bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeny and historical biogeography of the cave‐adapted shrimp genus Typhlatya (Atyidae) in the Caribbean Sea and western Atlantic
Authors: Hunter Rebecca L. , Webb Michael Scott , Iliffe Thomas M. , Bremer Jaime R. Alvarado 
Published: October 2007

AbstractAim  To infer phylogenetic relationships among five species of the cave‐adapted shrimp genus Typhlatya in order to test competing hypotheses of dispersal and colonization of the disjunct cave localities occupied by these five species.Location  Typhlatya species are found in caves and anchialine ponds across the northern margin of the Caribbean Sea, along the Mediterranean and Adriatic coasts and on oceanic islands in the Atlantic and eastern Pacific oceans. This study focuses on five species, one from Bermuda, one from the Caicos Islands and three from the Yucatan Peninsula of Mexico.Methods  Partial sequences (c. 1400 bp) from the mitochondrial cytochrome b, 16S rDNA and COI genes were obtained from representative samples of the five species. Phylogenetic inference was carried out with maximum parsimony and maximum likelihood analyses. Parsimony networks were constructed for the Bermudian species Typhlatya iliffei and one Yucatan species Typhlatya mitchelli, to determine the degree of connectivity among populations inhabiting different cave systems.Results  All three land masses were recovered as monophyletic. The two insular marine species from Bermuda and the Caicos Islands formed a clade, while the three continental freshwater species from the Yucatan Peninsula formed another. Within both Bermuda and the Yucatan, shared haplotypes were found in different cave systems, suggesting recent or ongoing gene flow among populations in both locales.Main conclusions  The two insular marine Typhlatya species originated from an ancestral marine population, possibly already cave‐adapted, that is suggested to have colonized the Caicos Islands and subsequently dispersed to Bermuda via the Gulf Stream. Divergence estimates suggest that colonization occurred before the formation of present‐day anchialine cave habitat, which did not form on either island until the late Pliocene to early Pleistocene. Divergence estimates also indicate that the Yucatan freshwater species split before the formation of freshwater cave habitat in the Yucatan. These species could have inhabited crevicular marine habitats before the late Pliocene/early Pleistocene in the Yucatan or elsewhere in the Caribbean, and subsequently migrated to freshwater caves once they formed.
Environmental setting of human migrations in the circum‐Pacific region
Authors: Pope Kevin O. , Terrell John E. 
Published: October 2007

AbstractAim  To assess the genetic and archaeological evidence for the migration of modern humans out of Africa to the circum‐Pacific region and compare the migration patterns with Late Pleistocene and Holocene changes in sea level and climate.Location  Southern and eastern Asia, Australia, and Oceania.Methods  Review of the literature and detailed compilations of data on early human settlements, sea level, and climate change.Results  The expansion of modern humans out of Africa, following a coastal route into southern Asia, was initially thwarted by a series of large and abrupt environmental changes. A period of relatively stable climate and sea level from c. 45,000 yr bp to 40,000 yr bp supported a rapid coastal expansion of modern humans throughout much of Southeast Asia, enabling them to reach the coasts of northeast Russia and Japan by 38,000–37,000 yr bp. Further northwards, migrations were delayed by cold northern climates, which began to deteriorate rapidly after 33,000 yr bp. Human migrations along the coast of the Bering Sea into the New World appear to have occurred much later, c. 14,000 yr bp, probably by people from central Asia who were better adapted to cold northern climates. Cold, dry climates and rapidly changing sea levels leading into and out of the Last Glacial Maximum inhibited coastal settlement, and many of the sites occupied prior to 33,000 yr bp were abandoned. After 16,000 yr bp, the sea‐level rise slowed enough to permit coastal ecosystems to develop and coasts to be re‐colonized, but abrupt changes in climate and sea level inhibited this development until after 12,000 yr bp. Between 12,000 yr bp and 7000 yr bp there was a dramatic increase in reef and estuary/lagoon ecosystems, concurrent with a major expansion of coastal settlements. This early Holocene increase in coastal environments and the concomitant expansion of human coastal‐resource exploitation were followed by corresponding declines in both phenomena in the mid‐Holocene, c. 6000–4000 yr bp. This decline in coastal resources is linked to the drop in sea level throughout the Pacific, which may have caused the widespread population dislocations that ultimately led to the human expansion throughout Oceania.Main conclusions  Climate and sea‐level changes played a central role in the peopling of the circum‐Pacific region.
A controlled trial of an educational programme for people with Parkinson's disease
Authors: Lindskov Susanne , Westergren Albert , Hagell Peter 
Published: October 2007

