17+ T cells were determined by immune staining. By coculture with isolated peripheral CD8+ T cells, the immune regulatory capacity of Foxp3+IL‐17+ T cells was examined. The results showed that a number of Foxp3+IL‐17+ T cells were found in CRC tissue (22.8 ± 2.6 cells/mm2 tissue) that was significantly more than in non‐cancer colonic mucosa (5.6 ± 1.04 cells/mm2 tissue). The Foxp3+IL‐17+ cells also CD4+, CCR6+, transforming growth factor (TGF)‐beta+ and IL‐6+. The CD8+ T cells proliferated markedly after exposure to tumour protein in culture that was suppressed in the presence of CRC–derived Foxp3+IL‐17+ T cells; the suppression was attenuated by pretreatment with anti‐IL‐17 antibody. We conclude that CRC–derived Foxp3+IL‐17+ T cells have the ability to suppress tumour‐specific CD8+ T cells. This subset of T cells may be a novel therapeutic target in the treatment of CRC.
Interleukin‐6 −174 G/C Promoter Polymorphism is Associated with Persistence of Chlamydia pneumoniae Antibodies in Young Men
Authors: Rantala A. , Lajunen T. , Juvonen R. , Paldanius M. , Silvennoinen‐Kassinen S. , Peitso A. , Vainio O. , Leinonen M. , Saikku P. 
Published: February 2011

AbstractA promoter polymorphism −174 G/C in the inflammatory cytokine interleukin‐6 (IL‐6) gene has been associated with differences in serum IL‐6 levels and a risk for inflammatory conditions, such as cardiovascular diseases. We investigated whether this polymorphism is associated with Chlamydia pneumoniae, a common causative agent of respiratory infection with tendency for persistent infections, in 867 Finnish military recruits. IgG seropositivity in arrival and departure serum samples during 6–12 months of military service was considered as persistence of antibodies and a possible prolonged or chronic infection. The −174C allele was significantly associated with IgG seropositivity (P = 0.0002) and the persistence of IgG antibodies (P = 0.0002) as well as with slightly elevated C‐reactive protein (CRP) levels (P = 0.003). In addition, the association was stronger when persistent C. pneumoniae antibodies were present together with elevated CRP than when either of them was positive alone (OR; 95% CI: 3.45; 2.00–5.98 and 1.41; 1.00–1.99, respectively). Our data suggest that IL‐6 −174 G/C polymorphism is associated with persistence of C. pneumoniae antibodies and may be linked to the chronic or prolonged infection with systemic low‐grade inflammation.
Defective Central Tolerance in Aire‐Deficient Mice is not Sufficient to Induce Symptomatic Autoimmunity During Lymphopenia‐Induced T cell Proliferation
Authors: Kekäläinen E. , Lehto M.‐K. , Smeds E. , Miettinen A. , Meri S. , Jarva H. , Petteri Arstila T. 
Published: February 2011

AbstractTranscriptional regulator autoimmune regulator (AIRE) controls thymic negative selection but it is also expressed in secondary lymphoid organs. The relative contribution of AIRE’s central and peripheral function to the maintenance of tolerance is unclear. We transferred mature lymphocytes from Aire−/− or wild‐type donors to Aire+/+ lymphopenic recipients, which allowed us to gauge the autoreactivity inherent in the cells originating in an Aire−/− thymus. In the ensuing lymphopenia‐induced proliferation (LIP), the recipients of cells from Aire−/− showed definite T cell hyperproliferation and developed autoantibodies at a higher frequency than the recipients of wild‐type cells. However, neither of the recipient groups developed clinical symptoms, and pathological tissue infiltrates were also absent. The recipients of Aire−/− cells showed hyperproliferation and increased accumulation of regulatory T cells (Tregs), especially in tissues susceptible to inflammation triggered by LIP. These data are consistent with the view that T cells developing in the absence of Aire are autoreactive. However, overt autoimmunity was prevented, most likely by the suppressive function of Treg cells in the Aire‐sufficient recipients. Our results support the importance of the peripheral AIRE expression in the maintenance of immunological tolerance.
The Long‐Term Survival of Plasma Cells
Authors: Chu V. T. , Beller A. , Nguyen T. T. N. , Steinhauser G. , Berek C. 
Published: February 2011

