Academic literature on the topic 'Protein-water systems'
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Journal articles on the topic "Protein-water systems"
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Barkalov, I. M., A. I. Bolshakov, V. I. Goldanskii, and Yu F. Krupyanskii. "Vitrification effects in water—protein systems." Chemical Physics Letters 208, no. 1-2 (June 1993): 1–4. http://dx.doi.org/10.1016/0009-2614(93)80066-x.
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Versace, Rodney E., and Themis Lazaridis. "Modeling Protein–Micelle Systems in Implicit Water." Journal of Physical Chemistry B 119, no. 25 (June 15, 2015): 8037–47. http://dx.doi.org/10.1021/acs.jpcb.5b00171.
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Versace, Rodney E., and Themis Lazaridis. "Modelling Protein-Micelle Systems in Implicit Water." Biophysical Journal 108, no. 2 (January 2015): 249a. http://dx.doi.org/10.1016/j.bpj.2014.11.1378.
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Palacios, Aida C., Carlo Sarnthein-Graf, and Camillo La Mesa. "Equilibrium between phases in water–protein–surfactant systems." Colloids and Surfaces A: Physicochemical and Engineering Aspects 228, no. 1-3 (November 2003): 25–35. http://dx.doi.org/10.1016/s0927-7757(03)00332-7.
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Vorob’ev, Mikhail. "Monitoring of water ordering in aqueous protein systems." Food Hydrocolloids 21, no. 2 (March 2007): 309–12. http://dx.doi.org/10.1016/j.foodhyd.2006.06.001.
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Goncharuk, Elena, Galyna Polishchuk, Iryna Shevchenko, and Tetiana Osmak. "Nature of water bonding in hydrated milk-protein systems." Ukrainian Food Journal 9, no. 1 (March 2020): 111–19. http://dx.doi.org/10.24263/2304-974x-2020-9-1-10.
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Tombs, M. P., B. G. Newsom, and P. Wilding. "PROTEIN SOLUBILITY: PHASE SEPARATION IN ARACHIN-SALT-WATER SYSTEMS." International Journal of Peptide and Protein Research 6, no. 4 (January 12, 2009): 253–77. http://dx.doi.org/10.1111/j.1399-3011.1974.tb02384.x.
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Potes, Naritchaya, Joseph P. Kerry, and Yrjö H. Roos. "Protein Modifications in High Protein-Oil and Protein-Oil-Sugar Systems at Low Water Activity." Food Biophysics 9, no. 1 (August 25, 2013): 49–60. http://dx.doi.org/10.1007/s11483-013-9316-1.
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Bellavia, Giuseppe, Sergio Giuffrida, Grazia Cottone, Antonio Cupane, and Lorenzo Cordone. "Protein Thermal Denaturation and Matrix Glass Transition in Different Protein−Trehalose−Water Systems." Journal of Physical Chemistry B 115, no. 19 (May 19, 2011): 6340–46. http://dx.doi.org/10.1021/jp201378y.
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Martini, Silvia, Claudia Bonechi, Alberto Foletti, and Claudio Rossi. "Water-Protein Interactions: The Secret of Protein Dynamics." Scientific World Journal 2013 (2013): 1–6. http://dx.doi.org/10.1155/2013/138916.
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Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS) and selective (R1SE) spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.
Dissertations / Theses on the topic "Protein-water systems"
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Pence, David N. "Protein partitioning in two-phase liquid-liquid acetonitrile-water systems." Ohio : Ohio University, 1996. http://www.ohiolink.edu/etd/view.cgi?ohiou1178047340.
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Konidala, Praveen. "Molecular dynamics simulations of glycolipid and carbohydrate binding protein systems in the explicit water environment." [S.l.] : [s.n.], 2006. http://deposit.ddb.de/cgi-bin/dokserv?idn=979967791.
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Ajaj, Yathrib [Verfasser], Hermann [Gutachter] Weingärtner, and Christian [Gutachter] Herrmann. "Dynamics and thermodynamics of protein folding and interactions in water-cosolvent systems / Yathrib Ajaj ; Gutachter: Hermann Weingärtner, Christian Herrmann." Bochum : Ruhr-Universität Bochum, 2012. http://d-nb.info/1131354575/34.
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Glättli, Alice [Verfasser]. "Computer simulation of biomolecular systems: From the formulation of models for water, to the interpretation of experiment, to the investigation of polypeptide folding and membrane protein dynamics / Alice Glättli." Aachen : Shaker, 2004. http://d-nb.info/1172613141/34.
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Ogden, Leanne Gaye. "Interfacial studies of oil-water systems containing fat crystals." Thesis, Oxford Brookes University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.283814.
