373 results on '"Russo, David A."'
Search Results
352. HYSWASOR — Simulation Model of Hysteretic Water and Solute Transport in the Root Zone
- Author
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Dirksen, C., Kool, J. B., Koorevaar, P., van Genuchten, M. Th., Yaron, B., editor, Van Keulen, H., editor, Thomas, G. W., editor, Van Vleck, L. D., editor, Russo, David, editor, and Dagan, Gedeon, editor
- Published
- 1993
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353. Constant-Rainfall Infiltration on Hillslopes and Slope Crests
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Philip, J. R., Yaron, B., editor, Van Keulen, H., editor, Thomas, G. W., editor, Van Vleck, L. D., editor, Russo, David, editor, and Dagan, Gedeon, editor
- Published
- 1993
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354. The Bresler-Dagan Model of Flow and Transport: Recent Theoretical Developments
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Dagan, G., Yaron, B., editor, Van Keulen, H., editor, Thomas, G. W., editor, Van Vleck, L. D., editor, Russo, David, editor, and Dagan, Gedeon, editor
- Published
- 1993
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355. Capillary Barrier at the Interface of Two Layers
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Morel-Seytoux, H. J., Yaron, B., editor, Van Keulen, H., editor, Thomas, G. W., editor, Van Vleck, L. D., editor, Russo, David, editor, and Dagan, Gedeon, editor
- Published
- 1993
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356. Solute Lifetime Correlations in Chemical Transport Through Field Soils
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Sposito, G., Yaron, B., editor, Van Keulen, H., editor, Thomas, G. W., editor, Van Vleck, L. D., editor, Russo, David, editor, and Dagan, Gedeon, editor
- Published
- 1993
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357. Analysis of Solute Transport in Partially Saturated Heterogeneous Soils
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Russo, D., Yaron, B., editor, Van Keulen, H., editor, Thomas, G. W., editor, Van Vleck, L. D., editor, Russo, David, editor, and Dagan, Gedeon, editor
- Published
- 1993
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358. Towards Pore-Scale Analysis of Preferential Flow and Chemical Transport
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Luxmoore, R. J., Ferrand, L. A., Yaron, B., editor, Van Keulen, H., editor, Thomas, G. W., editor, Van Vleck, L. D., editor, Russo, David, editor, and Dagan, Gedeon, editor
- Published
- 1993
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359. The Contribution of Eshel Bresler to Soil Science
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Kemper, W. Doral, Yaron, B., editor, Van Keulen, H., editor, Thomas, G. W., editor, Van Vleck, L. D., editor, Russo, David, editor, and Dagan, Gedeon, editor
- Published
- 1993
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360. Nitrate fluxes to groundwater under citrus orchards in a Mediterranean climate: Observations, calibrated models, simulations and agro-hydrological conclusions.
- Author
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Kurtzman, Daniel, Shapira, Roi H., Bar-Tal, Asher, Fine, Pinchas, and Russo, David
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- *
NITRATES , *FLUX (Energy) , *GROUNDWATER pollution , *CITRUS , *ORCHARDS , *MEDITERRANEAN climate , *AGROHYDROLOGY - Abstract
Abstract: Nitrate contamination of groundwater under land used for intensive-agriculture is probably the most worrisome agro-hydrological sustainability problem worldwide. Vadose-zone samples from 0 to 9m depth under citrus orchards overlying an unconfined aquifer were analyzed for variables controlling water flow and the fate and transport of nitrogen fertilizers. Steady-state estimates of water and NO3-N fluxes to groundwater were found to vary spatially in the ranges of 90–330mmyr−1 and 50–220kgha−1 yr−1, respectively. Calibration of transient models to two selected vadose-zone profiles required limiting the concentration of NO3-N in the solution that is taken up by the roots to 30mgL−1. Results of an independent lysimeter experiment showed a similar nitrogen-uptake regime. Simulations of past conditions revealed a significant correlation between NO3-N flux to groundwater and the previous year's precipitation. Simulations of different nitrogen-application rates showed that using half of the nitrogen fertilizer added to the irrigation water by farmers would reduce average NO3-N flux to groundwater by 70%, decrease root nitrogen uptake by 20% and reduce the average pore water NO3-N concentration in the deep vadose zone to below the Israeli drinking water standard; hence this rate of nitrogen application was found to be agro-hydrologically sustainable. Beyond the investigation of nitrate fluxes to groundwater under citrus orchards and the interesting case-study aspects, this work demonstrates a methodology that enables skillful decisions concerning joint sustainability of both the water resource and agricultural production in a common environmental setting. [Copyright &y& Elsevier]
- Published
- 2013
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361. The Immaculate Conception of Little Dizzle.