Aims and objective.  To evaluate patient‐reported health outcomes of a multidisciplinary group educational programme for people with Parkinson's disease (PD), delivered as part of routine clinical practice.Background.  Studies suggest that educational programmes for people with PD have potential to improve patients’ perceived health and well‐being. However, controlled trials of multidisciplinary group educational programmes are lacking.Design.  Naturalistic non‐randomized controlled trial.Methods.  Following ethical approval and informed consent, 48 people with PD (58% men; mean age, 69·3) received the intervention and 48 (52% men; mean age, 72) were allocated to a delayed intervention control group. The intervention was a six‐week (two hours per week) multidisciplinary group educational programme. Patient‐reported health outcomes were assessed by the 12‐item short‐form health survey (SF‐12) at baseline and one month postintervention.Results.  Changes in SF‐12 scores at follow‐up did not differ between the groups and there were no within‐group differences over time. Daily dopaminergic medication increased in the control group but not in the intervention group.Conclusions.  Slightly, but significantly, increased drug requirement in the control group may in part have masked deterioration in perceived health. However, failure to demonstrate improved patient‐reported health may relate to the intervention design, response shift (i.e. change in how people perceive their health), and/or quality and choice of outcome measures. Further studies that take these aspects into consideration are needed to determine the potential for patient education interventions in PD.Relevance to clinical practice.  Nurses and other healthcare professionals need to document the effects of patient educational programmes and to be aware of the importance of intervention design and challenges associated with evaluating programme outcomes. Otherwise, there is a risk that benefits cannot be demonstrated and that decision makers will not invest resources in interventions that actually are beneficial for chronically ill people.
Genetic structure in a tropical lek‐breeding bird, the blue manakin (Chiroxiphia caudata) in the Brazilian Atlantic Forest
Authors: FRANCISCO MERCIVAL R. , GIBBS H. LISLE , GALETTI MAURO , LUNARDI VITOR O. , JUNIOR PEDRO M. GALETTI 
Published: October 2007

AbstractDetermining the genetic structure of tropical bird populations is important for assessing potential genetic effects of future habitat fragmentation and for testing hypotheses about evolutionary mechanisms promoting diversification. Here we used 10 microsatellite DNA loci to describe levels of genetic differentiation for five populations of the lek‐mating blue manakin (Chiroxiphia caudata), sampled along a 414‐km transect within the largest remaining continuous tract of the highly endangered Atlantic Forest habitat in southeast Brazil. We found small but significant levels of differentiation between most populations.FSTvalues varied from 0.0 to 0.023 (overallFST = 0.012) that conformed to a strong isolation by distance relationship, suggesting that observed levels of differentiation are a result of migration–drift equilibrium.Nemvalues estimated using a coalescent‐based method were small (≤ 2 migrants per generation) and close to the minimum level required to maintain genetic similarity between populations. An implication of these results is that if future habitat fragmentation reduces dispersal between populations to even a small extent, then individual populations may undergo a loss of genetic diversity due to an increase in the relative importance of drift, since inbreeding effective population sizes are relatively small (Ne~1000). Our findings also demonstrate that population structuring can occur in a tropical bird in continuous habitat in the absence of geographical barriers possibly due to behavioural features of the species.
Comparative phylogeography and speciation of dung beetles from the Australian Wet Tropics rainforest
Authors: BELL KAREN L. , MORITZ CRAIG , MOUSSALLI ADNAN , YEATES DAVID K. 
Published: October 2007