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Salehi, Sayed Mohammad. "Engineering Cell-free Protein Synthesis Technology for Codon Reassignment, Biotherapeutics Production using Just-add-Water System, and Biosensing Endocrine Disrupting Compounds." BYU ScholarsArchive, 2017. https://scholarsarchive.byu.edu/etd/6711.
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Cell-free protein synthesis is an emerging technology that has many applications. The open nature of this system makes it a compelling technology that can be manipulated to answer many needs that are unavailable in other systems. This dissertation reports on engineering this technology for: 1) sense codon emancipation for incorporation of multiple unnatural amino acids; 2) expressing a hard-to-express anticancer biotherapeutic and introducing a just-add-water system; 3) a biosensing ligand that interacts with nuclear hormone receptors. Emancipating sense codons toward a minimized genetic code is of significant interest to science and engineering. A promising approach to sense codon emancipation is the targeted in vitro removal of native tRNA. Here we introduce a new in-vitro or "cell-free" approach to emancipate sense codons via efficient and affordable degradation of endogenous tRNA using RNase-coated superparamagnetic beads. The presented method removes greater than 99% of tRNA in cell lysates, while preserving cell-free protein synthesis activity. The resulting tRNA-depleted lysate is compatible with in vitro-transcribed synthetic tRNA for the production of peptides and proteins. Biotherapeutics have many promising applications, such as anti-cancer treatments, immune suppression, and vaccines. However, due to their biological nature, some biotherapeutics can be challenging to rapidly express and screen for activity through traditional recombinant methods. In this work, we demonstrate the use of cell-free systems for the expression and direct screening of the difficult-to-express cytotoxic protein onconase. Using cell-free systems, onconase can be rapidly expressed in soluble, active form. Furthermore, the open nature of the reaction environment allows for direct and immediate downstream characterization without the need of purification. Also, we report the ability of a "just-add-water" lyophilized cell-fee system to produce onconase. Here we introduce a Rapid Adaptable Portable In-vitro Detection biosensor platform (RAPID) for detecting ligands that interact with nuclear hormone receptors (NHRs). The biosensor is based on an engineered, allosterically-activated fusion protein, which contains the ligand binding domain from a target NHR. The presented RAPID biosensor platform is significantly faster and less labor intensive than commonly available technologies, making it a promising tool for detecting environmental EDC contamination and screening potential NHR-targeted pharmaceuticals.
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George, Mary. "Urea and Non-Protein Nitrogen Metabolism in Infants : With Special Reference to the Sudden Infant Death Syndrome (SIDS)." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Univ.-bibl. [distributör], 2001. http://publications.uu.se/theses/91-554-5141-1/.
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PANZICA, Massimo. "Protein-Sugar-Water Systems Far From Thermodynamic Ideality." Doctoral thesis, 2012. http://hdl.handle.net/10447/94736.
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Mondal, Sayantan. "Theoretical studies of chemical dynamics in complex systems: Nanoconfined water, microdroplets, biomolecular hydration layer, and water-mediated protein association." Thesis, 2020. https://etd.iisc.ac.in/handle/2005/4898.
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The thesis contains theoretical studies of the structure and dynamics in different complex systems. Depending on the systems and properties of interest we divide the thesis into five parts. In the first part, we study chemical dynamics in nanoconfined water. Here we primarily focus on the dielectric properties of dipolar fluids confined inside nano-containers of various sizes and shapes. We discover an extremely slow convergence of the static dielectric constant (ε) of water with the size of the nanospheres. Our studies reveal an ultrafast relaxation of the collective orientation of water which is absent in the Stockmayer fluid. We connect this anomaly to the substantially low value of the Kirkwood g-factor for spherically confined water. We extrapolate the values of ε to obtain its true value in the thermodynamic limit which corroborates well with the values in periodic systems. We perform molecular dynamics simulations with three different liquid-surface interactions to study the surface effects.
The dielectric response of water under becomes anisotropic in non-spherical confinements, namely, cylindrical and slab geometries. Because of the difference in the dielectric boundary conditions along the different directions, the eigenvalues of the dielectric tensor becomes unequal. We derive the fluctuation formulae for the anisotropic dielectric constants. For the cylindrical geometry, we find that the axial component (εz) and the perpendicular component (εx/y) converge to the bulk value, with the diameter of the nanotube, in an opposite manner. εx/y shows relatively slower convergence starting from a lower value whereas εz shows faster convergence starting from a higher value. For the slab system, the parallel component (ε∥) does not show much deviation from the bulk value. On the contrary, the perpendicular component (ε⊥) exhibits extremely low values for smaller systems and shows a slow convergence toward bulk. Interestingly, in the slab geometry, the dielectric relaxation along the perpendicular direction becomes ultrafast with pronounced oscillations. Our results match well with recent dielectric microscopy experiments. We perform a constrained Ising model-based analysis and to understand the inwardly propagating destructions among correlations.