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Congenital Engine, production company., Visit Films, publisher, film distributor., Russo, David, 1964- director., Case, Peggy, producer., Rosen, Lance, producer., Pruzan, Alan, producer., Allman, Marshall, actor., Lyonne, Natasha, actor., Raymonde, Tania, 1988- actor., Runyan, Tygh, actor., and Vieluf, Vince, 1970- actor.
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- 2010
362. A comparison of travel-time based catchment transport models, with application to numerical experiments
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David Russo, Aldo Fiori, Melkamu Ali, Ali', MELKAMU ALEBACHEW, Fiori, Aldo, and Russo, David
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Travel time ,LTI system theory ,Mathematical optimization ,Scope (project management) ,Computer science ,Calibration (statistics) ,Benchmark (surveying) ,Evapotranspiration ,Flow (psychology) ,Econometrics ,Level of detail ,Water Science and Technology - Abstract
Summary In this paper we analyze the performance of four different models of solute transport in catchments. The models employ the concept of travel time distribution. A recapitulation and critical analysis of the models and their basic assumptions is performed first, emphasizing their limitations and potential problems arising in their application. Then, detailed numerical experiments are used as a benchmark for the calibration and the assessment of the models’ capabilities to simulate transport. The scope of the exercise is to test the performance of the models and their limitations in the ideal case in which the catchment system and all the hydrological variables (flow, concentration, storage, etc.) are perfectly known at any level of detail. The performance of the models and their limitations is presented and discussed. The results suggest that a time invariant formulation of the travel time distribution is usually inappropriate and not much effective in predicting transport. The performance of all models generally decreases when in presence of evapotranspiration.
- Published
- 2014
363. EXCRETE workflow enables deep proteomics of the microbial extracellular environment.
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Russo DA, Oliinyk D, Pohnert G, Meier F, and Zedler JAZ
- Subjects
- Cyanobacteria metabolism, Secretome metabolism, Synechococcus metabolism, Mass Spectrometry methods, Proteome metabolism, Proteomics methods, Workflow, Bacterial Proteins metabolism
- Abstract
Extracellular proteins play a significant role in shaping microbial communities which, in turn, can impact ecosystem function, human health, and biotechnological processes. Yet, for many ubiquitous microbes, there is limited knowledge regarding the identity and function of secreted proteins. Here, we introduce EXCRETE (enhanced exoproteome characterization by mass spectrometry), a workflow that enables comprehensive description of microbial exoproteomes from minimal starting material. Using cyanobacteria as a case study, we benchmark EXCRETE and show a significant increase over current methods in the identification of extracellular proteins. Subsequently, we show that EXCRETE can be miniaturized and adapted to a 96-well high-throughput format. Application of EXCRETE to cyanobacteria from different habitats (Synechocystis sp. PCC 6803, Synechococcus sp. PCC 11901, and Nostoc punctiforme PCC 73102), and in different cultivation conditions, identified up to 85% of all potentially secreted proteins. Finally, functional analysis reveals that cell envelope maintenance and nutrient acquisition are central functions of the predicted cyanobacterial secretome. Collectively, these findings challenge the general belief that cyanobacteria lack secretory proteins and suggest that multiple functions of the secretome are conserved across freshwater, marine, and terrestrial species., (© 2024. The Author(s).)
