Granular packings of cohesive elongated particles

We report numerical results of effective attractive forces on the packing properties of two-dimensional elongated grains. In deposits of non-cohesive rods in 2D, the topology of the packing is mainly dominated by the formation of ordered structures of aligned rods. Elongated particles tend to align horizontally and the stress is mainly transmitted from top to bottom, revealing an asymmetric distribution of local stress. However, for deposits of cohesive particles, the preferred horizontal orientation disappears. Very elongated particles with strong attractive forces form extremely loose structures, characterized by an orientation distribution, which tends to a uniform behavior when increasing the Bond number. As a result of these changes, the pressure distribution in the deposits changes qualitatively. The isotropic part of the local stress is notably enhanced with respect to the deviatoric part, which is related to the gravity direction. Consequently, the lateral stress transmission is dominated by the enhanced disorder and leads to a faster pressure saturation with dept

Reverse taxonomy for elucidating diversity of insect-associated nematodes: a case study with termites

BACKGROUND: The molecular operational taxonomic unit(MOTU)has recently been applied to microbial and microscopic animal biodiversity surveys. However, in many cases, some of the MOTUs cannot be definitively tied to any of the taxonomic groups in current databases. To surmount these limitations, the concept of "reverse taxonomy" has been proposed, i.e. to primarily list the MOTUs with morphological information, and then identify and/or describe them at genus/species level using subsamples or by re-isolating the target organisms. Nevertheless, the application of "reverse taxonomy" has not been sufficiently evaluated. Therefore, the practical applicability of "reverse taxonomy" is tested using termite-associated nematodes as a model system for phoretic/parasitic organisms which have high habitat specificity and a potential handle (their termite host species) for re-isolation attempts. METHODOLOGY: Forty-eight species (from 298 colonies) of termites collected from the American tropics and subtropics were examined for their nematode associates using the reverse taxonomy method and culturing attempts (morphological identification and further sequencing efforts). The survey yielded 51 sequence types (= MOTUs) belonging to 19 tentatively identified genera. Within these, four were identified based on molecular data with preliminary morphological observation, and an additional seven were identified or characterized from successful culturing, leaving eight genera unidentified. CONCLUSIONS: That 1/3 of the genera were not successfully identified suggests deficiencies in the depth of available sequences in the database and biological characters, i.e. usually isolated as phoretic/parasitic stages which are not available for morphological identification, and too many undiscovered lineages of nematodes. Although there still is the issue of culturability of nematodes, culturing attempts could help to make reverse taxonomy methods more effective. However, expansion of the database, i.e., production of more DNA barcodes tied to biological information by finding and characterizing additional new and known lineages, is necessary for analyzing functional diversity.Natsumi Kanzaki, Robin M. Giblin-Davis, Rudolf H. Scheffrahn, Hisatomo Taki, Alejandro Esquivel, Kerrie A. Davies and E. Allen Herr

PCR-RFLP and sequencing analysis of ribosomal DNA of Bursaphelenchus nematodes related to pine wilt disease

La réaction en chaîne des polymérases/polymorphisme des fragments de restriction (PCR-RFLP) a été utilisée pour séparer des isolats du nématode #Bursaphelenchus. Les isolats de #B. xylophilus examinés provenaient du Japon, des USA, de Chine et du Canada, et ceux de #B. mucronatus du Japon, de Chine et de la France. L'ADN ribosomal contenant le gène 5.8S, les segments de transciption interne 1 et 2, et les segments partiels des gènes 18S et 28S ont été amplifiés par PCR. La digestion des produits amplifiés provenant de chaque isolat à l'aide de douze endonucléases de restriction et l'examen des données en RFLP qui en découlent révèlent, par une analyse en grappe, une séparation significative entre #B. xylophilus et #B. mucronatus. Parmi les isolats de #B. xylophilus examinés, les isolats pathogènes du Japon, ceux de Chine et des USA étaient tous identiques, tandis que les isloats non pathogènes du Japon étaient légèrement distincts et que ceux du Canada formaient une grappe séparée. Parmi les isolats de #B. mucronatus, deux isolats provenant du Japon étaient très semblables ; de même un autre isolat du Japon et un isolat de Chine étaient identiques. Les données provenant des séquences d'ADN montrent 98 différences (substitution nucléotidiques ou séparations) dans les 884 paires de bases examinées chez les isolats de #B. xylophilus et #B. mucronatus. Les données provenant des séquences d'ADN chez #Aphelenchus avenae et #Aphelenchoides fragariae diffèrent non seulement de celles des #Bursaphelenchus mais aussi entre elles. Afin de préciser les relations phylogéniques de ces espèces, les données séquentielles du gène 5.8S provenant de l'ADN ribosomal ont été examinées... (D'après résume d'auteur

