Phylogenetic relationships of the macaques (Cercopithecidae : Macaca), inferred from mitochondrial DNA sequences

To study the phylogenetic relationships of the macaques, five gene fragments were sequenced from 40 individuals of eight species: Macaca mulatta, M. cyclopis, M. fascicularis, M. arctoides, M. assamensis, M. thibetana, M. silenus, and M. leonina. In addition, sequences of M. sylvanus were obtained from Genbank. A baboon was used as the outgroup. The phylogenetic trees were constructed using maximum-parsimony and Bayesian methods. Because five gene fragments were from the mitochondrial genome and were inherited as a single entity without recombination, we combined the five genes into a single analysis. The parsimony bootstrap proportions we obtained were higher than those from earlier studies based on the combined mtDNA dataset. Excluding M. arctoides, our results are generally consistent with the classification of Delson (1980). Our phylogenetic analyses agree with earlier studies suggesting that the mitochondrial lineages of M. arctoides share a close evolutionary relationship with the mitochondrial lineages of the fascicularis group of macaques (and M. fascicularis, specifically). M. mulatta (with respect to M. cyclopis), M. assamensis assamensis (with respect to M. thibetana), and M. leonina (with respect to M. silenus) are paraphyletic based on our analysis of mitochondrial genes.

Phylogeny and biogeography of the Petaurista philippensis complex (Rodentia : Sciuridae), inter- and intraspecific relationships inferred from molecular and morphometric analysis

With modified DNA extraction and Purification protocols, the complete cytochrome b gene sequences (1140 bp) were determined from degraded museum specimens. Molecular analysis and morphological examination of cranial characteristics of the giant flying squirrels of Petaurista philippensis complex (P. grandis, P. hainana, and P. yunanensis) and other Petaurista species yielded new insights into long-standing controversies in the Petaurista systematics. Patterns of genetic variations and morphological differences observed in this study indicate that P. hainana, P. albiventer, and P. yunanensis can be recognized as distinct species, and P. grandis and P. petaurista are conspecific populations. Phylogenetic relationships reconstructed by using parsimony, likelihood, and Bayesian methods reveal that, with P. leucogenys as the basal branch, all Petaurista groups formed two distinct clades. Petaurista philippensis, P. hainana, P. yunanensis, and P. albiventer are clustered in the same clade, while P. grandis shows a close relationship to P. petaurista. Deduced divergence times based on Bayesian analysis and the transversional substitution at the third codon suggest that the retreating of glaciers and upheavals or movements of tectonic plates in the Pliocene-Pleistocene were the major factors responsible for the present geographical distributions of Petaurista groups. (c) 2005 Elsevier Inc. All rights reserved.

Ribosomal DNA gene and phylogenetic relationships of Diplura and lower Hexapods

The monophyly of Diplura and its phylogenetic relationship with other hexapods are important for understanding the phylogeny of Hexapoda. The complete 18SrRNA gene and partial 28SrRNA gene (D3-D5 region) from 2 dipluran species (Campodeidae and Japygidae), 2 proturan species, 3 collembolan species, and 1 locust species were sequenced. Combining related sequences in GenBank, phylogenetic trees of Hexapoda were constructed by MP method using a crustacean Artemia salina as an outgroup. The results indicated that: (i) the integrated data of 18SrDNA and 28SrDNA could provide better phylogenetic information, which well supported the monophyly of Diplura; (ii) Diplura had a close phylogenetic relationship to Protura with high bootstrap support.

Phylogenetic relationships of Danio within the order cypriniformes: A framework for comparative and evolutionary studies of a model species

