Mechanism of coliphage M13 contraction: intermediate structures trapped at low temperatures.

The filamentous coliphage M13 can be transformed into a spherical particle (termed spheroid) by exposure to an interface of water and slightly polar but hydrophobic solvent such as chloroform-water at 24 degrees C. We report here that exposure of M13 filaments to a chloroform-water interface at 2 degrees C trapped the phage particles in forms morphologically intermediate to filaments and spheroids. These structures were rods 250 nm long and 15 nm wide, and each had a closed, slightly pointed end, an open flaired end, and a hollow central channel. The final contraction of these intermediates (termed I-forms) into spheroids was dependent upon both temperature and the presence of the solvent-water interface but was apparently independent of both the minor phage coat proteins and the virion DNA. Although stable in an aqueous environment, I-forms, in contrast to filaments, were readily disrupted by detergents, suggesting that the phage structure had been altered to a form more easily solubilized by membrane lipids. These solvent-induced changes might be related to the initial steps of phage penetration in vivo

Hardware-conscious Query Processing in GPU-accelerated Analytical Engines

In order to improve their power efficiency and computational capacity, modern servers are adopting hardware accelerators, especially GPUs. Modern analytical DMBS engines have been highly optimized for multi-core multi-CPU query execution, but lack the necessary abstractions to support concurrent hardware-conscious query execution over multiple heterogeneous devices and, thus, are unable to take full advantage of the available accelerators. In this work, we present a Heterogeneity-conscious Analytical query Processing Engine (HAPE), a hardware-conscious analytical engines that targets efficient concurrent multi-CPU multi-GPU query execution. HAPE decomposes heterogeneous query execution into i) efficient single-device and ii) concurrent multi-device query execution. It uses hardware-conscious algorithms designed for single-device execution and combines them into efficient intra-device hardware-conscious execution modules, via code generation. HAPE combines these modules to achieve concurrent multi-device execution by handling data and control transfers. We validate our design by building a prototype and evaluate its performance on a co-processing radix-join and TPC-H queries. We show that it achieves up to 10x and 3.5x speed-up on the join against CPU and GPU alternatives and 1.6x-8x against state-of-the-art CPU- and GPU-based commercial DBMS on the queries

HetExchange: Encapsulating heterogeneous CPU-GPU parallelism in JIT compiled engines

Modern server hardware is increasingly heterogeneous as hardware accelerators, such as GPUs, are used together with multicore CPUs to meet the computational demands of modern data analytics workloads. Unfortunately, query parallelization techniques used by analytical database engines are designed for homogeneous multicore servers, where query plans are parallelized across CPUs to process data stored in cache coherent shared memory. Thus, these techniques are unable to fully exploit available heterogeneous hardware, where one needs to exploit task-parallelism of CPUs and data-parallelism of GPUs for processing data stored in a deep, non-cache-coherent memory hierarchy with widely varying access latencies and bandwidth. In this paper, we introduce HetExchange–a parallel query execution framework that encapsulates the heterogeneous parallelism of modern multi-CPU–multi-GPU servers and enables the parallelization of (pre-)existing sequential relational operators. In contrast to the interpreted nature of traditional Exchange, HetExchange is designed to be used in conjunction with JIT compiled engines in order to allow a tight integration with the proposed operators and generation of efficient code for heterogeneous hardware. We validate the applicability and efficiency of our design by building a prototype that can operate over both CPUs and GPUs, and enables its operators to be parallelism- and data-location-agnostic. In doing so, we show that efficiently exploiting CPU–GPU parallelism can provide 2.8x and 6.4x improvement in performance compared to state-of-the-art CPU-based and GPU-based DBMS

