Explicit Codes Uniformly Reducing Repair Bandwidth in Distributed Storage

A distributed storage setting is considered where a file of size B is to be stored across n storage nodes. A data collector should be able to reconstruct the entire data by downloading the symbols stored in any k nodes. When a node fails, it is replaced by a new node by downloading data from some of the existing nodes. The amount of download is termed as repair bandwidth. One way to implement such a system is to store one fragment of an (n, k) MDS code in each node, in which case the repair bandwidth is B. Since repair of a failed node consumes network bandwidth, codes reducing repair bandwidth are of great interest. Most of the recent work in this area focuses on reducing the repair bandwidth of a set of k nodes which store the data in uncoded form, while the reduction in the repair bandwidth of the remaining nodes is only marginal. In this paper, we present an explicit code which reduces the repair bandwidth for all the nodes to approximately B/2. To the best of our knowledge, this is the first explicit code which reduces the repair bandwidth of all the nodes for all feasible values of the system parameters.

Base excision and nucleotide excision repair pathways in mycobacteria

About a third of the human population is estimated to be infected with Mycobacterium tuberculosis. The bacterium displays an excellent adaptability to survive within the host macrophages. As the reactive environment of macrophages is capable of inducing DNA damage, the ability of the pathogen to safeguard its DNA against the damage is of paramount significance for its survival within the host. Analysis of the genome sequence has provided important insights into the DNA repair machinery of the pathogen, and the studies on DNA repair in mycobacteria have gained momentum in the past few years. The studies have revealed considerable differences in the mycobacterial DNA repair machinery when compared with those of the other bacteria. This review article focuses especially on the aspects of base excision, and nucleotide excision repair pathways in mycobacteria. (C) 2011 Elsevier Ltd. All rights reserved.

Distinct Roles of FANCO/RAD51C Protein in DNA Damage Signaling and Repair Implications for Fanconi Anemia and Breast Cancer Susceptibility

RAD51C, a RAD51 paralog, has been implicated in homologous recombination (HR), and germ line mutations in RAD51C are known to cause Fanconi anemia (FA)-like disorder and breast and ovarian cancers. The role of RAD51C in the FA pathway of DNA interstrand cross-link (ICL) repair and as a tumor suppressor is obscure. Here, we report that RAD51C deficiency leads to ICL sensitivity, chromatid-type errors, and G(2)/M accumulation, which are hallmarks of the FA phenotype. We find that RAD51C is dispensable for ICL unhooking and FANCD2 monoubiquitination but is essential for HR, confirming the downstream role of RAD51C in ICL repair. Furthermore, we demonstrate that RAD51C plays a vital role in the HR-mediated repair of DNA lesions associated with replication. Finally, we show that RAD51C participates in ICL and double strand break-induced DNA damage signaling and controls intra-S-phase checkpoint through CHK2 activation. Our analyses with pathological mutants of RAD51C that were identified in FA and breast and ovarian cancers reveal that RAD51C regulates HR and DNA damage signaling distinctly. Together, these results unravel the critical role of RAD51C in the FA pathway of ICL repair and as a tumor suppressor.

3D finite element modelling of a composite patch repair

Composite-patching on cracked/weak metallic aircraft structures improves structural integrity. A Boron Epoxy patch employed to repair a cracked Aluminum sheet is modeled employing 3D Finite Element Method (FEM). SIFs extracted using ''displacement extrapolation'' are used to measure the repair effectiveness. Two issues viz., patch taper and symmetry have been looked into.

Distributed Storage Codes With Repair-by-Transfer and Nonachievability of Interior Points on the Storage-Bandwidth Tradeoff

Regenerating codes are a class of recently developed codes for distributed storage that, like Reed-Solomon codes, permit data recovery from any subset of k nodes within the n-node network. However, regenerating codes possess in addition, the ability to repair a failed node by connecting to an arbitrary subset of d nodes. It has been shown that for the case of functional repair, there is a tradeoff between the amount of data stored per node and the bandwidth required to repair a failed node. A special case of functional repair is exact repair where the replacement node is required to store data identical to that in the failed node. Exact repair is of interest as it greatly simplifies system implementation. The first result of this paper is an explicit, exact-repair code for the point on the storage-bandwidth tradeoff corresponding to the minimum possible repair bandwidth, for the case when d = n-1. This code has a particularly simple graphical description, and most interestingly has the ability to carry out exact repair without any need to perform arithmetic operations. We term this ability of the code to perform repair through mere transfer of data as repair by transfer. The second result of this paper shows that the interior points on the storage-bandwidth tradeoff cannot be achieved under exact repair, thus pointing to the existence of a separate tradeoff under exact repair. Specifically, we identify a set of scenarios which we term as ``helper node pooling,'' and show that it is the necessity to satisfy such scenarios that overconstrains the system.

