209 research outputs found
Saccharopolyspora cebuensis sp. nov., a novel actinomycete isolated from a Philippine sponge (Porifera)
The taxonomic status of a marine actinomycete isolated from the sponge Haliclona sp. collected from Cebu, Philippines, was established using both phenotypic and genotypic data. Strain SPE 10-1(T) exhibited chemotaxonomic and morphological characteristics that were consistent with those of members of the genus Saccharopolyspora. It showed a strict requirement for salt and is the first obligate marine bacterium of the genus Saccharopolyspora to be isolated. The principal isoprenoid quinone detected was MK-9(H(4)). The fatty acid pattern consisted mainly of terminally branched iso and anteiso fatty acids. The DNA G+C content was 72.6 mol%. Analysis of the 16S rRNA gene sequence supported affiliation of the strain with the genus Saccharopolyspora; the type strain of Saccharopolyspora gregorii was the closest phylogenetic relative (96 % sequence similarity). Sequence similarities of strain SPE 10-1(T) to other type strains of this genus were 93-95 %. It is proposed that strain SPE 10-1(T) should be classified in the genus Saccharopolyspora as a representative of Saccharopolyspora cebuensis sp. nov. The type strain of Saccharopolyspora cebuensis is SPE 10-1(T) (=DSM 45019(T)=CIP 109355(T))
Novel biomarker SARIFA in colorectal cancer: highly prognostic, not genetically driven and histologic indicator of a distinct tumor biology
SARIFA (Stroma AReactive Invasion Front Areas) has recently emerged as a promising histopathological biomarker for colon and gastric cancer. To elucidate the underlying tumor biology, we assessed SARIFA-status in tissue specimens from The-Cancer-Genome-Atlas (TCGA) cohorts COAD (colonic adenocarcinoma) and READ (rectal adenocarcinoma). For the final analysis, 207 CRC patients could be included, consisting of 69 SARIFA-positive and 138 SARIFA-negative cases. In this external validation cohort, H&E-based SARIFA-positivity was strongly correlated with unfavorable overall, disease-specific, and progression-free survival, partly outperforming conventional prognostic factors. SARIFA-positivity was not associated with known high-risk genetic profiles, such as BRAF V600E mutations or microsatellite-stable status. Transcriptionally, SARIFA-positive CRCs exhibited an overlap with CRC consensus molecular subtypes CMS1 and CMS4, along with distinct differential gene expression patterns, linked to lipid metabolism and increased stromal cell infiltration scores (SIIS). Gene-expression-based drug sensitivity prediction revealed a differential treatment response in SARIFA-positive CRCs. In conclusion, SARIFA represents the H&E-based counterpart of an aggressive tumor biology, demonstrating a partial overlap with CMS1/4 and also adding a further biological layer related to lipid metabolism. Our findings underscore SARIFA-status as an ideal biomarker for refined patient stratification and novel drug developments, particularly given its cost-effective assessment based on routinely available H&E slides
Ionization of hydrogen and hydrogenic ions by antiprotons
Presented here is a description of the ionization of hydrogen and hydrogenic
ions by antiproton-impact, based on very large scale numerical solutions of the
time-dependent Schr\"odinger equation in three spatial dimensions and on
analysis of the topology of the electronic eigenenergy surfaces in the plane of
complex internuclear distance. Comparison is made with other theories and very
recent measurements.Comment: RevTex document, 11 pages, 4 Postscript figures are available from
the authors, in press Phys. Rev. Let
Doping the holographic Mott insulator
Mott insulators form because of strong electron repulsions, being at the
heart of strongly correlated electron physics. Conventionally these are
understood as classical "traffic jams" of electrons described by a short-ranged
entangled product ground state. Exploiting the holographic duality, which maps
the physics of densely entangled matter onto gravitational black hole physics,
we show how Mott-insulators can be constructed departing from entangled
non-Fermi liquid metallic states, such as the strange metals found in cuprate
superconductors. These "entangled Mott insulators" have traits in common with
the "classical" Mott insulators, such as the formation of Mott gap in the
optical conductivity, super-exchange-like interactions, and form "stripes" when
doped. They also exhibit new properties: the ordering wave vectors are detached
from the number of electrons in the unit cell, and the DC resistivity diverges
algebraically instead of exponentially as function of temperature. These
results may shed light on the mysterious ordering phenomena observed in
underdoped cuprates.Comment: 27 pages, 9 figures. Accepted in Nature Physic
The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081
The human enteropathogen, Yersinia enterocolitica, is a significant link in the range of Yersinia pathologies extending
from mild gastroenteritis to bubonic plague. Comparison at the genomic level is a key step in our understanding of the
genetic basis for this pathogenicity spectrum. Here we report the genome of Y. enterocolitica strain 8081 (serotype 0:8;
biotype 1B) and extensive microarray data relating to the genetic diversity of the Y. enterocolitica species. Our analysis
reveals that the genome of Y. enterocolitica strain 8081 is a patchwork of horizontally acquired genetic loci, including a
plasticity zone of 199 kb containing an extraordinarily high density of virulence genes. Microarray analysis has
provided insights into species-specific Y. enterocolitica gene functions and the intraspecies differences between the
high, low, and nonpathogenic Y. enterocolitica biotypes. Through comparative genome sequence analysis we provide
new information on the evolution of the Yersinia. We identify numerous loci that represent ancestral clusters of genes
potentially important in enteric survival and pathogenesis, which have been lost or are in the process of being lost, in
the other sequenced Yersinia lineages. Our analysis also highlights large metabolic operons in Y. enterocolitica that are
absent in the related enteropathogen, Yersinia pseudotuberculosis, indicating major differences in niche and nutrients
used within the mammalian gut. These include clusters directing, the production of hydrogenases, tetrathionate
respiration, cobalamin synthesis, and propanediol utilisation. Along with ancestral gene clusters, the genome of Y.