Hardware-conscious Hash-Joins on GPUs

Traditionally, analytical database engines have used task parallelism provided by modern multisocket multicore CPUs for scaling query execution. Over the past few years, GPUs have started gaining traction as accelerators for processing analytical queries due to their massively data-parallel nature and high memory bandwidth. Recent work on designing join algorithms for CPUs has shown that carefully tuned join implementations that exploit underlying hardware can outperform naive, hardware-oblivious counterparts and provide excellent performance on modern multicore servers. However, there has been no such systematic analysis of hardware-conscious join algorithms for GPUs that systematically explores the dimensions of partitioning (partitioned versus non-partitioned joins), data location (data fitting and not fitting in GPU device memory), and access pattern (skewed versus uniform). In this paper, we present the design and implementation of a family of novel, partitioning-based GPU-join algorithms that are tuned to exploit various GPU hardware characteristics for working around the two main limitations of GPUs–limited memory capacity and slow PCIe interface. Using a thorough evaluation, we show that: i) hardware-consciousness plays a key role in GPU joins similar to CPU joins and our join algorithms can process 1 Billion tuples/second even if no data is GPU resident, ii) radix partitioning-based GPU joins that are tuned to exploit GPU hardware can substantially outperform non-partitioned hash joins, iii) hardware-conscious GPU joins can effectively overcome GPU limitations and match, or even outperform, state-of-the-art CPU joins

Serendipity

Author Posting. © American Society for Biochemistry and Molecular Biology, 2009. This article is posted here by permission of American Society for Biochemistry and Molecular Biology for personal use, not for redistribution. The definitive version was published in Journal of Biological Chemistry 284 (2009): 10285-10290, doi:10.1074/jbc.X800013200.As I look back, I realize that serendipity has played a major role in my life. I grew up in Santiago, Chile. As far back as I can remember I was interested in plants and animals, enjoying my Aunt Olga's farm, where I could observe the reproduction of rabbits and crossed plants of different colors. When I was a teenager a devastating earthquake in the South killed an aunt and two infant cousins who happened to be at the epicenter just for one night. That unfair tragedy convinced me that life had been created by natural forces, and the way to prove it was by synthesizing a living cell in vitro

Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways

Escherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologies remain speculative. Here, we used single-molecule force and fluorescence spectroscopy to investigate E. coli SSB binding to ssDNA. Stretching a single ssDNA-SSB complex reveals discrete states that correlate with known binding modes, the likely ssDNA conformations and diffusion dynamics in each, and the kinetic pathways by which the protein wraps ssDNA and is dissociated. The data allow us to construct an energy landscape for the ssDNA-SSB complex, revealing that unwrapping energy costs increase the more ssDNA is unraveled. Our findings provide insights into the mechanism by which proteins gain access to ssDNA bound by SSB, as demonstrated by experiments in which SSB is displaced by the E. coli recombinase RecA. DOI: http://dx.doi.org/10.7554/eLife.08193.00

The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins

The regions of single-stranded (ss) DNA that result from DNA damage are immediately coated by the ssDNA-binding protein (SSB). RecF pathway proteins facilitate the displacement of SSB from ssDNA, allowing the RecA protein to form protein filaments on the ssDNA region, which facilitates the process of recombinational DNA repair. In this study, we examined the mechanism of SSB displacement from ssDNA using purified Thermus thermophilus RecF pathway proteins. To date, RecO and RecR are thought to act as the RecOR complex. However, our results indicate that RecO and RecR have distinct functions. We found that RecR binds both RecF and RecO, and that RecO binds RecR, SSB and ssDNA. The electron microscopic studies indicated that SSB is displaced from ssDNA by RecO. In addition, pull-down assays indicated that the displaced SSB still remains indirectly attached to ssDNA through its interaction with RecO in the RecO-ssDNA complex. In the presence of both SSB and RecO, the ssDNA-dependent ATPase activity of RecA was inhibited, but was restored by the addition of RecR. Interestingly, the interaction of RecR with RecO affected the ssDNA-binding properties of RecO. These results suggest a model of SSB displacement from the ssDNA by RecF pathway proteins

Characterization of the Single Stranded DNA Binding Protein SsbB Encoded in the Gonoccocal Genetic Island

