Trends in life science grid: from computing grid to knowledge grid

BACKGROUND: Grid computing has great potential to become a standard cyberinfrastructure for life sciences which often require high-performance computing and large data handling which exceeds the computing capacity of a single institution. RESULTS: This survey reviews the latest grid technologies from the viewpoints of computing grid, data grid and knowledge grid. Computing grid technologies have been matured enough to solve high-throughput real-world life scientific problems. Data grid technologies are strong candidates for realizing "resourceome" for bioinformatics. Knowledge grids should be designed not only from sharing explicit knowledge on computers but also from community formulation for sharing tacit knowledge among a community. CONCLUSION: Extending the concept of grid from computing grid to knowledge grid, it is possible to make use of a grid as not only sharable computing resources, but also as time and place in which people work together, create knowledge, and share knowledge and experiences in a community

Road to extinction: Archival samples unveiled the process of inbreeding depression during artificial breeding in an almost extinct butterfly species

国内で最も絶滅リスクの高いチョウ、オガサワラシジミの繁殖途絶の原因を解明 --近親交配による遺伝的多様性の減少が、繁殖の失敗につながっていた-- .京都大学プレスリリース. 2024-07-12.During ex-situ conservation of endangered species, reproductive disruption risk due to inbreeding depression increases when genetic diversity is reduced due to founder effects or population declines. Elucidating the population genetic process of reproductive disruption will help understand the risks and mechanisms associated with inbreeding depression. A comprehensive understanding of these processes would require a comparison of reproductive traits and genetic diversity in the populations of endangered species that have experienced reproductive disruption. However, such previous studies, which focus on endangered species, are limited. Ex-situ conservation was initiated for the Ogasawara Holly Blue (Celastrina ogasawaraensis) (Lepidoptera, Lycaenidae), endemic to the Ogasawara Islands, Japan, in 2016 using two mated females as founders. The wild populations might have already been extinct since 2020. All the ex-situ conserved populations were also disrupted in their 20th generation in 2020. Archival samples have been preserved for genetic analysis for the last 20 years. Here, we examined the population genetic background behind reproductive disruption in this ex-situ conserved species for these samples. We used ISSR genotyping by sequencing (MIG-seq) to analyse the individuals from the wild and ex-situ conserved populations collected during 2001–2020. Genetic diversity, hatchability and the number of sperm decreased after the start of progressive breeding in ex-situ conservation. At least 26 individuals were required to retain the genetic diversity of the wild populations at the start of ex-situ conservation. This study highlights the significant risk of failure in ex-situ conservation efforts due to the small number of founders and breeding individuals

Coincidence between transcriptome analyses on different microarray platforms using a parametric framework

A parametric framework for the analysis of transcriptome data is demonstrated to yield coincident results when applied to data acquired using two different microarray platforms. Discrepancies among transcriptome studies are frequently reported, casting doubt on the reliability of collected data. The inconsistency among observations can be largely attributed to differences among the analytical frameworks employed for data analysis. The existing frameworks normalizes data against a standard determined from the data to be analyzed. In the present study, a parametric framework based on a strict model for normalization is applied to data acquired using an in-house printed chip and GeneChip. The framework is based on a common statistical characteristic of microarray data, and each data is normalized on the basis of a linear relationship with this model. In the proposed framework, the expressional changes observed and genes selected are coincident between platforms, achieving superior universality of data compared to other methods

A non-perturbative study of 4d U(1) non-commutative gauge theory -- the fate of one-loop instability

Recent perturbative studies show that in 4d non-commutative spaces, the trivial (classically stable) vacuum of gauge theories becomes unstable at the quantum level, unless one introduces sufficiently many fermionic degrees of freedom. This is due to a negative IR-singular term in the one-loop effective potential, which appears as a result of the UV/IR mixing. We study such a system non-perturbatively in the case of pure U(1) gauge theory in four dimensions, where two directions are non-commutative. Monte Carlo simulations are performed after mapping the regularized theory onto a U(N) lattice gauge theory in d=2. At intermediate coupling strength, we find a phase in which open Wilson lines acquire non-zero vacuum expectation values, which implies the spontaneous breakdown of translational invariance. In this phase, various physical quantities obey clear scaling behaviors in the continuum limit with a fixed non-commutativity parameter $\theta$, which provides evidence for a possible continuum theory. The extent of the dynamically generated space in the non-commutative directions becomes finite in the above limit, and its dependence on $\theta$ is evaluated explicitly. We also study the dispersion relation. In the weak coupling symmetric phase, it involves a negative IR-singular term, which is responsible for the observed phase transition. In the broken phase, it reveals the existence of the Nambu-Goldstone mode associated with the spontaneous symmetry breaking.Comment: 29 pages, 23 figures, references adde

