Comparative shotgun proteomic analysis of Clostridium acetobutylicum from butanol fermentation using glucose and xylose

<p>Abstract</p> <p>Background</p> <p>Butanol is a second generation biofuel produced by <it>Clostridium acetobutylicum </it>through acetone-butanol-ethanol (ABE) fermentation process. Shotgun proteomics provides a direct approach to study the whole proteome of an organism in depth. This paper focuses on shotgun proteomic profiling of <it>C. acetobutylicum </it>from ABE fermentation using glucose and xylose to understand the functional mechanisms of <it>C. acetobutylicum </it>proteins involved in butanol production.</p> <p>Results</p> <p>We identified 894 different proteins in <it>C. acetobutylicum </it>from ABE fermentation process by two dimensional - liquid chromatography - tandem mass spectrometry (2D-LC-MS/MS) method. This includes 717 proteins from glucose and 826 proteins from the xylose substrate. A total of 649 proteins were found to be common and 22 significantly differentially expressed proteins were identified between glucose and xylose substrates.</p> <p>Conclusion</p> <p>Our results demonstrate that flagellar proteins are highly up-regulated with glucose compared to xylose substrate during ABE fermentation. Chemotactic activity was also found to be lost with the xylose substrate due to the absence of CheW and CheV proteins. This is the first report on the shotgun proteomic analysis of <it>C. acetobutylicum </it>ATCC 824 in ABE fermentation between glucose and xylose substrate from a single time data point and the number of proteins identified here is more than any other study performed on this organism up to this report.</p

Guidelines for measuring and reporting environmental parameters for experiments in greenhouses

Background: The importance of appropriate, accurate measurement and reporting of environmental parameters in plant sciences is a significant aspect of quality assurance for all researchers and their research. There is a clear need for ensuring research across the world can be compared, understood and where necessary replicated by fellow researchers. A common set of guidelines to educate, assist and encourage comparativeness is of great importance. On the other hand, the level of effort and attention to detail by an individual researcher should be commensurate with the particular research being conducted. For example, a researcher focusing on interactions of light and temperature should measure all relevant parameters and report a measurement summary that includes sufficient detail allowing for replication. Such detail may be less relevant when the impact of environmental parameters on plant growth and development is not the main research focus. However, it should be noted that the environmental experience of a plant during production can have significant impact when subsequent experiments investigate plants at a molecular, biochemical or genetic level or where species interactions are considered. Thus, researchers are encouraged to make a critical assessment of what parameters are of primary importance in their research and these parameters should be measured and reported. Content: This paper brings together a collection of parameters that the authors, as members of International Committee on Controlled Environment Guidelines (ICCEG) in consultation with members of our three parent organizations, believe constitute those which should be recorded and reported when publishing scientific data from experiments in greenhouses. It provides recommendations to end users on when, how and where these parameters should be measured along with the appropriate internationally standardized units that should be used

Shotgun Metaproteomics of the Human Distal Gut Microbiota

The human gut contains a dense, complex and diverse microbial community, comprising the gut microbiome. Metagenomics has recently revealed the composition of genes in the gut microbiome, but provides no direct information about which genes are expressed or functioning. Therefore, our goal was to develop a novel approach to directly identify microbial proteins in fecal samples to gain information about the genes expressed and about key microbial functions in the human gut. We used a non-targeted, shotgun mass spectrometry-based whole community proteomics, or metaproteomics, approach for the first deep proteome measurements of thousands of proteins in human fecal samples, thus demonstrating this approach on the most complex sample type to date. The resulting metaproteomes had a skewed distribution relative to the metagenome, with more proteins for translation, energy production and carbohydrate metabolism when compared to what was earlier predicted from metagenomics. Human proteins, including antimicrobial peptides, were also identified, providing a non-targeted glimpse of the host response to the microbiota. Several unknown proteins represented previously undescribed microbial pathways or host immune responses, revealing a novel complex interplay between the human host and its associated microbes

Mindfulness in Action: Discovering How U.S. Navy Seals Build Capacity for Mindfulness in High-Reliability Organizations (HROs)

This study of US Navy Sea Air and Land (SEAL) commandos contributes to research investigating mindfulness in High-Reliability Organizations (HROs) by identifying the individual and collective influences that allow SEALs to build capacity for mindful behaviors despite the complexity of their missions, the unpredictability of their operating environments, and the danger inherent in their work. Although the HRO literature identifies a number of hallmarks of reliability, less attention is paid to how mindfulness is operationally achieved in situ by individuals on the frontline working in HROs. This study addresses this gap using a multi-phase, multi-method investigation of US Navy SEALs, identifying new links between individual mindfulness attributes (comfort with uncertainty and chaos) and collective mindfulness influences (a positive orientation towards failure) that combine to co-create a phenomenon we call 'mindfulness in action'. Mindfulness in action occurs when HROs achieve an attentive yet flexible focus capable of incorporating multiple—sometimes competing—realities in order to assess alternative solutions and take action in dynamic situations. By providing a more nuanced conceptualization of the links between individual mindfulness attributes and collective mindfulness influences, this paper opens up new avenues of discovery for a wide range of reliability-seeking organizations.This study of US Navy Sea Air and Land (SEAL) commandos contributes to research investigating mindfulness in High-Reliability Organizations (HROs) by identifying the individual and collective influences that allow SEALs to build capacity for mindful behaviors despite the complexity of their missions, the unpredictability of their operating environments, and the danger inherent in their work. Although the HRO literature identifies a number of hallmarks of reliability, less attention is paid to how mindfulness is operationally achieved in situ by individuals on the frontline working in HROs. This study addresses this gap using a multi-phase, multi-method investigation of US Navy SEALs, identifying new links between individual mindfulness attributes (comfort with uncertainty and chaos) and collective mindfulness influences (a positive orientation towards failure) that combine to co-create a phenomenon we call 'mindfulness in action'. Mindfulness in action occurs when HROs achieve an attentive yet flexible focus capable of incorporating multiple—sometimes competing—realities in order to assess alternative solutions and take action in dynamic situations. By providing a more nuanced conceptualization of the links between individual mindfulness attributes and collective mindfulness influences, this paper opens up new avenues of discovery for a wide range of reliability-seeking organizations