In addition to the above, we study the heterogeneous dynamics of water inside nano-enclosures of different shapes. We investigate the position-dependent solvation of model ionic/dipolar probes and find that the slow components of solvation show highly non-monotonic behaviour with the distance of the probe from the surface. To study the static and dynamical heterogeneity, we obtain the non-Gaussian parameter [α2(t)] and non-linear density response function [χ4(t)]. α2(t) shows an anomalous long-time growth for non-spherical systems which we attribute to the slow dynamics of water along the non-periodic direction(s).
In the second part, we focus on the chemical dynamics in small-sized (~μm) droplets that exhibit noticeably different chemistry than bulk water. Several chemical reactions show markedly enhanced rates in the droplet media. Here we present a generalized theoretical model and analytically solve the adjoint equations for two- and three-dimensional systems. We obtain exact expressions for the mean search time (MST) that is found to be proportional to R2/D [R=radius, D=relative diffusion constant]. We carry out Brownian dynamics simulations and show that the MST of reactive partner search in droplets is orders of magnitude smaller than that in the bulk. As the experiments often use an external electric field to charge the droplets, we study the effect of ions and electric fields on the bond dissociation energy. We find that the presence of an ion or electric field weakens the bond and enhances the intrinsic reaction rate. Our results describe the interplay between diffusion control and activation controlled processes.
In the third part, we study the dynamics of interfacial water molecules in the biomolecular hydration layers. Here we first aim to resolve a long-standing controversy regarding the timescale of water dynamics in the protein hydration layer, that is, solvation dynamics and dielectric relaxation finds substantial slow relaxation whereas NMR experiments find retardation only by a factor of 2-3. To this goal, we obtain distributions of single-particle relaxation timescales and show that the average values obtained from experiments hide the true picture. To our surprise, we find the existence of both faster and slower than bulk water molecules in the hydration layer. We unravel the origin of disparate timescales (from sub-100 fs to hundreds of ps) observed in the solvation dynamics of natural probe tryptophan tagged to three different proteins- Lysozyme, Myoglobin, and sweet protein Monellin. We show that the neighbourhood charged residues and the intrinsic side-chain fluctuations contribute to the observed slow dynamics. We further decompose the response into protein core, side-chains, and water contributions to study the nature of coupling. We find surprising anti-correlation between the energy fluctuations of protein and water. Our simulation results support the widely discussed protein-solvent slaving picture developed from earlier Mössbauer spectroscopy experiments. We also study the origin of the power law decay observed in DNA solvation dynamics. We employ the Oosawa model, continuum model, mode coupling theory, and continuous time random walk based analyses to unearth the effect of counterion motions. We study the solvation dynamics of DNA bases and a minor groove bound probe.
In the fourth part, we characterize the various protonated forms of metformin hydrochloride (MET) by employing computational and spectroscopic techniques. We develop an AMBER based force-field for three protonation states of MET and validate them against available experimental results. We use this force-field to study the interaction of MET with double-stranded B-DNAs. As there is evidence of anti-tumour and anti-cancer activity of MET, we aim to understand its mode of binding with DNA. We employ metadynamics based advanced sampling techniques to obtain the free energy landscape of the binding process. We find that MET prefers AT-rich minor grooves through non-intercalative mode of binding. We confirm these claims from fluorescence spectroscopy and circular dichroism experiments.
In the fifth and last part of the thesis, we study the structure and aggregation of insulin oligomers (dimer and hexamer) in water and water-ethanol binary mixtures. Insulin is biologically active in its monomeric form but gets stored in the pancreas as hexamers. The inter-conversion between monomer and hexamer occurs via dimeric intermediates. Here we present the structural analysis of insulin hexamer in water and water-ethanol binary mixture by using atomistic molecular dynamics and X-ray crystallography. We find that the water molecules trapped inside the central hydrophilic cavity of hexamer play a central role in sustaining the robust barrel-shaped structure. The presence of ethanol (even in lower concentrations) deforms the hexameric assembly. Next, we study the energetics of the insulin dimer association/dissociation process. We obtain the free energy landscape from parallel tempering metadynamics simulations in a well-tempered ensemble with respect to two collective variables- inter-monomeric distance and the number of inter-monomeric contacts. We find that the activation barrier of dissociation drastically decreases in the presence of 5% and 10% (v/v) ethanol. We attribute this effect to the preferential solvation of the dimer forming hydrophobic surface of the monomers that results in the destruction of inter-monomeric hydrogen bonding. We analyze the evolving structures along the minimum energy pathway and establish the role of the solvent.