Granular packings of cohesive elongated particles

We report numerical results of effective attractive forces on the packing properties of two-dimensional elongated grains. In deposits of non-cohesive rods in 2D, the topology of the packing is mainly dominated by the formation of ordered structures of aligned rods. Elongated particles tend to align horizontally and the stress is mainly transmitted from top to bottom, revealing an asymmetric distribution of local stress. However, for deposits of cohesive particles, the preferred horizontal orientation disappears. Very elongated particles with strong attractive forces form extremely loose structures, characterized by an orientation distribution, which tends to a uniform behavior when increasing the Bond number. As a result of these changes, the pressure distribution in the deposits changes qualitatively. The isotropic part of the local stress is notably enhanced with respect to the deviatoric part, which is related to the gravity direction. Consequently, the lateral stress transmission is dominated by the enhanced disorder and leads to a faster pressure saturation with depth.Comment: 6 pages, 6 figure

A dominant function of p38 mitogen-activated protein kinase signaling in receptor activator of nuclear factor-κB ligand expression and osteoclastogenesis induction by Aggregatibacter actinomycetemcomitans and Escherichia coli lipopolysaccharide

Lipopolysaccharide from gram-negative bacteria is one of the microbial-associated molecular patterns that initiate the immune/inflammatory response, leading to the tissue destruction observed in periodontitis. The aim of this study was to evaluate the role of the p38 mitogen-activated protein kinase (MAPK) signaling pathway in lipopolysaccharide-induced receptor activator of nuclear factor-κB ligand (RANKL) expression by murine periodontal ligament cells. Material and Methods:  Expression of RANKL and osteoprotegerin mRNA was studied by reverse transcription-polymerase chain reaction upon stimulation with lipopolysaccharide from Escherichia coli and Aggregatibacter actinomycetemcomitans . The biochemical inhibitor SB203580 was used to evaluate the contribution of the p38 MAPK signaling pathway to lipopolysaccharide-induced RANKL and osteoprotegerin expression. Stable cell lines expressing dominant-negative forms of MAPK kinase (MKK)-3 and MKK6 were generated to confirm the role of the p38 MAPK pathway. An osteoclastogenesis assay using a coculture model of the murine monocytic cell line RAW 264.7 was used to determine if osteoclast differentiation induced by lipopolysaccharide-stimulated periodontal ligament was correlated with RANKL expression. Results:  Inhibiting p38 MAPK prior to lipopolysaccharide stimulation resulted in a significant decrease of RANKL mRNA expression. Osteoprotegerin mRNA expression was not affected by lipopolysaccharide or p38 MAPK. Lipopolysaccharide-stimulated periodontal ligament cells increased osteoclast differentiation, an effect that was completely blocked by osteoprotegerin and significantly decreased by inhibition of MKK3 and MKK6, upstream activators of p38 MAPK. Conditioned medium from murine periodontal ligament cultures did not increase osteoclast differentiation, indicating that periodontal ligament cells produced membrane-bound RANKL. Conclusion:  Lipopolysaccharide resulted in a significant increase of RANKL in periodontal ligament cells. The p38 MAPK pathway is required for lipopolysaccharide-induced membrane-bound RANKL expression in these cells.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/65788/1/j.1600-0765.2007.01013.x.pd