Establishing bioinformatics research in the Asia Pacific

In 1998, the Asia Pacific Bioinformatics Network (APBioNet), Asia's oldest bioinformatics organisation was set up to champion the advancement of bioinformatics in the Asia Pacific. By 2002, APBioNet was able to gain sufficient critical mass to initiate the first International Conference on Bioinformatics (InCoB) bringing together scientists working in the field of bioinformatics in the region. This year, the InCoB2006 Conference was organized as the 5(th )annual conference of the Asia-Pacific Bioinformatics Network, on Dec. 18–20, 2006 in New Delhi, India, following a series of successful events in Bangkok (Thailand), Penang (Malaysia), Auckland (New Zealand) and Busan (South Korea). This Introduction provides a brief overview of the peer-reviewed manuscripts accepted for publication in this Supplement. It exemplifies a typical snapshot of the growing research excellence in bioinformatics of the region as we embark on a trajectory of establishing a solid bioinformatics research culture in the Asia Pacific that is able to contribute fully to the global bioinformatics community

Particle simulation approach for subcellular dynamics and interactions of biological molecules

BACKGROUND: Spatio-temporal dynamics within cells can now be visualized at appropriate resolution, due to the advances in molecular imaging technologies. Even single-particle tracking (SPT) and single fluorophore video imaging (SFVI) are now being applied to observation of molecular-level dynamics. However, little is known concerning how molecular-level dynamics affect properties at the cellular level. RESULTS: We propose an algorithm designed for three-dimensional simulation of the reaction-diffusion dynamics of molecules, based on a particle model. Chemical reactions proceed through the interactions of particles in space, with activation energies determining the rates of these chemical reactions at each interaction. This energy-based model can include the cellular membrane, membranes of other organelles, and cytoskeleton. The simulation algorithm was tested for a reversible enzyme reaction model and its validity was confirmed. Snapshot images taken from simulated molecular interactions on the cell-surface revealed clustering domains (size ~0.2 μm) associated with rafts. Sample trajectories of raft constructs exhibited "hop diffusion". These domains corralled the diffusive motion of membrane proteins. CONCLUSION: These findings demonstrate that our approach is promising for modelling the localization properties of biological phenomena

Agrobacterium-mediated transformation of kabocha squash (Cucurbita moschata Duch) induced by wounding with aluminum borate whiskers

An efficient genetic transformation method for kabocha squash (Cucurbita moschata Duch cv. Heiankogiku) was established by wounding cotyledonary node explants with aluminum borate whiskers prior to inoculation with Agrobacterium. Adventitious shoots were induced from only the proximal regions of the cotyledonary nodes and were most efficiently induced on Murashige–Skoog agar medium with 1 mg/L benzyladenine. Vortexing with 1% (w/v) aluminum borate whiskers significantly increased Agrobacterium infection efficiency in the proximal region of the explants. Transgenic plants were screened at the T0 generation by sGFP fluorescence, genomic PCR, and Southern blot analyses. These transgenic plants grew normally and T1 seeds were obtained. We confirmed stable integration of the transgene and its inheritance in T1 generation plants by sGFP fluorescence and genomic PCR analyses. The average transgenic efficiency for producing kabocha squashes with our method was about 2.7%, a value sufficient for practical use

Tomato TFT1 Is Required for PAMP-Triggered Immunity and Mutations that Prevent T3S Effector XopN from Binding to TFT1 Attenuate Xanthomonas Virulence

XopN is a type III effector protein from Xanthomonas campestris pathovar vesicatoria that suppresses PAMP-triggered immunity (PTI) in tomato. Previous work reported that XopN interacts with the tomato 14-3-3 isoform TFT1; however, TFT1's role in PTI and/or XopN virulence was not determined. Here we show that TFT1 functions in PTI and is a XopN virulence target. Virus-induced gene silencing of TFT1 mRNA in tomato leaves resulted in increased growth of Xcv ΔxopN and Xcv ΔhrpF demonstrating that TFT1 is required to inhibit Xcv multiplication. TFT1 expression was required for Xcv-induced accumulation of PTI5, GRAS4, WRKY28, and LRR22 mRNAs, four PTI marker genes in tomato. Deletion analysis revealed that the XopN C-terminal domain (amino acids 344–733) is sufficient to bind TFT1. Removal of amino acids 605–733 disrupts XopN binding to TFT1 in plant extracts and inhibits XopN-dependent virulence in tomato, demonstrating that these residues are necessary for the XopN/TFT1 interaction. Phos-tag gel analysis and mass spectrometry showed that XopN is phosphorylated in plant extracts at serine 688 in a putative 14-3-3 recognition motif. Mutation of S688 reduced XopN's phosphorylation state but was not sufficient to inhibit binding to TFT1 or reduce XopN virulence. Mutation of S688 and two leucines (L64,L65) in XopN, however, eliminated XopN binding to TFT1 in plant extracts and XopN virulence. L64 and L65 are required for XopN to bind TARK1, a tomato atypical receptor kinase required for PTI. This suggested that TFT1 binding to XopN's C-terminal domain might be stabilized via TARK1/XopN interaction. Pull-down and BiFC analyses show that XopN promotes TARK1/TFT1 complex formation in vitro and in planta by functioning as a molecular scaffold. This is the first report showing that a type III effector targets a host 14-3-3 involved in PTI to promote bacterial pathogenesis