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Constantinescu, Aruxandei Diana [Verfasser]. "Patterns of protein stability and interactions in water-cosolvent systems / vorgelegt von Diana Constantinescu Aruxandei." 2010. http://d-nb.info/1007596546/34.
Full textBooks on the topic "Protein-water systems"
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Frontiers of engineering: Reports on leading-edge engineering from the 2008 symposium. Washington: National Academies Press, 2009.
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Symposium on Frontiers of Engineering (2008 New Mexico). Frontiers of engineering: Reports on leading-edge engineering from the 2008 symposium. Washington: National Academies Press, 2009.
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Symposium on Frontiers of Engineering (2008 New Mexico). Frontiers of engineering: Reports on leading-edge engineering from the 2008 symposium. Washington: National Academies Press, 2009.
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Kuwajima, Kunihiro. Water and biomolecules: Physical chemistry of life phenomena. Berlin: Springer, 2009.
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Roxtrom, Git. Towards Simulating Fully Charged Protein-DNA Systems in Water: Zif268-DNA As a Test Case (Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, 492). Uppsala Universitet, 1999.
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Kuwajima, Kunihiro, Fumio Hirata, Mikio Kataoka, Yuji Goto, and Masahide Terazima. Water and Biomolecules: Physical Chemistry of Life Phenomena. Springer, 2010.
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Nozière, Pierre. INRA feeding system for ruminants. Edited by Daniel Sauvant and Luc Delaby. Wageningen Academic Publishers, 2018. http://dx.doi.org/10.3920/978-90-8686-872-8.
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The INRA Feeding System for Ruminants has been renewed to better address emerging challenges for animal nutrition: prevision of productive responses, product quality, animal health and emissions to the environment, in a larger extent of breeding contexts. The new system is mainly built from meta-analyses of large data bases, and modelling. The dietary supply model accounts for digestive interactions and flows of individual nutrients, so that feed values depend on the final ration. Animal requirements account for variability in metabolic efficiency. Various productive and non-productive animal responses to diets are quantified. This book presents the whole system for dairy and meat, large and small ruminant production, including specificities for tropical and Mediterranean areas. The first two sections present biological concepts and equations (with their field of application and statistical accuracy) used to predict intake (including at grazing) and nutrient supply (Section 1), animal’s requirements and multiple responses to diets (Section 2). They apply to net energy, metabolisable protein and amino acids, water, minerals and vitamins. Section 3 presents the use of concepts and equations in rationing with two purposes: (1) diet calculation for a given performance objective; and (2) prediction of the multiple responses of animal to diet changes. Section 4 displays the tables of feed values, and their prevision. All the equations and concepts are embedded in the fifth version of INRAtion® software for practical use.
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Nutrient Requirements of Domesticated Ruminants. CSIRO Publishing, 2007. http://dx.doi.org/10.1071/9780643095106.
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Nutrient Requirements of Domesticated Ruminants draws on the most up-to-date research on the energy, protein, mineral, vitamin and water requirements of beef and dairy cattle, sheep and goats. It defines the responses of animals, in weight change, milk production and wool growth, to quantitative and qualitative changes in their feed supply. It has particular application to grazing animals.
Factors affecting the intake of feed are taken into account and recommendations are given according to the production systems being used; for instance, the feed intake of a grazing animal is affected by a larger number of variables than a housed animal. Examples of the estimation of the energy and nutrients required for the different production systems are given, as well as the production expected from predicted feed intakes. The interactions between the grazing animal, the pasture and any supplementary feeds are complex, involving herbage availability, diet selection and substitution. To facilitate the application of these recommendations to particular grazing situations, readers are directed to decision support tools and spreadsheet programs.
Nutrient Requirements of Domesticated Ruminants is based on the benchmark publication, Feeding Standards for Australian Livestock: Ruminants, published in 1990 by CSIRO Publishing on behalf of the Standing Committee on Agriculture.
It provides comprehensive and useful information for graziers, livestock advisors, veterinarians, feed manufacturers and animal nutrition researchers. The recommendations described are equally applicable to animals in feedlots or drought yards.
Book chapters on the topic "Protein-water systems"
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Otting, Gottfried, and Kurt Wüthrich. "Studies of Protein Hydration by Direct NMR Observation of Individual Protein-Bound Water Molecules." In Water and Ions in Biomolecular Systems, 141–47. Basel: Birkhäuser Basel, 1990. http://dx.doi.org/10.1007/978-3-0348-7253-9_13.
