573 research outputs found
Revision of Madagascar's Dwarf Lemurs (Cheirogaleidae:Cheirogaleus): Designation of Species, Candidate Species Status and Geographic Boundaries Based on Molecular and Morphological Data
The genus Cheirogaleus, the dwarf lemurs, is a radiation of strepsirrhine primates endemic to the island of Madagascar.
The dwarf lemurs are taxonomically grouped in the family Cheirogaleidae (Infraorder: Lemuriformes) along with the genera
Microcebus, Mirza, Allocebus, and Phaner. The taxonomic history of the genus Cheirogaleus has been controversial since its
inception due to a paucity of evidence in support of some proposed species. In this study, we addressed this issue by expanding the
geographic breadth of samples by 91 individuals and built upon existing mitochondrial (cytb and COII) and nuclear (FIBA and
vWF) DNA datasets to better resolve the phylogeny of Cheirogaleus. The mitochondrial gene fragments D-loop and PAST as well
as the CFTR-PAIRB nuclear loci were also sequenced. In agreement with previous genetic studies, numerous deep divergences
were resolved in the C. major, C. minor and C. medius lineages. Four of these lineages were segregated as new species, seven
were identified as confirmed candidate species, and four were designated as unconfirmed candidate species based on comparative
mitochondrial DNA sequence data gleaned from the literature or this study. Additionally, C. thomasi was resurrected. Given the
widespread distribution of the genus Cheirogaleus throughout Madagascar, the methodology employed in this study combined
all available lines of evidence to standardize investigative procedures in a genus with limited access to type material and a lack of
comprehensive sampling across its total distribution. Our results highlighted lineages that likely represent new species and identified
localities that may harbor an as-yet undescribed cryptic species diversity pending further field and laboratory work.We
are most grateful to the Ahmanson Foundation, the Theodore
F. and Claire M. Hubbard Family Foundation, the Primate
Action Fund / Conservation International, the Margot
Marsh Biodiversity Foundation, and the National Geographic
Society, for financial assistance
On the origine of the Boson peak
We show that the phonon-saddle transition in the ensemble of generalized
inherent structures (minima and saddles) happens at the same point as the
dynamical phase transition in glasses, that has been studied in the framework
of the mode coupling approximation. The Boson peak observed in glasses at low
temperature is a remanent of this transition.Comment: Proceeding of the Pisa conference September 2002, 13 pages+ 4
figures, To be publiched by Journal of Physic
Relaxation in glassforming liquids and amorphous solids
The field of viscousliquid and glassysolid dynamics is reviewed by a process of posing the key questions that need to be answered, and then providing the best answers available to the authors and their advisors at this time. The subject is divided into four parts, three of them dealing with behavior in different domains of temperature with respect to the glass transition temperature, Tg,and a fourth dealing with âshort time processes.â The first part tackles the high temperature regime T\u3eTg, in which the system is ergodic and the evolution of the viscousliquid toward the condition at Tg is in focus. The second part deals with the regime TâŒTg, where the system is nonergodic except for very long annealing times, hence has time-dependent properties (aging and annealing). The third part discusses behavior when the system is completely frozen with respect to the primary relaxation process but in which secondary processes, particularly those responsible for âsuperionicâ conductivity, and dopart mobility in amorphous silicon, remain active. In the fourth part we focus on the behavior of the system at the crossover between the low frequency vibrational components of the molecular motion and its high frequency relaxational components, paying particular attention to very recent developments in the short time dielectric response and the high Qmechanical response
PhyloMarkerâA Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny
Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/
A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease
Peer reviewedPublisher PD
Pseudopotential study of binding properties of solids within generalized gradient approximations: The role of core-valence exchange-correlation
In ab initio pseudopotential calculations within density-functional theory
the nonlinear exchange-correlation interaction between valence and core
electrons is often treated linearly through the pseudopotential. We discuss the
accuracy and limitations of this approximation regarding a comparison of the