Background: Most strains of Neisseria gonorrhoeae carry a Gonococcal Genetic Island which encodes a type IV secretion system involved in the secretion of ssDNA. We characterize the GGI-encoded ssDNA binding protein, SsbB. Close homologs of SsbB are located within a conserved genetic cluster found in genetic islands of different proteobacteria. This cluster encodes DNA-processing enzymes such as the ParA and ParB partitioning proteins, the TopB topoisomerase, and four conserved hypothetical proteins. The SsbB homologs found in these clusters form a family separated from other ssDNA binding proteins. Methodology/Principal Findings: In contrast to most other SSBs, SsbB did not complement the Escherichia coli ssb deletion mutant. Purified SsbB forms a stable tetramer. Electrophoretic mobility shift assays and fluorescence titration assays, as well as atomic force microscopy demonstrate that SsbB binds ssDNA specifically with high affinity. SsbB binds single-stranded DNA with minimal binding frames for one or two SsbB tetramers of 15 and 70 nucleotides. The binding mode was independent of increasing Mg 2+ or NaCl concentrations. No role of SsbB in ssDNA secretion or DNA uptake could be identified, but SsbB strongly stimulated Topoisomerase I activity

Physical and functional interactions between human mitochondrial single-stranded DNA-binding protein and tumour suppressor p53

Single-stranded DNA-binding proteins (SSB) form a class of proteins that bind preferentially single-stranded DNA with high affinity. They are involved in DNA metabolism in all organisms and serve a vital role in replication, recombination and repair of DNA. In this report, we identify human mitochondrial SSB (HmtSSB) as a novel protein-binding partner of tumour suppressor p53, in mitochondria. It binds to the transactivation domain (residues 1–61) of p53 via an extended binding interface, with dissociation constant of 12.7 (± 0.7) μM. Unlike most binding partners reported to date, HmtSSB interacts with both TAD1 (residues 1–40) and TAD2 (residues 41–61) subdomains of p53. HmtSSB enhances intrinsic 3′-5′ exonuclease activity of p53, particularly in hydrolysing 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) present at 3′-end of DNA. Taken together, our data suggest that p53 is involved in DNA repair within mitochondria during oxidative stress. In addition, we characterize HmtSSB binding to ssDNA and p53 N-terminal domain using various biophysical measurements and we propose binding models for both

Epidermal growth factor regulates Mcl-1 expression through the MAPK-Elk-1 signalling pathway contributing to cell survival in breast cancer

Myeloid cell leukaemia-1 (Mcl-1) is an anti-apoptotic member of the Bcl-2 family that is elevated in a variety of tumour types including breast cancer. In breast tumours, increased Mcl-1 expression correlates with high tumour grade and poor patient survival. We have previously demonstrated that Her-2 levels correspond to increased Mcl-1 expression in breast tumours. Epidermal growth factor (EGF) receptor signalling is frequently deregulated in breast cancer and leads to increased proliferation and survival. Herein, we determined the critical downstream signals responsible for the EGF mediated increase of Mcl-1 and their role in cell survival. We found that both Mcl-1 mRNA and protein levels are rapidly induced upon stimulation with EGF. Promoter analysis revealed that an Elk-1 transcription factor-binding site is critical for EGF activation of the Mcl-1 promoter. Furthermore, we found that knockdown of Elk-1or inhibition of the Erk signalling pathway was sufficient to block EGF upregulation of Mcl-1 and EGF mediated cell survival. Using chromatin immunoprecipitation and biotin labelled probes of the Mcl-1 promoter, we found that Elk-1 and serum response factor are bound to the promoter after EGF stimulation. To determine whether Mcl-1 confers a survival advantage, we found that knockdown of Mcl-1 expression increased apoptosis whereas overexpression of Mcl-1 inhibited drug induced cell death. In human breast tumours, we found a correlation between phosphorylated Elk-1 and Mcl-1 protein levels. These results indicate that the EGF induced activation of Elk-1 is an important mediator of Mcl-1 expression and cell survival and therefore a potential therapeutic target in breast cancer