bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene trees, species trees and Earth history combine to shed light on the evolution of migration in a model avian system
Authors: Voelker Gary , Bowie Rauri C. K. , Klicka John 
Published: May 2013

AbstractThe evolution of migration in birds has fascinated biologists for centuries. In this study, we performed phylogenetic‐based analyses of Catharus thrushes, a model genus in the study of avian migration, and their close relatives. For these analyses, we used both mitochondrial and nuclear genes, and the resulting phylogenies were used to trace migratory traits and biogeographic patterns. Our results provide the first robust assessment of relationships within Catharus and relatives and indicate that both mitochondrial and autosomal genes contribute to overall support of the phylogeny. Measures of phylogenetic informativeness indicated that mitochondrial genes provided more signal within Catharus than did nuclear genes, whereas nuclear loci provided more signal for relationships between Catharus and close relatives than did mitochondrial genes. Insertion and deletion events also contributed important support across the phylogeny. Across all taxa included in the study, and for Catharus, possession of long‐distance migration is reconstructed as the ancestral condition, and a North American (north of Mexico) ancestral area is inferred. Within Catharus, sedentary behaviour evolved after the first speciation event in the genus and is geographically and temporally correlated with Central American distributions and the final closure of the Central American Seaway. Migratory behaviour subsequently evolved twice in Catharus and is geographically and temporally correlated with a recolonization of North America in the late Pleistocene. By temporally linking speciation events with changes in migratory condition and events in Earth history, we are able to show support for several competing hypotheses relating to the geographic origin of migration.
Tracking climate change in a dispersal‐limited species: reduced spatial and genetic connectivity in a montane salamander
Authors: Velo‐Antón G. , Parra J. L. , Parra‐Olea G. , Zamudio K. R. 
Published: May 2013

AbstractTropical montane taxa are often locally adapted to very specific climatic conditions, contributing to their lower dispersal potential across complex landscapes. Climate and landscape features in montane regions affect population genetic structure in predictable ways, yet few empirical studies quantify the effects of both factors in shaping genetic structure of montane‐adapted taxa. Here, we considered temporal and spatial variability in climate to explain contemporary genetic differentiation between populations of the montane salamander, Pseudoeurycea leprosa. Specifically, we used ecological niche modelling (ENM) and measured spatial connectivity and gene flow (using both mtDNA and microsatellite markers) across extant populations of P. leprosa in the Trans‐Mexican Volcanic Belt (TVB). Our results indicate significant spatial and genetic isolation among populations, but we cannot distinguish between isolation by distance over time or current landscape barriers as mechanisms shaping population genetic divergences. Combining ecological niche modelling, spatial connectivity analyses, and historical and contemporary genetic signatures from different classes of genetic markers allows for inference of historical evolutionary processes and predictions of the impacts future climate change will have on the genetic diversity of montane taxa with low dispersal rates. Pseudoeurycea leprosa is one montane species among many endemic to this region and thus is a case study for the continued persistence of spatially and genetically isolated populations in the highly biodiverse TVB of central Mexico.
Genomic evidence for the parallel evolution of coastal forms in the Senecio lautus complex
Authors: Roda Federico , Ambrose Luke , Walter Gregory M. , Liu Huanle L. , Schaul Andrea , Lowe Andrew , Pelser Pieter B. , Prentis Peter , Rieseberg Loren H. , Ortiz‐Barrientos Daniel 
Published: May 2013

