ATM in focus:a damage sensor and cancer target

The ability of a cell to conserve and maintain its native DNA sequence is fundamental for the survival and normal functioning of the whole organism and protection from cancer development. Here we review recently obtained results and current topics concerning the role of the ataxia-telangiectasia mutated (ATM) protein kinase as a damage sensor and its potential as therapeutic target for treating cancer. This monograph discusses DNA repair mechanisms activated after DNA double-strand breaks (DSBs), i.e. non-homologous end joining, homologous recombination and single strand annealing and the role of ATM in the above types of repair. In addition to DNA repair, ATM participates in a diverse set of physiological processes involving metabolic regulation, oxidative stress, transcriptional modulation, protein degradation and cell proliferation. Full understanding of the complexity of ATM functions and the design of therapeutics that modulate its activity to combat diseases such as cancer necessitates parallel theoretical and experimental efforts. This could be best addressed by employing a systems biology approach, involving mathematical modelling of cell signalling pathways

Survey of congestion control techniques for an ATM network

The emerging broadband integrated services digital network is expected to adopt ATM (Asynchronous Transfer Mode) as the transport network. This new network must support several classes of service with varying delay and loss requirements. It must also operate with link speeds in the hundreds of megabits per second and be scalable up to potential link speeds on the order of gigabits per second. The requirements to support multiple services and high speed make the congestion control in an ATM network difficult. This paper reviews sorne of the techniques for prevention and control of congestion in an ATM network

Pressure and temperature dependence of growth and morphology of Escherichia coli: Experiments and Stochastic Model

We have investigated the growth of Escherichia coli E.coli, a mesophilic bacterium, as a function of pressure $P$ and temperature $T$. E.coli can grow and divide in a wide range of pressure (1-400atm) and temperature ($23-40^{\circ}$C). For $T>30^{\circ}$ C, the division time of E.coli increases exponentially with pressure and exhibit a departure from exponential behavior at pressures between 250-400 atm for all the temperatures studied in our experiments. For $T<30^{\circ}$ C, the division time shows an anomalous dependence on pressure -- first decreases with increasing pressure and then increases upon further increase of pressure. The sharp change in division time is followed by a sharp change in phenotypic transition of E. Coli at high pressures where bacterial cells switch to an elongating cell type. We propose a model that this phenotypic changes in bacteria at high pressures is an irreversible stochastic process whereas the switching probability to elongating cell type increases with increasing pressure. The model fits well the experimental data. We discuss our experimental results in the light of structural and thus functional changes in proteins and membranes.Comment: 28 pages, 12 figure

Modeling cancer genomic data in yeast reveals selection against ATM function during tumorigenesis

The DNA damage response (DDR) comprises multiple functions that collectively preserve genomic integrity and suppress tumorigenesis. The Mre11 complex and ATM govern a major axis of the DDR and several lines of evidence implicate that axis in tumor suppression. Components of the Mre11 complex are mutated in approximately five percent of human cancers. Inherited mutations of complex members cause severe chromosome instability syndromes, such as Nijmegen Breakage Syndrome, which is associated with strong predisposition to malignancy. And in mice, Mre11 complex mutations are markedly more susceptible to oncogene- induced carcinogenesis. The complex is integral to all modes of DNA double strand break (DSB) repair and is required for the activation of ATM to effect DNA damage signaling. To understand which functions of the Mre11 complex are important for tumor suppression, we undertook mining of cancer genomic data from the clinical sequencing program at Memorial Sloan Kettering Cancer Center, which includes the Mre11 complex among the 468 genes assessed. Twenty five mutations in MRE11 and RAD50 were modeled in S. cerevisiae and in vitro. The mutations were chosen based on recurrence and conservation between human and yeast. We found that a significant fraction of tumor-borne RAD50 and MRE11 mutations exhibited separation of function phenotypes wherein Tel1/ATM activation was severely impaired while DNA repair functions were mildly or not affected. At the molecular level, the gene products of RAD50 mutations exhibited defects in ATP binding and hydrolysis. The data reflect the importance of Rad50 ATPase activity for Tel1/ATM activation and suggest that inactivation of ATM signaling confers an advantage to burgeoning tumor cells