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Siódmiak, Jacek. "Water Molecules Organization Surrounding Ions, Amphiphilic Protein Residues, and Hyaluronan." In Biologically-Inspired Systems, 131–54. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-67227-0_7.
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Tombs, M. P., and S. E. Harding. "Protein Transport Processes in the Water-Water Interface in Incompatible Two Phase Systems." In Separations Using Aqueous Phase Systems, 229–32. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4684-5667-7_38.
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Tombs, M. P. "Phase Separation in Protein — Water Systems and the Formation of Structure." In Properties of Water in Foods, 25–36. Dordrecht: Springer Netherlands, 1985. http://dx.doi.org/10.1007/978-94-009-5103-7_2.
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Römisch, Jürgen, Uwe Harnisch, Ulrich Schulte, and Hanns Weiss. "Crystallisation of Water-Soluble Preparations of the Iron-Sulfur-Protein and Cytochrome C1 of Ubiquinol:Cytochrome Reductase from Neurospora Mitochondria." In Cytochrome Systems, 303–8. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4613-1941-2_39.
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Muegge, I., A. Irgens-Defregger, and E. W. Knapp. "Model Calculations of Protein-Water Systems and of Long Time Dynamics of Proteins." In Informatik aktuell, 89–100. Berlin, Heidelberg: Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-642-78072-1_10.
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Hongsprabhas, P., and K. Israkarn. "Water and Protein Modifier Effects on the Phase Transitions and Microstructure of Mung-Bean Starch Granules." In Water Properties in Food, Health, Pharmaceutical and Biological Systems: ISOPOW 10, 507–13. Oxford, UK: Wiley-Blackwell, 2010. http://dx.doi.org/10.1002/9780470958193.ch43.
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Herrero, Mario, Daniel Mason-D’Croz, Philip K. Thornton, Jessica Fanzo, Jonathan Rushton, Cecile Godde, Alexandra Bellows, et al. "Livestock and Sustainable Food Systems: Status, Trends, and Priority Actions." In Science and Innovations for Food Systems Transformation, 375–99. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-15703-5_20.
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AbstractLivestock are a critically important component of the food system, although the sector needs a profound transformation to ensure that it contributes to a rapid transition towards sustainable food systems. This chapter reviews and synthesises the evidence available on changes in demand for livestock products in the last few decades, and the multiple socio-economic roles that livestock have around the world. We also describe the nutrition, health, and environmental impacts for which the sector is responsible. We propose eight critical actions for transitioning towards a more sustainable operating space for livestock. (1) Facilitate shifts in the consumption of animal source foods (ASF), recognising that global reductions will be required, especially in communities with high consumption levels, while promoting increased levels in vulnerable groups, including the undernourished, pregnant women and the elderly. (2) Continue work towards the sustainable intensification of livestock systems, paying particular attention to animal welfare, food-feed competition, blue water use, disease transmission and perverse economic incentives. (3) Embrace the potential of circularity in livestock systems as a way of partially decoupling livestock from land. (4) Adopt practices that lead to the direct or indirect mitigation of greenhouse gases. (5) Adopt some of the vast array of novel technologies at scale and design incentive mechanisms for their rapid deployment. (6) Diversify the protein sources available for human consumption and feed, focusing on the high-quality alternative protein sources that have lower environmental impacts. (7) Tackle antimicrobial resistance effectively through a combination of technology and new regulations, particularly for the fast-growing poultry and pork sectors and for feedlot operations. (8) Implement true cost of food and true-pricing approaches to ASF consumption.
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Hensey, C. E., D. Boscoboinik, and A. Azzi. "Control of Protein Kinase C Function: An Inhibitor Study." In Water and Ions in Biomolecular Systems, 101–13. Basel: Birkhäuser Basel, 1990. http://dx.doi.org/10.1007/978-3-0348-7253-9_10.
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Mărgineanu, Doru-Georg. "Effect of Protein Cross-Linking on Excitable and Non-Excitable Membranes." In Water and Ions in Biological Systems, 367–75. Boston, MA: Springer US, 1985. http://dx.doi.org/10.1007/978-1-4899-0424-9_35.
Full textConference papers on the topic "Protein-water systems"
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Liu, Zhen, Zhitao Zhou, Hu Tao, and Keyin Liu. "Direct patterning using protein-based water lithography." In 2018 IEEE Micro Electro Mechanical Systems (MEMS). IEEE, 2018. http://dx.doi.org/10.1109/memsys.2018.8346600.