AbstractInstances of parallel ecotypic divergence where adaptation to similar conditions repeatedly cause similar phenotypic changes in closely related organisms are useful for studying the role of ecological selection in speciation. Here we used a combination of traditional and next generation genotyping techniques to test for the parallel divergence of plants from the Senecio lautus complex, a phenotypically variable groundsel that has adapted to disparate environments in the South Pacific. Phylogenetic analysis of a broad selection of Senecio species showed that members of the S. lautus complex form a distinct lineage that has diversified recently in Australasia. An inspection of thousands of polymorphisms in the genome of 27 natural populations from the S. lautus complex in Australia revealed a signal of strong genetic structure independent of habitat and phenotype. Additionally, genetic differentiation between populations was correlated with the geographical distance separating them, and the genetic diversity of populations strongly depended on geographical location. Importantly, coastal forms appeared in several independent phylogenetic clades, a pattern that is consistent with the parallel evolution of these forms. Analyses of the patterns of genomic differentiation between populations further revealed that adjacent populations displayed greater genomic heterogeneity than allopatric populations and are differentiated according to variation in soil composition. These results are consistent with a process of parallel ecotypic divergence in face of gene flow.
Melanins and melanogenesis: methods, standards, protocols
Authors: d'Ischia Marco , Wakamatsu Kazumasa , Napolitano Alessandra , Briganti Stefania , Garcia‐Borron José‐Carlos , Kovacs Daniela , Meredith Paul , Pezzella Alessandro , Picardo Mauro , Sarna Tadeusz , Simon John D. , Ito Shosuke 
Published: May 2013

SummaryDespite considerable advances in the past decade, melanin research still suffers from the lack of universally accepted and shared nomenclature, methodologies, and structural models. This paper stems from the joint efforts of chemists, biochemists, physicists, biologists, and physicians with recognized and consolidated expertise in the field of melanins and melanogenesis, who critically reviewed and experimentally revisited methods, standards, and protocols to provide for the first time a consensus set of recommended procedures to be adopted and shared by researchers involved in pigment cell research. The aim of the paper was to define an unprecedented frame of reference built on cutting‐edge knowledge and state‐of‐the‐art methodology, to enable reliable comparison of results among laboratories and new progress in the field based on standardized methods and shared information.
Modulation of the Photophysical Properties of Pyrene by the Microstructures of Five Poly(alkyl methacrylate)s Over a Broad Temperature Range
Authors: Atvars Teresa D. Z. , Abraham Shibu , Hill Anita J. , Pas Steven J. , Chesta Carlos , Weiss Richard G. 
Published: May 2013

AbstractPyrene fluorescence spectra have been recorded in five poly(alkyl methacrylate)s (where alkyl is ethyl butyl, isobutyl, cyclohexyl and hexadecyl) over a 20–400 K temperature range. The changes in the position and the full width at half maximum (FWHM) of the 0–0 emission band (peak I) have been correlated with the structural characteristics of the alkyl groups in the different relaxation regimes of the polymers to assess the degree of coupling of the excited singlet states with the polymer cybotactic regions. Data treatment of the peak I positions using an electron–phonon model indicates that longitudinal optical modes are involved, and that the magnitude of coupling depends on the polymer structure and follows the same trend as the glass transition temperatures. The same spectral parameters have been correlated also with “hole” free volumes from positron annihilation spectroscopy over temperature ranges which span the glass or melting transitions of the polymers. Reasons why free volume and FWHM measurements follow the same trends, and other aspects of the systems, are discussed.
Erythema dose ‐ a novel global objective index for facial erythema by computer‐aided image analysis
Authors: Choi Jae Woo , Kwon Soon Hyo , Jo Seong Moon , Youn Sang Woong 
Published: May 2013

BackgroundFacial erythema is a common but morbid condition caused by several inflammatory disorders. Since most of the current severity indexes lack objectivity and global assessment, the computer‐aided image analysis (CAIA) has been suggested.ObjectiveThe purpose of this study is to compare the validity and efficacy of novel CAIA erythema index – erythema dose (ED) with two other CAIA indexes.MethodsFor mild, moderated and severe erytherotelangiectatic rosacea patients, their photographs of right cheek were assessed with red‐blue difference index in image (RBI), a*, and ED. For each index, the differences between severity groups were analyzed. The correlations between the three indexes were evaluated. To evaluate the capability of differentiating the pathologic erythema from the red component of the normal skin, each index was calculated at both the erythema and normal area.ResultsThe a* and ED significantly changed according to the severity, while the RBI did not. The ED was different between both mild‐moderate and moderate‐severe, while the a* only between mild‐moderate. There was a strong positive correlation between a* and ED. The difference between erythema and normal skin was more prominent in ED than in a*.ConclusionWe confirmed that the ED is well correlated with both subjective assessment, as well as the other CAIA index a*. The ED has the advantage of specifically visualizing and analyzing the pathologic erythema.
Extraplastidial cytidinediphosphate diacylglycerol synthase activity is required for vegetative development in Arabidopsis thaliana
Authors: Zhou Yonghong , Peisker Helga , Weth Agnes , Baumgartner Werner , Dörmann Peter , Frentzen Margrit 
Published: May 2013

