Protein phosphatase 2A is required for the initiation of chromosomal DNA replication

Protein phosphatase 2A (PP2A) is an abundant, multifunctional serine/threonine-specific phosphatase that stimulates simian virus 40 DNA replication. The question as to whether chromosomal DNA replication also depends on PP2A was addressed by using a cell-free replication system derived from Xenopus laevis eggs. Immunodepletion of PP2A from Xenopus egg extract resulted in strong inhibition of DNA replication. PP2A was required for the initiation of replication but not for the elongation of previously engaged replication forks. Therefore, the initiation of chromosomal DNA replication depends not only on phosphorylation by protein kinases but also on dephosphorylation by PP2A.

The replication initiation protein of the broad-host-range plasmid RK2 is activated by the ClpX chaperone

Initiation and control of replication of the broad-host-range plasmid RK2 requires two plasmid-encoded elements, the replication origin (oriV) and the initiation protein TrfA. Purified TrfA is largely in the form of a dimer; however, only the monomeric form of the protein can bind specifically to the direct repeats (iterons) at the RK2 origin. The largely dimeric form of wild-type TrfA is inactive in the initiation of replication of RK2 in an in vitro replication system reconstituted from purified components. However, preincubation of the TrfA protein with the ClpX molecular chaperone isolated from Escherichia coli activates the initiator protein for replication in the purified system. We further observed that ClpX, in an ATP-dependent reaction, greatly increases the proportion of TrfA monomers and, therefore, the ability of this protein to bind to iterons localized within RK2 origin. Finally, a copy-up mutant of the TrfA protein which is largely in the monomer form is active in the reconstituted in vitro replication system, and its activity is not affected by ClpX.

DNA polymerase ɛ is required for coordinated and efficient chromosomal DNA replication in Xenopus egg extracts

DNA polymerase ɛ (Polɛ) is thought to be involved in DNA replication, repair, and cell-cycle checkpoint control in eukaryotic cells. Although the requirement of other replicative DNA polymerases, DNA polymerases α and δ (Polα and δ), for chromosomal DNA replication has been well documented by genetic and biochemical studies, the precise role, if any, of Polɛ in chromosomal DNA replication is still obscure. Here we show, with the use of a cell-free replication system with Xenopus egg extracts, that Xenopus Polɛ is indeed required for chromosomal DNA replication. In Polɛ-depleted extracts, the elongation step of chromosomal DNA replication is markedly impaired, resulting in significant reduction of the overall DNA synthesis as well as accumulation of small replication intermediates. Moreover, despite the decreased DNA synthesis, excess amounts of Polα are loaded onto the chromatin template in Polɛ-depleted extracts, indicative of the failure of proper assembly of DNA synthesis machinery at the fork. These findings strongly suggest that Polɛ, along with Polα and Polδ, is necessary for coordinated chromosomal DNA replication in eukaryotic cells.

A neural system for human visual working memory

Working memory is the process of actively maintaining a representation of information for a brief period of time so that it is available for use. In monkeys, visual working memory involves the concerted activity of a distributed neural system, including posterior areas in visual cortex and anterior areas in prefrontal cortex. Within visual cortex, ventral stream areas are selectively involved in object vision, whereas dorsal stream areas are selectively involved in spatial vision. This domain specificity appears to extend forward into prefrontal cortex, with ventrolateral areas involved mainly in working memory for objects and dorsolateral areas involved mainly in working memory for spatial locations. The organization of this distributed neural system for working memory in monkeys appears to be conserved in humans, though some differences between the two species exist. In humans, as compared with monkeys, areas specialized for object vision in the ventral stream have a more inferior location in temporal cortex, whereas areas specialized for spatial vision in the dorsal stream have a more superior location in parietal cortex. Displacement of both sets of visual areas away from the posterior perisylvian cortex may be related to the emergence of language over the course of brain evolution. Whereas areas specialized for object working memory in humans and monkeys are similarly located in ventrolateral prefrontal cortex, those specialized for spatial working memory occupy a more superior and posterior location within dorsal prefrontal cortex in humans than in monkeys. As in posterior cortex, this displacement in frontal cortex also may be related to the emergence of new areas to serve distinctively human cognitive abilities.

