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The ARB (from Latin arbor, tree) project was initiated almost 10 years ago. The ARB program package comprises a variety of directly interacting software tools for sequence database maintenance and analysis which are controlled by a common graphical user interface. Although it was initially designed for ribosomal RNA data, it can be used for any nucleic and(More)
MOTIVATION The computation of large phylogenetic trees with statistical models such as maximum likelihood or bayesian inference is computationally extremely intensive. It has repeatedly been demonstrated that these models are able to recover the true tree or a tree which is topologically closer to the true tree more frequently than less elaborate methods(More)
Inference of phylogenetic trees comprising hundreds or even thousands of organisms based on the Maximum Likelihood (ML) method is computationally extremely intensive. In order to accelerate computations we implemented RAxML-OMP, an efficient OpenMP-parallelization for Symmetric Multi-Processing machines (SMPs) based on the sequential program RAxML-V(More)
Cellular senescence has been theorized to oppose neoplastic transformation triggered by activation of oncogenic pathways in vitro, but the relevance of senescence in vivo has not been established. The PTEN and p53 tumour suppressors are among the most commonly inactivated or mutated genes in human cancer including prostate cancer. Although they are(More)
Cell-cycle arrest, apoptosis, and senescence are widely accepted as the major mechanisms by which p53 inhibits tumor formation. Nevertheless, it remains unclear whether they are the rate-limiting steps in tumor suppression. Here, we have generated mice bearing lysine to arginine mutations at one (p53(K117R)) or three (p53(3KR); K117R+K161R+K162R) of p53(More)
The computation of large phylogenetic trees with maximum likelihood is computationally intensive. In previous work we have introduced and implemented algorithmic optimizations in <b>PAxML.</b> The program shows run time improvements &gt; 25% over <b>parallel fastDNAml</b> yielding exactly the same results. This paper is focusing on computations of large(More)
We have investigated the distribution of newly synthesized lysosomal enzymes in endocytic compartments of normal rat kidney (NRK) cells. The mannose-6-phosphate (Man6-P) containing lysosomal enzymes could be iodinated in situ after internalization of lactoperoxidase (LPO) by fluid phase endocytosis and isolated on CI-MPR affinity columns. For EM studies,(More)
Inference of phylogenetic trees comprising hundreds or even thousands of organisms based on the maximum likelihood method is computationally extremely expensive. We present simple new heuristics which yield accurate trees for synthetic (simulated) as well as real data and significantly reduce execution time. The new heuristics have been implemented in a(More)
Leptin is required for normal energy and glucose homeostasis. The hypothalamic arcuate nucleus (ARH) has been proposed as an important site of leptin action. To assess the physiological significance of leptin signaling in the ARH, we used mice homozygous for a FLPe-reactivatable, leptin receptor null allele (Lepr(neo/neo) mice). Similar to Lepr(db/db) mice,(More)
The levels of H2A and H2B mRNAs as a function of cell-cycle stage were determined by hybridization methods. The analysis was extended to H3 and H4 mRNAs by in vitro translation. Cells were partitioned into cell-cycle stages either by centrifugal elutriation or by G1 synchronization with the yeast mating pheromone, alpha factor. The data lead to the(More)