SummaryCytidinediphosphate diacylglycerol synthase (CDS) catalyzes the activation of phosphatidic acid to cytidinediphosphate (CDP)‐diacylglycerol, a central intermediate in glycerolipid biosynthesis in prokaryotic and eukaryotic organisms. Cytidinediphosphate‐diacylglycerol is the precursor to phosphatidylinositol, phosphatidylglycerol (PG) and cardiolipin of eukaryotic phospholipids that are essential for various cellular functions. Isoforms of CDS are located in plastids, mitochondria and the endomembrane system of plants and are encoded by five genes in Arabidopsis. Two genes have previously been shown to code for the plastidial isoforms which are indispensable for the biosynthesis of plastidial PG, and thus biogenesis and function of thylakoid membranes. Here we have focused on the extraplastidial CDS isoforms, encoded by CDS1 and CDS2 which are constitutively expressed contrary to CDS3. We provide evidence that these closely related CDS genes code for membrane proteins located in the endoplasmic reticulum and possess very similar enzymatic properties. Development and analysis of Arabidopsis mutants lacking either one or both CDS1 and CDS2 genes clearly shows that these two genes have redundant functions. As reflected in the seedling lethal phenotype of the cds1cds2 double mutant, plant cells require at least one catalytically active microsomal CDS isoform for cell division and expansion. According to the altered glycerolipid composition of the double mutant in comparison with wild‐type seedlings, it is likely that the drastic decrease in the level of phosphatidylinositol and the increase in phosphatidic acid cause defects in cell division and expansion.
Structural characterizations of the chloroplast translocon protein Tic110
Authors: Tsai Jia‐Yin , Chu Chiung‐Chih , Yeh Yi‐Hung , Chen Lih‐Jen , Li Hsou‐min , Hsiao Chwan‐Deng 
Published: May 2013

SummaryTic110 is a major component of the chloroplast protein import translocon. Two functions with mutually exclusive structures have been proposed for Tic110: a protein‐conducting channel with six transmembrane domains and a scaffold with two N‐terminal transmembrane domains followed by a large soluble domain for binding transit peptides and other stromal translocon components. To investigate the structure of Tic110, Tic110 from Cyanidioschyzon merolae (CmTic110) was characterized. We constructed three fragments, CmTic110A, CmTic110B and CmTic110C, with increasing N‐terminal truncations, to perform small‐angle X‐ray scattering (SAXS) and X‐ray crystallography analyses and Dali structural comparison. Here we report the molecular envelope of CmTic110B and CmTic110C determined by SAXS, and the crystal structure of CmTic110C at 4.2 Å. Our data indicate that the C‐terminal half of CmTic110 possesses a rod‐shaped helix‐repeat structure that is too flattened and elongated to be a channel. The structure is most similar to the HEAT‐repeat motif that functions as scaffolds for protein–protein interactions.
Serial haemostatic monitoring of dogs with multicentric lymphoma
Authors: Kol A. , Marks S. L. , Skorupski K. A. , Kass P. H. , Guerrero T. , Gosselin R. C. , Borjesson D. L. 
Published: May 2013

AbstractLymphoma is the most common haematopoietic malignancy in dogs and it has been associated with hypercoagulability and subsequent thromboembolism. The objectives of this study were to serially characterize the haemostatic status of dogs with multicentric lymphoma. Thromboelastography, thrombin–antithrombin complex concentration and routine haematology and coagulation panels were measured. Twenty‐seven dogs were included in the study and 15 completed the study in remission. At presentation, 81% (22/27) of dogs with multicentric lymphoma had altered haemostatic profiles consistent with hypercoagulability. Laboratory evidence of hypercoagulability did not resolve during treatment or for up to 1 month following attainment of clinical remission. Accelerated rate of clot formation at the time of chemotherapeutic protocol completion was associated with decreased survival time. We concluded that dogs with multicentric lymphoma were frequently hypercoagulable from presentation through 4 weeks after the completion of chemotherapy. Increased angle and shortenedKin dogs that have successfully completed their chemotherapeutic protocol may be associated with shorter survival times.
Collection, processing and testing of bone, corneas, umbilical cord blood and haematopoietic stem cells by European Blood Alliance members
Authors: Närhi M. , Natri O. , Desbois I. , Kinggaard Holm D. , Galea G. , Aranko K. , Korhonen M. , Nordstrom K. 
Published: May 2013

