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Pinto A.,Berkeley Networks | Krishnamurthy S.,UTRC - United Technologies Research Center
2010 48th Annual Allerton Conference on Communication, Control, and Computing, Allerton 2010 | Year: 2010

We motivate the need for a cyber-physical system analysis and design tool that embraces uncertainty as key characteristic of these type of systems. We outline the features that such tool should provide and we present a prototype implementation. The challenges faced during its development go beyond the sheer complexity of analyzing large Markov Models. We close the paper with some examples of analysis of uncertain systems. ©2010 IEEE.


Keller K.L.,University of Missouri | Keller K.L.,Berkeley Networks | Keller K.L.,William Woods University | Rapp-Giles B.J.,University of Missouri | And 7 more authors.
Applied and Environmental Microbiology | Year: 2014

To understand the energy conversion activities of the anaerobic sulfate-reducing bacteria, it is necessary to identify the components involved in electron flow. The importance of the abundant type I tetraheme cytochrome c3 (TpIc3) as an electron carrier during sulfate respiration was questioned by the previous isolation of a null mutation in the gene encoding TpIc3, cycA, in Desulfovibrio alaskensis G20. Whereas respiratory growth of the CycA mutant with lactate and sulfate was little affected, growth with pyruvate and sulfate was significantly impaired. We have explored the phenotype of the CycA mutant through physiological tests and transcriptomic and proteomic analyses. Data reported here show that electrons from pyruvate oxidation do not reach adenylyl sulfate reductase, the enzyme catalyzing the first redox reaction during sulfate reduction, in the absence of either CycA or the type I cytochrome c3:menaquinone oxidoreductase transmembrane complex, QrcABCD. In contrast to the wild type, the CycA and QrcA mutants did not grow with H2 or formate and sulfate as the electron acceptor. Transcriptomic and proteomic analyses of the CycA mutant showed that transcripts and enzymes for the pathway from pyruvate to succinate were strongly decreased in the CycA mutant regardless of the growth mode. Neither the CycA nor the QrcA mutant grew on fumarate alone, consistent with the omics results and a redox regulation of gene expression. We conclude that TpIc3 and the Qrc complex are D. alaskensis components essential for the transfer of electrons released in the periplasm to reach the cytoplasmic adenylyl sulfate reductase and present a model that may explain the CycA phenotype through confurcation of electrons. © 2014, American Society for Microbiology.


Brileya K.A.,Montana State University | Camilleri L.B.,Montana State University | Zane G.M.,University of Missouri | Wall J.D.,University of Missouri | And 3 more authors.
Frontiers in Microbiology | Year: 2014

Sulfate-reducing bacteria (SRB) can interact syntrophically with other community members in the absence of sulfate, and interactions with hydrogen-consuming methanogens are beneficial when these archaea consume potentially inhibitory H2 produced by the SRB. A dual continuous culture approach was used to characterize population structure within a syntrophic biofilm formed by the SRB Desulfovibrio vulgaris Hildenborough and the methanogenic archaeum Methanococcus maripaludis. Under the tested conditions, monocultures of D. vulgaris formed thin, stable biofilms, but monoculture M. maripaludis did not. Microscopy of intact syntrophic biofilm confirmed that D. vulgaris formed a scaffold for the biofilm, while intermediate and steady-state images revealed that M. maripaludis joined the biofilm later, likely in response to H2 produced by the SRB. Close interactions in structured biofilm allowed efficient transfer of H2 to M. maripaludis, and H2 was only detected in cocultures with a mutant SRB that was deficient in biofilm formation (δpilA). M. maripaludis produced more carbohydrate (uronic acid, hexose, and pentose) as a monoculture compared to total coculture biofilm, and this suggested an altered carbon flux during syntrophy. The syntrophic biofilm was structured into ridges (~300 × 50 μm) and models predicted lactate limitation at ~50 μm biofilm depth. The biofilm had structure that likely facilitated mass transfer of H2 and lactate, yet maximized biomass with a more even population composition (number of each organism) when compared to the bulk-phase community. Total biomass protein was equivalent in lactate-limited and lactate-excess conditions when a biofilm was present, but in the absence of biofilm, total biomass protein was significantly reduced. The results suggest that multispecies biofilms create an environment conducive to resource sharing, resulting in increased biomass retention, or carrying capacity, for cooperative populations. © 2014 Brileya, Camilleri, Zane, Wall and Fields.