Sesbania Mosaic Virus (SeMV) Infectious Clone: Possible Mechanism of 3 ` and 5 ` End Repair and Role of Polyprotein Processing in Viral Replication

Sesbania mosaic virus (SeMV) is a positive stranded RNA virus belonging to the genus Sobemovirus. Construction of an infectious clone is an essential step for deciphering the virus gene functions in vivo. Using Agrobacterium based transient expression system we show that SeMV icDNA is infectious on Sesbania grandiflora and Cyamopsis tetragonoloba plants. The efficiency of icDNA infection was found to be significantly high on Cyamopsis plants when compared to that on Sesbania grandiflora. The coat protein could be detected within 6 days post infiltration in the infiltrated leaves. Different species of viral RNA (double stranded and single stranded genomic and subgenomic RNA) could be detected upon northern analysis, suggesting that complete replication had taken place. Based on the analysis of the sequences at the genomic termini of progeny RNA from SeMV icDNA infiltrated leaves and those of its 3' and 5' terminal deletion mutants, we propose a possible mechanism for 3' and 5' end repair in vivo. Mutation of the cleavage sites in the polyproteins encoded by ORF 2 resulted in complete loss of infection by the icDNA, suggesting the importance of correct polyprotein processing at all the four cleavage sites for viral replication. Complementation analysis suggested that ORF 2 gene products can act in trans. However, the trans acting ability of ORF 2 gene products was abolished upon deletion of the N-terminal hydrophobic domain of polyprotein 2a and 2ab, suggesting that these products necessarily function at the replication site, where they are anchored to membranes.

Self Repair in Circuits-Automating Open Fault Repair in Integrated Circuits Using Field-Induced Aggregation of Carbon Nanotubes

This paper presents studies on the use of carbon nanotubes dispersed in an insulating fluid to serve as an automaton for healing open-circuit interconnect faults in integrated circuits. The physics behind the repair mechanism is the electric-field-induced diffusion limited aggregation. On the occurrence of an open fault, the repair is automatically triggered due to the presence of an electric field across the gap. We perform studies on the repair time as a function of the electric field and dispersion concentrations with the above application in mind.

Distinct mechanisms of DNA repair in mycobacteria and their implications in attenuation of the pathogen growth

About a third of the human population is estimated to be infected with Mycobacterium tuberculosis. Emergence of drug resistant strains and the protracted treatment strategies have compelled the scientific community to identify newer drug targets, and to develop newer vaccines. In the host macrophages, the bacterium survives within an environment rich in reactive nitrogen and oxygen species capable of damaging its genome. Therefore, for its successful persistence in the host, the pathogen must need robust DNA repair mechanisms. Analysis of M. tuberculosis genome sequence revealed that it lacks mismatch repair pathway suggesting a greater role for other DNA repair pathways such as the nucleotide excision repair, and base excision repair pathways. In this article, we summarize the outcome of research involving these two repair pathways in mycobacteria focusing primarily on our own efforts. Our findings, using Mycobacterium smegmatis model, suggest that deficiency of various DNA repair functions in single or in combinations severely compromises their DNA repair capacity and attenuates their growth under conditions typically encountered in macrophages. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

An Inhibitor of Nonhomologous End-Joining Abrogates Double-Strand Break Repair and Impedes Cancer Progression

DNA Ligase IV is responsible for sealing of double-strand breaks (DSBs) during nonhomologous end-joining (NHEJ). Inhibiting Ligase IV could result in amassing of DSBs, thereby serving as a strategy toward treatment of cancer. Here, we identify a molecule, SCR7 that inhibits joining of DSBs in cell-free repair system. SCR7 blocks Ligase IV-mediated joining by interfering with its DNA binding but not that of T4 DNA Ligase or Ligase I. SCR7 inhibits NHEJ in a Ligase IV-dependent manner within cells, and activates the intrinsic apoptotic pathway. More importantly, SCR7 impedes tumor progression in mouse models and when coadministered with DSB-inducing therapeutic modalities enhances their sensitivity significantly. This inhibitor to target NHEJ offers a strategy toward the treatment of cancer and improvement of existing regimens.

