bluuebunny/crossref_metadata_2025_split huggingface dataset:
Finding a (pine) needle in a haystack: chloroplast genome sequence divergence in rare and widespread pines
Authors: WHITTALL J. B. , SYRING J. , PARKS M. , BUENROSTRO J. , DICK C. , LISTON A. , CRONN R. 
Published: February 2010

AbstractCritical to conservation efforts and other investigations at low taxonomic levels, DNA sequence data offer important insights into the distinctiveness, biogeographic partitioning and evolutionary histories of species. The resolving power of DNA sequences is often limited by insufficient variability at the intraspecific level. This is particularly true of studies involving plant organelles, as the conservative mutation rate of chloroplasts and mitochondria makes it difficult to detect polymorphisms necessary to track genealogical relationships among individuals, populations and closely related taxa, through space and time. Massively parallel sequencing (MPS) makes it possible to acquire entire organelle genome sequences to identify cryptic variation that would be difficult to detect otherwise. We are using MPS to evaluate intraspecific chloroplast‐level divergence across biogeographic boundaries in narrowly endemic and widespread species of Pinus. We focus on one of the world’s rarest pines – Torrey pine (Pinus torreyana) – due to its conservation interest and because it provides a marked contrast to more widespread pine species. Detailed analysis of nearly 90% (∼105 000 bp each) of these chloroplast genomes shows that mainland and island populations of Torrey pine differ at five sites in their plastome, with the differences fixed between populations. This is an exceptionally low level of divergence (1 polymorphism/∼21 kb), yet it is comparable to intraspecific divergence present in widespread pine species and species complexes. Population‐level organelle genome sequencing offers new vistas into the timing and magnitude of divergence within species, and is certain to provide greater insight into pollen dispersal, migration patterns and evolutionary dynamics in plants.
Characterization of a hotspot for mimicry: assembly of a butterfly wing transcriptome to genomic sequence at the HmYb/Sb locus
Authors: FERGUSON LAURA , LEE SIU FAI , CHAMBERLAIN NICOLA , NADEAU NICOLA , JORON MATHIEU , BAXTER SIMON , WILKINSON PAUL , PAPANICOLAOU ALEXIE , KUMAR SUJAI , KEE THUAN‐JIN , CLARK RICHARD , DAVIDSON CLAIRE , GLITHERO REBECCA , BEASLEY HELEN , VOGEL HEIKO , FFRENCH‐CONSTANT RICHARD , JIGGINS CHRIS 
Published: February 2010

AbstractThe mimetic wing patterns of Heliconius butterflies are an excellent example of both adaptive radiation and convergent evolution. Alleles at the HmYb and HmSb loci control the presence/absence of hindwing bar and hindwing margin phenotypes respectively between divergent races of Heliconius melpomene, and also between sister species. Here, we used fine‐scale linkage mapping to identify and sequence a BAC tilepath across the HmYb/Sb loci. We also generated transcriptome sequence data for two wing pattern forms of H. melpomene that differed in HmYb/Sb alleles using 454 sequencing technology. Custom scripts were used to process the sequence traces and generate transcriptome assemblies. Genomic sequence for the HmYb/Sb candidate region was annotated both using the MAKER pipeline and manually using transcriptome sequence reads. In total, 28 genes were identified in the HmYb/Sb candidate region, six of which have alternative splice forms. None of these are orthologues of genes previously identified as being expressed in butterfly wing pattern development, implying previously undescribed molecular mechanisms of pattern determination on Heliconius wings. The use of next‐generation sequencing has therefore facilitated DNA annotation of a poorly characterized genome, and generated hypotheses regarding the identity of wing pattern at the HmYb/Sb loci.
Bacterial diversity in a glacier foreland of the high Arctic
Authors: SCHÜTTE URSEL M.E. , ABDO ZAID , FOSTER JAMES , RAVEL JACQUES , BUNGE JOHN , SOLHEIM BJØRN , FORNEY LARRY J. 
Published: February 2010