Maintenance of cross-sector partnerships: the role of frames in sustained collaboration

We examine the framing mechanisms used to maintain a cross-sector partnership (XSP) that was created to address a complex long-term social issue. We study the first eight years of existence of an XSP that aims to create a market for recycled phosphorus, a nutrient that is critical to crop growth but whose natural reserves have dwindled significantly. Drawing on 27 interviews and over 3,000 internal documents, we study the evolution of different frames used by diverse actors in an XSP. We demonstrate the role of framing in helping actors to avoid some of the common pitfalls for an XSP, such as debilitating conflict, and in creating sufficient common ground to sustain collaboration. As opposed to a commonly held assumption in the XSP literature, we find that collaboration in a partnership does not have to result in a unanimous agreement around a single or convergent frame regarding a contentious issue. Rather, successful collaboration between diverse partners can also be achieved by maintaining a productive tension between different frames through ‘optimal’ frame plurality – not excessive frame variety that may prevent agreements from emerging, but the retention of a select few frames and the deletion of others towards achieving a narrowing frame bandwidth. One managerial implication is that resources need not be focussed on reaching a unanimous agreement among all partners on a single mega-frame vis-à-vis a contentious issue, but can instead be used to kindle a sense of unity in diversity that allows sufficient common ground to emerge, despite the variety of actors and their positions

The interplay between HQ legitimation and subsidiary legitimacy judgments in HQ relocation : a social psychological approach

This paper marks a departure from the focus on external stakeholders in much research on legitimacy and multinational corporations, adopting a social psychological approach to study how MNCs build internal legitimacy for controversial decisions with their subsidiaries. We explore this through a longitudinal, real-time qualitative case study of a regional office relocation, since office relocations represent rare yet significant strategic decisions. We analyze the interplay between the legitimation strategies of senior managers and subsidiary legitimacy judgments, based in instrumental, relational, and moral considerations, and how the relationship between the two develops over time. From this analysis, we derive inductively a process model that reveals the dynamics of building internal legitimacy with subsidiaries, and how an MNC moves on even in the absence of full legitimacy, when dealing with controversial MNC decisions. The model highlights two important dynamics. The first is a dynamic between legitimation strategies and legitimacy judgments and how this is influenced by local subsidiary contexts. The second is a temporal dynamic in how both the legitimation strategies and legitimacy judgments evolve over time. Our model contributes to research on legitimacy in MNCs, what we know about tensions that characterize MNC–subunit relationships, and research on headquarters relocation

Towards an articulation of the material and visual turn in organization studies

International audienceContemporary organizations increasingly rely on images, logos, videos, building materials, graphic andproduct design, and a range of other material and visual artifacts to compete, communicate, form identityand organize their activities. This Special Issue focuses on materiality and visuality in the course of objectifyingand reacting to novel ideas, and, more broadly, contributes to organizational theory by articulating theemergent contours of a material and visual turn in the study of organizations. In this Introduction, weprovide an overview of research on materiality and visuality. Drawing on the articles in the special issue, wefurther explore the affordances and limits of the material and visual dimensions of organizing in relation tonovelty. We conclude by pointing out theoretical avenues for advancing multimodal research, and discusssome of the ethical, pragmatic and identity-related challenges that a material and visual turn could pose fororganizational research

Pigment Concentrations among Heat-tolerant Turfgrasses

Heat-tolerant bluegrass varieties were developed to resist dormancy and retain pigmentation during heat stress events. The objective of this study was to investigate the influence of grass species, nitrogen (N) fertilization, and seasonality on the accumulation patterns of lutein, β-carotene, and chlorophyll a and b in the leaf tissues of turfgrass. The heat-tolerant bluegrass cultivars Dura Blue and Thermal Blue (Poa pratensis L. x Poa arachnifera Torr.), Apollo kentucky bluegrass (Poa pratensis L.), and Kentucky 31 tall fescue (Festuca arundinacea Schreb.) were compared for the accumulation of plant pigments. Evaluations were conducted over 2 consecutive years (Years 4 and 5 after establishment) during two different seasons (spring and summer) and under varying N fertilization. Fertilizer applications of 5, 14, and 27 g N/m2/year resulted in a significant positive correlation for the accumulation of leaf blade lutein and chlorophyll a and b, but not for β-carotene. The accumulation of the four measured plant pigments among the grasses was significantly different with ‘Apollo’ having the largest concentration of pigments followed by ‘Dura Blue’, ‘Thermal Blue’, and finally ‘Kentucky 31’. Specifically, when comparing the cultivars Apollo and Kentucky 31, the pigment levels decreased 27%, 26%, 26%, and 23% for lutein, β-carotene, and chlorophyll a and b, respectively. The interesting observation of the analysis of the grass pigment concentrations was that the least reported heat-tolerant cultivar in our study (‘Apollo’) had the largest measured pigment concentrations