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- 2024
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364. Self-Assembly of Nanofilaments in Cyanobacteria for Protein Co-localization.
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Zedler JAZ, Schirmacher AM, Russo DA, Hodgson L, Gundersen E, Matthes A, Frank S, Verkade P, and Jensen PE
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- Photosynthesis, Protein Transport, Bacterial Proteins metabolism, Synechocystis metabolism
- Abstract
Cyanobacteria offer great potential as alternative biotechnological hosts due to their photoautotrophic capacities. However, in comparison to established heterotrophic hosts, several key aspects, such as product titers, are still lagging behind. Nanobiotechnology is an emerging field with great potential to improve existing hosts, but so far, it has barely been explored in microbial photosynthetic systems. Here, we report the establishment of large proteinaceous nanofilaments in the unicellular model cyanobacterium Synechocystis sp. PCC 6803 and the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973. Transmission electron microscopy and electron tomography demonstrated that expression of pduA* , encoding a modified bacterial microcompartment shell protein, led to the generation of bundles of longitudinally aligned nanofilaments in S. elongatus UTEX 2973 and shorter filamentous structures in Synechocystis sp. PCC 6803. Comparative proteomics showed that PduA* was at least 50 times more abundant than the second most abundant protein in the cell and that nanofilament assembly had only a minor impact on cellular metabolism. Finally, as a proof-of-concept for co-localization with the filaments, we targeted a fluorescent reporter protein, mCitrine, to PduA* by fusion with an encapsulation peptide that natively interacts with PduA. The establishment of nanofilaments in cyanobacterial cells is an important step toward cellular organization of heterologous pathways and the establishment of cyanobacteria as next-generation hosts.
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- 2023
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365. Transcriptomics-guided identification of an algicidal protease of the marine bacterium Kordia algicida OT-1.
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Syhapanha KS, Russo DA, Deng Y, Meyer N, Poulin RX, and Pohnert G
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- Peptide Hydrolases genetics, Peptide Hydrolases metabolism, Transcriptome, Plankton, Endopeptidases genetics, Flavobacteriaceae metabolism, Diatoms genetics, Diatoms metabolism
- Abstract
In recent years, interest in algicidal bacteria has risen due to their ecological importance and their potential as biotic regulators of harmful algal blooms. Algicidal bacteria shape the plankton communities of the oceans by inhibiting or lysing microalgae and by consuming the released nutrients. Kordia algicida strain OT-1 is a model marine algicidal bacterium that was isolated from a bloom of the diatom Skeletonema costatum. Previous work has suggested that algicidal activity is mediated by secreted proteases. Here, we utilize a transcriptomics-guided approach to identify the serine protease gene KAOT1_RS09515, hereby named alpA1 as a key element in the algicidal activity of K. algicida. The protease AlpA1 was expressed and purified from a heterologous host and used in in vitro bioassays to validate its activity. We also show that K. algicida is the only algicidal species within a group of four members of the Kordia genus. The identification of this algicidal protease opens the possibility of real-time monitoring of the ecological impact of algicidal bacteria in natural phytoplankton blooms., (© 2023 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.)
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- 2023
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366. Interlaboratory Reproducibility in Growth and Reporter Expression in the Cyanobacterium Synechocystis sp. PCC 6803.