AbstractIn tropical rainforests, insects show especially high species richness and local endemism of species relative to vertebrates. One possible cause is that insects respond to historical fluctuations of rainforests on a smaller spatial scale than do vertebrates. To evaluate this hypothesis, we combine environmental niche models and mitochondrial DNA phylogeography for two pairs of sister species of the dung beetle genus Temnoplectron (T. aeneopiceum–T. subvolitans and T. politulum–T. reyi) from the rainforests of northeastern Australia, where climate‐driven rainforest fluctuations in the Quaternary have strongly influenced genetic and species diversity of vertebrates. Within both species pairs, the bioclimatic niche was conserved, but the T. aeneopiceum–T. subvolitans species pair had the narrower environmental range, and thus more restricted potential distribution. Coalescent analyses indicated Late Pliocene or Early Pleistocene divergences for both species pairs, and earlier speciation in (T. aeneopiceum–T. subvolitans) than in (T. politulum–T. reyi). Phylogeographic structure in (T. aeneopiceum–T. subvolitans) was more pronounced than in (T. politulum–T. reyi), with significant isolation‐by‐distance in the former species‐pair only. Nested clade and coalescence analyses indicated local range expansions for the T. aeneopiceum–subvolitans species pair and range‐wide expansion for both T. politulum and T. reyi. We suggest that stronger phylogeographic structure and earlier divergence in (T. aeneopiceum–T. subvolitans) than in (T. politulum–T. reyi) reflects a stronger influence of environmental barriers to gene flow under the present climate and greater sensitivity to warmer and drier periods of the Quaternary. The two species pairs evidently responded to Quaternary rainforest fluctuations at spatial scales similar to those seen within low‐vagility species of vertebrate. Despite this similarity of scale, these insect lineages are reproductively isolated at parapatric boundaries, whereas analogous lineages of vertebrates often are not. We suggest that rapid evolution of genitalia may facilitate geographic speciation in rainforest beetles.
Rangewide phylogeography in the greater horseshoe bat inferred from microsatellites: implications for population history, taxonomy and conservation
Authors: ROSSITER STEPHEN J. , BENDA PETR , DIETZ CHRISTIAN , ZHANG SHUYI , JONES GARETH 
Published: October 2007

AbstractThe distribution of genetic variability across a species’ range can provide valuable insights into colonization history. To assess the relative importance of European and Asian refugia in shaping current levels of genetic variation in the greater horseshoe bats, we applied a microsatellite‐based approach to data collected from 56 localities ranging from the UK to Japan. A decline in allelic richness from west Asia to the UK and analyses of FST both imply a northwestward colonization across Europe. However, sharp discontinuities in gene frequencies within Europe and between the Balkans and west Asia (Syria/Russia) are consistent with suture zones following expansion from multiple refugia, and a lack of recent gene flow from Asia Minor. Together, these results suggest European populations originated from west Asia in the ancient past, and experienced a more recent range expansion since the Last Glacial Maximum. Current populations in central Europe appear to originate from the Balkans and those from west Europe from either Iberia and/or Italy. Comparisons of RST and FST suggest that stepwise mutation has contributed to differentiation between island and continental populations (France/UK and China/Japan) and also among distant samples. However, pairwise RST values between distant populations appear to be unreliable, probably due to size homoplasy. Our findings also highlight two priorities for conservation. First, stronger genetic subdivision within the UK than across 4000 km of continental Eurasia is most likely the result of population fragmentation and highlights the need to maintain gene flow in this species. Second, deep splits within China and between Europe and China are indicative of cryptic taxonomic divisions which need further investigation.
The solution structure of the periplasmic domain of the TonB system ExbD protein reveals an unexpected structural homology with siderophore‐binding proteins
Authors: Garcia‐Herrero Alicia , Peacock R. Sean , Howard S. Peter , Vogel Hans J. 
Published: October 2007