The evolutionary relationships of species of Danio and the monophyly and phylogenetic placement of the genus within the family Cyprinidae and subfamily Rasborinae provide fundamentally important phyloinformatics necessary for direct evaluations of an array of pertinent questions in modern comparative biology. Although the genus Danio is not one of the most diverse within the family, Danio rerio is one of the most important model species in biology. Many investigations have used this species or presumed close relatives to address specific questions that have lasting impact on the hypothesis and theory of development in vertebrates. Largely lacking from this approach has been a holistic picture of the exact phylogenetic or evolutionary relationships of this species and its close relatives. One thing that has been learned over the previous century is that many organismal attributes (e.g., developmental pathways, ecologies, behaviors, speciation) are historically constrained and their origins and functions are best explained via a phylogenetic approach. Herein, we provide a molecular evaluation of the phylogenetic placement of the model species Danio rerio within the genus Danio and among hypothesized closely related species and genera. Our analysis is derived from data using two nuclear genes (RAG1, rhodopsin) and five mitochondrial genes (ND4, ND4L, ND5, COI, cyt b) evaluated using parsimony, maximum likelihood, and Bayesian analyses. The family Cyprinidae is resolved as monophyletic but the subfamily Rasborinae (priority over Danioinae) is an unnatural assemblage. Danio is identified as a monophyletic group sister to a clade inclusive of the genera Chela, Microrasbora, Devario, and Inlecypris, not Devario nor Esomus as hypothesized in previous studies. Danio rerio is sister to D. kyathit among the species of Danio evaluated in this analysis. Microrasbora and Rasbora are non-monophyletic assemblages; however, Boraras is monophyletic.

A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta

Background: There are many advantages to the application of complete mitochondrial (mt) genomes in the accurate reconstruction of phylogenetic relationships in Metazoa. Although over one thousand metazoan genomes have been sequenced, the taxonomic sampling is highly biased, left with many phyla without a single representative of complete mitochondrial genome. Sipuncula (peanut worms or star worms) is a small taxon of worm-like marine organisms with an uncertain phylogenetic position. In this report, we present the mitochondrial genome sequence of Phascolosoma esculenta, the first complete mitochondrial genome of the phylum. Results: The mitochondrial genome of P. esculenta is 15,494 bp in length. The coding strand consists of 32.1% A, 21.5% C, 13.0% G, and 33.4% T bases (AT = 65.5%; AT skew = -0.019; GC skew = -0.248). It contains thirteen protein-coding genes (PCGs) with 3,709 codons in total, twenty-two transfer RNA genes, two ribosomal RNA genes and a non-coding AT-rich region (AT = 74.2%). All of the 37 identified genes are transcribed from the same DNA strand. Compared with the typical set of metazoan mt genomes, sipunculid lacks trnR but has an additional trnM. Maximum Likelihood and Bayesian analyses of the protein sequences show that Myzostomida, Sipuncula and Annelida (including echiurans and pogonophorans) form a monophyletic group, which supports a closer relationship between Sipuncula and Annelida than with Mollusca, Brachiopoda, and some other lophotrochozoan groups. Conclusion: This is the first report of a complete mitochondrial genome as a representative within the phylum Sipuncula. It shares many more similar features with the four known annelid and one echiuran mtDNAs. Firstly, sipunculans and annelids share quite similar gene order in the mitochondrial genome, with all 37 genes located on the same strand; secondly, phylogenetic analyses based on the concatenated protein sequences also strongly support the sipunculan + annelid clade (including echiurans and pogonophorans). Hence annelid "key-characters" including segmentation may be more labile than previously assumed.

Morphology and localization of interstitial cells in the guinea pig bladder: structural relationships with smooth muscle and neurons.

PURPOSE: In the current study we examined the location of interstitial cell of Cajal (ICC)-like cells in the guinea pig bladder wall and studied their structural interactions with nerves and smooth muscle cells. MATERIALS AND METHODS: Whole mount samples and cryosections of bladder tissue were labeled with primary and fluorescent secondary antibodies, and imaged using confocal and multiphoton microscopy. RESULTS: Kit positive ICC-like cells were located below the urothelium, in the lamina propria region and throughout the detrusor. In the suburothelium they had a stellate morphology and appeared to network. They made connections with nerves, as shown by double labeling experiments with anti-kit and anti-protein gene product 9.5. A network of vimentin positive cells was also found, of which many but not all were kit positive. In the detrusor kit positive cells were most often seen at the edge of smooth muscle bundles. They were elongated with lateral branches, running in parallel with the bundles and closely associated with intramural nerves. Another population of kit positive cells was seen in the detrusor between muscle bundles. These cells had a more stellate-like morphology and made connections with each other. Kit positive cells were seen tracking nerve bundles and close to intramural ganglia. Vimentin positive cells were present in the detrusor, of which some were also kit positive. CONCLUSIONS: There are several populations of ICC-like cells throughout the guinea pig bladder wall. They differ in morphology and orientation but all make connections with intramural nerves and in the detrusor they are closely associated with smooth muscle cells.

