bluuebunny/crossref_metadata_2025_split huggingface dataset:
Range‐wide distribution of genetic diversity in the North American treeJuglans cinerea: a product of range shifts, not ecological marginality or recent population decline
Authors: HOBAN SEAN M. , BORKOWSKI DANIEL S. , BROSI SUNSHINE L. , McCLEARY TIM S. , THOMPSON LAURA M. , McLACHLAN JASON S. , PEREIRA MARIE A. , SCHLARBAUM SCOTT E. , ROMERO‐SEVERSON JEANNE 
Published: October 2010

AbstractThe spatial distribution of genetic diversity is a product of recent and historical ecological processes, as well as anthropogenic activities. A current challenge in population and conservation genetics is to disentangle the relative effects of these processes, as a first step in predicting population response to future environmental change. In this investigation, we compare the influence of contemporary population decline, contemporary ecological marginality and postglacial range shifts. Using classical model comparison procedures and Bayesian methods, we have identified postglacial range shift as the clear determinant of genetic diversity, differentiation and bottlenecks in 29 populations of butternut,Juglans cinereaL., a North American outcrossing forest tree. Although butternut has experienced dramatic 20th century decline because of an introduced fungal pathogen, our analysis indicates that recent population decline has had less genetic impact than postglacial recolonization history. Location within the range edge vs. the range core also failed to account for the observed patterns of diversity and differentiation. Our results suggest that the genetic impact of large‐scale recent population losses in forest trees should be considered in the light of Pleistocene‐era large‐scale range shifts that may have had long‐term genetic consequences. The data also suggest that the population dynamics and life history of wind‐pollinated forest trees may provide a buffer against steep population declines of short duration, a result having important implications for habitat management efforts,ex situconservation sampling and population viability analysis.
Divergence genetics analysis reveals historical population genetic processes leading to contrasting phylogeographic patterns in co‐distributed species
Authors: McGOVERN TAMARA M. , KEEVER CARSON C. , SASKI CHRISTOPHER A. , HART MICHAEL W. , MARKO PETER B. 
Published: October 2010

AbstractCoalescent samplers are computational time machines for inferring the historical demographic genetic processes that have given rise to observable patterns of spatial genetic variation among contemporary populations. We have used traditional characterizations of population structure and coalescent‐based inferences about demographic processes to reconstruct the population histories of two co‐distributed marine species, the frilled dog whelk, Nucella lamellosa, and the bat star, Patiria miniata. Analyses of population structure were consistent with previous work in both species except that additional samples of N. lamellosa showed a larger regional genetic break on Vancouver Island (VI) rather than between the southern Alexander Archipelago as in P. miniata. Our understanding of the causes, rather than just the patterns, of spatial genetic variation was dramatically improved by coalescent analyses that emphasized variation in population divergence times. Overall, gene flow was greater in bat stars (planktonic development) than snails (benthic development) but spatially homogeneous within species. In both species, these large phylogeographic breaks corresponded to relatively ancient divergence times between populations rather than regionally restricted gene flow. Although only N. lamellosa shows a large break on VI, population separation times on VI are congruent between species, suggesting a similar response to late Pleistocene ice sheet expansion. The absence of a phylogeographic break in P. miniata on VI can be attributed to greater gene flow and larger effective population size in this species. Such insights put the relative significance of gene flow into a more comprehensive historical biogeographic context and have important implications for conservation and landscape genetic studies that emphasize the role of contemporary gene flow and connectivity in shaping patterns of population differentiation.
The effect of habitat fragmentation on the genetic structure of a top predator: loss of diversity and high differentiation among remnant populations of Atlantic Forest jaguars (Panthera onca)
Authors: HAAG T. , SANTOS A. S. , SANA D. A. , MORATO R. G. , CULLEN JR L. , CRAWSHAW JR P. G. , DE ANGELO C. , DI BITETTI M. S. , SALZANO F. M. , EIZIRIK E. 
Published: October 2010

