Molecular systematics and evolution of the Cyanocorax jays

Phylogenetic relationships were studied in the genus Cyanocorax (Aves: Corvidae) and related genera, Psilorhinus and Calocitta, a diverse group of New World jays distributed from the southern United States south to Argentina. Although the ecology and behavior of some species in the group have been studied extensively, lack of a molecular phylogeny has precluded rigorous interpretations in an evolutionary framework. Given the diverse combinations of plumage coloration, size, and morphology, the taxonomy of the group has been inconsistent and understanding of biogeographic patterns problematic. Moreover, plumage similarity between two geographically disjuct species, the Tufted Jay (Cyanocorax dickeyi) from western Mexico and the White-tailed Jay (C. mystacalis) from western Ecuador and Peru, has puzzled ornithologists for decades. Here, a phylogeny of all species in the three genera is presented, based on study of two mitochondrial and three nuclear genes. Phylogenetic trees revealed the non-monophyly of Cyanocorax, and the division of the whole assemblage in two groups: “Clade A” containing Psilorhinus morio, both species in Calocitta, Cyanocorax violaceus, C. caeruleus, C. cristatellus, and C. cyanomelas, and “Clade B” consisting of the remaining species in Cyanocorax. Relationships among species in Clade A were ambiguous and, in general, not well resolved. Within Clade B, analyses revealed the monophyly of the “Cissilopha” jays and showed no evidence for a sister relationship between C. mystacalis and C. dickeyi. The phylogenetic complexity of lineages in the group suggests several complications for the understanding biogeographic patterns, as well as for proposing a taxonomy that is consistent with morphological variation. Although multiple taxonomic arrangements are possible, recommendations are for recognizing only one genus, Cyanocorax, with Psilorhinus and Calocitta as synonyms. Se estudiaron las relaciones filogenéticas en los géneros Cyanocorax, Psilorhinus y Calocitta (Aves: Corvidae), un grupo diverso de urracas del Nuevo Mundo cuyas especies se distribuyen desde el sur de los Estados Unidos hasta Argentina. Aunque la ecología y el comportamiento de algunas especies en el grupo han sido estudiadas extensamente, la falta de una filogenia molecular ha impedido la interpretación rigurosa de estos estudios en un marco evolutivo. Dadas las diversas combinaciones de coloración de plumaje, tamaño y morfología presentes en las especies del grupo, su taxonomía ha sido inconsistente y la interpretación de sus patrones biogeográficos ha sido problemática. Mas aún, la similitud de plumaje en especies que están geográficamente distantes, como Cyanocorax dickeyi del oeste de Mexico y C. mystacalis del oeste de Ecuador y Perú, ha sido difícil de interpretar. Se presenta una filogenia para todas las especies en los tres géneros, basada en el estudio de dos genes nucleares y dos genes mitocondriales. Los árboles filogenéticos mostraron la parafilia de Cyanocorax y la división de todas las especies en dos grupos: “Clado A” en el cual se encuentran Psilorhinus morio, ambas especies Calocitta, Cyanocorax violaceus, C. caeruleus, C. cristatellus, y C. cyanomelas, y “Clado B” en el cual se encuentran el resto de las especies de Cyanocorax. Las relaciones entre especies del Clado A fueron ambiguas y, en general, poco resueltas. En el Clado B, los análisis mostraron la monofilia de las especies en “Cissilopha”, pero no indicaron la monofilia de C. mystacalis + C. dickeyi. La complejidad filogenética de los linajes en el grupo sugiere varias complicaciones en el entendimiento de su biogeografía y taxonomía. Con base en los resultados filogenéticos se reconoce un solo género, Cyanocorax, con Psilorhinus y Calocitta como sinónimos

Unified dark energy thermodynamics: varying w and the -1-crossing

We investigate, in a unified and general way, the thermodynamic properties of dark energy with an arbitrary, varying equation-of-state parameter w(a). We find that all quantities are well defined and regular for every w(a), including at the -1-crossing, with the temperature being negative in the phantom regime (w(a)-1). The density and entropy are always positive while the chemical potential can be arbitrary. At the -1-crossing, both temperature and chemical potential are zero. The temperature negativity can only be interpreted in the quantum framework. The regular behavior of all quantities at the -1-crossing, leads to the conclusion that such a crossing does not correspond to a phase transition, but rather to a smooth cross-over.Comment: 5 pages, version published in Class. Quant. Gra