enterocolitica has revealed species-specific and enteropathogen-specific loci. This has provided important insights into
the pathology of this bacterium and, more broadly, into the evolution of the genus. Moreover, wider investigations
looking at the patterns of gene loss and gain in the Yersinia have highlighted common themes in the genome evolution
of other human enteropathogens
Ionization via Chaos Assisted Tunneling
A simple example of quantum transport in a classically chaotic system is
studied. It consists in a single state lying on a regular island (a stable
primary resonance island) which may tunnel into a chaotic sea and further
escape to infinity via chaotic diffusion. The specific system is realistic : it
is the hydrogen atom exposed to either linearly or circularly polarized
microwaves. We show that the combination of tunneling followed by chaotic
diffusion leads to peculiar statistical fluctuation properties of the energy
and the ionization rate, especially to enhanced fluctuations compared to the
purely chaotic case. An appropriate random matrix model, whose predictions are
analytically derived, describes accurately these statistical properties.Comment: 30 pages, 11 figures, RevTeX and postscript, Physical Review E in
pres
The host response to the probiotic Escherichia coli strain Nissle 1917: Specific up-regulation of the proinflammatory chemokine MCP-1
BACKGROUND: The use of live microorganisms to influence positively the course of intestinal disorders such as infectious diarrhea or chronic inflammatory conditions has recently gained increasing interest as a therapeutic alternative. In vitro and in vivo investigations have demonstrated that probiotic-host eukaryotic cell interactions evoke a large number of responses potentially responsible for the effects of probiotics. The aim of this study was to improve our understanding of the E. coli Nissle 1917-host interaction by analyzing the gene expression pattern initiated by this probiotic in human intestinal epithelial cells. METHODS: Gene expression profiles of Caco-2 cells treated with E. coli Nissle 1917 were analyzed with microarrays. A second human intestinal cell line and also pieces of small intestine from BALB/c mice were used to confirm regulatory data of selected genes by real-time RT-PCR and cytometric bead array (CBA) to detect secretion of corresponding proteins. RESULTS: Whole genome expression analysis revealed 126 genes specifically regulated after treatment of confluent Caco-2 cells with E. coli Nissle 1917. Among others, expression of genes encoding the proinflammatory molecules monocyte chemoattractant protein-1 ligand 2 (MCP-1), macrophage inflammatory protein-2 alpha (MIP-2α) and macrophage inflammatory protein-2 beta (MIP-2β) was increased up to 10 fold. Caco-2 cells cocultured with E. coli Nissle 1917 also secreted high amounts of MCP-1 protein. Elevated levels of MCP-1 and MIP-2α mRNA could be confirmed with Lovo cells. MCP-1 gene expression was also up-regulated in mouse intestinal tissue. CONCLUSION: Thus, probiotic E. coli Nissle 1917 specifically upregulates expression of proinflammatory genes and proteins in human and mouse intestinal epithelial cells
The usability of recycled carbon fibres in short fibre thermoplastics: interfacial properties
The objective of this study was to investigate the feasibility of combining discontinuous recycled carbon fibres with polypropylene, to produce a low-cost, high specific stiffness material for high-volume applications. The inherent low affinity of carbon fibre and polypropylene motivated a detailed study of the surface characteristics of carbon fibre and interfacial behaviour between the two materials, using the microbond test. The effects of removing the sizing from the fibres, as well as introducing a maleic anhydride-grafted polypropylene coupling agent, were extensively investigated. Polypropylene was found to degrade when prepared under atmospheric conditions; therefore, it was necessary to form droplets under nitrogen. Removal of the sizing from the fibre using pyrolysis and solvolysis techniques altered the surface morphology of the fibre and increased the interfacial shear strength (IFSS) by 4 and 33 %, respectively. A more significant improvement in the fibre–matrix adhesion was achieved by adding a maleic anhydride coupling agent at 2 wt%, which increased the IFSS by 320 %
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