AbstractHabitat fragmentation may disrupt original patterns of gene flow and lead to drift‐induced differentiation among local population units. Top predators such as the jaguar may be particularly susceptible to this effect, given their low population densities, leading to small effective sizes in local fragments. On the other hand, the jaguar’s high dispersal capabilities and relatively long generation time might counteract this process, slowing the effect of drift on local populations over the time frame of decades or centuries. In this study, we have addressed this issue by investigating the genetic structure of jaguars in a recently fragmented Atlantic Forest region, aiming to test whether loss of diversity and differentiation among local populations are detectable, and whether they can be attributed to the recent effect of drift. We used 13 microsatellite loci to characterize the genetic diversity present in four remnant populations, and observed marked differentiation among them, with evidence of recent allelic loss in local areas. Although some migrant and admixed individuals were identified, our results indicate that recent large‐scale habitat removal and fragmentation among these areas has been sufficiently strong to promote differentiation induced by drift and loss of alleles at each site. Low estimated effective sizes supported the inference that genetic drift could have caused this effect within a short time frame. These results indicate that jaguars’ ability to effectively disperse across the human‐dominated landscapes that separate the fragments is currently very limited, and that each fragment contains a small, isolated population that is already suffering from the effects of genetic drift.
Landscape effects on extremely fragmented populations of a rare solitary bee, Colletes floralis
Authors: DAVIS EMILY S. , MURRAY TOMÁS E. , FITZPATRICK ÚNA , BROWN MARK J. F. , PAXTON ROBERT J. 
Published: October 2010

AbstractGlobally, there is concern over the decline of bees, an ecologically important group of pollinating insects. Genetic studies provide insights into population structure that are crucial for conservation management but that would be impossible to obtain by conventional ecological methods. Yet conservation genetic studies of bees have primarily focussed on social species rather than the more species‐rich solitary bees. Here, we investigate the population structure of Colletes floralis, a rare and threatened solitary mining bee, in Ireland and Scotland using nine microsatellite loci. Genetic diversity was surprisingly as high in Scottish (Hebridean island) populations at the extreme northwestern edge of the species range as in mainland Irish populations further south. Extremely high genetic differentiation among populations was detected; multilocus FST was up to 0.53, and and Dest were even higher (maximum: 0.85 and 1.00, respectively). A pattern of isolation by distance was evident for sites separated by land. Water appears to act as a substantial barrier to gene flow yet sites separated by sea did not exhibit isolation by distance. C. floralis populations are extremely isolated and probably not in regional migration‐drift equilibrium. GIS‐based landscape genetic analysis reveals urban areas as a potential and substantial barrier to gene flow. Our results highlight the need for urgent site‐specific management action to halt the decline of this and potentially other rare solitary bees.
Chemoreceptors in signalling complexes: shifted conformation and asymmetric coupling
Authors: Amin Divya N. , Hazelbauer Gerald L. 
Published: October 2010

SummaryBacterial chemotaxis is mediated by signalling complexes of chemoreceptors, histidine kinase CheA and coupling protein CheW. Interactions in complexes profoundly affect the kinase. We investigated effects of these interactions on chemoreceptors by comparing receptors alone and in complexes. Assays of initial rates of methylation indicated that signalling complexes shifted receptor conformation towards the methylation‐on, higher‐ligand‐affinity, kinase‐off state, tuning receptors for greater sensitivity. In contrast, transmembrane and conformational signalling within chemoreceptors was essentially unaltered, consistent with other evidence identifying receptor dimers as the fundamental units of such signalling. In signalling complexes, coupling of ligand binding to kinase activity is cooperative and the dynamic range of kinase control expanded > 100‐fold by receptor adaptational modification. We observed no cooperativity in influence of ligand on receptor conformation, only on kinase activity. However, receptor modification generated increased dynamic range in a stepwise fashion, partly in coupling ligand to receptor conformation and partly in coupling receptor conformation to kinase activity. Thus, receptors and kinase were not equivalently affected by interactions in signalling complexes or by ligand binding and adaptational modification, indicating asymmetrical coupling between them. This has implications for mechanisms of precise adaptation. Coupling might vary, providing a previously unappreciated locus for sensory control.
CGDEase, a Pseudomonas fluorescens protein of the PLC/APase superfamily with CDP‐ethanolamine and (dihexanoyl)glycerophosphoethanolamine hydrolase activity induced by osmoprotectants under phosphate‐deficient conditions
Authors: Costas María Jesús , Pinto Rosa María , Cordero Paloma Martín , Cabezas Alicia , Alves‐Pereira Isabel , Cameselle José Carlos , Ribeiro João Meireles 
Published: October 2010

