Universal primers that amplify RNA from all three flavivirus subgroups

Background: Species within the Flavivirus genus pose public health problems around the world. Increasing cases of Dengue and Japanese encephalitis virus in Asia, frequent outbreaks of Yellow fever virus in Africa and South America, and the ongoing spread of West Nile virus throughout the Americas, show the geographical burden of flavivirus diseases. Flavivirus infections are often indistinct from and confused with other febrile illnesses. Here we review the specificity of published primers, and describe a new universal primer pair that can detect a wide range of flaviviruses, including viruses from each of the recognised subgroups

Fish and chips: Various methodologies demonstrate utility of a 16,006-gene salmonid microarray

BACKGROUND: We have developed and fabricated a salmonid microarray containing cDNAs representing 16,006 genes. The genes spotted on the array have been stringently selected from Atlantic salmon and rainbow trout expressed sequence tag (EST) databases. The EST databases presently contain over 300,000 sequences from over 175 salmonid cDNA libraries derived from a wide variety of tissues and different developmental stages. In order to evaluate the utility of the microarray, a number of hybridization techniques and screening methods have been developed and tested. RESULTS: We have analyzed and evaluated the utility of a microarray containing 16,006 (16K) salmonid cDNAs in a variety of potential experimental settings. We quantified the amount of transcriptome binding that occurred in cross-species, organ complexity and intraspecific variation hybridization studies. We also developed a methodology to rapidly identify and confirm the contents of a bacterial artificial chromosome (BAC) library containing Atlantic salmon genomic DNA. CONCLUSION: We validate and demonstrate the usefulness of the 16K microarray over a wide range of teleosts, even for transcriptome targets from species distantly related to salmonids. We show the potential of the use of the microarray in a variety of experimental settings through hybridization studies that examine the binding of targets derived from different organs and tissues. Intraspecific variation in transcriptome expression is evaluated and discussed. Finally, BAC hybridizations are demonstrated as a rapid and accurate means to identify gene content

Dynamical Evolution in Noncommutative Discrete Phase Space and the Derivation of Classical Kinetic Equations

By considering a lattice model of extended phase space, and using techniques of noncommutative differential geometry, we are led to: (a) the conception of vector fields as generators of motion and transition probability distributions on the lattice; (b) the emergence of the time direction on the basis of the encoding of probabilities in the lattice structure; (c) the general prescription for the observables' evolution in analogy with classical dynamics. We show that, in the limit of a continuous description, these results lead to the time evolution of observables in terms of (the adjoint of) generalized Fokker-Planck equations having: (1) a diffusion coefficient given by the limit of the correlation matrix of the lattice coordinates with respect to the probability distribution associated with the generator of motion; (2) a drift term given by the microscopic average of the dynamical equations in the present context. These results are applied to 1D and 2D problems. Specifically, we derive: (I) The equations of diffusion, Smoluchowski and Fokker-Planck in velocity space, thus indicating the way random walk models are incorporated in the present context; (II) Kramers' equation, by further assuming that, motion is deterministic in coordinate spaceComment: LaTeX2e, 40 pages, 1 Postscript figure, uses package epsfi

What are communities of practice? A comparative review of four seminal works

This paper is a comparative review of four seminal works on communities of practice. It is argued that the ambiguities of the terms community and practice are a source of the concept's reusability allowing it to be reappropriated for different purposes, academic and practical. However, it is potentially confusing that the works differ so markedly in their conceptualizations of community, learning, power and change, diversity and informality. The three earlier works are underpinned by a common epistemological view, but Lave and Wenger's 1991 short monograph is often read as primarily about the socialization of newcomers into knowledge by a form of apprenticeship, while the focus in Brown and Duguid's article of the same year is, in contrast, on improvising new knowledge in an interstitial group that forms in resistance to management. Wenger's 1998 book treats communities of practice as the informal relations and understandings that develop in mutual engagement on an appropriated joint enterprise, but his focus is the impact on individual identity. The applicability of the concept to the heavily individualized and tightly managed work of the twenty-first century is questionable. The most recent work by Wenger – this time with McDermott and Snyder as coauthors – marks a distinct shift towards a managerialist stance. The proposition that managers should foster informal horizontal groups across organizational boundaries is in fact a fundamental redefinition of the concept. However it does identify a plausible, if limited, knowledge management (KM) tool. This paper discusses different interpretations of the idea of 'co-ordinating' communities of practice as a management ideology of empowerment

