Special section dedicated to The Sixth q-bio Conference : meeting report and preface

This special section consists of ten original research reports that elaborate on work presented at The Sixth q-bio Conference, which took place on 8-12 August 2012 on the campus of St John's College in Santa Fe, NM, USA. The q-bio community is a vibrant group of researchers that develop and promote integrated modeling, theoretical and quantitative experimental approaches aimed at understanding cellular information processing and other related complex biological phenomena with the quantitative rigor of the physical sciences. This community is transforming the way research in biology is done, making it more quantitative, and using the power of mathematics to discover and systematize biological knowledge in a way that has long eluded the field. The q-bio Conference is our annual flagship conference, held every August in Santa Fe, NM, USA. It is a major system biology forum for exchanging results and ideas, networking and continued education in q-bio. Since its beginning in 2007, the conference has emphasized studies of cellular regulation, and it was originally called The q-bio Conference on Cellular Information Processing. To more effectively serve the community and impact other fields of biology, we later decided that the conference should broaden to include ecological and evolutionary contexts, and bridge into other areas in systems biology, cell biology, physical chemistry, bioengineering and biophysics. The scope of the conference has gradually expanded, and thus, since 2012, the conference has become known simply as The q-bio Conference. Even with its expanded scope, a majority of contributions to the conference continue to focus on cellular information processing and decision-making. In a field that spans a diverse array of biological systems and emphasizes multidisciplinary approaches, a unifying conference that brings together all of its constitutive groups (researchers from the life, physical and engineering sciences) continues to be as crucial as ever. With The q-bio Conference, we have aimed at creating a dynamic atmosphere where junior researchers can meet and interact with senior investigators in an intimate setting and also present their work in posters and talks. There is ample time for impromptu discussions and opportunities for interactions amongst attendees, which is not always the case at larger meetings. The q-bio Conference features a single-track programme, which unfolds over four days. The meeting continues its tradition of being hosted at the campus of St John's College in Santa Fe, NM, USA. This unique location in the foothills of the Sangre de Cristo Mountains has allowed the conference to capitalize, on the one hand, on the solitude of the campus, where most of the attendees sleep and eat on site, promoting spontaneous informal meetings and discussions, and, on the other hand, on the relative closeness to arts, culture and outdoors of Santa Fe, which provide participants and their families with recreational opportunities. The size of the conference (about 200-50 attendees) is aimed to be large enough to sustain a diverse field, and yet small enough to foster intimate interactions. The Sixth q-bio Conference included (see http://q-bio.org/wiki/2012_schedule for the detailed program): 21 invited talks (including four special talks), 27 contributed talks, 17 short poster spotlight talks and 131 poster presentations. The emphasis on contributed talks and posters places the focus of the conference on junior investigators, and, indeed, more than half of the attendees in 2012 were graduate students and postdoctoral scientists. Contributed and invited talks were anchored by four special presentations and events. For 2012, these included the following

Report of the first international liver transplantation society expert panel consensus conference on renal insufficiency in liver transplantation

No abstract.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64330/1/21877_ftp.pd

The Dense Gas Mass Fraction and the Relationship to Star Formation in M51

Observations of 12CO J = 1 - 0 and HCN J = 1 - 0 emission from NGC 5194 (M51) made with the 50 m Large Millimeter Telescope and the SEQUOIA focal plane array are presented. Using the HCN-to-CO ratio, we examine the dense gas mass fraction over a range of environmental conditions within the galaxy. Within the disk, the dense gas mass fraction varies along the spiral arms but the average value over all spiral arms is comparable to the mean value of interarm regions. We suggest that the near-constant dense gas mass fraction throughout the disk arises from a population of density-stratified, self-gravitating molecular clouds and the required density threshold to detect each spectral line. The measured dense gas fraction significantly increases in the central bulge in response to the effective pressure, P e , from the weight of the stellar and gas components. This pressure modifies the dynamical state of the molecular cloud population and, possibly, the HCN-emitting regions in the central bulge from self-gravitating to diffuse configurations in which P e is greater than the gravitational energy density of individual clouds. Diffuse molecular clouds comprise a significant fraction of the molecular gas mass in the central bulge, which may account for the measured sublinear relationships between the surface densities of the star formation rate and molecular and dense gas

Floral gene resources from basal angiosperms for comparative genomics research

BACKGROUND: The Floral Genome Project was initiated to bridge the genomic gap between the most broadly studied plant model systems. Arabidopsis and rice, although now completely sequenced and under intensive comparative genomic investigation, are separated by at least 125 million years of evolutionary time, and cannot in isolation provide a comprehensive perspective on structural and functional aspects of flowering plant genome dynamics. Here we discuss new genomic resources available to the scientific community, comprising cDNA libraries and Expressed Sequence Tag (EST) sequences for a suite of phylogenetically basal angiosperms specifically selected to bridge the evolutionary gaps between model plants and provide insights into gene content and genome structure in the earliest flowering plants. RESULTS: Random sequencing of cDNAs from representatives of phylogenetically important eudicot, non-grass monocot, and gymnosperm lineages has so far (as of 12/1/04) generated 70,514 ESTs and 48,170 assembled unigenes. Efficient sorting of EST sequences into putative gene families based on whole Arabidopsis/rice proteome comparison has permitted ready identification of cDNA clones for finished sequencing. Preliminarily, (i) proportions of functional categories among sequenced floral genes seem representative of the entire Arabidopsis transcriptome, (ii) many known floral gene homologues have been captured, and (iii) phylogenetic analyses of ESTs are providing new insights into the process of gene family evolution in relation to the origin and diversification of the angiosperms. CONCLUSION: Initial comparisons illustrate the utility of the EST data sets toward discovery of the basic floral transcriptome. These first findings also afford the opportunity to address a number of conspicuous evolutionary genomic questions, including reproductive organ transcriptome overlap between angiosperms and gymnosperms, genome-wide duplication history, lineage-specific gene duplication and functional divergence, and analyses of adaptive molecular evolution. Since not all genes in the floral transcriptome will be associated with flowering, these EST resources will also be of interest to plant scientists working on other functions, such as photosynthesis, signal transduction, and metabolic pathways

Who Benefits From Teams? Comparing Workers, Supervisors, and Managers

This paper offers a political explanation for the diffusion and sustainability of team-based work systems by examining the differential outcomes of team structures for 1200 workers, supervisors, and middle managers in a large unionized telecommunications company. Regression analyses show that participation in self-managed teams is associated with significantly higher levels of perceived discretion, employment security, and satisfaction for workers and the opposite for supervisors. Middle managers who initiate team innovations report higher employment security, but otherwise are not significantly different from their counterparts who are not involved in innovations. By contrast, there are no significant outcomes for employees associated with their participation in offline problem-solving teams