SummaryA novel enzyme, induced by choline, ethanolamine, glycine betaine or dimethylglycine, was released at low temperature and phosphate from Pseudomonas fluorescens (CECT 7229) suspensions at low cell densities. It is a CDP‐ethanolamine pyrophosphatase/(dihexanoyl)glycerophosphoethanolamine phosphodiesterase (CGDEase) less active on choline derivatives, and inactive on long‐chain phospholipids, CDP‐glycerol and other NDP‐X compounds. The reaction pattern was typical of phospholipase C (PLC), as either phosphoethanolamine or phosphocholine was produced. Peptide‐mass analyses, gene cloning and expression provided a molecular identity for CGDEase. Bioinformatic studies assigned it to the PLC branch of the phospholipase C/acid phosphatase (PLC/APase) superfamily, revealed an irregular phylogenetic distribution of close CGDEase relatives, and suggested their genes are not in operons or conserved contexts. A theoretical CGDEase structure was supported by mutagenesis of two predicted active‐site residues, which yielded essentially inactive mutants. Biological relevance is supported by comparisons with CGDEase relatives, induction by osmoprotectants (not by osmotic stress itself) and repression by micromolar phosphate. The low bacterial density requirement was related to phosphate liberation from lysed bacteria in denser populations, rather than to a classical quorum‐sensing effect. The results fit better a CGDEase role in phosphate scavenging than in osmoprotection.
The critical role of S‐lactoylglutathione formation during methylglyoxal detoxification in Escherichia coli
Authors: Ozyamak Ertan , Black Susan S. , Walker Claire A. , MacLean Morag J. , Bartlett Wendy , Miller Samantha , Booth Ian R. 
Published: October 2010

SummarySurvival of exposure to methylglyoxal (MG) in Gram‐negative pathogens is largely dependent upon the operation of the glutathione‐dependent glyoxalase system, consisting of two enzymes, GlxI (gloA) and GlxII (gloB). In addition, the activation of the KefGB potassium efflux system is maintained closed by glutathione (GSH) and is activated by S‐lactoylGSH (SLG), the intermediate formed by GlxI and destroyed by GlxII. Escherichia coli mutants lacking GlxI are known to be extremely sensitive to MG. In this study we demonstrate that a ΔgloB mutant is as tolerant of MG as the parent, despite having the same degree of inhibition of MG detoxification as a ΔgloA strain. Increased expression of GlxII from a multicopy plasmid sensitizes E. coli to MG. Measurement of SLG pools, KefGB activity and cytoplasmic pH shows these parameters to be linked and to be very sensitive to changes in the activity of GlxI and GlxII. The SLG pool determines the activity of KefGB and the degree of acidification of the cytoplasm, which is a major determinant of the sensitivity to electrophiles. The data are discussed in terms of how cell fate is determined by the relative abundance of the enzymes and KefGB.
Small RNAs promote mRNA stability to activate the synthesis of virulence factors
Authors: Podkaminski Dimitri , Vogel Jörg 
Published: October 2010

SummaryAlthough most bacterial small RNAs act to repress target mRNAs, some also activate messengers. The predominant mode of activation has been seen in ‘anti‐antisense’ regulation whereby a small RNA prevents the formation of an inhibitory 5′ mRNA structure that otherwise impairs translational initiation and protein synthesis. The translational activation might also stabilize the target yet this was considered a secondary effect in the examples known thus far. Two recent papers in Molecular Microbiology investigate post‐transcriptional activation of collagenase mRNA by Clostridium VR‐RNA, and streptokinase mRNA by Streptococcus FasX RNA, to suggest that small RNAs exert positive regulation of virulence genes primarily at the level of mRNA stabilization.
Rapid phylogenetic identification of members of the Pseudomonas syringae species complex using the rpoD locus
Authors: Parkinson N. , Bryant R. , Bew J. , Elphinstone J. 
Published: October 2010