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Barajas, John, Jana Latayan, Sheree Pagsuyoin, Florinda Bacani, Joost Santos, Raymond Tan, Aileen Orbecido, Luis Razon, and Michelle Almendrala. "Water disinfection using moringa protein adsorbed on rice husk ash." In 2016 Systems and Information Engineering Design Symposium (SIEDS). IEEE, 2016. http://dx.doi.org/10.1109/sieds.2016.7489291.
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Kasztelanic, R., M. Olszewski, and R. Buczynski. "Heavy metal water pollution sensor based on Green Fluorescent Protein." In CLEO: Applications and Technology. Washington, D.C.: Optica Publishing Group, 2023. http://dx.doi.org/10.1364/cleo_at.2023.jw2a.108.
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In this study, the possibility of monitoring heavy metal pollution in water using Green Fluorescent Protein was analyzed. Two measurement systems based on glass capillary and fluorescence signal fading measurements were considered and optimized.
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Sargautis, Darius, Tatjana Kince, and Vanda Sargautiene. "Review: current trends in oat protein recovery and utilization in aqueous food systems." In Research for Rural Development 2021 : annual 27th International scientific conference proceedings. Latvia University of Life Sciences and Technologies, 2021. http://dx.doi.org/10.22616/rrd.27.2021.011.
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Oat protein itself, as a substance, has extensively been studied providing information on its nutritional value, some functional properties and possible applicability in food systems. Chosen protein isolation methods and technological aspects define final composition of obtained oat protein product, its concentration, nutrition value and its functionality in food industry. Scientific data on oat protein recovery methods, typically relying on protein solubility or dry fractionation, provides an insufficient knowledge about the success in commercialization of oat protein recovery technologies and their derivatives in form of oat protein. The aim of the study was to analyse and summarize the research findings on oat protein extraction methods and functional properties of oat protein. Semi-systematic, monographic methods were used to analyse the oat protein isolation techniques, functional properties of oat protein in aqueous food systems, covering the latest information on oat protein extraction methods. Wet and dry isolation methods were demonstrated as main methods in oat protein extraction. Functional properties of oat protein, such as thermal stability, solubility, emulsification, water hydration capacity and foaming were reviewed and evaluated, identifying limitations and protein alterations which occur through the oat protein extraction process. The study provides recent trends in oat protein recovery technologies, along with an overview of current and potential oat protein utilization in food systems.
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Hötzer, Benjamin, Timo Scheu, Gregor Jung, and Stefan Castritius. "Measurement of the copper concentration in drinking water based on changes of the fluorescence lifetime of the green fluorescent protein." In SPIE Optical Systems Design, edited by Laurent Mazuray, Rolf Wartmann, Andrew P. Wood, Marta C. de la Fuente, Jean-Luc M. Tissot, Jeffrey M. Raynor, Tina E. Kidger, et al. SPIE, 2012. http://dx.doi.org/10.1117/12.981170.
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Creasy, M. Austin, and Donald J. Leo. "Modeling Bilayer Systems as Electrical Networks." In ASME 2010 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. ASMEDC, 2010. http://dx.doi.org/10.1115/smasis2010-3791.
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Bilayers are synthetically made cell membranes that are used to study cell membrane properties or make functional devices that use the properties of the cell membrane components. Lipids and proteins are two of the main components of a cell membrane. Lipids are amphiphilic molecules that can self assemble into organized structures in the presences of water and this self assembly property can be used to form bilayers. Because of the amphiphilic nature of the lipids, a bilayer is impermeable to ion flow. Proteins are the active structures of a cell membrane that opens pores through the membrane for ions and other molecules to pass. Proteins are made from amino acids and have varying properties that depend on its configuration. Some proteins are activated by reactions (chemical, thermal, etc) or gradients induced across the bilayer. One way of testing bilayers to find bilayer properties is to induce a potential gradient across a membrane that induces ion flow and this flow can be measured as an electrical current. But, these pores may be voltage gated or activated by some other stimuli and therefore cannot be modeled as a linear conductor. Usually the conductance of the protein is a nonlinear function of the input that activates the protein. A small system that consists of a single bilayer and protein with few changing components can be easily modeled, but as systems become larger with multiple bilayers, multiple variables, and multiple proteins, the models will become more complex. This paper looks at how to model a system of multiple bilayers and the peptide alamethicin. An analytical expression for this peptide is used to match experimental data and a short study on the sensitivity of the variables is performed.
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Yesiltas, Betul, Charlotte Jacobsen, Egon B. Hansen, Michael Overgaard, Paolo Marcatili, Pedro Garcia-Moreno, Rasmus K. Mikkelsen, and Simon Gregersen. "Physical and oxidative stability of emulsions stabilized with fractionated potato protein hydrolysates obtained from starch production byproduct: Use of bioinformatics and proteomics." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/xxty9713.