AbstractPlasma cells sustain antibody production and hence are an essential part of immune protection. In the mucosa‐associated lymphoid tissues plasma cells secrete IgA antibodies which protect the organism from invasion by pathogenic bacteria while in the bone marrow they produce the antibodies which guarantee long‐term humoral immune protection. The various lymphoid organs provide specific microenvironments which support plasma cell survival. In particular, in the bone marrow, highly specialized survival niches are established by the underlying stromal reticular cells which permit plasma cells to survive for years. In some situations, however, the antibody may be detrimental to the organism. In those auto immune diseases, where plasma cells play a pathological role by producing the auto antibodies, new strategies are needed to interfere with the lifespan of plasma cells and thus to diminish their numbers. The recent finding that eosinophils are essential for the long‐term survival of plasma cells in the bone marrow provides a new therapeutic target to modulate the plasma cell survival niche.
Carbonate facies patterns in surface sediments of upwelling and non‐upwelling shelf environments (Panama, East Pacific)
Authors: REIJMER JOHN J. G. , BAUCH THORSTEN , SCHÄFER PRISKA 
Published: February 2011

AbstractIn this study two carbonate environments are compared and contrasted; the Gulf of Panama and the Gulf of Chiriquí on the Pacific side of Panama. These two embayments are in close geographic proximity at latitudes between 7° N and 9° N. The Gulf of Panama and the Gulf of Chiriquí are characterized by contrasting oceanographic conditions with year‐round stable non‐upwelling conditions in the Gulf of Chiriquí and strong seasonal upwelling in the dry season (December to April) in the Gulf of Panama. The upwelling variations only have a limited influence on the amount of carbonate produced; however, they do have a major impact on the occurrence of specific carbonate producing biota. In addition, carbonate production and distribution is influenced in both gulfs by the occurrence of islands and by terrigenous input. Terrigenous material is found mainly in the smaller grain sizes (<63 to 250 μm) that can be transported easily by currents and waves. Carbonate dominant sediments (carbonate sands and mixed carbonate–siliciclastic sands) mainly occur around the islands and are dominated by larger grain‐sizes (>500 μm). The Gulf of Panama and the Gulf of Chiriquí both show warm and temperate carbonate‐producing biota, with carbonate producers from tropical (corals) to mixed tropical to cool‐water (coralline red algae) and cold‐water (balanids) environments. The Gulf of Chiriquí is characterized by oligotrophic to mesotrophic conditions resulting in a photozoan (coral) and/or rhodolith‐facies in shallow‐water areas surrounding the islands and a mollusc‐dominated facies in deeper waters towards the shelf edge. Seasonal upwelling causes temporary eutrophic conditions in the Gulf of Panama, which results in a heterozoan facies around the islands dominated by balanids, echinoderms and molluscs. Thus a ‘cool‐water’ carbonate fauna and eutrophic conditions can exist in the tropics within an area prone to seasonal upwelling. The distinct facies differences found on the Pacific shelf of Panama stress the importance of variations in oceanographic conditions, upwelling versus non‐upwelling, in determining carbonate production and associated facies patterns in the tropics.
Experimental evidence for rapid biotic and abiotic reduction of Fe (III) at low temperatures in salt marsh sediments: a possible mechanism for formation of modern sedimentary siderite concretions
Authors: MORTIMER ROBERT J. G. , GALSWORTHY AMANDA M. J. , BOTTRELL SIMON H. , WILMOT LUCY E. , NEWTON ROBERT J. 
Published: February 2011

AbstractFe (III) reduction is a key component of the global iron cycle, and an important control on carbon mineralization. However, little is known about the relative roles and rates of microbial (biotic) iron reduction, which utilizes organic matter, versus abiotic iron reduction, which occurs without carbon mineralization. This paper reports on the capacity for salt marsh sediments, which typically are rich in iron, to support abiotic reduction of mineral Fe (III) driven by oxidation of sulphide. Sediment was reacted with amorphous FeS under strictly anaerobic conditions at a range of temperatures in biotic and abiotic microcosm experiments. Fe (III) reduction driven by sulphide oxidation occurs abiotically at all temperatures, leading to Fe (II) and elemental sulphur production in all abiotic experiments. In biotic experiments elemental sulphur is also the oxidized sulphur product but higher bicarbonate production leads to FeCO3 precipitation. Abiotic reduction of Fe (III) occurs at rates that are significant compared with microbial Fe (III) reduction in salt marsh sediments. The solid phases produced by coupled abiotic and biotic reactions, namely elemental sulphur and FeCO3, are comparable to those seen in nature at Warham, Norfolk, UK. Furthermore, the rates of these processes measured in the microcosm experiments are sufficient to generate siderite concretions on the rapid time scales observed in the field. This work highlights the importance of abiotic Fe (III) reduction alongside heterotrophic reduction, which has implications for iron cycling and carbon mineralization in modern and ancient sediments.