Phylogenies based on four loci confirmed the relatedness of all nine validly published species type strains within the Pseudomonas syringae species complex. To further establish the phylogenetic structure within the complex, all 67 pathovar type strains (with defined host ranges) were sequenced using a 578‐nucleotide rpoD locus. Since this locus encompassed that used in a previous seven‐locus study, it was possible to relate these strains to the existing phylogroup, genomospecies and binomial classifications. All species type strains were distinguished by relatively long branch lengths with all four loci, except for P. savastanoi, P. ficuserectae, P. meliae, P. amygdali and P. tremae, which were attributed to phylogroup 3. The grouping of P. tremae with these genomospecies‐2 species was surprising since this species was previously designated as the sole representative of genomospecies 5. The oat pathogen P. syringae pv. coronafaciens was also distinguished by relatively long branch lengths with all four loci. The rpoD phylogeny grouped all the pathovar type strains into major clades that corresponded to previously defined phylogroups, except for two genomospecies‐7 strains and P. caricapapayae, which were identified as a new phylogroup (6). There was good correlation between phylogroup and genomospecies classifications, except that two genomospecies‐8 strains (P. avellanae and P. syringae pv. theae) were found as a distinct clade within phylogroup 1 along with P. syringae pvs morsprunorum and actinidiae. The rpoD locus will provide a common reference framework to improve monitoring and surveillance of these important pathogens.
A nested‐PCR method for rapid detection of Sclerotinia sclerotiorum on petals of oilseed rape (Brassica napus)
Authors: Qin L. , Fu Y. , Xie J. , Cheng J. , Jiang D. , Li G. , Huang J. 
Published: October 2010

This study established a quick and accurate method to detect petal infection of oilseed rape (Brassica napus) by Sclerotinia sclerotiorum using a nested‐PCR technique. DNA samples were extracted from each petal using a microwave method, followed by two rounds of PCR amplification. The first‐round PCR amplification was performed using the universal fungal primer pair ITS4/ITS5, and the second‐round amplification with a specific primer pair XJJ21/XJJ222, which was designed using the single‐nucleotide polymorphisms among nuclear rDNA ITS sequences of Sclerotinia spp., Botrytis spp. and other selected fungi. The established technique is rapid and inexpensive, and has a high degree of specificity and sensitivity. This assay can distinguish Sclerotinia spp. from other fungi, including Botrytis cinerea, a closely related and frequent cohabitant on oilseed rape petals, and can detect 50 fg genomic DNA, five ascospores of S. sclerotiorumin vitro or 50 ascospores of S. sclerotiorum on one petal in approximately 6 h, even in the presence of a high background of oilseed rape DNA. This technique was successfully applied in detecting natural petal infections.
Phenotypic and molecular genetic characterization indicate no major race‐specific interactions between Xanthomonas translucens pv. graminis and Lolium multiflorum
Authors: Wichmann F. , Müller Hug B. , Widmer F. , Boller B. , Studer B. , Kölliker R. 
Published: October 2010

Bacterial wilt of forage grasses, caused by the pathogen Xanthomonas translucens pv. graminis (Xtg), is a major disease of forage grasses such as Italian ryegrass (Lolium multiflorum). The plant genotype‐bacterial isolate interaction was analysed to elucidate the existence of race‐specific responses and to assist the identification of plant disease resistance genes. In a greenhouse experiment, 62 selected plant genotypes were artificially inoculated with six different bacterial isolates. Significant differences in resistance were observed among L. multiflorum genotypes (P < 0·001) and in virulence (intensity of disease symptoms) among Xtg isolates (P < 0·001) using the area under the disease progress curve (AUDPC). No significant genotype‐isolate interaction (P > 0·05) could be observed using linear regression modelling. However, additive main effects and multiplicative interaction effects (ammi) analysis revealed five genotypes which did not cluster close to the origin of the biplot, indicating specific interactions between these genotypes and some bacterial isolates. Simple sequence repeat (SSR) markers were used to identify marker‐resistance associations using the same plant genotypes and bacterial isolates. The SSR marker NFA027 located on linkage group (LG) 5 was significantly associated with bacterial wilt resistance across all six bacterial isolates and explained up to 37·4% of the total variance of AUDPC values. Neither the inoculation experiment nor the SSR analyses revealed major host genotype‐pathogen isolate interactions, thus suggesting that Xtg resistance, observed so far, is effective across a broad range of different bacterial isolates and plant genotypes.
Development of Lymphocyte Subpopulations in Preterm Infants
Authors: Walker J. C. , Smolders M. A. J. C. , Gemen E. F. A. , Antonius T. A. J. , Leuvenink J. , De Vries E. 
Published: October 2010