The gut mycobiome of the Human Microbiome Project healthy cohort

Background: Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease centric or in small cohorts of healthy individuals. To contribute to existing knowledge of the human mycobiome, we investigated the gut mycobiome of the Human Microbiome Project (HMP) cohort by sequencing the Internal Transcribed Spacer 2 (ITS2) region as well as the 18S rRNA gene. Results: Three hundred seventeen HMP stool samples were analyzed by ITS2 sequencing. Fecal fungal diversity was significantly lower in comparison to bacterial diversity. Yeast dominated the samples, comprising eight of the top 15 most abundant genera. Specifically, fungal communities were characterized by a high prevalence of Saccharomyces, Malassezia, and Candida, with S. cerevisiae, M. restricta, and C. albicans operational taxonomic units (OTUs) present in 96. 8, 88.3, and 80.8% of samples, respectively. There was a high degree of inter- and intra-volunteer variability in fungal communities. However, S. cerevisiae, M. restricta, and C. albicans OTUs were found in 92.2, 78.3, and 63.6% of volunteers, respectively, in all samples donated over an approximately 1-year period. Metagenomic and 18S rRNA gene sequencing data agreed with ITS2 results; however, ITS2 sequencing provided greater resolution of the relatively low abundance mycobiome constituents. Conclusions: Compared to bacterial communities, the human gut mycobiome is low in diversity and dominated by yeast including Saccharomyces, Malassezia, and Candida. Both inter- and intra-volunteer variability in the HMP cohort were high, revealing that unlike bacterial communities, an individual’s mycobiome is no more similar to itself over time than to another person’s. Nonetheless, several fungal species persisted across a majority of samples, evidence that a core gut mycobiome may exist. ITS2 sequencing data provided greater resolution of the mycobiome membership compared to metagenomic and 18S rRNA gene sequencing data, suggesting that it is a more sensitive method for studying the mycobiome of stool samples

Widespread sex differences in gene expression and splicing in the adult human brain

There is strong evidence to show that men and women differ in terms of neurodevelopment, neurochemistry and susceptibility to neurodegenerative and neuropsychiatric disease. The molecular basis of these differences remains unclear. Progress in this field has been hampered by the lack of genome-wide information on sex differences in gene expression and in particular splicing in the human brain. Here we address this issue by using post-mortem adult human brain and spinal cord samples originating from 137 neuropathologically confirmed control individuals to study whole-genome gene expression and splicing in 12 CNS regions. We show that sex differences in gene expression and splicing are widespread in adult human brain, being detectable in all major brain regions and involving 2.5% of all expressed genes. We give examples of genes where sex-biased expression is both disease-relevant and likely to have functional consequences, and provide evidence suggesting that sex biases in expression may reflect sex-biased gene regulatory structures

Thirty Years After Michael E. Porter: What Do We Know About Business Exit?

Although a business exit is an important corporate change initiative, the buyer’s side seems to be more appealing to management researchers than the seller’s because acquisitions imply growth, i.e., success. Yet from an optimistic viewpoint, business exit can effectively create value for the selling company. In this paper we attempt to bring the relevance of the seller’s side back into our consciousness by asking: What do we know about business exit? We start our exploration with Porter (1976), focusing on literature that investigates the antecedents of, barriers to, and outcomes of business exit. We also include studies from related fields such as finance and economics.1 Through this research we determine three clusters of findings: factors promoting business exit, exit barriers, and exit outcomes. Overall, it is the intention of this paper to highlight the importance of business exit for research and practice. Knowing what we know about business exits and their high financial value we should bear in mind that exit need not mean failure but a new beginning for a corporation

Coherent Stranski-Krastanov growth in 1+1 dimensions with anharmonic interactions: An equilibrium study

The formation of coherently strained three-dimensional islands on top of the wetting layer in Stranski-Krastanov mode of growth is considered in a model in 1+1 dimensions accounting for the anharmonicity and non-convexity of the real interatomic forces. It is shown that coherent 3D islands can be expected to form in compressed rather than in expanded overlayers beyond a critical lattice misfit. In the latter case the classical Stranski-Krastanov growth is expected to occur because the misfit dislocations can become energetically favored at smaller island sizes. The thermodynamic reason for coherent 3D islanding is the incomplete wetting owing to the weaker adhesion of the edge atoms. Monolayer height islands with a critical size appear as necessary precursors of the 3D islands. The latter explains the experimentally observed narrow size distribution of the 3D islands. The 2D-3D transformation takes place by consecutive rearrangements of mono- to bilayer, bi- to trilayer islands, etc., after exceeding the corresponding critical sizes. The rearrangements are initiated by nucleation events each next one requiring to overcome a lower energetic barrier. The model is in good qualitative agreement with available experimental observations.Comment: 12 pages text, 15 figures, Accepted in Phys.Rev.B, Vol.61, No2