AbstractOver the past 100 years, Arctic temperatures have increased at almost twice the global average rate. One consequence is the acceleration of glacier retreat, exposing new habitats that are colonized by microorganisms whose diversity and function are unknown. Here, we characterized bacterial diversity along two approximately parallel chronosequences in an Arctic glacier forefield that span six time points following glacier retreat. We assessed changes in phylotype richness, evenness and turnover rate through the analysis of 16S rRNA gene sequences recovered from 52 samples taken from surface layers along the chronosequences. An average of 4500 sequences was obtained from each sample by 454 pyrosequencing. Using parametric methods, it was estimated that bacterial phylotype richness was high, and that it increased significantly from an average of 4000 (at a threshold of 97% sequence similarity) at locations exposed for 5 years to an average of 7050 phylotypes per 0.5 g of soil at sites that had been exposed for 150 years. Phylotype evenness also increased over time, with an evenness of 0.74 for 150 years since glacier retreat reflecting large proportions of rare phylotypes. The bacterial species turnover rate was especially high between sites exposed for 5 and 19 years. The level of bacterial diversity present in this High Arctic glacier foreland was comparable with that found in temperate and tropical soils, raising the question whether global patterns of bacterial species diversity parallel that of plants and animals, which have been found to form a latitudinal gradient and be lower in polar regions compared with the tropics.
A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush)
Authors: GOETZ FREDERICK , ROSAUER DANIEL , SITAR SHAWN , GOETZ GILES , SIMCHICK CRYSTAL , ROBERTS STEVEN , JOHNSON RONALD , MURPHY CHERYL , BRONTE CHARLES R. , MACKENZIE SIMON 
Published: February 2010

AbstractIn Lake Superior there are three principal forms of lake trout (Salvelinus namaycush): lean, siscowet and humper. Wild lean and siscowet differ in the shape and relative size of the head, size of the fins, location and size of the eyes, caudal peduncle shape and lipid content of the musculature. To investigate the basis for these phenotypic differences, lean and siscowet lake trout, derived from gametes of wild populations in Lake Superior, were reared communally under identical environmental conditions for 2.5 years. Fish were analysed for growth, morphometry and lipid content, and differences in liver transcriptomics were investigated using Roche 454 GS‐FLX pyrosequencing. The results demonstrate that key phenotypic differences between wild lean and siscowet lake trout such as condition factor, morphometry and lipid levels, persist in these two forms when reared in the laboratory under identical environmental conditions. This strongly suggests that these differences are genetic and not a result of environmental plasticity. Transcriptomic analysis involving the comparison of hepatic gene frequencies (RNA‐seq) and expression (quantitative reverse transcription–polymerase chain reaction (qPCR)) between the two lake trout forms, indicated two primary gene groups that were differentially expressed; those involving lipid synthesis, metabolism and transport (acyl‐CoA desaturase, acyl‐CoA binding protein, peroxisome proliferator‐activated receptor gamma, and apolipoproteins), and those involved with immunity (complement component C3, proteasome, FK506 binding protein 5 and C1q proteins). The results demonstrate that RNA‐seq can be used to identify differentially expressed genes; however, some discrepancies between RNA‐seq analysis and qPCR indicate that methods for deep sequencing may need to be refined and/or different RNA‐seq platforms utilized.
Massively parallel 454‐sequencing of fungal communities in Quercus spp. ectomycorrhizas indicates seasonal dynamics in urban and rural sites
Authors: JUMPPONEN ARI , JONES KENNETH L. , DAVID MATTOX J. , YAEGE CHULEE 
Published: February 2010

AbstractWe analysed two sites within and outside an urban development in a rural background to estimate the fungal richness, diversity and community composition in Quercus spp. ectomycorrhizas using massively parallel 454‐sequencing in combination with DNA‐tagging. Our analyses indicated that shallow sequencing (∼150 sequences) of a large number of samples (192 in total) provided data that allowed identification of seasonal trends within the fungal communities: putative root‐associated antagonists and saprobes that were abundant early in the growing season were replaced by common ectomycorrhizal fungi in the course of the growing season. Ordination analyses identified a number of factors that were correlated with the observed communities including host species as well as soil organic matter, nutrient and heavy metal enrichment. Overall, our application of the high throughput 454 sequencing provided an expedient means for characterization of fungal communities.
Microbial ecological response of the intestinal flora of Peromyscus maniculatus and P. leucopus to heavy metal contamination
Authors: COOLON JOSEPH D. , JONES KENNETH L. , NARAYANAN SANJEEV , WISELY SAMANTHA M. 
Published: February 2010