local density approximation (LDA) and generalized gradient approximations
(GGA), which we find to describe core-valence exchange-correlation markedly
different. (1) Evaluating the binding properties of a number of typical solids
we demonstrate that the pseudopotential approach and namely the linearization
of core-valence exchange-correlation are both accurate and limited in the same
way in GGA as in LDA. (2) Examining the practice to carry out GGA calculations
using pseudopotentials derived within LDA we show that the ensuing results
differ significantly from those obtained using pseudopotentials derived within
GGA. As principal source of these differences we identify the distinct behavior
of core-valence exchange-correlation in LDA and GGA which, accordingly,
contributes substantially to the GGA induced changes of calculated binding
properties.Comment: 13 pages, 6 figures, submitted to Phys. Rev. B, other related
publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm
Building democracy from below : lessons from Western Uganda
How to achieve democratisation in the neopatrimonial and agrarian environments that predominate in sub-Saharan Africa continues to present a challenge for both development theory and practice. Drawing on intensive fieldwork in Western Uganda, this paper argues that Charles Tillyâs âdemocratisation as processâ provides us with the framework required to explain the ways in which particular kinds of association can advance democratisation from below. Moving beyond the current focus on how elite-bargaining and certain associational forms may contribute to liberal forms of democracy, this approach helps identify the intermediate mechanisms involved in building democracy from below, including the significance of challenging categorical inequalities, notably through the role of producer groups, and of building trust networks, cross-class alliances and synergistic relations between civil and political society. The evidence and mode of analysis deployed here help suggest alternative routes for supporting local efforts to build democracy from below in sub-Saharan Africa
Frequency behavior of Raman coupling coefficient in glasses
Low-frequency Raman coupling coefficient of 11 different glasses is
evaluated. It is found that the coupling coefficient demonstrates a universal
linear frequency behavior near the boson peak maximum and a superlinear
behavior at very low frequencies. The last observation suggests vanishing of
the coupling coefficient when frequency tends to zero. The results are
discussed in terms of the vibration wavefunction that combines features of
localized and extended modes.Comment: 8 pages, 9 figure
Oral and Fecal Campylobacter concisus Strains Perturb Barrier Function by Apoptosis Induction in HT-29/B6 Intestinal Epithelial Cells
Campylobacter concisus infections of the gastrointestinal tract can be accompanied by diarrhea and inflammation, whereas colonization of the human oral cavity might have a commensal nature. We focus on the pathophysiology of C. concisus and the effects of different clinical oral and fecal C. concisus strains on human HT-29/B6 colon cells. Six oral and eight fecal strains of C. concisus were isolated. Mucus-producing HT-29/B6 epithelial monolayers were infected with the C. concisus strains. Transepithelial electrical resistance (Rt) and tracer fluxes of different molecule size were measured in Ussing chambers. Tight junction (TJ) protein expression was determined by Western blotting, and subcellular TJ distribution was analyzed by confocal laser-scanning microscopy. Apoptosis induction was examined by TUNEL-staining and Western blot of caspase-3 activation. All strains invaded confluent HT-29/B6 cells and impaired epithelial barrier function, characterized by a time- and dose-dependent decrease in Rt either after infection from the apical side but even more from the basolateral compartment. TJ protein expression changes were sparse, only in apoptotic areas of infected monolayers TJ proteins were redistributed. Solely the barrier-forming TJ protein claudin-5 showed a reduced expression level to 66±8% (P<0.05), by expression regulation from the gene. Concomitantly, Lactate dehydrogenase release was elevated to 3.1±0.3% versus 0.7±0.1% in control (P<0.001), suggesting cytotoxic effects. Furthermore, oral and fecal C. concisus strains elevated apoptotic events to 5-fold. C. concisus-infected monolayers revealed an increased permeability for 332 Da fluorescein (1.74±0.13 vs. 0.56±0.17 10â6 cm/s in control, P<0.05) but showed no difference in permeability for 4 kDa FITC-dextran (FD-4). The same was true in camptothecin-exposed monolayers, where camptothecin was used for apoptosis induction
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