SummaryThe transport of iron complexes through outer membrane transporters from Gram‐negative bacteria is highly dependent on the TonB system. Together, the three components of the system, TonB, ExbB and ExbD, energize the transport of iron complexes through the outer membrane by utilizing the proton motive force across the cytoplasmic membrane. The three‐dimensional (3D) structure of the periplasmic domain of TonB has previously been determined. However, no detailed structural information for the other two components of the TonB system is currently available and their role in the iron‐uptake process is not yet clearly understood. ExbD from Escherichia coli contains 141 residues distributed in three domains: a small N‐terminal cytoplasmic region, a single transmembrane helix and a C‐terminal periplasmic domain. Here we describe the first well‐defined solution structure of the periplasmic domain of ExbD (residues 44–141) solved by multidimensional nuclear magnetic resonance (NMR) spectroscopy. The monomeric structure presents three clearly distinct regions: an N‐terminal flexible tail (residues 44–63), a well‐defined folded region (residues 64–133) followed by a small C‐terminal flexible region (residues 134–141). The folded region is formed by two α‐helices that are located on one side of a single β‐sheet. The central β‐sheet is composed of five β‐strands, with a mixed parallel and antiparallel arrangement. Unexpectedly, this fold closely resembles that found in the C‐terminal lobe of the siderophore‐binding proteins FhuD and CeuE. The ExbD periplasmic domain has a strong tendency to aggregate in vitro and 3D‐TROSY (transverse relaxation optimized spectroscopy) NMR experiments of the deuterated protein indicate that the multimeric protein has nearly identical secondary structure to that of the monomeric form. Chemical shift perturbation studies suggest that the Glu‐Pro region (residues 70–83) of TonB can bind weakly to the surface and the flexible C‐terminal region of ExbD. At the same time the Lys‐Pro region (residues 84–102) and the folded C‐terminal domain (residues 150–239) of TonB do not show significant binding to ExbD, suggesting that the main interactions forming the TonB complex occur in the cytoplasmic membrane.
Auto‐regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation
Authors: Schöning Jan C. , Streitner Corinna , Page Damian R. , Hennig Sven , Uchida Kenko , Wolf Eva , Furuya Masaki , Staiger Dorothee 
Published: October 2007

SummaryThe clock‐regulated RNA‐binding protein AtGRP7 (Arabidopsis thaliana glycine‐rich RNA‐binding protein) influences circadian oscillations of its transcript by negative feedback at the post‐transcriptional level. Here we show that site‐specific mutation of one conserved arginine to glutamine within the RNA recognition motif impairs binding of recombinant AtGRP7 to its pre‐mRNA in vitro. This correlates with the loss of the negative auto‐regulation in vivo: in transgenic plants constitutively overexpressing AtGRP7 (AtGRP7‐ox), a shift occurs to an alternatively spliced AtGRP7 transcript that decays rapidly, and thus does not accumulate to high levels. In contrast, constitutive ectopic overexpression of the AtGRP7‐RQ mutant does not lead to alternative splicing of the endogenous AtGRP7 transcript and concomitant damping of the oscillations. This highlights the importance of AtGRP7 binding to its own transcript for the negative auto‐regulatory circuit. Moreover, regulation of AtGRP7 downstream targets also depends on its RNA‐binding activity, as AtGRP8 and other targets identified by transcript profiling of wild‐type and AtGRP7‐ox plants using fluorescent differential display are negatively affected by AtGRP7 but not by AtGRP7‐RQ. In mutants impaired in the nonsense‐mediated decay (NMD) components UPF1 or UPF3, levels of the alternatively spliced AtGRP7 and AtGRP8 transcripts that contain premature termination codons are strongly elevated, implicating UPF1 and UPF3 in the decay of these clock‐regulated transcripts.
BTNL2 allele associations with chronic beryllium disease in HLA‐DPB1*Glu69–negative individuals
Authors: Sato H. , Spagnolo P. , Silveira L. , Welsh K. I. , Du Bois R. M. , Newman L. S. , Maier L. A. 
Published: October 2007

AbstractButyrophilin‐like 2 (BTNL2) polymorphisms have been associated with sarcoidosis. We hypothesized that BTNL2 variants might confer a human leukocyte antigen (HLA)‐independent risk for chronic beryllium disease (CBD), a granulomatous lung disease with similar clinical, radiological, and pathological features to sarcoidosis. Genomic DNA was obtained from CBD (n= 88), beryllium sensitized (BeS, n= 86), and beryllium exposed nondiseased control subjects (Be‐exp, n= 173). Six BTNL2 polymorphisms, HLA‐DPB1, DRB1, and DQB1 alleles were determined by sequence‐specific primer‐PCR. All BTNL2 polymorphisms were in Hardy–Weinberg equilibrium. No significant differences were found between BTNL2 polymorphisms or haplotypes and CBD, BeS, or Be‐exp. In HLA‐DPB1*Glu69–negative subjects (n= 10 CBD, n= 13 BeS, n= 102 Be‐exp), DRB1*13 and BTNL2 rs3117099TT homozygosity were increased in CBD (70% and 40%, respectively) vs Be‐exp (16%, P= 0.001 and 2.9%, P= 0.001, respectively). The BTNL2 rs3117099T–HLA‐DRB1*13 combination was significantly increased in CBD (50%) compared with Be‐exp (6.9%, P= 0.001). In conclusion, both DRB1*13 and rs3117099TT homozygosity are associated with CBD in *Glu69‐negative subjects, while DPB1*Glu69 is associated with CBD and BeS compared with Be‐exp. As a result of the small sample size and strong linkage disequilibrium between DRB1*13‐DQB1*0603/4/9 and the BTNL2 rs3117099T allele, it is difficult to assess the primary association in DPB1*Glu69‐negative CBD cases.
Toll‐like receptor 4 (TLR4) gene polymorphisms in celiac disease
Authors: Santin I. , Castellanos‐Rubio A. , Hualde I. , Castaño L. , Vitoria J. C. , Bilbao J. R. 
Published: October 2007