Background and ObjectivesA questionnaire study was carried out in collaboration with the European Blood Alliance (EBA) Tissues and Cells (T&C) working group. The aim was to assess the level of involvement and commonality of processes on the procurement, testing and storage of bone, corneas, umbilical cord blood (UCB) and haematopoietic stem cells (HSC) in order to identify different practices and to explore whether recommendations can be made for harmonization.Materials and MethodsAn online questionnaire was used for data collection in 2011, and 43 replies were received covering 71 product answers from 13 countries.Results and conclusionsEstimated percentages of tissue and cell banking covered by EBA member blood banks as a proportion of all collections of each individual country varied markedly. There were also major differences in the amounts of products collected and discarded and in proportions tissues provided for grafting. However, discarding of certain collections also reflects the practice of increasing the likelihood of the very best units being used for transplantation. Harmonization of possible practices should focus on matching supply with demand and on identifying the most efficient operators. This could allow for the development of practices for minimizing unnecessary collections.
Q Fever in Alberta, Canada: 1998–2011
Authors: Snedeker K. G. , Sikora C. 
Published: May 2013

SummaryEstablishing the diagnosis of Q fever (Coxiella burnetii) is important in directing the application of therapy to prevent severe manifestations of the infection. In Alberta, Canada, the presence of high livestock density creates a significant risk of infection, but to date, there has been no comprehensive analysis of local Q fever epidemiological trends and exposure patterns. Between 1998 and 2011, there were 39 cases and an overall adjusted case rate of 0.087 per 100 000 person‐years. Cases were identified most commonly during the May–June season (Figure 2). The median age at date of diagnosis was 49.0 (range: 8.7–71.5) with slightly higher percentage of cases in men (56.4%) than in women (43.6%). There was an apparent geographical clustering of cases. The majority of these cases, with exposure data (n = 31), reported contact with farms and/or livestock, predominantly cattle (6), sheep (5) and goats (5). Cases tended to occur in census divisions with higher density of sheep, goats and cattle. Our findings suggest the need for an increase in targeted messages about Q fever to those in the livestock industry, as more targeted case finding among patients with a high index of suspicion for Q fever. In addition, widespread implementation of a standard questionnaire for cases would enhance surveillance of Q fever in Alberta.
Impairment of pancreatic β‐cell function by chronic intermittent hypoxia
Authors: Wang Ning , Khan Shakil A. , Prabhakar Nanduri R. , Nanduri Jayasri 
Published: May 2013