Superficial Characteristics and Functionalization Effectiveness of Non-Toxic Glutathione-Capped Magnetic, Fluorescent, Metallic and Hybrid Nanoparticles for Biomedical Applications

An optimal design of nanoparticles suitable for biomedical applications requires proper functionalization, a key step in the synthesis of such nanoparticles, not only for subsequent crosslinking to biological targets and to avoid cytotoxicity, but also to endow these materials with colloidal stability. In this sense, a reliable characterization of the effectiveness of the functionalization process would, therefore, be crucial for subsequent bioconjugations. In this work, we have analyzed glutathione as a means to functionalize four of the most widely used nanoparticles in biomedicine, one of which is a hybrid gold-magnetic-iron-oxide nanoparticle synthetized by a simple and novel method that we propose in this article. We have analyzed the colloidal characteristics that the glutathione capping provides to the different nanoparticles and, using information on the Z-potential, we have deduced the chemical group used by glutathione to link to the nanoparticle core. We have used electron microscopy for further structural and chemical characterization of the nanoparticles. Finally, we have evaluated nanoparticle cytotoxicity, studying cell viability after incubation with different concentrations of nanoparticles, showing their suitability for biomedical applications

Development and Validation of Hepamet Fibrosis Scoring System-a Simple, Non-invasive Test to Identify Patients With Nonalcoholic Fatty liver Disease With Advanced Fibrosis

BACKGROUND & AIMS: Fibrosis affects prognoses for patients with nonalcoholic fatty liver disease (NAFLD). Several non-invasive scoring systems have aimed to identify patients at risk for advanced fibrosis, but inconclusive results and variations in features of patients (diabetes, obesity and older age) reduce their diagnostic accuracy. We sought to develop a scoring system based on serum markers to identify patients with NAFLD at risk for advanced fibrosis. METHODS: We collected data from 2452 patients with NAFLD at medical centers in Italy, France, Cuba, and China. We developed the Hepamet fibrosis scoring system using demographic, anthropometric, and laboratory test data, collected at time of liver biopsy, from a training cohort of patients from Spain (n=768) and validated the system using patients from Cuba (n=344), Italy (n=288), France (n=830), and China (n=232). Hepamet fibrosis score (HFS) were compared with those of previously developed fibrosis scoring systems (the NAFLD fibrosis score [NFS] and FIB-4). The diagnostic accuracy of the Hepamet fibrosis scoring system was assessed based on area under the receiver operating characteristic (AUROC) curve, sensitivity, specificity, diagnostic odds ratio, and positive and negative predictive values and likelihood ratios. RESULTS: Variables used to determine HFS were patient sex, age, homeostatic model assessment score, presence of diabetes, levels of aspartate aminotransferase, and albumin, and platelet counts; these were independently associated with advanced fibrosis. HFS discriminated between patients with and without advanced fibrosis with an AUROC curve value of 0.85 whereas NFS or FIB-4 did so with AUROC values of 0.80 (P=.0001). In the validation set, cut-off HFS of 0.12 and 0.47 identified patients with and without advanced fibrosis with 97.2% specificity, 74% sensitivity, a 92% negative predictive value, a 76.3% positive predictive value, a 13.22 positive likelihood ratio, and a 0.31 negative likelihood ratio. HFS were not affected by patient age, body mass index, hypertransaminasemia, or diabetes. The Hepamet fibrosis scoring system had the greatest net benefit in identifying patients who should undergo liver biopsy analysis and led to significant improvements in reclassification, reducing the number of patients with undetermined results to 20% from 30% for the FIB-4 and NFS systems (P<.05). CONCLUSIONS: Using clinical and laboratory data from patients with NAFLD, we developed and validated the Hepamet fibrosis scoring system, which identified patients with advanced fibrosis with greater accuracy than the FIB-4 and NFS systems. the Hepamet system provides a greater net benefit for the decision-making process to identify patients who should undergo liver biopsy analysis

Growth and Competitive Effects of Centaurea stoebe Populations in Response to Simulated Nitrogen Deposition