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Mager M, Pineda Hernandez H, Brandenburg F, López-Maury L, McCormick AJ, Nürnberg DJ, Orthwein T, Russo DA, Victoria AJ, Wang X, Zedler JAZ, Branco Dos Santos F, and Schmelling NM
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- Reproducibility of Results, Biomass, Genes, Reporter, Promoter Regions, Genetic, Synechocystis genetics
- Abstract
In recent years, a plethora of new synthetic biology tools for use in cyanobacteria have been published; however, their reported characterizations often cannot be reproduced, greatly limiting the comparability of results and hindering their applicability. In this interlaboratory study, the reproducibility of a standard microbiological experiment for the cyanobacterial model organism Synechocystis sp. PCC 6803 was assessed. Participants from eight different laboratories quantified the fluorescence intensity of mVENUS as a proxy for the transcription activity of the three promoters P
J 23100 , PrhaBAD , and PpetE over time. In addition, growth rates were measured to compare growth conditions between laboratories. By establishing strict and standardized laboratory protocols, reflecting frequently reported methods, we aimed to identify issues with state-of-the-art procedures and assess their effect on reproducibility. Significant differences in spectrophotometer measurements across laboratories from identical samples were found, suggesting that commonly used reporting practices of optical density values need to be supplemented by cell count or biomass measurements. Further, despite standardized light intensity in the incubators, significantly different growth rates between incubators used in this study were observed, highlighting the need for additional reporting requirements of growth conditions for phototrophic organisms beyond the light intensity and CO2 supply. Despite the use of a regulatory system orthogonal to Synechocystis sp. PCC 6803, PrhaBAD , and a high level of protocol standardization, ∼32% variation in promoter activity under induced conditions was found across laboratories, suggesting that the reproducibility of other data in the field of cyanobacteria might be affected similarly.- Published
- 2023
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367. Recent developments in the production and utilization of photosynthetic microorganisms for food applications.
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Barone GD, Cernava T, Ullmann J, Liu J, Lio E, Germann AT, Nakielski A, Russo DA, Chavkin T, Knufmann K, Tripodi F, Coccetti P, Secundo F, Fu P, Pfleger B, Axmann IM, and Lindblad P
- Abstract
The growing use of photosynthetic microorganisms for food and food-related applications is driving related biotechnology research forward. Increasing consumer acceptance, high sustainability, demand of eco-friendly sources for food, and considerable global economic concern are among the main factors to enhance the focus on the novel foods. In the cases of not toxic strains, photosynthetic microorganisms not only provide a source of sustainable nutrients but are also potentially healthy. Several published studies showed that microalgae are sources of accessible protein and fatty acids. More than 400 manuscripts were published per year in the last 4 years. Furthermore, industrial approaches utilizing these microorganisms are resulting in new jobs and services. This is in line with the global strategy for bioeconomy that aims to support sustainable development of bio-based sectors. Despite the recognized potential of the microalgal biomass value chain, significant knowledge gaps still exist especially regarding their optimized production and utilization. This review highlights the potential of microalgae and cyanobacteria for food and food-related applications as well as their market size. The chosen topics also include advanced production as mixed microbial communities, production of high-value biomolecules, photoproduction of terpenoid flavoring compounds, their utilization for sustainable agriculture, application as source of nutrients in space, and a comparison with heterotrophic microorganisms like yeast to better evaluate their advantages over existing nutrient sources. This comprehensive assessment should stimulate further interest in this highly relevant research topic., Competing Interests: The authors declare no conflict of interest., (© 2023 Published by Elsevier Ltd.)
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- 2023
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368. A droplet-based microfluidic platform enables high-throughput combinatorial optimization of cyanobacterial cultivation.
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Cao J, Russo DA, Xie T, Groß GA, and Zedler JAZ
- Subjects
- Nitrates, Phosphates, Microfluidics, Synechocystis
- Abstract
Cyanobacteria are fast-growing, genetically accessible, photoautotrophs. Therefore, they have attracted interest as sustainable production platforms. However, the lack of techniques to systematically optimize cultivation parameters in a high-throughput manner is holding back progress towards industrialization. To overcome this bottleneck, here we introduce a droplet-based microfluidic platform capable of one- (1D) and two-dimension (2D) screening of key parameters in cyanobacterial cultivation. We successfully grew three different unicellular, biotechnologically relevant, cyanobacteria: Synechocystis sp. PCC 6803, Synechococcus elongatus UTEX 2973 and Synechococcus sp. UTEX 3154. This was followed by a highly-resolved 1D screening of nitrate, phosphate, carbonate, and salt concentrations. The 1D screening results suggested that nitrate and/or phosphate may be limiting nutrients in standard cultivation media. Finally, we use 2D screening to determine the optimal N:P ratio of BG-11. Application of the improved medium composition in a high-density cultivation setup led to an increase in biomass yield of up to 15.7%. This study demonstrates that droplet-based microfluidics can decrease the volume required for cyanobacterial cultivation and screening up to a thousand times while significantly increasing the multiplexing capacity. Going forward, microfluidics have the potential to play a significant role in the industrial exploitation of cyanobacteria., (© 2022. The Author(s).)