AbstractToll‐like receptors (TLRs) participate in the first line of immune defense through antigen pattern recognition, and ligands include exogenous and host‐derived molecules. Coding variants in TLR4 have been associated with autoimmune diseases like ulcerative colitis, Crohn’s disease, and rheumatoid arthritis. Our aim was to determine whether these polymorphisms are associated with celiac disease (CD). Two coding single nucleotide polymorphisms of TLR4 (Asp299Gly and Thr399Ile) were genotyped in 95 family trios with CD as well as in 186 patients and 186 unrelated controls. There were no differences in allele, genotype or haplotype distribution, or transmission between patient and control groups. Our results do not support association of these TLR4 variants with CD.
The North American P group of Heterobasidion annosum s.l. is widely distributed in Pinus pinea forests of the western coast of central Italy
Authors: D’Amico L. , Motta E. , Annesi T. , Scire’ M. , Luchi N. , Hantula J. , Korhonen K. , Capretti P. 
Published: October 2007

SummaryThe distribution of the North American P group of Heterobasidion annosum s.l., recently reported from a Pinus pinea forest in the surroundings of Rome, was studied using mating tests and DNA fingerprinting (mitochondrial DNA, random amplified microsatellite technique and two group‐specific markers). This fungus is present in several forests and small plantations along the Tyrrhenian coast of the Italian peninsula, within an area approximately 100 km long, extending from Fregene in the north to the National Park of Circeo in the south, and 27 km wide including the city of Rome. In pine forests of Castelporziano, Castel Fusano and Anzio, where US troops resided during the Second World War, the North American P group is more frequent than the European P group. The low number of mating alleles in the Italian population of the North American P group supports the hypothesis of its origin from a small number of introductions. The near 100% sexual compatibility between the North American and European P groups, together with inconsistencies in results obtained with different identification methods of these groups, suggests that hybridization between the North American and European P populations occurs occasionally.
Identification of Botrytis spp. on Plants Grown in Iran
Authors: Mirzaei S. , Goltapeh E. Mohammadi , Shams‐Bakhsh M. , Safaie N. 
Published: October 2007

AbstractA total of 363 isolates were collected from all over Iran. They were isolated from apple, arum lily, briar rose, bride wort, broad bean, camellia, canola, carnation, cucumber, egg plant, feijoa, geranium, gerbera, gladiolus, grape, guilder rose, hibiscus, iris, kiwifruit, oleander, onion, orange, pear, pomegranate, primrose, quince, redbud, robinia, rose, rubber plant, sow thiste, spathe flower, strawberry, tomato, violet, wall flower and wheat. To identify the species, morphological characters such as conidiophore length, conidial and sclerotial dimensions were measured. According to morphological and cultural characters, eight Botrytis species were identified: B. aclada sensu lato, B. cinerea, B. fabae, B. convoluta, B. gladiolorum, B. paeoniae, B. pelargonii and B. porri. As far as we are aware, this is the first report of the last five species from Iran. These species were examined by polymerase chain reaction (PCR) using necrosis and ethylene‐inducing protein (NEP2) and C729 primers. A 835 bp band was amplified in B. cinerea, B. fabae and B. pelargonii, using NEP2, but not in others. However, C729 primers amplified a 700 bp band in B. cinerea and B. pelargonii and a 600 bp in B. fabae.