Exotic behavior and crystal structures of calcium under pressure

Experimental studies established that calcium undergoes several counterintuitive transitions under pressure: fcc \rightarrow bcc \rightarrow simple cubic \rightarrow Ca-IV \rightarrow Ca-V, and becomes a good superconductor in the simple cubic and higher-pressure phases. Here, using ab initio evolutionary simulations, we explore the behavior of Ca under pressure and find a number of new phases. Our structural sequence differs from the traditional picture for Ca, but is similar to that for Sr. The {\beta}-tin (I41/amd) structure, rather than simple cubic, is predicted to be the theoretical ground state at 0 K and 33-71 GPa. This structure can be represented as a large distortion of the simple cubic structure, just as the higher-pressure phases stable between 71 and 134 GPa. The structure of Ca-V, stable above 134 GPa, is a complex host-guest structure. According to our calculations, the predicted phases are superconductors with Tc increasing under pressure and reaching ~20 K at 120 GPa, in good agreement with experiment

Genomic stability in response to high versus low linear energy transfer radiation in Arabidopsis thaliana.

Low linear energy transfer (LET) gamma rays and high LET HZE (high atomic weight, high energy) particles act as powerful mutagens in both plants and animals. DNA damage generated by HZE particles is more densely clustered than that generated by gamma rays. To understand the genetic requirements for resistance to high versus low LET radiation, a series of Arabidopsis thaliana mutants were exposed to either 1GeV Fe nuclei or gamma radiation. A comparison of effects on the germination and subsequent growth of seedlings led us to conclude that the relative biological effectiveness (RBE) of the two types of radiation (HZE versus gamma) are roughly 3:1. Similarly, in wild-type lines, loss of somatic heterozygosity was induced at an RBE of about a 2:1 (HZE versus gamma). Checkpoint and repair defects, as expected, enhanced sensitivity to both agents. The "replication fork" checkpoint, governed by ATR, played a slightly more important role in resistance to HZE-induced mutagenesis than in resistance to gamma induced mutagenesis

hSSB1 interacts directly with the MRN complex stimulating its recruitment to DNA double-strand breaks and its endo-nuclease activity

hSSB1 is a recently discovered single-stranded DNA binding protein that is essential for efficient repair of DNA double-strand breaks (DSBs) by the homologous recombination pathway. hSSB1 is required for the efficient recruitment of the MRN complex to sites of DSBs and for the efficient initiation of ATM dependent signalling. Here we explore the interplay between hSSB1 and MRN. We demonstrate that hSSB1 binds directly to NBS1, a component of the MRN complex, in a DNA damage independent manner. Consistent with the direct interaction, we observe that hSSB1 greatly stimulates the endo-nuclease activity of the MRN complex, a process that requires the C-terminal tail of hSSB1. Interestingly, analysis of two point mutations in NBS1, associated with Nijmegen breakage syndrome, revealed weaker binding to hSSB1, suggesting a possible disease mechanism.Publisher PDFPeer reviewe

Electronic and photonic switching in the atm era

Broadband networks require high-capacity switches in order to properly manage large amounts of traffic fluxes. Electronic and photonic technologies are being used to achieve this objective both allowing different multiplexing and switching techniques. Focusing on the asynchronous transfer mode (ATM), the inherent different characteristics of electronics and photonics makes different architectures feasible. In this paper, different switching structures are described, several ATM switching architectures which have been recently implemented are presented and the implementation characteristics discussed. Three diverse points of view are given from the electronic research, the photonic research and the commercial switches. Although all the architectures where successfully tested, they should also follow different market requirements in order to be commercialised. The characteristics are presented and the architectures projected over them to evaluate their commercial capabilities.Peer ReviewedPostprint (published version

Infinitely Complex Machines

Infinite machines (IMs) can do supertasks. A supertask is an infinite series of operations done in some finite time. Whether or not our universe contains any IMs, they are worthy of study as upper bounds on finite machines. We introduce IMs and describe some of their physical and psychological aspects. An accelerating Turing machine (an ATM) is a Turing machine that performs every next operation twice as fast. It can carry out infinitely many operations in finite time. Many ATMs can be connected together to form networks of infinitely powerful agents. A network of ATMs can also be thought of as the control system for an infinitely complex robot. We describe a robot with a dense network of ATMs for its retinas, its brain, and its motor controllers. Such a robot can perform psychological supertasks - it can perceive infinitely detailed objects in all their detail; it can formulate infinite plans; it can make infinitely precise movements. An endless hierarchy of IMs might realize a deep notion of intelligent computing everywhere