U-duality Covariant M-theory Cosmology

A manifestly U-duality covariant approach to M-theory cosmology is developed and applied to cosmologies in dimensions D=4,5. Cosmological properties such as expansion powers and Hubble parameters turn out to be U-duality invariant in certain asymptotic regions. U-duality transformations acting on cosmological solutions, on the other hand, shift the transition time between two asymptotic regions and determine the details of the transition. Moreover, in D=5, we show that U-duality can map expanding negative and positive branch solutions into each other.Comment: 18 pages, LATEX, 1 Postscript figure include

Heterotic M-Theory Cosmology in Four and Five Dimensions

We study rolling radii solutions in the context of the four- and five-dimensional effective actions of heterotic M-theory. For the standard four-dimensional solutions with varying dilaton and T-modulus, we find approximate five-dimensional counterparts. These are new, generically non-separating solutions corresponding to a pair of five-dimensional domain walls evolving in time. Loop corrections in the four-dimensional theory are described by certain excitations of fields in the fifth dimension. We point out that the two exact separable solutions previously discovered are precisely the special cases for which the loop corrections are time-independent. Generically, loop corrections vary with time. Moreover, for a subset of solutions they increase in time, evolving into complicated, non-separating solutions. In this paper we compute these solutions to leading, non-trivial order. Using the equations for the induced brane metric, we present a general argument showing that the accelerating backgrounds of this type cannot evolve smoothly into decelerating backgrounds.Comment: 15 pages, Latex, 1 eps figur

Five-Dimensional Moving Brane Solutions with Four-Dimensional Limiting Behaviour

Under certain conditions some solutions to five-dimensional heterotic M-theory can be accurately described by the four-dimensional action of the theory - they have a four-dimensional limit. We consider the connection between solutions of four and five-dimensional heterotic M-theory when moving five-branes are present in the bulk. We begin by describing how to raise the known four-dimensional moving brane solutions to obtain approximate solutions to the five-dimensional theory, presenting for the first time the metric template necessary for this procedure. We then present the first solutions to the five-dimensional theory containing moving five-branes. We can then discuss the connection between our new exact five-dimensional solution and the four-dimensional ones. It is shown that our new solution corresponds to a solution with a static brane in four-dimensions. In other words our new solution could not have been identified as containing a moving brane from a purely four-dimensional viewpoint.Comment: 18 pages, 6 figure

Analysis of Ultra Low Genome Conservation in Clostridium difficile

Microarray-based comparative genome hybridisations (CGH) and genome sequencing of Clostridium difficile isolates have shown that the genomes of this species are highly variable. To further characterize their genome variation, we employed integration of data from CGH, genome sequencing and putative cellular pathways. Transcontinental strain comparison using CGH data confirmed the emergence of a human-specific hypervirulent cluster. However, there was no correlation between total toxin production and hypervirulent phenotype, indicating the possibility of involvement of additional factors towards hypervirulence. Calculation of C. difficile core and pan genome size using CGH and sequence data estimated that the core genome is composed of 947 to 1,033 genes and a pan genome comprised of 9,640 genes. The reconstruction, annotation and analysis of cellular pathways revealed highly conserved pathways despite large genome variation. However, few pathways such as tetrahydrofolate biosynthesis were found to be variable and could be contributing to adaptation towards virulence such as antibiotic resistance

A quick guide for student-driven community genome annotation

High quality gene models are necessary to expand the molecular and genetic tools available for a target organism, but these are available for only a handful of model organisms that have undergone extensive curation and experimental validation over the course of many years. The majority of gene models present in biological databases today have been identified in draft genome assemblies using automated annotation pipelines that are frequently based on orthologs from distantly related model organisms. Manual curation is time consuming and often requires substantial expertise, but is instrumental in improving gene model structure and identification. Manual annotation may seem to be a daunting and cost-prohibitive task for small research communities but involving undergraduates in community genome annotation consortiums can be mutually beneficial for both education and improved genomic resources. We outline a workflow for efficient manual annotation driven by a team of primarily undergraduate annotators. This model can be scaled to large teams and includes quality control processes through incremental evaluation. Moreover, it gives students an opportunity to increase their understanding of genome biology and to participate in scientific research in collaboration with peers and senior researchers at multiple institutions