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With the increasing demand for sustainable and functional proteins from alternative sources, it is necessary to use advanced proteomics and bioinformatics tools for more time and cost-efficient research. The identification and release of abundant proteins/peptides from plant-based sources has been gaining significant attention by the food industry in the last decade. Despite its low protein content (1–2%), the magnitude of proteins obtained from the starch industry (~240,000 tons/year) makes potatoes a highly relevant source as a plant-based protein. Previously, we have identified and validated abundant peptides with good emulsifying and antioxidant properties using bioinformatics and proteomics tools as well as in vitro model systems. Using data-driven targeted hydrolysis, we were able to release validated, functional peptides from the potato protein obtained from potato fruit juice, a protein rich by-product of potato starch production. This work focuses on fractionation of potato protein hydrolysates (PPH) obtained through such targeted hydrolysis using trypsin and subsequent fraction characterization. Unfractionated (PPH1) and membrane-fractionated (PPH2 as >10kDa, PPH3 as 10-5kDa, PPH4 as 5-0.8kDa and PPH5 as < 0.8kDa) PPH was characterized for emulsifying and antioxidant properties/potential. Pendant drop technique and dilatational rheology were applied for determining interfacial tension and viscoelasticity of the PPH fractions at the oil-water interface. PPH2 (>10kDa) showed higher decrease of oil-water interfacial tension. All fractions predominantly provided elastic, weak and easily stretchable interfaces. PPH2 provided more rigid interfacial layer than the other fractions. Radical scavenging and metal chelating activities of PPHs were also tested and the best activities were provided by fractions >5kDa. Furthermore, their ability to form physically and oxidatively stable 5% fish oil-in-water emulsions were investigated during 8-day storage and results generally showed that fractions >5kDa provided the best stability followed by the 5–0.8kDa fraction.
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Vatansever, Serap, Rachel Mitacek, Vaidehi Narkar, and Pam Ismail. "Comparing the Structural and Functional Characteristics of Novel Proteins from Pennycress (Thlaspi Arvense) and Camelina Sativa." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/xbog8744.
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Justification:Global demand sustainable plant protein ingredients is peaking. Camelina and pennycress are sustainable, short season cover crops with high protein content (25-35% protein) and are thus great potential sources of protein ingredients. Developing commercially viable protein ingredients may expand the use of these sustainable crops for various food applications. Objective: The objective was to evaluate and compare the structural and functional attributes of both proteins extracted under optimized and industry feasible conditions. Methods: Defatted meals from seeds of both crops were used to extract protein following optimized salt solubilization coupled with ultrafiltration and alkaline solubilization coupled with isoelectric precipitation. Structural characterization of the protein isolates included evaluating surface hydrophobicity and charge, protein profiles, and state of denaturation. Functional properties including protein solubility, gelation, water holding capacity, and emulsification were also assessed and compared through principal component analysis. Results: Camelina and pennycress protein isolates (CPI, PcPI) from salt extraction were less denatured, and had lower surface charge and hydrophobicity than the alkaline extracted counterparts. There were significant differences in surface properties between CPI and PcPI. Salt-extracted CPI had higher surface charge and lower surface hydrophobicity than PcPI. Both PcPIs had a greater solubility than CPIs. Furthermore, salt-extracted CPI did not form a gel, while CPI from alkaline extraction had good gelation properties. PcPI also had good gelation properties, while its emulsification capacity was significantly lower compared to CPI. Significance: Results indicates that CPI and PcPI have a great potential to be utilized as novel protein ingredients that can replace partially or wholly traditional protein ingredients in various food applications. Knowledge of differences in the structural and functional attributes of these novel proteins allows for targeted selection of most suitable applications. Successful incorporation of these proteins in food systems will result in increasing the value and use of these sustainable crops.
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Lamsal, Buddhi, and Md Mahfuzur Rahman. "Conventional and novel technologies for extraction of protein and their impact on structure and functionality as ingredient." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/dhxf1174.
