Penn Center for Boinformatics

In biological systems, gene expression takes place when genes generate gene products and gene expression levels correspond to concentration levels of these products. Gene expression levels within a single cell are determined by a network of regulatory interactions among genes mediated by gene products. In spatially extended systems consisting of multiple cells gene expression levels within a cell are also affected by gene activity taking place in neighbouring cells.

Abstract Detection of stem rust race TTKSK (Ug99) from Uganda in 1998/99 highlighted not only the extremely high vulnerability of the global wheat crop to stem rust, but also a lack of adequate global systems to monitor such a threat. Progress in the development and expansion of the Global Cereal Rust Monitoring System (GCRMS) is described. The current situation regarding the Ug99 lineage of races is outlined and the potential for expansion into important wheat areas is considered.

Genome architecture and the regulation of gene expression are expected to be interdependent. Understanding this interdependence is key to successful genome engineering. Evidence for non-random arrangement of genes along genomes, defined as the relative positioning of co-functional or co-regulated genes, stems from two main approaches. Firstly, the analysis of contiguous genome segments across species has highlighted the conservation of gene order (synteny) along chromosome regions. Secondly, the study of long-range regularities along chromosomes of one given species has emphasized periodic positioning of microbial genes that are either co-regulated, evolutionarily correlated, or highly codon-biased. Software tools to detect, visualise, systematically analyse, and exploit gene position regularities along genomes can facilitate the studies of such non-random genome layouts, the inference of transcription factor binding sites, and potentially guide rational genome design. Here a computational protocol is demonstrated for the analysis and exploitation of regular patterns in a set of genomic features of interest (e.g., co-functional or co-regulated genes, Chromatin ImmunoPrecipitation results, etc.). This case study is conducted for genes involved in hydrocarbon metabolism of a marine petroleum-degrading bacterium Alkanivorax borkumensis.

The phenolic profile of the grape berries is a key quality factor for the red grapevine varieties and several techniques have been applied to improve it. An innovative technique is the application of resistance elicitors and phytohormones. In the present study, leaves and berries of a Greek red indigenous variety (Mouhtaro) sprayed with two elicitors, benzothiadiazole and chitosan and a plant hormone abscisic acid, during veraison. Physicochemical and phenolic characteristics of the berries and microbial communities of rhizosphere, phyllosphere and carposphere were analyzed at harvest. Differences in the microbial communities on different plant compartments were observed after the application of the plant activators. Chitosan treatment increased the abundance of the beneficial lactic acid bacteria, while the abscisic acid treatment decreased the presence of spoilage fungi on the carposphere. Treatments differentiate total phenolics, anthocyanins and in the chemical characteristics o...

In biological systems, gene expression takes place when genes generate gene products and gene expression levels correspond to concentration levels of these products. Gene expression levels within a single cell are determined by a network of regulatory interactions among genes mediated by gene products. In spatially extended systems consisting of multiple cells gene expression levels within a cell are also affected by gene activity taking place in neighbouring cells. The interplay between spatial interactions among ...

Embryonic stem cells (ESCs) fate is regulated both at transcriptional and post-transcriptional levels. Indeed, several studies showed that, in addition to gene transcription, mRNA stability and protein synthesis are finely tuned and strongly control the ESCs pluripotency and fate changes. An increasing number of RNA-binding proteins (RBPs) involved in post-transcriptional and translational regulation of gene expression has been identified as regulators of ESC identity. The major lysine methyltransferase Setdb1 is essential for the self-renewal and viability of ESCs. Setdb1 was primarily known to methylate the lysine 9 of histone 3 (H3K9) in the nucleus, where it regulates chromatin functions. However, Setdb1 is also massively localized in the cytoplasm, including in mouse ESCs, where its role remains unknown. Here we show that the cytoplasmic Setdb1 (cSetdb1) is essential for the survival of mESCs. Functional assays further demonstrate that cSetdb1 regulates gene expression post-tra...

Aegilops sharonensis Eig (Sharon goatgrass) is a wild diploid relative of wheat within the Sitopsis section of Aegilops. This species represents an untapped reservoir of genetic diversity for traits of agronomic importance, especially as a source of novel disease resistance. To gain a foothold in this genetic resource, we sequenced the cDNA from leaf tissue of two geographically distinct Ae. sharonensis accessions (1644 and 2232) using the 454 Life Sciences platform. We compared the results of two different assembly programs using different parameter sets to generate 13 distinct assemblies in an attempt to maximize representation of the gene space in de novo transcriptome assembly. The most sensitive assembly (71,029 contigs; N50 674 nts) retrieved 18,684 unique best reciprocal BLAST hits (BRBH) against six previously characterised grass proteomes while the most specific assembly (30,609 contigs; N50 815 nts) retrieved 15,687 BRBH. We combined these two assemblies into a set of 62,2...

MotivationNetwork biology is a dominant player in today’s multi-omics era. Therefore, the need for visualization tools which can efficiently cope with intra-network heterogeneity emerges.ResultsNORMA-2.0 is a web application which uses efficient layouts to group together areas of interest in a network. In this version, NORMA-2.0 utilizes three different strategies to make such groupings as distinct as possible while it preserves all of the properties from its first version where one can handle multiple networks and annotation files simultaneously.AvailabilityThe web resource is available at http://norma.pavlopouloslab.info/The source code is freely available at https://github.com/PavlopoulosLab/NORMAContactpavlopoulos@fleming.gr

SUMMARYThe histone lysine methyltransferase SETDB1 is involved in muscle differentiation and has been shown as a regulator of the TGFβ pathway in cancer contexts. Here, we investigated the role of SETDB1 in Duchenne muscular dystrophy (DMD) myotubes harboring an overactivated TGFβ pathway. Our data show that challenging healthy myotubes with TGFβ induces nuclear accumulation of SETDB1, while in DMD myotubes SETDB1 is constantly accumulated in nuclei in TGFβ-dependent fashion. SETDB1 loss-of-function (LOF) leads to a decrease of the TGFβ downstream target genes in DMD myotubes, suggesting the involvement of a TGFβ/SETDB1 axis in DMD physiopathology. Transcriptomics show that many targets of SETDB1 code for secreted factors involved in fibrosis, extracellular matrix remodeling and inflammation and are downregulated when SETDB1 is silenced. Conditioned medium assays show that SETDB1 LOF in DMD myotubes abrogates the deleterious effect of the secretome on myoblast differentiation and im...