Enabling node repair in any erasure code for distributed storage

Erasure codes are an efficient means of storing data across a network in comparison to data replication, as they tend to reduce the amount of data stored in the network and offer increased resilience in the presence of node failures. The codes perform poorly though, when repair of a failed node is called for, as they typically require the entire file to be downloaded to repair a failed node. A new class of erasure codes, termed as regenerating codes were recently introduced, that do much better in this respect. However, given the variety of efficient erasure codes available in the literature, there is considerable interest in the construction of coding schemes that would enable traditional erasure codes to be used, while retaining the feature that only a fraction of the data need be downloaded for node repair. In this paper, we present a simple, yet powerful, framework that does precisely this. Under this framework, the nodes are partitioned into two types and encoded using two codes in a manner that reduces the problem of node-repair to that of erasure-decoding of the constituent codes. Depending upon the choice of the two codes, the framework can be used to avail one or more of the following advantages: simultaneous minimization of storage space and repair-bandwidth, low complexity of operation, fewer disk reads at helper nodes during repair, and error detection and correction.

Enabling node repair in any erasure code for distributed storage

Erasure codes are an efficient means of storing data across a network in comparison to data replication, as they tend to reduce the amount of data stored in the network and offer increased resilience in the presence of node failures. The codes perform poorly though, when repair of a failed node is called for, as they typically require the entire file to be downloaded to repair a failed node. A new class of erasure codes, termed as regenerating codes were recently introduced, that do much better in this respect. However, given the variety of efficient erasure codes available in the literature, there is considerable interest in the construction of coding schemes that would enable traditional erasure codes to be used, while retaining the feature that only a fraction of the data need be downloaded for node repair. In this paper, we present a simple, yet powerful, framework that does precisely this. Under this framework, the nodes are partitioned into two types and encoded using two codes in a manner that reduces the problem of node-repair to that of erasure-decoding of the constituent codes. Depending upon the choice of the two codes, the framework can be used to avail one or more of the following advantages: simultaneous minimization of storage space and repair-bandwidth, low complexity of operation, fewer disk reads at helper nodes during repair, and error detection and correction.

ATM- and ATR-mediated phosphorylation of XRCC3 regulates DNA double-strand break-induced checkpoint activation and repair

The RAD51 paralogs XRCC3 and RAD51C have been implicated in homologous recombination (HR) and DNA damage responses. However, the molecular mechanism(s) by which these paralogs regulate HR and DNA damage signaling remains obscure. Here, we show that an SQ motif serine 225 in XRCC3 is phosphorylated by ATR kinase in an ATM signaling pathway. We find that RAD51C but not XRCC2 is essential for XRCC3 phosphorylation, and this modification follows end resection and is specific to S and G(2) phases. XRCC3 phosphorylation is required for chromatin loading of RAD51 and HR-mediated repair of double-strand breaks (DSBs). Notably, in response to DSBs, XRCC3 participates in the intra-S-phase checkpoint following its phosphorylation and in the G(2)/M checkpoint independently of its phosphorylation. Strikingly, we find that XRCC3 distinctly regulates recovery of stalled and collapsed replication forks such that phosphorylation is required for the HR-mediated recovery of collapsed replication forks but is dispensable for the restart of stalled replication forks. Together, these findings suggest that XRCC3 is a new player in the ATM/ATR-induced DNA damage responses to control checkpoint and HR-mediated repair.

Evidence for the role of Mycobacteriumtuberculosis RecG helicase in DNA repair and recombination

In order to survive and replicate in a variety of stressful conditions during its life cycle, Mycobacteriumtuberculosis must possess mechanisms to safeguard the integrity of the genome. Although DNA repair and recombination related genes are thought to play key roles in the repair of damaged DNA in all organisms, so far only a few of them have been functionally characterized in the tubercle bacillus. In this study, we show that M.tuberculosis RecG (MtRecG) expression was induced in response to different genotoxic agents. Strikingly, expression of MtRecG in Escherichiacoli recG mutant strain provided protection against mitomycin C, methyl methane sulfonate and UV induced cell death. Purified MtRecG exhibited higher binding affinity for the Holliday junction (HJ) compared with a number of canonical recombinational DNA repair intermediates. Notably, although MtRecG binds at the core of the mobile and immobile HJs, and with higher binding affinity for the immobile HJ, branch migration was evident only in the case of the mobile HJ. Furthermore, immobile HJs stimulate MtRecG ATPase activity less efficiently than mobile HJs. In addition to HJ substrates, MtRecG exhibited binding affinity for a variety of branched DNA structures including three-way junctions, replication forks, flap structures, forked duplex and a D-loop structure, but demonstrated strong unwinding activity on replication fork and flap DNA structures. Together, these results support that MtRecG plays an important role in processes related to DNA metabolism under normal as well as stress conditions.