Activity of Japanese Society of Grassland Science

The Japanese Society of Grassland Science (JSGS) was founded in 1954 for the purposes of progressing grassland and forage crop sciences and fostering grassland agriculture and better management of grassland for animal production in Japan. From the first, the members of JSGS have included interdisciplinary scientists from forage crop science, forestry, animal science, agribusiness and many related fields. In the 50 years since its foundation, JSGS has made large contributions to the progress of both science and industry in Japan. The number of JSGS members is now declining slightly, but there are still about 950 including 800 individual members and 150 organisations or private companies. The profile of the current members is mainly scientists working in university or governmental and private research institutes

DDBJ dealing with mass data produced by the second generation sequencer

DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) collected and released 2 368 110 entries or 1 415 106 598 bases in the period from July 2007 to June 2008. The releases in this period include genome scale data of Bombyx mori, Oryzas latipes, Drosophila and Lotus japonicus. In addition, from this year we collected and released trace archive data in collaboration with National Center for Biotechnology Information (NCBI). The first release contains those of O. latipes and bacterial meta genomes in human gut. To cope with the current progress of sequencing technology, we also accepted and released more than 100 million of short reads of parasitic protozoa and their hosts that were produced by using a Solexa sequencer

Predicting Secondary Structures, Contact Numbers, and Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence by Critical Random Networks

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we present a new machine-learning method, critical random networks (CRNs), for predicting one-dimensional structures, and apply it, with position-specific scoring matrices, to the prediction of secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO). The present method achieves, on average, $Q_3$ accuracy of 77.8% for SS, correlation coefficients of 0.726 and 0.601 for CN and RWCO, respectively. The accuracy of the SS prediction is comparable to other state-of-the-art methods, and that of the CN prediction is a significant improvement over previous methods. We give a detailed formulation of critical random networks-based prediction scheme, and examine the context-dependence of prediction accuracies. In order to study the nonlinear and multi-body effects, we compare the CRNs-based method with a purely linear method based on position-specific scoring matrices. Although not superior to the CRNs-based method, the surprisingly good accuracy achieved by the linear method highlights the difficulty in extracting structural features of higher order from amino acid sequence beyond that provided by the position-specific scoring matrices.Comment: 20 pages, 1 figure, 5 tables; minor revision; accepted for publication in BIOPHYSIC

Searching for plasticity in dissociated cortical cultures on multi-electrode arrays

We attempted to induce functional plasticity in dense cultures of cortical cells using stimulation through extracellular electrodes embedded in the culture dish substrate (multi-electrode arrays, or MEAs). We looked for plasticity expressed in changes in spontaneous burst patterns, and in array-wide response patterns to electrical stimuli, following several induction protocols related to those used in the literature, as well as some novel ones. Experiments were performed with spontaneous culture-wide bursting suppressed by either distributed electrical stimulation or by elevated extracellular magnesium concentrations as well as with spontaneous bursting untreated. Changes concomitant with induction were no larger in magnitude than changes that occurred spontaneously, except in one novel protocol in which spontaneous bursts were quieted using distributed electrical stimulation

Collective dynamics of two-mode stochastic oscillators

We study a system of two-mode stochastic oscillators coupled through their collective output. As a function of a relevant parameter four qualitatively distinct regimes of collective behavior are observed. In an extended region of the parameter space the periodicity of the collective output is enhanced by the considered coupling. This system can be used as a new model to describe synchronization-like phenomena in systems of units with two or more oscillation modes. The model can also explain how periodic dynamics can be generated by coupling largely stochastic units. Similar systems could be responsible for the emergence of rhythmic behavior in complex biological or sociological systems.Comment: 4 pages, RevTex, 5 figure

Admission to hospital following head injury in England: Incidence and socio-economic associations

BACKGROUND: Head injury in England is common. Evidence suggests that socio-economic factors may cause variation in incidence, and this variation may affect planning for services to meet the needs of those who have sustained a head injury. METHODS: Socio-economic data were obtained from the UK Office for National Statistics and merged with Hospital Episodes Statistics obtained from the Department of Health. All patients admitted for head injury with ICD-10 codes S00.0–S09.9 during 2001–2 and 2002–3 were included and collated at the level of the extant Health Authorities (HA) for 2002, and Primary Care Trust (PCT) for 2003. Incidence was determined, and cluster analysis and multiple regression analysis were used to look at patterns and associations. Results: 112,718 patients were admitted during 2001–2 giving a hospitalised incidence rate for England of 229 per 100,000. This rate varied across the English HA's ranging from 91–419 per 100,000. The rate remained unchanged for 2002–3 with a similar magnitude of variation across PCT's. Three clusters of HA's were identified from the 2001–2 data; those typical of London, those of the Shire counties, and those of Other Urban authorities. Socio-economic factors were found to account for a high proportion of the variance in incidence for 2001–2. The same pattern emerged for 2002–3 at the PCT level. The use of public transport for travel to work is associated with a decreased incidence and lifestyle indicators, such as the numbers of young unemployed, increase the incidence. CONCLUSION: Head injury incidence in England varies by a factor of 4.6 across HA's and PCT's. Planning head injury related services at the local level thus needs to be based on local incidence figures rather than regional or national estimates. Socio-economic factors are shown to be associated with admission, including travel to work patterns and lifestyle indicators, which suggests that incidence is amenable to policy initiatives at the macro level as well as preventive programmes targeted at key groups

eGenomics: Cataloguing our complete genome collection III

This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS) specification (v1.1), consensus on a variety of features to be added to the Genome Catalogue (GCat), agreement by several researchers to adopt MIGS for imminent genome publications, and an agreement by the EBI and NCBI to input their genome collections into GCat for the purpose of quantifying the amount of optional data already available (e.g., for geographic location coordinates) and working towards a single, global list of all public genomes and metagenomes

The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions

The Genomes TO Protein Structures and Functions (GTOP) database (http://spock.genes.nig.ac.jp/~genome/gtop.html) freely provides an extensive collection of information on protein structures and functions obtained by application of various computational tools to the amino acid sequences of entirely sequenced genomes. GTOP contains annotations of 3D structures, protein families, functions, and other useful data of a protein of interest in user-friendly ways to give a deep insight into the protein structure. From the initial 1999 version, GTOP has been continually updated to reap the fruits of genome projects and augmented to supply novel information, in particular intrinsically disordered regions. As intrinsically disordered regions constitute a considerable fraction of proteins and often play crucial roles especially in eukaryotes, their assignments give important additional clues to the functionality of proteins. Additionally, we have incorporated the following features into GTOP: a platform independent structural viewer, results of HMM searches against SCOP and Pfam, secondary structure predictions, color display of exon boundaries in eukaryotic proteins, assignments of gene ontology terms, search tools, and master files