Rabus R.,Carl von Ossietzky University | Venceslau S.S.,New University of Lisbon | Wohlbrand L.,Carl von Ossietzky University | Voordouw G.,University of Calgary | And 3 more authors.
Advances in Microbial Physiology | Year: 2015

Dissimilatory sulphate reduction is the unifying and defining trait of sulphate-reducing prokaryotes (SRP). In their predominant habitats, sulphate-rich marine sediments, SRP have long been recognized to be major players in the carbon and sulphur cycles. Other, more recently appreciated, ecophysiological roles include activity in the deep biosphere, symbiotic relations, syntrophic associations, human microbiome/health and long-distance electron transfer. SRP include a high diversity of organisms, with large nutritional versatility and broad metabolic capacities, including anaerobic degradation of aromatic compounds and hydrocarbons. Elucidation of novel catabolic capacities as well as progress in the understanding of metabolic and regulatory networks, energy metabolism, evolutionary processes and adaptation to changing environmental conditions has greatly benefited from genomics, functional OMICS approaches and advances in genetic accessibility and biochemical studies. Important biotechnological roles of SRP range from (i) wastewater and off gas treatment, (ii) bioremediation of metals and hydrocarbons and (iii) bioelectrochemistry, to undesired impacts such as (iv) souring in oil reservoirs and other environments, and (v) corrosion of iron and concrete. Here we review recent advances in our understanding of SRPs focusing mainly on works published after 2000. The wealth of publications in this period, covering many diverse areas, is a testimony to the large environmental, biogeochemical and technological relevance of these organisms and how much the field has progressed in these years, although many important questions and applications remain to be explored. © 2015 Elsevier Ltd.


Ramos A.R.,New University of Lisbon | Keller K.L.,University of Missouri | Keller K.L.,Berkeley Networks | Wall J.D.,University of Missouri | And 2 more authors.
Frontiers in Microbiology | Year: 2012

The adenosine 5′-phosphosulfate reductase (AprAB) is the enzyme responsible for the reduction of adenosine 5'-phosphosulfate (APS) to sulfite in the biological process of dissimilatory sulfate reduction, which is carried out by a ubiquitous group of sulfate reducing prokaryotes. The electron donor for AprAB has not been clearly identified, but was proposed to be the QmoABC membrane complex, since an aprBA-qmoABC gene cluster is found in many sulfate reducing and sulfur-oxidizing bacteria. The QmoABC complex is essential for sulfate reduction, but electron transfer between QmoABC and AprAB has not been reported. In this work we provide the first direct evidence that QmoABC and AprAB interact in Desulfovibrio spp., using co-immunoprecipitation, cross-linking Far-Western blot, tag-affinity purification, and surface plasmon resonance studies. This showed that the QmoABC-AprAB complex has a strong steady-state affinity (KD= 90± 3nM), but has a transient character due to a fast dissociation rate. Far-Western blot identified QmoA as the Qmo subunit most involved in the interaction. Nevertheless, electron transfer from menaquinol analogs to APS through anaerobically purified QmoABC and AprAB could not be detected. We propose that this reaction requires the involvement of a third partner to allow electron flow driven by a reverse electron bifurcation process, i.e., electron confurcation. This process is deemed essential to allow coupling of APS reduction to chemiosmotic energy conservation. © 2012 Ramos, Keller, Wall and Pereira.


Keller K.L.,University of Missouri | Keller K.L.,Virtual Institute for Microbial Stress and Survival | Wall J.D.,University of Missouri | Wall J.D.,Virtual Institute for Microbial Stress and Survival | Wall J.D.,Berkeley Networks
Frontiers in Microbiology | Year: 2011

Progress in the genetic manipulation of the Desulfovibrio strains has provided an opportunity to explore electron flow pathways during sulfate respiration. Most bacteria in this genus couple the oxidation of organic acids or ethanol with the reduction of sulfate, sulfite, or thiosulfate. Both fermentation of pyruvate in the absence of an alternative terminal electron acceptor, disproportionation of fumarate and growth on H2 with CO2 during sulfate reduction are exhibited by some strains. The ability to produce or consume H2 provides Desulfovibrio strains the capacity to participate as either partner in interspecies H2 transfer. Interestingly the mechanisms of energy conversion, pathways of electron flow and the parameters determining the pathways used remain to be elucidated. Recent application of molecular genetic tools for the exploration of the metabolism of Desulfovibrio vulgaris Hildenborough has provided several new datasets that might provide insights and constraints to the electron flow pathways.These datasets include (1) gene expression changes measured in microarrays for cells cultured with different electron donors and acceptors, (2) relative mRNA abundances for cells growing exponentially in defined medium with lactate as carbon source and electron donor plus sulfate as terminal electron acceptor, and (3) a random transposon mutant library selected on medium containing lactate plus sulfate supplemented with yeast extract. Studies of directed mutations eliminating apparent key components, the quinone-interacting membrane-bound oxidoreductase (Qmo) complex, the Type 1 tetraheme cytochrome c3 (Tp1-c3), or the Type 1 cytochrome c3:menaquinone oxidoreductase (Qrc) complex, suggest a greater flexibility in electron flow than previously considered. The new datasets revealed the absence of random transposons in the genes encoding an enzyme with homology to Coo membrane-bound hydrogenase. From this result, we infer that Coo hydrogenase plays an important role in D. vulgaris growth on lactate plus sulfate. These observations along with those reported previously have been combined in a model showing dual pathways of electrons from the oxidation of both lactate and pyruvate during sulfate respiration. Continuing genetic and biochemical analyses of key genes in Desulfovibrio strains will allow further clarification of a general model for sulfate respiration. © 2011 Keller and Wall.