Bundles over Nearly-Kahler Homogeneous Spaces in Heterotic String Theory

We construct heterotic vacua based on six-dimensional nearly-Kahler homogeneous manifolds and non-trivial vector bundles thereon. Our examples are based on three specific group coset spaces. It is shown how to construct line bundles over these spaces, compute their properties and build up vector bundles consistent with supersymmetry and anomaly cancelation. It turns out that the most interesting coset is $SU(3)/U(1)^2$. This space supports a large number of vector bundles which lead to consistent heterotic vacua, some of them with three chiral families.Comment: 32 pages, reference adde

solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database

BACKGROUND: A common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL). Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furthermore, as entire genomes are being sequenced and an increasing amount of genetic and expression data are being generated, a challenge remains: linking phenotypic variation to the underlying genomic variation. To identify candidate genes and understand the molecular basis underlying the phenotypic variation of traits, bioinformatic approaches are needed to exploit information such as genetic map, expression and whole genome sequence data of organisms in biological databases. DESCRIPTION: The Sol Genomics Network (SGN, http://solgenomics.net) is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids species and houses a variety of bioinformatics tools. SGN has implemented a new approach to QTL data organization, storage, analysis, and cross-links with other relevant data in internal and external databases. The new QTL module, solQTL, http://solgenomics.net/qtl/, employs a user-friendly web interface for uploading raw phenotype and genotype data to the database, R/QTL mapping software for on-the-fly QTL analysis and algorithms for online visualization and cross-referencing of QTLs to relevant datasets and tools such as the SGN Comparative Map Viewer and Genome Browser. Here, we describe the development of the solQTL module and demonstrate its application. CONCLUSIONS: solQTL allows Solanaceae researchers to upload raw genotype and phenotype data to SGN, perform QTL analysis and dynamically cross-link to relevant genetic, expression and genome annotations. Exploration and synthesis of the relevant data is expected to help facilitate identification of candidate genes underlying phenotypic variation and markers more closely linked to QTLs. solQTL is freely available on SGN and can be used in private or public mode

Coffee and tomato share common gene repertoires as revealed by deep sequencing of seed and cherry transcripts

An EST database has been generated for coffee based on sequences from approximately 47,000 cDNA clones derived from five different stages/tissues, with a special focus on developing seeds. When computationally assembled, these sequences correspond to 13,175 unigenes, which were analyzed with respect to functional annotation, expression profile and evolution. Compared with Arabidopsis, the coffee unigenes encode a higher proportion of proteins related to protein modification/turnover and metabolism—an observation that may explain the high diversity of metabolites found in coffee and related species. Several gene families were found to be either expanded or unique to coffee when compared with Arabidopsis. A high proportion of these families encode proteins assigned to functions related to disease resistance. Such families may have expanded and evolved rapidly under the intense pathogen pressure experienced by a tropical, perennial species like coffee. Finally, the coffee gene repertoire was compared with that of Arabidopsis and Solanaceous species (e.g. tomato). Unlike Arabidopsis, tomato has a nearly perfect gene-for-gene match with coffee. These results are consistent with the facts that coffee and tomato have a similar genome size, chromosome karyotype (tomato, n=12; coffee n=11) and chromosome architecture. Moreover, both belong to the Asterid I clade of dicot plant families. Thus, the biology of coffee (family Rubiacaeae) and tomato (family Solanaceae) may be united into one common network of shared discoveries, resources and information

TobEA: an atlas of tobacco gene expression from seed to senescence.

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.BACKGROUND: Transcriptomics has resulted in the development of large data sets and tools for the progression of functional genomics and systems biology in many model organisms. Currently there is no commercially available microarray to allow such expression studies in Nicotiana tabacum (tobacco). RESULTS: A custom designed Affymetrix tobacco expression microarray was generated from a set of over 40k unigenes and used to measure gene expression in 19 different tobacco samples to produce the Tobacco Expression Atlas (TobEA). TobEA provides a snap shot of the transcriptional activity for thousands of tobacco genes in different tissues throughout the lifecycle of the plant and enables the identification of the biological processes occurring in these different tissues. 772 of 2513 transcription factors previously identified in tobacco were mapped to the array, with 87% of them being expressed in at least one tissue in the atlas. Putative transcriptional networks were identified based on the co-expression of these transcription factors. Several interactions in a floral identity transcription factor network were consistent with previous results from other plant species. To broaden access and maximise the benefit of TobEA a set of tools were developed to provide researchers with expression information on their genes of interest via the Solanaceae Genomics Network (SGN) web site. The array has also been made available for public use via the Nottingham Arabidopsis Stock Centre microarray service. CONCLUSIONS: The generation of a tobacco expression microarray is an important development for research in this model plant. The data provided by TobEA represents a valuable resource for plant functional genomics and systems biology research and can be used to identify gene targets for both fundamental and applied scientific applications in tobacco

M-theory resolution of four-dimensional cosmological singularities via U-duality

We consider cosmological solutions of string and M-theory compactified to four dimensions by giving a general prescription to construct four-dimensional modular cosmologies with two commuting Killing vectors from vacuum solutions. By lifting these solutions to higher dimensions we analyze the existence of cosmological singularities and find that, in the case of non-closed Friedmann-Robertson-Walker universes, singularities can be removed from the higher-dimensional model when only one of the extra dimensions is time-varying. By studying the moduli space of compactifications of M-theory resulting in homogeneous cosmologies in four dimensions we show that U-duality transformations map singular cosmologies into non-singular ones.Comment: 21 pages, harvmac. No figures. Minor changes. Typos corrected, a footnote added in Sec. 3 and two words added to the title. Final version to appear in Nuclear Physics