Genome-scale resources for Thermoanaerobacterium saccharolyticum

Background Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. A major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation. Results Here we present a set of genome-scale resources to enable the systems level investigation and development of this potentially important industrial organism. Resources include a complete genome sequence for strain JW/SL-YS485, a genome-scale reconstruction of metabolism, tiled microarray data showing transcription units, mRNA expression data from 71 different growth conditions or timepoints and GC/MS-based metabolite analysis data from 42 different conditions or timepoints. Growth conditions include hemicellulose hydrolysate, the inhibitors HMF, furfural, diamide, and ethanol, as well as high levels of cellulose, xylose, cellobiose or maltodextrin. The genome consists of a 2.7 Mbp chromosome and a 110 Kbp megaplasmid. An active prophage was also detected, and the expression levels of CRISPR genes were observed to increase in association with those of the phage. Hemicellulose hydrolysate elicited a response of carbohydrate transport and catabolism genes, as well as poorly characterized genes suggesting a redox challenge. In some conditions, a time series of combined transcription and metabolite measurements were made to allow careful study of microbial physiology under process conditions. As a demonstration of the potential utility of the metabolic reconstruction, the OptKnock algorithm was used to predict a set of gene knockouts that maximize growth-coupled ethanol production. The predictions validated intuitive strain designs and matched previous experimental results. Conclusion These data will be a useful asset for efforts to develop T. saccharolyticum for efficient industrial production of biofuels. The resources presented herein may also be useful on a comparative basis for development of other lignocellulose degrading microbes, such as Clostridium thermocellum. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0159-x) contains supplementary material, which is available to authorized users

The return of inhibition in visual marking

Dissertation (Ph.D.)--University of Kansas, Psychology, 2007.Visual marking (Watson & Humphreys, 1997) and inhibition of return (IOR; Posner & Cohen, 1984) are thought to be distinct visual effects, despite similarities between the two in terms of their time course, their possible use of an inhibitory component, and advantages that each deliver to visual search in general. The present research provided a comparison of the visual marking and IOR effects through two experiments, the first examining patterns of individual differences in the effects, and the second utilizing a task which combined the IOR and visual marking paradigms. Overall, the results suggest that IOR and visual marking occur because of separate processes, but that the two effects may be complementary components in visual search, or related in some other way. The discussion centers on how the results contribute to understanding the similarities and differences between IOR and visual marking, the individual differences finding that some show a preference in using IOR over visual marking in search, and the proposal that IOR might account for a portion of the preview benefit in visual marking studies

Judgments of Size Change Trends in Static and Animated Graduated Circle Displays

Despite the abundance of research on the perception of information presented as graduated or proportional circles on static maps, such experiments have been rare for animated map displays. However, such experimental results might be beneficial for selecting optimal methods for depicting temporal change on graduated circle maps. In the present experiment, participants judged whether a greater number of circles in an n x n array increased or decreased during a 1500-millisecond (ms) observation interval. The variable n represented values of 6, 8, and 10,and all circles changed size (some larger, some smaller) from a common starting size either in a discrete shift (static condition) in the middle of the observation interval, or in a smooth, apparently continuous shift (animated condition) over the same interval. In addition, the size changes were relatively small, moderate, or large. The proportion of “more bigger” judgments, plotted against the actual proportions of enlarged circles, produced an ogive function (a cumulative normal) with similar slopes in all conditions. However, the bias towards “bigger” judgments increased with the size discrepancies between the initial and final circle diameters, and the bias towards “bigger” judgments was greater for animated than for static circle diameter changes. The results are interpreted in terms of attentional precedence for larger items and also for those that appear to be continuously increasing in size (looming). These results have implications for the presentation of information on static and animated graduated circle maps

Genome-scale resources for Thermoanaerobacterium saccharolyticum

Abstract Background Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. A major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation. Results Here we present a set of genome-scale resources to enable the systems level investigation and development of this potentially important industrial organism. Resources include a complete genome sequence for strain JW/SL-YS485, a genome-scale reconstruction of metabolism, tiled microarray data showing transcription units, mRNA expression data from 71 different growth conditions or timepoints and GC/MS-based metabolite analysis data from 42 different conditions or timepoints. Growth conditions include hemicellulose hydrolysate, the inhibitors HMF, furfural, diamide, and ethanol, as well as high levels of cellulose, xylose, cellobiose or maltodextrin. The genome consists of a 2.7 Mbp chromosome and a 110 Kbp megaplasmid. An active prophage was also detected, and the expression levels of CRISPR genes were observed to increase in association with those of the phage. Hemicellulose hydrolysate elicited a response of carbohydrate transport and catabolism genes, as well as poorly characterized genes suggesting a redox challenge. In some conditions, a time series of combined transcription and metabolite measurements were made to allow careful study of microbial physiology under process conditions. As a demonstration of the potential utility of the metabolic reconstruction, the OptKnock algorithm was used to predict a set of gene knockouts that maximize growth-coupled ethanol production. The predictions validated intuitive strain designs and matched previous experimental results. Conclusion These data will be a useful asset for efforts to develop T. saccharolyticum for efficient industrial production of biofuels. The resources presented herein may also be useful on a comparative basis for development of other lignocellulose degrading microbes, such as Clostridium thermocellum