AbstractHeavy metal contamination negatively affects natural systems including plants, birds, fish and bacteria by reducing biodiversity at contaminated sites. At the Tri‐State Mining District, efforts have been made to remediate sites to mitigate the detrimental effects that contamination has caused on human health. While the remediation effort has returned the site to within federal safety standards, it is unclear if this effort is sufficient to restore floral and faunal communities. Intrinsic to ecosystem and organism health is the biodiversity and composition of microbial communities. We have taken advantage of recent advances in sequencing technology and surveyed the bacterial community of remediated and reference soils as well as the intestinal microbial community of two ubiquitous rodent species to provide insight on the impacts of residual heavy metal contamination on the ecosystem. Rodents found on the remediated site had reduced body mass, smaller body size and lower body fat than animals on reference sites. Using bar‐coded, massively parallel sequencing, we found that bacterial communities in both the soil and Peromyscus spp. gastrointestinal tracts had no difference in diversity between reference and remediated sites but assemblages differed in response to contamination. These results suggest that niche voids left by microbial taxa that were unable to deal with the remnant levels of heavy metals on remediated sites were replaced by taxa that could persist in this environment. Whether this replacement provided similar ecosystem services as ancestral bacterial communities is unknown.
Key considerations for measuring allelic expression on a genomic scale using high‐throughput sequencing
Authors: FONTANILLAS PIERRE , LANDRY CHRISTIAN R. , WITTKOPP PATRICIA J. , RUSS CARSTEN , GRUBER JONATHAN D. , NUSBAUM CHAD , HARTL DANIEL L. 
Published: February 2010

AbstractDifferences in gene expression are thought to be an important source of phenotypic diversity, so dissecting the genetic components of natural variation in gene expression is important for understanding the evolutionary mechanisms that lead to adaptation. Gene expression is a complex trait that, in diploid organisms, results from transcription of both maternal and paternal alleles. Directly measuring allelic expression rather than total gene expression offers greater insight into regulatory variation. The recent emergence of high‐throughput sequencing offers an unprecedented opportunity to study allelic transcription at a genomic scale for virtually any species. By sequencing transcript pools derived from heterozygous individuals, estimates of allelic expression can be directly obtained. The statistical power of this approach is influenced by the number of transcripts sequenced and the ability to unambiguously assign individual sequence fragments to specific alleles on the basis of transcribed nucleotide polymorphisms. Here, using mathematical modelling and computer simulations, we determine the minimum sequencing depth required to accurately measure relative allelic expression and detect allelic imbalance via high‐throughput sequencing under a variety of conditions. We conclude that, within a species, a minimum of 500–1000 sequencing reads per gene are needed to test for allelic imbalance, and consequently, at least five to 10 millions reads are required for studying a genome expressing 10 000 genes. Finally, using 454 sequencing, we illustrate an application of allelic expression by testing for cis‐regulatory divergence between closely related Drosophila species.
From signal perception to signal transduction: ligand‐induced dimeric switch of DctB sensory domain in solution
Authors: Nan Beiyan , Liu Xin , Zhou Yanfeng , Liu Jiwei , Zhang Le , Wen Jin , Zhang Xiaodong , Su Xiao‐Dong , Wang Yi‐Ping 
Published: February 2010

Summary Sinorhizobium meliloti DctB is a typical transmembrane sensory histidine kinase, which senses C4‐dicarboxylic acids (DCA) and regulates the expression of DctA, the DCA transporter. We previously reported the crystal structures of its periplasmic sensory domain (DctBp) in apo and succinate‐bound states, and these structures showed dramatic conformational changes at dimeric level. Here we show a ligand‐induced dimeric switch in solution and a strong correlation between DctBp's dimerization states and the in vivo activities of DctB. Using site‐directed mutagenesis, we identify important determinants for signal perception and transduction. Specifically, we show that the ligand‐binding pocket is essential for DCA‐induced ‘on’ activity of DctB. Mutations at different sections of DctBp's dimerization interface can lock full‐length DctB at either ‘on’ or ‘off’ state, independent of ligand binding. Taken together, these results suggest that DctBp's signal perception and transduction occur through a ‘ligand‐induced dimeric switch’, in which the changes in the dimeric conformations upon ligand binding are responsible for the signal transduction in DctB.
A high‐affinity putrescine‐cadaverine transporter from Trypanosoma cruzi
Authors: Hasne Marie‐Pierre , Coppens Isabelle , Soysa Radika , Ullman Buddy 
Published: February 2010

