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The notion that there might be a cellular basis for aging stems from research that began several decades ago and was proposed to explain the loss of proliferative homeostasis, which is a hallmark of complex animals. Recent years have seen growing support for the idea that two cell fates-apoptosis and cellular senescence, both now well-established tumor suppressor mechanisms-may be important drivers of aging phenotypes and age-related disease. However, there remain many unanswered questions, some quite basic, about how these processes change with age and how they might contribute to aging. It is now clear that failures in apoptosis or senescence can result in hyperproliferative diseases such as cancer. Less is known about whether and how increased apoptosis or senescence can cause tissue degeneration and aging. In addition, there is now a growing recognition that cellular senescence can have cell-nonautonomous effects within tissues. New molecular tools and model organisms, some already on the horizon, will need to be developed to better understand the roles of apoptosis and cellular senescence in age-associated changes in proliferative homeostasis. [ABSTRACT FROM AUTHOR]

We introduce Cryoscope, a method for sampling on-chip baseband pulses used to dynamically control qubit frequency in a quantum processor. We specifically use Cryoscope to measure the step response of the dedicated flux control lines of two-junction transmon qubits in circuit QED processors with the temporal resolution of the room-temperature arbitrary waveform generator producing the control pulses. As a first application, we iteratively improve this step response using optimized real-time digital filters to counter the linear-dynamical distortion in the control line, as needed for high-fidelity repeatable one- and two-qubit gates based on dynamical control of qubit frequency. [ABSTRACT FROM AUTHOR]

Nucleostemin (NS), a nucleolar GTPase, is highly expressed in stem/progenitor cells and in most cancer cells. However, little is known about the regulation of its expression. Here, we identify the NS gene as a novel direct transcriptional target of the c-Myc oncoprotein. We show that Myc overexpression enhances NS transcription in cultured cells and in pre-neoplastic B cells from Eμ-myc transgenic mice. Consistent with NS being downstream of Myc, NS expression parallels that of Myc in a large panel of human cancer cell lines. Using chromatin immunoprecipitation we show that c-Myc binds to a well-conserved E-box in the NS promoter. Critically, we show NS haploinsufficiency profoundly delays Myc-induced cancer formation in vivo. NS+/−Eμ-myc transgenic mice have much slower rates of B-cell lymphoma development, with life spans twice that of their wild-type littermates. Moreover, we demonstrate that NS is essential for the proliferation of Myc-overexpressing cells in cultured cells and in vivo: impaired lymphoma development was associated with a drastic decrease of c-Myc-induced proliferation of pre-tumoural B cells. Finally, we provide evidence that in cell culture NS controls cell proliferation independently of p53 and that NS haploinsufficiency significantly delays lymphomagenesis in p53-deficient mice. Together these data indicate that NS functions downstream of Myc as a rate-limiting regulator of cell proliferation and transformation, independently from its putative role within the p53 pathway. Targeting NS is therefore expected to compromise early tumour development irrespectively of the p53 status. [ABSTRACT FROM AUTHOR]

We address the problem of finding large-scale functional and structural relationships between genes, given a time series of gene expression data, namely mRNA concentration values measured from genetically engineered rat fibroblasts cell lines responding to conditional cMyc proto-oncogene activation. We show how it is possible to retrieve suitable information about molecular mechanisms governing the cell response to conditional perturbations. This task is complex because typical high-throughput genomics experiments are performed with high number of probesets (103–104 genes) and a limited number of observations (< 102 time points). In this paper, we develop a deepest analysis of our previous work [Remondini et al., 2005] in which we characterized some of the main features of a gene-gene interaction network reconstructed from temporal correlation of gene expression time series. One first advancement is based on the comparison of the reconstructed network with networks obtained from randomly generated data, in order to characterize which features retrieve real biological information, and which are instead due to the characteristics of the network reconstruction method. The second and perhaps more relevant advancement is the characterization of the global change in co-expression pattern following cMyc activation as compared to a basal unperturbed state. We propose an analogy with a physical system in a critical state close to a phase transition (e.g. Potts ferromagnet), since the cell responds to the stimulus with high susceptibility, such that a single gene activation propagates to almost the entire genome. Our result is relative to temporal properties of gene network dynamics, and there are experimental evidence that this can be related to spatial properties regarding the global organization of chromatine structure [Knoepfler et al., 2006]. [ABSTRACT FROM AUTHOR]