Biogeographic and palaeoclimatic relationships of the Middle Pliocene ichthyofauna of the Samoggia Torrent (Bologna, Italy)

New Middle Pliocene ichthyofauna (2.4-2.2 Ma) from central-eastern Italy (Samoggia Torrent, Bologna) are described. These ichthyolites were found in a rather thin laminated layer that was deposited after the 2.4 Ma climatic crisis. The origin of this deposit, in which 31 taxa have been classified, is to be related to anoxic events on a regional and, probably, supraregional scale. This ichthyofaunistic association, which consists of living genera, is characterized by a clearcut predominance of mesopelagic species. The palaeoclimatic characters of these ichthyofauna indicate subtropical-type waters, while from a palaeobiogeographic point of view there is a close relationship with the present-day Atlantic-Mediterranean bioprovince. The Samoggia deposit has yielded six taxa that are absent or only occasionally present in the Mediterranean: one of these, Spratelloides gracilis, is exclusive of the Indo-Pacific bioprovince.

Hurry up and slow down : education to close the ingenuity gap /

To explore the idea of education to close the ingenuity gap I use Thomas Homer-Dixon's work to define ingenuity. The notion that the supply of ingenuity to solve our technical and social problems is not keeping pace with the ingenuity required to solve those problems is called the ingenuity gap. Man-made technological developments are increasing the density, intensity, and pace of globalisation. People must reorganise decision-making organisations and problem-solving methods to pragmatically combat the growing ingenuity gap. John Dewey's work illustrates the fundamental attitudes for the thinking and judgment associated with educating for ingenuity. Howard Gardner's idea that truth, beauty, and morality ought to form the core values and tenets of the philosophy of educating for ingenuity is integral to this thesis. The act of teaching facilitates the invitation to the communication necessary to foster ingenuity. John Novak-discusses the five relationships of educational leadership that enhance an environment of ingenuity. The International Baccalaureate (IB) is an existing model of global education, one that defines some of the school experiences and academic development of core values of educating for ingenuity. Expanding upon the structure of the IB and other research within this thesis, I speculate upon what my school, where educating for ingenuity so as to close the ingenuity gap is the goal, would be like.

Plasticity of neuroanatomical relationships between cholinergic and dopaminergic axon varicosities and pyramidal cells in the rat medial prefrontal cortex

Les systèmes cholinergique et dopaminergique jouent un rôle prépondérant dans les fonctions cognitives. Ce rôle est exercé principalement grâce à leur action modulatrice de l’activité des neurones pyramidaux du cortex préfrontal. L’interaction pharmacologique entre ces systèmes est bien documentée mais les études de leurs interactions neuroanatomiques sont rares, étant donné qu’ils sont impliqués dans une transmission diffuse plutôt que synaptique. Ce travail de thèse visait à développer une expertise pour analyser ce type de transmission diffuse en microscopie confocale. Nous avons étudié les relations de microproximité entre ces différents systèmes dans le cortex préfrontal médian (mPFC) de rats et souris. En particulier, la densité des varicosités axonales en passant a été quantifiée dans les segments des fibres cholinergiques et dopaminergiques à une distance mutuelle de moins de 3 µm ou à moins de 3 µm des somas de cellules pyramidales. Cette microproximité était considérée comme une zone d’interaction probable entre les éléments neuronaux. La quantification était effectuée après triple-marquage par immunofluorescence et acquisition des images de 1 µm par microscopie confocale. Afin d’étudier la plasticité de ces relations de microproximité, cette analyse a été effectuée dans des conditions témoins, après une activation du mPFC et dans un modèle de schizophrénie par déplétion des neurones cholinergiques du noyau accumbens. Les résultats démontrent que 1. Les fibres cholinergiques interagissent avec des fibres dopaminergiques et ce sur les mêmes neurones pyramidaux de la couche V du mPFC. Ce résultat suggère différents apports des systèmes cholinergique et dopaminergique dans l’intégration effectuée par une même cellule pyramidale. 2. La densité des varicosités en passant cholinergiques et dopaminergiques sur des segments de fibre en microproximité réciproque est plus élevée comparé aux segments plus distants les uns des autres. Ce résultat suggère un enrichissement du nombre de varicosités axonales dans les zones d’interaction. 3. La densité des varicosités en passant sur des segments de fibre cholinergique en microproximité de cellules pyramidales, immunoúactives pour c-Fos après une stimulation visuelle et une stimulation électrique des noyaux cholinergiques projetant au mPFC est plus élevée que la densité des varicosités de segments en microproximité de cellules pyramidales non-activées. Ce résultat suggère un enrichissement des varicosités axonales dépendant de l’activité neuronale locale au niveau de la zone d'interaction avec d'autres éléments neuronaux. 4. La densité des varicosités en passant des fibres dopaminergiques a été significativement diminuée dans le mPFC de rats ayant subi une déplétion cholinergique dans le noyau accumbens, comparée aux témoins. Ces résultats supportent des interrelations entre la plasticité structurelle des varicosités dopaminergiques et le fonctionnement cortical. L’ensemble des donneès démontre une plasticité de la densité locale des varicosités axonales en fonction de l’activité neuronale locale. Cet enrichissement activité-dépendant contribue vraisemblablement au maintien d’une interaction neurochimique entre deux éléments neuronaux.