Increased resource availability can promote invasion by exotic plants, raising concerns over the potential effects of global increases in the deposition of nitrogen (N). It is poorly understood why increased N favors exotics over natives. Fast growth may be a general trait of good invaders and these species may have exceptional abilities to increase growth rates in response to N deposition. Additionally, invaders commonly displace locals, and thus may have inherently greater competitive abilities. The mean growth response of Centaurea stoebe to two N levels was significantly greater than that of North American (NA) species. Growth responses to N did not vary among C. stoebe populations or NA species. Without supplemental N, NA species were better competitors than C. stoebe, and C. stoebe populations varied in competitive effects. The competitive effects of C. stoebe populations increased with N whereas the competitive effects of NA species decreased, eliminating the overall competitive advantage demonstrated by NA species in soil without N added. These results suggest that simulated N deposition may enhance C. stoebe invasion through increasing its growth and relative competitive advantage, and also indicate the possibility of local adaptation in competitive effects across the introduced range of an invader

The role of historical and contemporary processes on phylogeographic structure and genetic diversity in the Northern Cardinal, Cardinalis cardinalis

Background Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, Cardinalis cardinalis. Results Phylogenetic analysis revealed deep mtDNA structure with six lineages across the species\u27 range. Ecological niche models supported the same geographic breaks revealed by the mtDNA. A paleoecological niche model for the Last Glacial Maximum indicated that cardinals underwent a dramatic range reduction in eastern North America, whereas their ranges were more stable in México. In eastern North America cardinals expanded out of glacial refugia, but we found no signature of decreased genetic diversity in areas colonized after the Last Glacial Maximum. Present-day demographic data suggested that population growth across the expansion cline is positively correlated with latitude. We propose that there was no loss of genetic diversity in areas colonized after the Last Glacial Maximum because recent high-levels of gene flow across the region have homogenized genetic diversity in eastern North America. Conclusion We show that both deep historical events as well as demographic processes that occurred following these events are critical in shaping genetic pattern and diversity in C. cardinalis. The general implication of our results is that patterns of genetic diversity are best understood when information on species history, ecology, and demography are considered simultaneously

Influenza A Viruses from Wild Birds in Guatemala Belong to the North American Lineage

The role wild bird species play in the transmission and ecology of avian influenza virus (AIV) is well established; however, there are significant gaps in our understanding of the worldwide distribution of these viruses, specifically about the prevalence and/or significance of AIV in Central and South America. As part of an assessment of the ecology of AIV in Guatemala, we conducted active surveillance in wild birds on the Pacific and Atlantic coasts. Cloacal and tracheal swab samples taken from resident and migratory wild birds were collected from February 2007 to January 2010.1913 samples were collected and virus was detected by real time RT-PCR (rRT-PCR) in 28 swab samples from ducks (Anas discors). Virus isolation was attempted for these positive samples, and 15 isolates were obtained from the migratory duck species Blue-winged teal. The subtypes identified included H7N9, H11N2, H3N8, H5N3, H8N4, and H5N4. Phylogenetic analysis of the viral sequences revealed that AIV isolates are highly similar to viruses from the North American lineage suggesting that bird migration dictates the ecology of these viruses in the Guatemalan bird population

The role of historical and contemporary processes on phylogeographic structure and genetic diversity in the Northern Cardinal, Cardinalis cardinalis

<p>Abstract</p> <p>Background</p> <p>Earth history events such as climate change are believed to have played a major role in shaping patterns of genetic structure and diversity in species. However, there is a lag between the time of historical events and the collection of present-day samples that are used to infer contemporary population structure. During this lag phase contemporary processes such as dispersal or non-random mating can erase or reinforce population differences generated by historical events. In this study we evaluate the role of both historical and contemporary processes on the phylogeography of a widespread North American songbird, the Northern Cardinal, <it>Cardinalis cardinalis</it>.</p> <p>Results</p> <p>Phylogenetic analysis revealed deep mtDNA structure with six lineages across the species' range. Ecological niche models supported the same geographic breaks revealed by the mtDNA. A paleoecological niche model for the Last Glacial Maximum indicated that cardinals underwent a dramatic range reduction in eastern North America, whereas their ranges were more stable in México. In eastern North America cardinals expanded out of glacial refugia, but we found no signature of decreased genetic diversity in areas colonized after the Last Glacial Maximum. Present-day demographic data suggested that population growth across the expansion cline is positively correlated with latitude. We propose that there was no loss of genetic diversity in areas colonized after the Last Glacial Maximum because recent high-levels of gene flow across the region have homogenized genetic diversity in eastern North America.</p> <p>Conclusion</p> <p>We show that both deep historical events as well as demographic processes that occurred following these events are critical in shaping genetic pattern and diversity in <it>C. cardinalis</it>. The general implication of our results is that patterns of genetic diversity are best understood when information on species history, ecology, and demography are considered simultaneously.</p