The CECAM Electronic Structure Library and the modular software development paradigm

First-principles electronic structure calculations are very widely used thanks to the many successful software packages available. Their traditional coding paradigm is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, from the compiler up, with the exception of linear-algebra and message-passing libraries. This model has been quite successful for decades. The rapid progress in methodology, however, has resulted in an ever increasing complexity of those programs, which implies a growing amount of replication in coding and in the recurrent re-engineering needed to adapt to evolving hardware architecture. The Electronic Structure Library (\esl) was initiated by CECAM (European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure programs and redesign them as free, open-source libraries. They include ``heavy-duty'' ones with a high degree of parallelisation, and potential for adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by scientists when implementing new ideas. It is a community effort, undertaken by developers of various successful codes, now facing the challenges arising in the new model. This modular paradigm will improve overall coding efficiency and enable specialists (computer scientists or computational scientists) to use their skills more effectively. It will lead to a more sustainable and dynamic evolution of software as well as lower barriers to entry for new developers

Die Ausbildung von Pre-Replikationskomplexen im Epstein-Barr-Virus und dem Menschen: Eine Genom-weite Analyse.

Die Replikationskompetenz eines eukaryonten Genoms wird in der G1-Phase des Zellzyklus durch die Ausbildung von Pre-Replikationskomplexen (Pre-RCs) auf der DNA festgelegt, wobei nur ein geringer Anteil in der S-Phase aktiviert wird. In höheren Eukaryonten sind die Kriterien, die die Positionen von Replikationsursprüngen auf dem Genom festlegen, nur unzureichend charakterisiert. Zudem sind die Faktoren, die bei der selektiven Aktivierung eines Pre-RCs eine Rolle spielen, noch weitgehend unverstanden. Der limitierende Faktor, der die Analyse von Replikationsursprüngen auf dem Human-Genom bisher erschwert, ist die geringe Anzahl bisher bekannter Pre-RC-Bindestellen. Ziel dieser Arbeit war es, durch Genom-weite ChIP-Chip-Analysen potentielle Replikationsursprünge anhand von Pre-RC-Bindestellen identifizieren und Kriterien zu analysieren, die zur Ausbildung von Replikationskomplexen beitragen. Die Experimente erfolgten auf 1% des Human-Genoms sowie Genom-weit in EBV (Epstein-Barr-Virus), das in Latenz die humane Replikationsmaschinerie nutzt. Es konnten erfolgreich ChIP- und ChIP-Chip-Techniken etabliert werden. Die humanen Pre-RC-Proteine Orc2, Mcm3, Mcm7 und Cdt1 sowie das EBV-Protein EBNA1 wurden spezifisch am viralen Replikationsursprung oriP angereichert nachgewiesen. Das Replikator-Element DS in oriP zeigt eine Zellzyklus-abhängige Pre-RCAusbildung sowie 3‘ von DS eine lokale Anreicherung des Remodeling-Faktors Snf2h in der G1-Phase und eine Zellzyklus-unabhängige Histon H4-Lysin3-Trimethylierung. Des Weiteren wurde gezeigt, dass das virale Protein EBNA1 mit dem humanen Pre-RC-Protein Cdt1 interagiert und so Cdt1 lokal an EBNA1-Bindestellen auf dem EBVGenom rekrutiert. Ferner wurde in EBV der Q-Promoter (Qp) als aktiver Replikationsursprung identifiziert, wobei EBNA1 und Cdt1 sowie die Histon-Modifikation H3K4me3 lokal angereichert an Qp nachgewiesen wurden. Qp lässt in ChIP-Chip-Analysen jedoch keine spezifische Ausbildung von Pre-RCs erkennen. Analog zu dem Replikationsursprung Qp zeigen auch die Genom-weiten Bindungsprofile der Pre-RC-Komponenten in EBV und dem Menschen eine insgesamt sehr niedrige Signalintensitäten ohne signifikante Signalanreicherungen. Anhand der Pre-RC-Bindungsprofile wird postuliert, dass die Ausbildung von Pre-Replikationskomplexen auf dem EBV- und dem Human-Genom sehr flexibel und delokalisiert erfolgt und daher mittels ChIP-Chip nur schwer nachzuweisen ist

Why are we where we are? Understanding replication origins and initiation sites in eukaryotes using ChIP-approaches.