Mutations in mitochondrial DNA (mtDNA) accumulate in tissues ofmammalian species and have been hypothesized to contribute to aging. Weshow that mice expressing a proofreading-deficient version of themitochondrial DNA polymerase γ (POLG) accumulate mtDNA mutationsand display features of accelerated aging. Accumulation of mtDNAmutations was not associated with increased markers of oxidative stressor a defect in cellular proliferation, but was correlated with theinduction of apoptotic markers, particularly in tissues characterized byrapid cellular turnover. The levels of apoptotic markers were also foundto increase during aging in normal mice. Thus, accumulation of mtDNAmutations that promote apoptosis may be a central mechanism drivingmammalian aging. [ABSTRACT FROM AUTHOR]

This work studies the dynamics of a gene expression time series network. The network, which is obtained from the correlation of gene expressions, exhibits global dynamic properties that emerge after a cell state perturbation. The main features of this network appear to be more robust when compared with those obtained with a network obtained from a linear Markov model. In particular, the network properties strongly depend on the exact time sequence relationships between genes and are destroyed by random temporal data shuffling. We discuss in detail the problem of finding targets of the c-myc protooncogene, which encodes a transcriptional regulator whose inappropriate expression has been correlated with a wide array of malignancies. The data used for network construction are a time series of gene expression, collected by microarray analysis of a rat fibroblast cell line expressing a conditional Myc-estrogen receptor oncoprotein. We show that the correlation-based model can establish a clear relationship between network structure and the cascade of c-myc-activated genes. [ABSTRACT FROM AUTHOR]

Abstract: Premature aging of the skin is a prominent side-effect of psoralen photoactivation, a therapy used for different skin disorders. Recently, we demonstrated that treatment of fibroblasts with 8-methoxypsoralen and ultraviolet A irradiation resulted in growth arrest with morphological and functional changes reminiscent of replicative senescence. To further elucidate the underlying molecular mechanisms, we analysed the cell-cycle phases of the growth-arrested fibroblasts. After PUVA treatment, fibroblasts arrested in G2/M, in contrast to spontaneously senesced fibroblasts arresting in a cell-cycle phase with many features similar to G1. To address the role of the cell-cycle controlling genes p16[sup INK4a] , p21[sup CIP1] and p53, we analysed the expression of these genes. p16[sup INK4a] , p21[sup CIP1] and p53 protein levels increased substantially with different time kinetics in growth-arrested fibroblasts. Because p16[sup INK4a] , p21[sup CIP1] and p53 are involved in replicative senescence, we applied the PUVA regimen to fibroblasts deficient in either of these genes. p16[sup INK4a] , p21[sup CIP1] and p53 null mutant fibroblast strains underwent growth arrest with a senescent phenotype similar to wild-type human fibroblasts. Based on these results, we propose that redundant or alternate pathways are involved in the response of dermal fibroblasts to PUVA treatment resulting in a phenocopy of replicative senescence in vitro . [ABSTRACT FROM AUTHOR]

c-myc nullizygous fibroblasts (KO cells) were used to compare the abilities of c-myc, N-myc and L-myc oncoproteins to accelerate growth, promote apoptosis, revert morphology, and regulate the expression of previously described c-myc target genes. All three myc oncoproteins were expressed following retroviral transduction of KO cells. The proteins all enhanced the growth rate of KO cells and significantly shortened the cell cycle transition time. They also accelerated apoptosis following serum deprivation, reverted the abnormal KO cell morphology, and modulated the expression of previously described c-myc target genes. In most cases, Lmyc was equivalent to c-myc and N-myc in restoring all of the c-myc-dependent activities. These findings contrast with the previously reported weak transforming and transactivating properties of L-myc. Myc oncoproteins may thus impart both highly similar as well as dissimilar signals to the cells in which they are expressed. [ABSTRACT FROM AUTHOR]