Trademark
Berkeley Networks | Date: 2012-07-31

Downloadable software in the nature of an application enabling consumers to access, store and/or share information relating to personal preferences and/or coupons, discounts, and/or other promotions for a wide variety of consumer products and/or services of others; downloadable software in the nature of an application enabling consumers to enter and manage information and/or personal preferences about a wide variety of consumer products and/or services of others in a user profile; downloadable software in the nature of an application enabling consumers to share with each other information relating to personal preferences about a wide variety of consumer products and/or services of others; downloadable software in the nature of a mobile application for displaying and sharing a users location, finding, locating, and interacting with other users and places in the field of consumer products and services; computer application software for mobile phones, namely, software for posting reviews and recommendations on consumer products and services of others; downloadable software in the nature of an application enabling a user to locate businesses or places in proximity to the user in the field of consumer products and services; none of the aforesaid goods relating to financial indices.


Trademark
Berkeley Networks | Date: 2015-07-31

downloadable software in the nature of an application enabling consumers to access, store and/or share information relating to personal preferences and/or coupons, discounts, and/or other promotions for a wide variety of consumer products and/or services of others; downloadable software in the nature of an application enabling consumers to enter and manage information and/or personal preferences about a wide variety of consumer products and/or services of others in a user profile; downloadable software in the nature of an application enabling consumers to share with each other information relating to personal preferences about a wide variety of consumer products and/or services of others; downloadable software in the nature of a mobile application for displaying and sharing a users location, finding, locating, and interacting with other users and places in the field of consumer products and services; computer application software for mobile phones, namely, software for posting reviews and recommendations on consumer products and services of others; downloadable software in the nature of an application enabling a user to locate businesses or places in proximity to the user in the field of consumer products and services; none of the aforesaid goods relating to financial indices. Electronic commerce services, namely, dissemination of advertising in the field of discount programs, customer loyalty programs and customer reward programs for others via global computer networks, telecommunications networks, and wireless communication networks; providing a database of customer profiles featuring information from loyalty programs, discount programs and customer reward programs. Communication services, namely, the electronic transmission and reception of text, data, voice, audio, video, images, sound, information, and other digital and interactive information via global computer networks, telecommunications networks, and wireless communication networks for the purpose of facilitating electronic commerce; providing user access to multi-channel interactive global computer networks, telecommunication networks, and wireless communication networks. Providing online, non-downloadable software that enables the interactive exchange of information between retailers, vendors and customers via global computer networks, telecommunications networks, and wireless communication networks; providing non-downloadable software for a multi-channel interactive network that enables individuals to capture, record and share information about items they wish to purchase or to have purchased via global computer networks, telecommunications networks, and wireless communication networks; providing an online database of customer profiles featuring technology that enables customers to centralize information from loyalty programs, discount programs and customer reward programs, and to organize, manage and share shopping lists and customer profile information with retailers, vendors and other consumers.


Cue

Trademark
Berkeley Networks | Date: 2015-07-28

Downloadable software in the nature of an application enabling consumers to access, store and share information relating to personal preferences, coupons, discounts, and other promotions for a wide variety of consumer products and/or services of others; downloadable software in the nature of an application enabling consumers to enter and manage information and personal preferences about a wide variety of consumer products and/or services of others in a user profile; downloadable software in the nature of an application enabling consumers to share with each other information relating to personal preferences about a wide variety of consumer products and/or services of others; downloadable software in the nature of a mobile application for displaying and sharing a users location, finding, locating, and interacting with other users and places in the field of consumer products and services; computer application software for mobile phones, namely, software for posting reviews and recommendations on consumer products and services of others; downloadable software in the nature of an application enabling a user to locate businesses or places in proximity to the user in the field of consumer products and services; none of the aforesaid goods relating to financial indices. Electronic commerce services, namely, dissemination of advertising in the field of discount programs, customer loyalty programs and customer reward programs for others via global computer networks, telecommunications networks, and wireless communication networks; providing a database of customer profiles featuring information from loyalty programs, discount programs and customer reward programs. Providing online, non-downloadable software that enables the interactive exchange of information between retailers, vendors and customers via global computer networks, telecommunications networks, and wireless communication networks; providing non-downloadable software for a multi-channel interactive network that enables individuals to capture, record and share information about items they wish to purchase or to have purchased via global computer networks, telecommunications networks, and wireless communication networks; providing an online database of customer profiles featuring technology that enables customers to centralize information from loyalty programs, discount programs and customer reward programs, and to organize, manage and share shopping lists and customer profile information with retailers, vendors and other consumers.


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