Young caregiving and HIV in the UK: caring relationships and mobilities in African migrant families

Recent research in Sub-Saharan Africa has revealed the importance of children’s caring roles in families affected by HIV and AIDS. However, few studies have explored young caregiving in the context of HIV in the UK, where recently arrived African migrant and refugee families are adversely affected by the global epidemic. This paper explores young people’s socio-spatial experiences of caring for a parent with HIV, based on qualitative research with 37 respondents in London and other urban areas in England. In-depth semi-structured interviews were conducted with young people with caring responsibilities and mothers with HIV, who were predominantly African migrants, as well as with service providers. Drawing on their perspectives, the paper discusses the ways that young people and mothers negotiate the boundaries of young people’s care work within and beyond homespace, according to norms of age, gender, generational relations and cultural constructions of childhood. Despite close attachments within the family, the emotional effects of living with a highly stigmatised life-limiting illness, pressures associated with insecure immigration status, transnational migration and low income undermined African mothers’ and young people’s sense of security and belonging to homespace. These factors also restricted their mobility and social participation in school/college and neighbourhood spaces. While young people and mothers valued supportive safe spaces within the community, the stigma surrounding HIV significantly affected their ability to seek support. The article identifies security, privacy, independence and social mobility as key dimensions of African young people’s and mothers’ imagined futures of ‘home’ and ‘family’.

Phylogenetic relationships withinPelargonium sect. Peristera (Geraniaceae) inferred from nrDNA and cpDNA sequence comparisons

Phylogenetic analysis of nrDNA ITS and trnL (UAA) 5′ exon-trnF (GAA) chloroplast DNA sequences from 17 species ofPelargonium sect.Peristera, together with nine putative outgroups, suggests paraphyly for the section and a close relationship between the highly disjunct South African and Australian species of sect.Peristera. Representatives fromPelargonium sectt.Reniformia, Ligularia s. l. andIsopetalum (the St. Helena endemicP. cotyledonis) appear to be nested within thePeristera clade. The close relationship between the South African and AustralianPeristera is interpreted as being caused by long-range dispersal to Australia, probably as recent as the late Pliocene.

The dynamics and relationships of precipitation, temperature and convection boundaries in the dayside auroral ionosphere