Modeling of Distributed Generation under Next Generation Interconnection Requirements

Thesis (Master's)--University of Washington, 2016-06

A structural method for the design of fault tolerant distributed control systems

Distributed digital control systems provide alternatives to conventional, centralised digital control systems. Typically, a modern distributed control system will comprise a multi-processor or network of processors, a communications network, an associated set of sensors and actuators, and the systems and applications software. This thesis addresses the problem of how to design robust decentralised control systems, such as those used to control event-driven, real-time processes in time-critical environments. Emphasis is placed on studying the dynamical behaviour of a system and identifying ways of partitioning the system so that it may be controlled in a distributed manner. A structural partitioning technique is adopted which makes use of natural physical sub-processes in the system, which are then mapped into the software processes to control the system. However, communications are required between the processes because of the disjoint nature of the distributed (i.e. partitioned) state of the physical system. The structural partitioning technique, and recent developments in the theory of potential controllability and observability of a system, are the basis for the design of controllers. In particular, the method is used to derive a decentralised estimate of the state vector for a continuous-time system. The work is also extended to derive a distributed estimate for a discrete-time system. Emphasis is also given to the role of communications in the distributed control of processes and to the partitioning technique necessary to design distributed and decentralised systems with resilient structures. A method is presented for the systematic identification of necessary communications for distributed control. It is also shwon that the structural partitions can be used directly in the design of software fault tolerant concurrent controllers. In particular, the structural partition can be used to identify the boundary of the conversation which can be used to protect a specific part of the system. In addition, for certain classes of system, the partitions can be used to identify processes which may be dynamically reconfigured in the event of a fault. These methods should be of use in the design of robust distributed systems.

The immune system as drug target

The immune system is perhaps the largest yet most diffuse and distributed somatic system in vertebrates. It plays vital roles in fighting infection and in the homeostatic control of chronic disease. As such, the immune system in both pathological and healthy states is a prime target for therapeutic interventions by drugs-both small-molecule and biologic. Comprising both the innate and adaptive immune systems, human immunity is awash with potential unexploited molecular targets. Key examples include the pattern recognition receptors of the innate immune system and the major histocompatibility complex of the adaptive immune system. Moreover, the immune system is also the source of many current and, hopefully, future drugs, of which the prime example is the monoclonal antibody, the most exciting and profitable type of present-day drug moiety. This brief review explores the identity and synergies of the hierarchy of drug targets represented by the human immune system, with particular emphasis on the emerging paradigm of systems pharmacology. © the authors, publisher and licensee Libertas Academica Limited.

Identification and Characterization of New Small Molecule Inhibitors of Picornavirus Replication

The Picornaviridae family consists of positive-strand RNA viruses that are the causative agents of a variety of diseases in humans and animals. Few drugs targeting picornaviruses are available, making the discovery of new antivirals a high priority. Here, we identified and characterized three compounds from a library of kinase inhibitors that block replication of poliovirus, coxsackievirus B3, and encephalomyocarditis virus. The antiviral effect of these compounds is not likely related to their known cellular targets because other inhibitors targeting the same pathways did not inhibit viral replication. Using an in vitro translation-replication system, we showed that these drugs inhibit different stages of the poliovirus life cycle. A4(1) inhibited the formation of a functional replication complex, while E5(1) and E7(2) affected replication after the replication complex had formed. A4(1) demonstrated partial protection from paralysis in a murine model of poliomyelitis. Poliovirus resistant to E7(2) had a single mutation in the 3A protein. This mutation was previously found to confer resistance to enviroxime-like compounds, which target either PI4KIIIβ (major enviroxime-like compounds) or OSBP (minor enviroxime-like compounds), cellular factors involved in lipid metabolism and shown to be important for replication of diverse positive-strand RNA viruses. We classified E7(2) as a minor enviroxime-like compound, because the localization of OSBP changed in the presence of this inhibitor. Interestingly, both E7(2) and major enviroxime-like compound GW5074 interfered with the viral polyprotein processing. Multiple attempts to isolate resistant mutants in the presence of A4(1) or E5(1) were unsuccessful, showing that effective broad-spectrum antivirals could be developed on the basis of these compounds. Studies with these compounds shed light on pathways shared by diverse picornaviruses that could be potential targets for the development of broad-spectrum antiviral drugs.

Solution to reduce nonlinearity in LTE RoF system for an efficient das topology:a brief review

In this paper, a review on radio-over-fiber (RoF) technology is conducted to support the exploding growth of mobile broadband. An RoF system will provide a platform for distributed antenna system (DAS) as a fronthaul of long term evolution (LTE) technology. A higher splitting ratio from a macrocell is required to support large DAS topology, hence higher optical launch power (OLP) is the right approach. However, high OLP generates undesired nonlinearities, namely the stimulated Brillouin scattering (SBS). Three different aspects of solving the SBS process are covered in this paper, where the solutions ultimately provided an additional 4 dB link budget.

