Search for single production of a heavy vector-like T quark decaying to a Higgs boson and a top quark with a lepton and jets in the final state

Peer reviewe

Identification of fungal DNA barcode targets and PCR primers based on Pfam protein families and taxonomic hierarchy

Abstract: DNA barcoding is the application of DNA sequences of standardized genetic markers for the identification of eukaryotic organisms. We attempted to identify alternative candidate barcode gene targets for the fungal biota from available fungal genomes using a taxonomy-aware processing pipeline. Putative-protein coding sequences were matched to Pfam protein families and aligned to reference Pfam accessions. Conserved sequence blocks were identified in the resulting alignments and degenerate primers were designed. The processing pipeline is described and the resulting candidate gene targets are discussed. The pipeline allows analysis of subsets at various hierarchical, taxonomic levels (selectable by GenBank taxonomy ID or scientific name) of the available reference data, allowing discrete taxonomic groups to be combined into a single subset, or for subordinate taxa to be excluded from the analysis of higher-level taxa. Putative degenerate primer pairs were designed as high as the superkingdom rank for the set of organisms included in the analysis. The identified targets have essential housekeeping functions, like the well known phylogenetic or barcode markers, and most have a better resolution potential to differentiate species among fully sequenced genomes than the most presently used markers. Some of the commonly used species-level phylogenetic markers for fungi, especially tef1-α and rpb2, were not recovered in our analysis because of their existence in multiple copies in single organisms, and because Pfam families do not always correlate with complete proteins. Keywords: Fungi, barcoding, internal transcribed spacer (ITS), translation elongation factor 1A (tef1a), ribosomal polymerase B2 (rpb2), cytochrome oxidase 1 (cox1, COI)

The quest for a general and reliable fungal DNA barcode

DNA sequences are key elements for both identification and classification of living organisms. Mainly for historical reasons, a limited number of genes are currently used for this purpose. From a mathematical point of view, any DNA segment, at any location, even outside of coding regions and even if they do not align, could be used as long as PCR primers could be designed to amplify them. This paper describes two methods to search genomic data for the most efficient DNA segments that can be used for identification and classification

Distinct loiasis infection states and associated clinical and hematological manifestations in patients from Gabon

BACKGROUND: Loiasis-a filarial disease endemic in Central and West Africa-is increasingly recognized as significant individual and public health concern. While the understanding of the disease characteristics remains limited, significant morbidity and excess mortality have been demonstrated. Here, we characterize clinical and hematological findings in a large cohort from Gabon. METHODS: Loiasis-related clinical manifestations and microfilaremia, hemoglobin and differential blood counts were recorded prospectively during a cross-sectional survey. For analysis, participants were categorized into distinct infection states by the diagnostic criteria of eye worm history and microfilaremia. RESULTS: Analysis of data from 1,232 individuals showed that occurrence of clinical and hematological findings differed significantly between the infection states. Eye worm positivity was associated with a wide range of clinical manifestations while microfilaremia by itself was not. Loa loa infection was associated with presence of eosinophilia and absolute eosinophil counts were associated with extent of microfilaremia (p-adj. = 0.012, ß-estimate:0.17[0.04-0.31]). CONCLUSIONS: Loiasis is a complex disease, causing different disease manifestations in patients from endemic regions. The consequences for the affected individuals or populations as well as the pathophysiological consequences of correlating eosinophilia are largely unknown. High-quality research on loiasis should be fostered to improve patient care and understanding of the disease

The Amsterdam Declaration on Fungal Nomenclature

The Amsterdam Declaration on Fungal Nomenclature was agreed at an international symposium convened in Amsterdam on 19–20 April 2011 under the auspices of the International Commission on the Taxonomy of Fungi (ICTF). The purpose of the symposium was to address the issue of whether or how the current system of naming pleomorphic fungi should be maintained or changed now that molecular data are routinely available. The issue is urgent as mycologists currently follow different practices, and no consensus was achieved by a Special Committee appointed in 2005 by the International Botanical Congress to advise on the problem. The Declaration recognizes the need for an orderly transitition to a single-name nomenclatural system for all fungi, and to provide mechanisms to protect names that otherwise then become endangered. That is, meaning that priority should be given to the first described name, except where that is a younger name in general use when the first author to select a name of a pleomorphic monophyletic genus is to be followed, and suggests controversial cases are referred to a body, such as the ICTF, which will report to the Committee for Fungi. If appropriate, the ICTF could be mandated to promote the implementation of the Declaration. In addition, but not forming part of the Declaration, are reports of discussions held during the symposium on the governance of the nomenclature of fungi, and the naming of fungi known only from an environmental nucleic acid sequence in particular. Possible amendments to the Draft BioCode (2011) to allow for the needs of mycologists are suggested for further consideration, and a possible example of how a fungus only known from the environment might be described is presented

On the Way to a Gutzwiller Density Functional Theory

Abstract. Multi-band Gutzwiller-correlated wave functions reconcile the contrasting concepts of itinerant band electrons versus electrons localized in partially filled atomic shells. The exact evaluation of these variational ground states in the limit of large coordination number allows the identification of quasi-particle band structures, and the calculation of a variational spinwave dispersion. The study of a generic two-band model elucidates the co-operation of the Coulomb repulsion and the Hund’s-rule exchange for itinerant ferromagnetism. We present results of calculations for ferromagnetic nickel, using a realistic 18 spin-orbital basis of 4s, 4p and 3d valence electrons. The quasiparticle energy bands agree much better with the photo-emission and Fermi surface data than the band structure obtained from spin-density functional theory (SDFT). 1 Exchange versus Correlations More than 50 years ago two basically different scenarios had emerged from early quantum-mechanical considerations on electrons in metals with partly filled d bands. Scenario I: As proposed by Slater [1] and Stoner [2], band theory alone wa