SummaryWhereas mammalian cells and most other organisms can synthesize polyamines from basic amino acids, the protozoan parasite Trypanosoma cruzi is incapable of polyamine biosynthesis de novo and therefore obligatorily relies upon putrescine acquisition from the host to meet its nutritional requirements. The cell surface proteins that mediate polyamine transport into T. cruzi, as well as most eukaryotes, however, have by‐in‐large eluded discovery at the molecular level. Here we report the identification and functional characterization of two polyamine transporters, TcPOT1.1 and TcPOT1.2, encoded by alleles from two T. cruzi haplotypes. Overexpression of the TcPOT1.1 and TcPOT1.2 genes in T. cruzi epimastigotes revealed that TcPOT1.1 and TcPOT1.2 were high‐affinity transporters that recognized both putrescine and cadaverine but not spermidine or spermine. Furthermore, the activities and subcellular locations of both TcPOT1.1 and TcPOT1.2 in intact parasites were profoundly influenced by extracellular putrescine availability. These results establish TcPOT1.1 and TcPOT1.2 as key components of the T. cruzi polyamine transport pathway, an indispensable nutritional function for the parasite that may be amenable to therapeutic manipulation.
Discovery of an operon that participates in agmatine metabolism and regulates biofilm formation in Pseudomonas aeruginosa
Authors: Williams Bryan J. , Du Rui‐Hong , Calcutt M. Wade , Abdolrasulnia Rasul , Christman Brian W. , Blackwell Timothy S. 
Published: February 2010

SummaryAgmatine is the decarboxylation product of arginine and a number of bacteria have devoted enzymatic pathways for its metabolism. Pseudomonas aeruginosa harbours the aguBA operon that metabolizes agmatine to putrescine, which can be subsequently converted into other polyamines or shunted into the TCA cycle for energy production. We discovered an alternate agmatine operon in the P. aeruginosa strain PA14 named agu2ABCA′ that contains two genes for agmatine deiminases (agu2A and agu2A′). This operon was found to be present in 25% of clinical P. aeruginosa isolates. Agu2A′ contains a twin‐arginine translocation signal at its N‐terminus and site‐directed mutagenesis and cell fractionation experiments confirmed this protein is secreted to the periplasm. Analysis of the agu2ABCA′ promoter demonstrates that agmatine induces expression of the operon during the stationary phase of growth and during biofilm growth and agu2ABCA′ provides only weak complementation of aguBA, which is induced during log phase. Biofilm assays of mutants of all three agmatine deiminase genes in PA14 revealed that deletion of agu2ABCA′, specifically its secreted product Agu2A′, reduces biofilm production of PA14 following addition of exogenous agmatine. Together, these findings reveal a novel role for the agu2ABCA′ operon in the biofilm development of P. aeruginosa.
Identification of the gate regions in the primary structure of the secretin pIV
Authors: Spagnuolo Julian , Opalka Natacha , Wen Wesley X. , Gagic Dragana , Chabaud Elodie , Bellini Pierdomenico , Bennett Matthew D. , Norris Gillian E. , Darst Seth A. , Russel Marjorie , Rakonjac Jasna 
Published: February 2010