Controlo de um gerador hidroeléctrico utilizado na recuperação de energia numa conduta de abastecimento de água

O presente trabalho pretende contribuir para a melhoria da eficiência dos sistemas de transporte e distribuição de água, possível de conseguir através da recuperação de energia potencial que, em certas situações, existe em excesso em condutas gravíticas. Sendo uma questão já abordada em diversos estudos, as poupanças de energia a que poderá conduzir, justificam a análise de todas as oportunidades, em especial no nosso País, cuja dependência energética do exterior é bem conhecida. Todavia, a implementação de soluções que recorrem à instalação de turbinas em condutas de abastecimento de água, causam naturalmente alguma apreensão às respectivas entidades gestoras, uma vez que pode pôr em causa a integridade das condutas e, em consequência, o abastecimento de água. Neste contexto, o estudo de modelos de controlo específicos para os referidos equipamentos poderá ser um contributo para a implementação mais alargada das soluções de melhoria da eficiência de sistemas de abastecimento de água, através da instalação de geradores hidroeléctricos, que terão a dupla função de controlo de caudal e produção de energia. O estudo e simulação dos modelos de controlo contidos neste trabalho permite concluir que é possível garantir a segurança das condutas e produzir energia eléctrica com turbinas nelas instaladas. Interessa assim aprofundar este tipo de estudos de forma a conseguir modelos de controlo que, com as premissas indicadas, possibilitem a optimização da produção de energia.

Meta-heuristics self-configuration for scheduling

Scheduling resolution requires the intervention of highly skilled human problemsolvers. This is a very hard and challenging domain because current systems are becoming more and more complex, distributed, interconnected and subject to rapidly changing. A natural Autonomic Computing evolution in relation to Current Computing is to provide systems with Self-Managing ability with a minimum human interference. This paper addresses the resolution of complex scheduling problems using cooperative negotiation. A Multi-Agent Autonomic and Meta-heuristics based framework with self-configuring capabilities is proposed.

Disseminating data using broadcast when topology is unknown

Consider the problem of disseminating data from an arbitrary source node to all other nodes in a distributed computer system, like Wireless Sensor Networks (WSNs). We assume that wireless broadcast is used and nodes do not know the topology. We propose new protocols which disseminate data faster and use fewer broadcasts than the simple broadcast protocol.

Uma arquitectura para a monitorização de computações paralelas e distribuídas

O recurso à monitorização do comportamento dos programas durante a execução é necessário em diversos contextos de aplicação. Por exemplo, para verificar a utilização dos recursos computacionais durante a execução, para calcular métricas que permitam melhor definir o perfil da aplicação ou para melhor identificar em que pontos da execução estão as causas de desvios do comportamento desejado de um programa e, noutros casos, para controlar a configuração da aplicação ou do sistema que suporta a sua execução. Esta técnica tem sido aplicada, quer no caso de programas sequenciais, quer se trate de programas distribuídos. Em particular, no caso de computações paralelas, dada a complexidade devida ao seu não determinismo, estas técnicas têm sido a melhor fonte de informação para compreender a execução da aplicação, quer em termos da sua correcção, quer na avaliação do seu desempenho e utilização dos recursos computacionais. As principais dificuldades no desenvolvimento e na adopção de ferramentas de monitorização, prendem-se com a complexidade dos sistemas de computação paralela e distribuída e com a necessidade de desenvolver soluções específicas para cada plataforma, para cada arquitectura e para cada objectivo. No entanto existem funcionalidades genéricas que, se presentes em todos os casos, podem ajudar ao desenvolvimento de novas ferramentas e à sua adaptação a diferentes ambientes computacionais. Esta dissertação propõe um modelo para suportar a observação e o controlo de aplicações paralelas e distribuídas (DAMS - Distributed ApplicationsMonitoring System). O modelo define uma arquitectura abstracta de monitorização baseada num núcleo mínimo sobre o qual assentam conjuntos de serviços que realizam as funcionalidades pretendidas em cada cenário de utilização. A sua organização em camadas de abstracção e a capacidade de extensão modular, permitem suportar o desenvolvimento de conjuntos de funcionalidades que podem ser partilhadas por distintas ferramentas. Por outro lado, o modelo proposto facilita o desenvolvimento de ferramentas de observação e controlo, sobre diferentes plataformas de suporte à execução. Nesta dissertação, são apresentados exemplos da utilização do modelo e da infraestrutura que o suporta, em diversos cenários de observação e controlo. Descreve-se também a experimentação realizada, com base em protótipos desenvolvidos sobre duas plataformas computacionais distintas.

The utilization bound of non-preemptive rate-monotonic scheduling in controller area networks is 25%

Consider a distributed computer system comprising many computer nodes, each interconnected with a controller area network (CAN) bus. We prove that if priorities to message streams are assigned using rate-monotonic (RM) and if the requested capacity of the CAN bus does not exceed 25% then all deadlines are met.

Using a prioritized MAC protocol to efficiently compute aggregated quantities

Consider a distributed computer system such that every computer node can perform a wireless broadcast and when it does so, all other nodes receive this message. The computer nodes take sensor readings but individual sensor readings are not very important. It is important however to compute the aggregated quantities of these sensor readings. We show that a prioritized medium access control (MAC) protocol for wireless broadcast can compute simple aggregated quantities in a single transaction, and more complex quantities with many (but still a small number of) transactions. This leads to significant improvements in the time-complexity and as a consequence also similar reduction in energy “consumption”.