2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles

Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 9 E.coli isolates from the 2011 German outbreak against existing E. coli genomes using the alignment-free feature frequency profile method. In addition, we looked for gene elements that distinguish the outbreak group from the other E. coli strains and possibly accounted for the emergence of the outbreak isolates using the distinguishing feature analysis

Entanglement dynamics of two-qubit system in different types of noisy channels

In this paper, we study entanglement dynamics of a two-qubit extended Werner-like state locally interacting with independent noisy channels, i.e., amplitude damping, phase damping and depolarizing channels. We show that the purity of initial entangled state has direct impacts on the entanglement robustness in each noisy channel. That is, if the initial entangled state is prepared in mixed instead of pure form, the state may exhibit entanglement sudden death (ESD) and/or be decreased for the critical probability at which the entanglement disappear.Comment: 11 pages, 6 figure

2011 German Escherichia coli O104:H4 outbreak: whole-genome phylogeny without alignment

<p>Abstract</p> <p>Background</p> <p>A large-scale <it>Escherichia coli </it>O104:H4 outbreak occurred in Germany from May to July 2011, causing numerous cases of hemolytic-uremic syndrome (HUS) and deaths. Genomes of ten outbreak isolates and a historical O104:H4 strain isolated in 2001 were sequenced using different new generation sequencing platforms. Phylogenetic analyses were performed using various approaches which either are not genome-wide or may be subject to errors due to poor sequence alignment. Also, detailed pathogenicity analyses on the 2001 strain were not available.</p> <p>Findings</p> <p>We reconstructed the phylogeny of <it>E. coli </it>using the genome-wide and alignment-free feature frequency profile method and revealed the 2001 strain to be the closest relative to the 2011 outbreak strain among all available <it>E. coli </it>strains at present and confirmed findings from previous alignment-based phylogenetic studies that the HUS-causing O104:H4 strains are more closely related to typical enteroaggregative <it>E. coli </it>(EAEC) than to enterohemorrhagic <it>E. coli</it>. Detailed re-examination of pathogenicity-related virulence factors and secreted proteins showed that the 2001 strain possesses virulence factors shared between typical EAEC and the 2011 outbreak strain.</p> <p>Conclusions</p> <p>Our study represents the first attempt to elucidate the whole-genome phylogeny of the 2011 German outbreak using an alignment-free method, and suggested a direct line of ancestry leading from a putative EAEC-like ancestor through the 2001 strain to the 2011 outbreak strain.</p

2011 German Escherichia coli outbreak: Prophage analysis of close-assembled TY2482 against 55989 using PHAST

Using the Hiseq data of the German E. coli outbreak isolate TY2482, preliminary prophage analyses have been performed by some researchers previously. With the closed assembly of the same isolate being available, another round of analysis might help in resolving questions that remain unclear due to the incompleteness of the dataset

The immunomodulatory functions and molecular mechanism of a new bursal heptapeptide (BP7) in immune responses and immature B cells

International audienceAbstractThe bursa of Fabricius (BF) is the acknowledged central humoural immune organ unique to birds and plays a vital role in B lymphocyte development. In addition, the unique molecular immune features of bursal-derived biological peptides involved in B cell development are rarely reported. In this paper, a novel bursal heptapeptide (BP7) with the sequence GGCDGAA was isolated from the BF and was shown to enhance the monoclonal antibody production of a hybridoma. A mouse immunization experiment showed that mice immunized with an AIV antigen and BP7 produced strong antibody responses and cell-mediated immune responses. Additionally, BP7 stimulated increased mRNA levels of sIgM in immature mouse WEHI-231 B cells. Gene microarray results confirmed that BP7 regulated 2465 differentially expressed genes in BP7-treated WEHI-231 cells and induced 13 signalling pathways and various immune-related functional processes. Furthermore, we found that BP7 stimulated WEHI-231 cell autophagy and AMPK-ULK1 phosphorylation and regulated Bcl-2 protein expression. Finally, chicken immunization showed that BP7 enhanced the potential antibody and cytokine responses to the AIV antigen. These results suggested that BP7 might be an active biological factor that functions as a potential immunopotentiator, which provided some novel insights into the molecular mechanisms of the effects of bursal peptides on immune functions and B cell differentiation