New Findings
What is the central question of this study?Periodic decreases in arterial blood O2 or chronic intermittent hypoxia (CIH) is a hallmark feature of sleep apnoea patients. Despite a large body of clinical evidence linking sleep‐disordered breathing with apnoeas to diabetes, the causal relationships between CIH and β‐cell function and the underlying molecular mechanisms have not been established.
What is the main finding and its importance?In a rodent model, we show that mitochondrial oxidative stress generated by CIH leads to pancreatic β‐cell dysfunction manifested by augmented basal insulin secretion, insulin resistance, defective proinsulin processing and impaired glucose‐stimulated insulin secretion. The results of the present study provide evidence for direct effects of CIH on β‐cell function, which may be an underlying molecular mechanism contributing to the development of type 2 diabetes among sleep apnoea patients.
Breathing disorders with recurrent apnoea produce periodic decreases in arterial blood O2, i.e. chronic intermittent hypoxia (CIH). Recurrent apnoea patients and CIH‐exposed rodents exhibit several co‐morbidities, including diabetes. However, the effects of CIH on pancreatic β‐cell function are not known. In the present study, we investigated pancreatic β‐cell function in C57BL6 mice exposed to 30 days of CIH. Compared with control animals, the CIH‐exposed mice exhibited elevated levels of fasting plasma insulin but comparable glucose levels and higher homeostasis model assessment, indicating insulin resistance. Pancreatic β‐cell morphology was unaltered in CIH‐exposed mice. Insulin content was decreased in CIH‐exposed β‐cells, and this effect was associated with increased proinsulin levels. The mRNA and protein levels of the enzyme prohormone convertase 1, which converts proinsulin to insulin, were downregulated in CIH‐treated islets. More importantly, glucose‐stimulated insulin secretion was impaired in CIH‐exposed mice and in isolated islets. Mitochondrial levels of reactive oxygen species (ROS) were elevated in CIH‐exposed pancreatic islets. Treatment of mice with mito‐tempol, a scavenger of mitochondrial ROS, during exposure to CIH prevented the augmented insulin secretion and restored the proinsulin and homeostasis model assessment values to control levels. These results demonstrate that CIH leads to pancreatic β‐cell dysfunction, manifested by augmented basal insulin secretion, insulin resistance, defective proinsulin processing, impaired glucose‐stimulated insulin secretion and increased mitochondrial ROS, which mediate the effects of CIH on pancreatic β‐cell function.
Sternohyoid and diaphragm muscle form and function during postnatal development in the rat
Authors: O’Connell R. A. , Carberry J. , O’Halloran K. D. 
Published: May 2013

New Findings
What is the central question of this study?Co‐ordinated activity of the thoracic pump and pharyngeal dilator muscles is critical for maintaining airway calibre and respiratory homeostasis. Whilst postnatal maturation of the diaphragm has been well characterized, surprisingly little is known about the developmental programme in the airway dilator muscles.
What is the main finding and its importance?Developmental increases in force‐generating capacity and fatigue in the sternohyoid and diaphragm muscles are attributed to a maturational shift in muscle myosin heavy chain phenotype. This maturation is accelerated in the sternohyoid muscle relative to the diaphragm and may have implications for the control of airway calibre in vivo.
The striated muscles of breathing, including the thoracic pump and pharyngeal dilator muscles, play a critical role in maintaining respiratory homeostasis. Whilst postnatal maturation of the diaphragm has been well characterized, surprisingly little is known about the developmental programme in airway dilator muscles given that co‐ordinated activity of both sets of muscles is needed for the maintenance of airway calibre and effective pulmonary ventilation. The form and function of sternohyoid and diaphragm muscles from Wistar rat pups [postnatal day (PD) 10, 20 and 30] was determined. Isometric contractile and endurance properties were examined in tissue baths containing Krebs solution at 35°C. Myosin heavy chain (MHC) isoform composition was determined using immunofluorescence. Muscle oxidative and glycolytic capacity was assessed by measuring the activities of succinate dehydrogenase and glycerol‐3‐phosphate dehydrogenase using semi‐quantitative histochemistry. Sternohyoid and diaphragm peak isometric force and fatigue increased significantly with postnatal maturation. Developmental myosin disappeared by PD20, whereas MHC2B areal density increased significantly from PD10 to PD30, emerging earlier and to a much greater extent in the sternohyoid muscle. The numerical density of fibres expressing MHC2X and MHC2B increased significantly during development in the sternohyoid. Diaphragm succinate dehydrogenase activity and sternohyoid glycerol‐3‐phosphate dehydrogenase activity increased significantly with age. Developmental increases in force‐generating capacity and fatigue in the sternohyoid and diaphragm muscles are attributed to a postnatal shift in muscle MHC phenotype. The accelerated maturation of the sternohyoid muscle relative to the diaphragm may have implications for the control of airway calibre in vivo.
Enterococcus faecalis Grows on Ascorbic Acid
Authors: Mehmeti Ibrahim , Solheim Margrete , Nes Ingolf F. , Holo Helge 
Published: May 2013

ABSTRACT

We show that
Enterococcus faecalis
can utilize ascorbate for fermentative growth. In chemically defined media, growth yield was limited by the supply of amino acids, and the cells showed a much higher demand for amino acids than when they were grown on glucose.