A continuous band of high ion temperature, which persisted for about 8 h and zigzagged north-south across more than five degrees in latitude in the dayside (07:00– 15:00MLT) auroral ionosphere, was observed by the EISCAT VHF radar on 23 November 1999. Latitudinal gradients in the temperature of the F-region electron and ion gases (Te and Ti , respectively) have been compared with concurrent observations of particle precipitation and field-perpendicular convection by DMSP satellites, in order to reveal a physical explanation for the persistent band of high Ti , and to test the potential role of Ti and Te gradients as possible markers for the open-closed field line boundary. The north/south movement of the equatorward Ti boundary was found to be consistent with the contraction/expansion of the polar cap due to an unbalanced dayside and nightside reconnection. Sporadic intensifications in Ti , recurring on _10-min time scales, indicate that frictional heating was modulated by time-varying reconnection, and the band of high Ti was located on open flux. However, the equatorward Ti boundary was not found to be a close proxy of the open-closed boundary. The closest definable proxy of the open-closed boundary is the magnetosheath electron edge observed by DMSP. Although Te appears to be sensitive to magnetosheath electron fluxes, it is not found to be a suitable parameter for routine tracking of the open-closed boundary, as it involves case dependent analysis of the thermal balance. Finally, we have documented a region of newly-opened sunward convecting flux. This region is situated between the convection reversal boundary and the magnetosheath electron edge defining the openclosed boundary. This is consistent with a delay of several minutes between the arrival of the first (super-Alfv´enic) magnetosheath electrons and the response in the ionospheric convection, conveyed to the ionosphere by the interior Alfv´en wave. It represents a candidate footprint of the low-latitude boundary mixing layer on sunward convecting open flux

Investigating relationships within and between category networks in Wikipedia

This work maps and analyses cross-citations in the areas of Biology, Mathematics, Physics and Medicine in the English version of Wikipedia, which are represented as an undirected complex network where the entries correspond to nodes and the citations among the entries are mapped as edges. We found a high value of clustering coefficient for the areas of Biology and Medicine, and a small value for Mathematics and Physics. The topological organization is also different for each network, including a modular structure for Biology and Medicine, a sparse structure for Mathematics and a dense core for Physics. The networks have degree distributions that can be approximated by a power-law with a cut-off. The assortativity of the isolated networks has also been investigated and the results indicate distinct patterns for each subject. We estimated the betweenness centrality of each node considering the full Wikipedia network, which contains the nodes of the four subjects and the edges between them. In addition, the average shortest path length between the subjects revealed a close relationship between the subjects of Biology and Physics, and also between Medicine and Physics. Our results indicate that the analysis of the full Wikipedia network cannot predict the behavior of the isolated categories since their properties can be very different from those observed in the full network. (C) 2011 Elsevier Ltd. All rights reserved.

Using mitochondrial nucleotide sequences to investigate diversity and genealogical relationships within common carp (Cyprinus carpio L.)

Direct sequencing of mitochondrial DNA (mtDNA) D-loop (745 bp) and MTATPase6/MTATPase8 (857 bp) regions was used to investigate genetic variation within common carp and develop a global genealogy of common carp strains. The D-loop region was more variable than the MTATPase6/MTATPase8 region, but given the wide distribution of carp the overall levels of sequence divergence were low. Levels of haplotype diversity varied widely among countries with Chinese, Indonesian and Vietnamese carp showing the greatest diversity whereas Japanese Koi and European carp had undetectable nucleotide variation. A genealogical analysis supports a close relationship between Vietnamese, Koi and Chinese Color carp strains and to a lesser extent, European carp. Chinese and Indonesian carp strains were the most divergent, and their relationships do not support the evolution of independent Asian and European lineages and current taxonomic treatments.

Evolutionary relationships among bluetongue and related orbiviruses

Polymerase chain reaction (PCR) sequencing of specific viral gene segments was used to investigate the phylogenetic relationships among the orbiviruses. Sequence comparisons of the bluetongue virus (BTV) RNA3 from different regions of the world (North America, South Africa, India, Indonesian, Malaysia, Australia and the Caribbean region) showed that geographic separation had resulted in significant divergence, consistent with the evolution of distinct viral populations. There were at least 3 topotypes (Gould, 1987); the Australasian, African - American and another topotype represented by BTV 15 isolated in Australia in 1986. The topotypes of BTV had RNA3 nucleotide sequences that differed by approximately 20 per cent. Analysis of BTV-specific gene segments from animal and insect specimens showed that bluetongue viruses had entered northern Australia from South East Asia, possibly by wind-borne vectors. Nucleotide sequence comparisons were used to show the close genetic relationship between BTV 2 (Ona-A strain) from Florida and BTV 12 from Jamaica, and to investigate the reassortment of BTV genome segments in nature. The mutation rates of the BTV RNA2 and RNA3 segments were estimated to be of the order of 10(-4) nucleotide changes/site/year, similar in magnitude to that reported for other RNA viruses.