SummarySecretins are a family of large bacterial outer membrane channels that serve as exit ports for folded proteins, filamentous phage and surface structures. Despite the large size of their substrates, secretins do not compromise the barrier function of the outer membrane, implying a gating mechanism. The region in the primary structure that forms the putative gate has not previously been determined for any secretin. To identify residues involved in gating the pIV secretin of filamentous bacteriophage f1, we used random mutagenesis of the gene followed by positive selection for mutants with compromised barrier function (‘leaky’ mutants). We identified mutations in 34 residues, 30 of which were clustered into two regions located in the centre of the conserved C‐terminal secretin family domain: GATE1 (that spanned 39 residues) and GATE2 (that spanned 14 residues). An internal deletion constructed in the GATE2 region resulted in a severely leaky phenotype. Three of the four remaining mutations are located in the region that encodes the N‐terminal, periplasmic portion of pIV and could be involved in triggering gate opening. Two missense mutations in the 24‐residue region that separates GATE1 and GATE2 were also constructed. These mutant proteins were unstable, defective in multimerization and non‐functional.
Update on Legionnaires’ disease: pathogenesis, epidemiology, detection and control
Authors: Hilbi Hubert , Jarraud Sophie , Hartland Elizabeth , Buchrieser Carmen 
Published: February 2010

SummaryLegionellosis or Legionnaires’ disease is an emerging and often‐fatal form of pneumonia that is most severe in elderly and immunocompromised people, an ever‐increasing risk group for infection. In recent years, the genomics of Legionella spp. has significantly increased our knowledge of the pathogenesis of this disease by providing new insights into the evolution and genetic and physiological basis of Legionella–host interactions. The seventh international conference on Legionella, Legionella 2009, illustrated many recent conceptual advances in epidemiology, pathogenesis and ecology. Experts in different fields presented new findings on basic mechanisms of pathogen–host interactions and bacterial evolution, as well as the clinical management and environmental prevalence and persistence of Legionella. The presentations revealed remarkable facts about the genetic and metabolic basis of the intracellular lifestyle of Legionella and reported on its striking ability to manipulate host cell processes by molecular mimicry. Together, these investigations will lead to new approaches for the treatment and prevention of Legionnaires’ disease.
CC Chemokine Receptor 4 (CCR4) in human allergen‐induced late nasal responses
Authors: Banfield G. , Watanabe H. , Scadding G. , Jacobson M. R. , Till S. J. , Hall D. A. , Robinson D. S. , Lloyd C. M. , Nouri‐Aria K. T. , Durham S. R. 
Published: February 2010

To cite this article: Banfield G, Watanabe H, Scadding G, Jacobson MR, Till SJ, Hall DA, Robinson DS, Lloyd CM, Nouri‐Aria KT, Durham SR. CC Chemokine Receptor 4 (CCR4) in human allergen‐induced late nasal responses. Allergy 2010; 65: 1126–1133.AbstractBackground:  CC Chemokine receptor 4 (CCR4) is preferentially expressed on Th2 lymphocytes. CCR4‐mediated inflammation may be important in the pathology of allergic rhinitis. Disruption of CCR4 – ligand interaction may abrogate allergen‐induced inflammation.Methods:  Sixteen allergic rhinitics and six nonatopic individuals underwent both allergen and control (diluent) nasal challenges. Symptom scores and peak nasal inspiratory flow were recorded. Nasal biopsies were taken at 8 h post challenge. Sections were immunostained and examined by light or dual immunofluorescence microscopy for eosinophils, T‐lymphocytes, CCR4+CD3+ and CXCR3+CD3+ cells and examined by in situ hybridization for CCR4, IL‐4 and IFN‐γ mRNA+ cells. Peripheral blood mononuclear cells were obtained from peripheral blood of nine normal donors and the CCR4+CD4+ cells assessed for actin polymerization in response to the CCR4 ligand macrophage‐derived chemokine (MDC/CCL22) and the influence of a CCR4 antagonist tested.Results:  Allergic rhinitics had increased early and late phase symptoms after allergen challenge compared to diluent; nonatopics did not respond to either challenge. Eosinophils, but not total numbers of CD3+ T cells, were increased in rhinitics following allergen challenge. In rhinitics, there was an increase in CCR4+CD3+ protein‐positive cells relative to CXCR3+CD3+ cells; CCR4 mRNA+ cells were increased and IL‐4 increased to a greater extent than IFN‐γ. CCR4+CD4+ T cells responded to MDC in vitro, and this response was inhibited by the selective CCR4 antagonist.Conclusion:  Lymphocyte CCR4 expression is closely associated with induction of human allergen‐induced late nasal responses. Blocking CCR4‐ligand interaction may provide a novel therapeutic approach in allergic disease.