The mechanism of word satiation in Tibetan reading: Evidence from eye movements

Two eye-tracking experiments were used to investigate the mechanism of word satiation in Tibetan reading. The results revealed that, at a low repetition level, gaze duration and total fixation duration in the semantically unrelated condition were significantly longer than in the semantically related condition; at a medium repetition level, reaction time in the semantically related condition was significantly longer than in the semantically unrelated condition; at a high repetition level, the total fixation duration and reaction time in the semantically related condition were significantly longer than in the semantically unrelated condition. However, fixation duration and reaction time showed no significant difference between the similar and dissimilar orthography at any repetition level. These findings imply that there are semantic priming effects in Tibetan reading at a low repetition level, but semantic satiation effects at greater repetition levels, which occur in the late stage of lexical processing

Entanglement and quantum phase transition in alternating XY spin chain with next-nearest neighbour interactions

By using the method of density-matrix renormalization-group to solve the different spin-spin correlation functions, the nearest-neighbouring entanglement(NNE) and next-nearest-neighbouring entanglement(NNNE) of one-dimensional alternating Heisenberg XY spin chain is investigated in the presence of alternating nearest neighbour interactions of exchange couplings, external magnetic fields and next-nearest neighbouring interactions. For dimerized ferromagnetic spin chain, NNNE appears only above the critical dimerized interaction, meanwhile, the dimerized interaction effects quantum phase transition point and improves NNNE to a large value. We also study the effect of ferromagnetic or antiferromagnetic next-nearest neighboring (NNN) interactions on the dynamics of NNE and NNNE. The ferromagnetic NNN interaction increases and shrinks NNE below and above critical frustrated interaction respectively, while the antiferromagnetic NNN interaction always decreases NNE. The antiferromagnetic NNN interaction results to a larger value of NNNE in comparison to the case when the NNN interaction is ferromagnetic.Comment: 13 pages, 4 figures,. accepted by Chinese Physics B 2008 11 (in press

Genome sequence and genetic linkage analysis of Shiitake mushroom _Lentinula edodes_

_Lentinula edodes_ (Shiitake/Xianggu) is an important cultivated mushroom. Understanding the genomics and functional genomics of _L. edodes_ allows us to improve its cultivation and quality. Genome sequence is a key to develop molecular genetic markers for breeding and genetic manipulation. We sequenced the genome of _L. edodes_ monokaryon L54A using Roche 454 and ABI SOLiD genome sequencing. Sequencing reads of about 1400Mb were de novo assembled into a 40.2 Mb genome sequence. We compiled the genome sequence into a searchable database with which we have been annotating the genes and analyzing the metabolic pathways. In addition, we have been using many molecular techniques to analyze genes differentially expressed during development. Gene ortholog groups of _L. edodes_ genome sequence compared across genomes of several fungi including mushrooms identified gene families unique to mushroom-forming fungi. We used a mapping population of haploid basidiospores of dikaryon L54 for genetic linkage analysis. High-quality variations such as single nucleotide polymorphisms, insertions, and deletions of the mapping population formed a high-density genetic linkage map. We compared the linkage map to the _L. edodes_ L54A genome sequence and located selected quantitative trait loci. The Shiitake community will benefit from these resources for genetic studies and breeding.&#xd;&#xa

Entanglement control in one-dimensional s=1/2s=1/2 random XY spin chain

The entanglement in one-dimensional random XY spin systems where the impurities of exchange couplings and the external magnetic fields are considered as random variables is investigated by solving the different spin-spin correlation functions and the average magnetization per spin. The entanglement dynamics near particular locations of the system is also studied when the exchange couplings (or the external magnetic fields) satisfy three different distributions(the Gaussian distribution, double-Gaussian distribution, and bimodal distribution). We find that the entanglement can be controlled by varying the strength of external magnetic field and the different distributions of impurities. Moreover, the entanglement of some nearest-neighboring qubits can be increased for certain parameter values of the three different distributions.Comment: 13 pages, 4 figure