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- 2022
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369. Genomic insights into cyanobacterial protein translocation systems.
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Russo DA and Zedler JAZ
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- Bacterial Proteins metabolism, Biological Transport, Cyanobacteria metabolism, Protein Translocation Systems metabolism, Bacterial Proteins genetics, Cyanobacteria genetics, Protein Translocation Systems genetics
- Abstract
Cyanobacteria are ubiquitous oxygenic photosynthetic bacteria with a versatile metabolism that is highly dependent on effective protein targeting. Protein sorting in diderm bacteria is not trivial and, in cyanobacteria, even less so due to the presence of a complex membrane system: the outer membrane, the plasma membrane and the thylakoid membrane. In cyanobacteria, protein import into the thylakoids is essential for photosynthesis, export to the periplasm fulfills a multifunctional role in maintaining cell homeostasis, and secretion mediates motility, DNA uptake and environmental interactions. Intriguingly, only one set of genes for the general secretory and the twin-arginine translocation pathways seem to be present. However, these systems have to operate in both plasma and thylakoid membranes. This raises the question of how substrates are recognized and targeted to their correct, final destination. Additional complexities arise when a protein has to be secreted across the outer membrane, where very little is known regarding the mechanisms involved. Given their ecological importance and biotechnological interest, a better understanding of protein targeting in cyanobacteria is of great value. This review will provide insights into the known knowns of protein targeting, propose hypotheses based on available genomic sequences and discuss future directions., (© 2020 Walter de Gruyter GmbH, Berlin/Boston.)
- Published
- 2020
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370. A force awakens: exploiting solar energy beyond photosynthesis.
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Russo DA, Zedler JAZ, and Jensen PE
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- Biotechnology, Catalysis, Plants radiation effects, Solar Energy, Photosynthesis, Plant Physiological Phenomena radiation effects, Plants metabolism, Sunlight
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In recent years, efforts to exploit sunlight, a free and abundant energy source, have sped up dramatically. Oxygenic photosynthetic organisms, such as higher plants, algae, and cyanobacteria, can convert solar energy into chemical energy very efficiently using water as an electron donor. By providing organic building blocks for life in this way, photosynthesis is undoubtedly one of the most important processes on Earth. The aim of light-driven catalysis is to harness solar energy, in the form of reducing power, to drive enzymatic reactions requiring electrons for their catalytic cycle. Light-driven enzymes have been shown to have a large number of biotechnological applications, ranging from the production of high-value secondary metabolites to the development of green chemistry processes. Here, we highlight recent key developments in the field of light-driven catalysis using biological components. We will also discuss strategies to design and optimize light-driven systems in order to develop the next generation of sustainable solutions in biotechnology., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Experimental Biology.)
- Published
- 2019
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371. Metaproteomics of Freshwater Microbial Communities.
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Russo DA, Couto N, Beckerman AP, and Pandhal J
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- Chromatography, Liquid, Computational Biology methods, Solvents, Tandem Mass Spectrometry, Workflow, Microbiota, Proteome, Proteomics methods, Water Microbiology
- Abstract
Recent advances in metaproteomics have provided us a link between genomic expression and functional characterization of environmental microbial communities. Therefore, the large-scale identification of proteins expressed by environmental microbiomes allows an unprecedented view of their in situ metabolism and function. However, one of the main challenges in metaproteomics remains the lack of robust analytical pipelines. This is especially true for aquatic environments with low protein concentrations and the presence of compounds that are known to interfere with traditional sample preparation pipelines and downstream LC-MS/MS analyses. In this chapter, a semiquantitative method that spans from sample preparation to functional annotation is provided. This method has been shown to provide in-depth and representative results of both the eukaryotic and prokaryotic fractions of freshwater microbiomes.