DNA replication initiates from origins of replication following a strict sequential activation programme and a conserved temporal order of activation. The number of replication initiation sites varies between species, according to the complexity of the genomes, with an average spacing of 100,000 bp. In contrast to yeast genomes, the location and definition of origins in mammalian genomes has been elusive. Historically, mammalian replication initiation sites have been mapped in situ by systematically searching specific genomic loci for sites that preferentially initiated DNA replication, potential origins by start-site mapping and autonomously replicating sequence experiments, and potential ORC and pre-replicative complex (pre-RC) sites by chromatin immunoprecipitation (ChIP) using antibodies for pre-RC proteins. In the past decade, ChIP has become an important method for analyzing protein/DNA interactions. Classically, ChIP is combined with Southern blotting or PCR. Recently, whole genome-ChIP methods have been very successful in unicellular eukaryotes to understand molecular mechanisms coordinating replication initiation and its flexibility in response to environmental changes. However, in mammalian systems, ChIP with pre-RC antibodies has often been challenging and genome-wide studies are scarce. In this review, we will appraise the progress that has been made in understanding replication origin organization using immunoprecipitation of the ORC and Mcm2-7 complexes. A special focus will be on the advantages and disadvantages of genome-wide ChIP-technologies and their potential impact on understanding metazoan replicators

Open chromatin structures regulate the efficiencies of pre-RC formation and replication initiation in Epstein-Barr virus.

Whether or not metazoan replication initiates at random or specific but flexible sites is an unsolved question. The lack of sequence specificity in origin recognition complex (ORC) DNA binding complicates genome-scale chromatin immunoprecipitation (ChIP)-based studies. Epstein-Barr virus (EBV) persists as chromatinized minichromosomes that are replicated by the host replication machinery. We used EBV to investigate the link between zones of pre-replication complex (pre-RC) assembly, replication initiation, and micrococcal nuclease (MNase) sensitivity at different cell cycle stages in a genome-wide fashion. The dyad symmetry element (DS) of EBV's latent origin, a well-established and very efficient pre-RC assembly region, served as an internal control. We identified 64 pre-RC zones that correlate spatially with 57 short nascent strand (SNS) zones. MNase experiments revealed that pre-RC and SNS zones were linked to regions of increased MNase sensitivity, which is a marker of origin strength. Interestingly, although spatially correlated, pre-RC and SNS zones were characterized by different features. We propose that pre-RCs are formed at flexible but distinct sites, from which only a few are activated per single genome and cell cycle

PML contributes to a cellular mechanism of repression of herpes simplex virus type 1 infection that is inactivated by ICP0

Promyelocytic leukemia (PML) nuclear bodies (also known as ND10) are nuclear substructures that contain several proteins, including PML itself, Sp100, and hDaxx. PML has been implicated in many cellular processes, and ND10 are frequently associated with the replicating genomes of DNA viruses. During herpes simplex virus type 1 (HSV-1) infection, the viral regulatory protein ICP0 localizes to ND10 and induces the degradation of PML, thereby disrupting ND10 and dispersing their constituent proteins. ICP0-null mutant viruses are defective in PML degradation and ND10 disruption, and concomitantly they initiate productive infection very inefficiently. Although these data are consistent with a repressive role for PML and/or ND10 during HSV-1 infection, evidence in support of this hypothesis has been inconclusive. By use of short interfering RNA technology, we demonstrate that depletion of PML increases both gene expression and plaque formation by an ICP0-negative HSV-1 mutant, while having no effect on wild-type HSV-1. We conclude that PML contributes to a cellular antiviral repression mechanism that is countered by the activity of ICP0

A comprehensive study of chromosome 16q in invasive ductal and lobular breast carcinoma using array CGH.

We analysed chromosome 16q in 106 breast cancers using tiling-path array-comparative genomic hybridization (aCGH). About 80% of ductal cancers (IDCs) and all lobular cancers (ILCs) lost at least part of 16q. Grade I (GI) IDCs and ILCs often lost the whole chromosome arm. Grade II (GII) and grade III (GIII) IDCs showed less frequent whole-arm loss, but often had complex changes, typically small regions of gain together with larger regions of loss. The boundaries of gains/losses tended to cluster, common sites being 54.5-55.5 Mb and 57.4-58.8 Mb. Overall, the peak frequency of loss (83% cancers) occurred at 61.9-62.9 Mb. We also found several 'minimal' regions of loss/gain. However, no mutations in candidate genes (TRADD, CDH5, CDH8 and CDH11) were detected. Cluster analysis based on copy number changes identified a large group of cancers that had lost most of 16q, and two smaller groups (one with few changes, one with a tendency to show copy number gain). Although all morphological types occurred in each cluster group, IDCs (especially GII/GIII) were relatively overrepresented in the smaller groups. Cluster groups were not independently associated with survival. Use of tiling-path aCGH prompted re-evaluation of the hypothetical pathways of breast carcinogenesis. ILCs have the simplest changes on 16q and probably diverge from the IDC lineage close to the stage of 16q loss. Higher-grade IDCs probably develop from low-grade lesions in most cases, but there remains evidence that some GII/GIII IDCs arise without a GI precursor