AbstractIn preterm neonates the immune system is thought to be less developed at birth, but very little is known about the actual size of lymphocyte subpopulations, and even less about the maturation of these subpopulations during the first months after a premature birth. To evaluate the development of lymphocyte subpopulations in preterm infants during the first 3 months after birth, we performed a prospective longitudinal study in two hospitals in the Netherlands. Preterm neonates (n = 38) of all post‐menstrual ages were included and blood samples were taken from cord blood, and at 1 week, 6 weeks, and 3 months. Lymphocyte subpopulations were measured by four‐colour flow cytometry. The data were compared with follow‐up data obtained in healthy term neonates (n = 8), and with single samples from school age children (n = 5) and adults (n = 5). Overall, we found a similar pattern of post‐natal development of lymphocyte subpopulations in the term and preterm infants. Both B lymphocytes and helper and cytotoxic T lymphocytes mainly consist of naive cells at birth and during the 3 months of follow‐up in all neonatal age groups. So, the preterm immune system seems to be able to generate an outburst of naive T and B lymphocytes from the thymus and bone marrow within the same time span after the start of post‐natal antigenic stimulation from the environment as the term immune system, but, with lower post‐menstrual age, the absolute counts of naive helper T lymphocytes are lower.
Molecular Characterization of the Porcine TIM‐3 Gene
Authors: Zhao W. , Li Y. , Wang Z. , Li K. , Yang S. 
Published: October 2010

AbstractTIM‐3 is a member of the TIM (T‐cell immunoglobulin domain and mucin domain) family, which plays an important role in TH1 responses and autoimmune diseases. In this study, we cloned and characterized the porcine TIM‐3 gene. Real‐time PCR showed little expression of porcine TIM‐3 in muscle and stomach, low expression in kidney, brain, stomach and muscle, moderate expression in liver, small intestine and lymph, and high expression in spleen and lung. Transient transfection indicated that porcine TIM‐3 fusion protein was found to localize on the cell membranes or cytoplasm. Association analysis indicated that the SNP AccI in exon2 was significantly associated (P < 0.05) with red blood cell count mean corpuscular haemoglobin, packed cell volume, Lymphocyte percentage and Lymphocyte modulus. In conclusion, our results provide some information for conducting further studies on the functions of porcine TIM‐3 gene in type I diabetes and suggest that SNP AccI in exon2 may be utilized as a marker for molecular‐assisted selection in animal breeding.
Improving transfusion practice: ongoing education and audit at two tertiary speciality hospitals in Western Australia
Authors: Gallagher‐Swann M. , Ingleby B. , Cole C. , Barr A. 
Published: October 2010

Background: Institutions undertaking transfusion have a responsibility to ensure safe and appropriate practice. The hospital transfusion committee (HTC) plays a major role in monitoring all aspects of transfusion. Dedicated staff with the responsibility of undertaking transfusion education and audit have been employed at many hospitals. The question is ‘Do these positions improve practice?’. Study design and methods: In 2005, a transfusion coordinator was employed by the King Edward Memorial Hospital (KEMH) and Princess Margaret Hospital (PMH) in Perth, Western Australia. After an initial audit to collect baseline data on transfusion documentation and compliance with national guidelines, a series of interventions was undertaken. In addition, the transfusion protocols were rewritten and published electronically. Further audits were undertaken in 2006, 2007 and 2009. Results: Sequential audits show measured improvements in transfusion documentation. Baseline, hourly and completion observations are now correctly recorded in >94% of records at KEMH and >96% of records at PMH. Compliance with recording of 15 min observations has shown a 23% magnitude increase at KEMH and 36% at PMH. Compliance with recording of consent has increased by 20% at KEMH and 31% at PMH. Promotion of positive patient identification, when collecting specimens and administering blood, has been undertaken. Conclusion: The initiatives implemented by the transfusion coordinator and endorsed by the HTCs have improved the standard of transfusion documentation and practice at both institutions.