- Published
- 2019
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372. Quantitative proteomics of a B 12 -dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism.
- Author
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Helliwell KE, Pandhal J, Cooper MB, Longworth J, Kudahl UJ, Russo DA, Tomsett EV, Bunbury F, Salmon DL, Smirnoff N, Wright PC, and Smith AG
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- Algal Proteins metabolism, Amino Acids metabolism, Chlorophyta drug effects, Chlorophyta genetics, Coculture Techniques, Computational Biology, Electron Transport drug effects, Gene Expression Regulation, Plant drug effects, Mesorhizobium drug effects, Photosynthesis drug effects, RNA, Messenger genetics, RNA, Messenger metabolism, Chlorophyta growth & development, Chlorophyta metabolism, Mesorhizobium growth & development, Proteomics, Symbiosis drug effects, Vitamin B 12 pharmacology
- Abstract
The unicellular green alga Lobomonas rostrata requires an external supply of vitamin B
12 (cobalamin) for growth, which it can obtain in stable laboratory cultures from the soil bacterium Mesorhizobium loti in exchange for photosynthate. We investigated changes in protein expression in the alga that allow it to engage in this mutualism. We used quantitative isobaric tagging (iTRAQ) proteomics to determine the L. rostrata proteome grown axenically with B12 supplementation or in coculture with M. loti. Data are available via ProteomeXchange (PXD005046). Using the related Chlamydomonas reinhardtii as a reference genome, 588 algal proteins could be identified. Enzymes of amino acid biosynthesis were higher in coculture than in axenic culture, and this was reflected in increased amounts of total cellular protein and several free amino acids. A number of heat shock proteins were also elevated. Conversely, photosynthetic proteins and those of chloroplast protein synthesis were significantly lower in L. rostrata cells in coculture. These observations were confirmed by measurement of electron transfer rates in cells grown under the two conditions. The results indicate that, despite the stability of the mutualism, L. rostrata experiences stress in coculture with M. loti, and must adjust its metabolism accordingly., (© 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.)- Published
- 2018
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373. Competitive growth experiments with a high-lipid Chlamydomonas reinhardtii mutant strain and its wild-type to predict industrial and ecological risks.
- Author
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Russo DA, Beckerman AP, and Pandhal J
- Abstract
Key microalgal species are currently being exploited as biomanufacturing platforms using mass cultivation systems. The opportunities to enhance productivity levels or produce non-native compounds are increasing as genetic manipulation and metabolic engineering tools are rapidly advancing. Regardless of the end product, there are both environmental and industrial risks associated to open pond cultivation of mutant microalgal strains. A mutant escape could be detrimental to local biodiversity and increase the risk of algal blooms. Similarly, if the cultivation pond is invaded by a wild-type (WT) microalgae or the mutant reverts to WT phenotypes, productivity could be impacted. To investigate these potential risks, a response surface methodology was applied to determine the competitive outcome of two Chlamydomonas reinhardtii strains, a WT (CC-124) and a high-lipid accumulating mutant (CC-4333), grown in mixotrophic conditions, with differing levels of nitrogen and initial WT to mutant ratios. Results of the growth experiments show that mutant cells have double the exponential growth rate of the WT in monoculture. However, due to a slower transition from lag phase to exponential phase, mutant cells are outcompeted by the WT in every co-culture treatment. This suggests that, under the conditions tested, outdoor cultivation of the C. reinhardtii cell wall-deficient mutant strains does not carry a significant environmental risk to its WT in an escape scenario. Furthermore, lipid results show the mutant strain accumulates over 200% more TAGs per cell, at 50 mg L
-1 NH4 Cl, compared to the WT, therefore, the fragility of the mutant strain could impact on overall industrial productivity.- Published
- 2017
- Full Text
- View/download PDF
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