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Proteins possess their techno-functionalities by virtues of their state of being, i.e., their molecular makeup and structure, which in turn, is affected by the technologies employed to extract them from the matrices they belong to. This is true for both plant proteins and cell-based proteins. While pH-modulated solubility based aqueous extraction, followed by isolation, is the overwhelming method for plant protein preparations, other technologies, for example dry fractionation (separation based on density, air drag or electrostatic charges), enzyme-, microwave-, ultrasound-, pulsed electric energy- and high pressure-assisted extraction, subcritical water, reverse micelles extraction, and aqueous two-phase systems extraction have been researched for better yields and functionality. Physical separation or dry fractionation preserves the molecular structure and protein possesses better techno-functional and sensory properties than conventional alkaline and acid-based methods. However, dry fractionation can produce only protein concentrate, not isolate. Although alkaline and acid-based methods can prepare to isolate efficiently, subsequent acid precipitation and drying methods form insoluble aggregates and enhance oxidation, which in turn, affect solubility and related functional properties as well as contribute to off-flavor. This presentation will summarize such technologies for extraction, potential for sustainability and their impact on protein's structure and techno-functionalities such as solubility, foaming/emulsion, gelation etc. It will also present authors' recent research on ultrasound-assisted extraction of soy protein and changes in major isolate structure/ function.
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Grandum, Svein, Yasunori Kobayashi, Akira Yabe, Sohei Matsumoto, Fumio Takemura, Kazuya Nakagomi, and Per-Erling Frivik. "Molecular Dynamics Simulation of Ice Crystal Growth From a Surface Containing Adsorbed Antifreeze Protein." In ASME 1997 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 1997. http://dx.doi.org/10.1115/imece1997-0957.
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Abstract In order to develop advanced low temperature storage systems based on slurry ice, resistant to recrystallization, Antifreeze Protein (AFP) has been introduced as an effective additive. In this paper, the mechanism of crystal growth when AFPs are adsorbing to the surface of ice has been investigated by Molecular Dynamics simulation. Liquid water molecules were located above the adsorption plane, containing a simplified model of the AFP and the growth potential, corresponding to a supercooling of approximately 40 K was applied. Growth was not easily occurring close to the AFP but at sites where the molecules easily could generate at least two hydrogen bonds to the crystal lattice. This resulted in a curved ice surface, similar to the previously observations using a Scanning Tunneling Microscope.
Reports on the topic "Protein-water systems"
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Wong, Eric A., and Zehava Uni. Nutrition of the Developing Chick Embryo: Nutrient Uptake Systems of the Yolk Sac Membrane and Embryonic Intestine. United States Department of Agriculture, June 2012. http://dx.doi.org/10.32747/2012.7697119.bard.
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We have examined the developmental changes in composition, amount, and uptake of yolk nutrients (fat, protein, water and carbohydrates) and the expression ofnutrient transporters in the yolk sac membrane (YSM) from embryonic day 11 (Ell) to 21 (E21) and small intestine from embryonic day 15 (E15) to E21 in embryos from young (22-25 wk) and old (45-50 wk) Cobb and Leghorn breeder flocks. The developmental expression profiles for the peptide transporter 1 (PepTl), the amino acid transporters, EAAT3, CAT-1 and BOAT, the sodium glucose transporter (SGLTl), the fructose transporter (GLUT5), the digestive enzymes aminopeptidase N (APN) and sucraseisomaltase (SI) were assayed by the absolute quantification real time PCR method in the YSM and embryonic intestine. Different temporal patterns of expression were observed for these genes. The effect of in ovo injection of peptides (the dipeptide Gly-Sar, purified peptides, trypsin hydrolysate) on transporter gene expression has been examined in the embryonic intestine. Injection of a partial protein hydrolysate resulted in an increase in expression of the peptide transporter PepT2. We have initiated a transcriptome analysis of genes expressed in the YSM at different developmental ages to better understand the function of the YSM.
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Vakharia, Vikram, Shoshana Arad, Yonathan Zohar, Yacob Weinstein, Shamila Yusuff, and Arun Ammayappan. Development of Fish Edible Vaccines on the Yeast and Redmicroalgae Platforms. United States Department of Agriculture, February 2013. http://dx.doi.org/10.32747/2013.7699839.bard.
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Betanodaviruses are causative agents of viral nervous necrosis (VNN), a devastating disease of cultured marine fish worldwide. Betanodavirus (BTN) genome is composed of two single-stranded, positive-sense RNA molecules. The larger genomic segment, RNA1 (3.1 kb), encodes the RNA-dependent RNA polymerase, while the smaller genomic segment, RNA 2 (1.4kb), encodes the coat protein. This structural protein is the host-protective antigen of VNN which assembles to form virus-like particles (VLPs). BTNs are classified into four genotypes, designated red-spotted grouper nervous necrosis virus (RGNNV), barfin flounder nervous necrosis virus (BFNNV), tiger puffer nervous necrosis virus (TPNNV), and striped jack nervous necrosis virus (SJNNV), based on phylogenetic analysis of the coat protein sequences. RGNNV type is quite important as it has a broad host-range, infecting warm-water fish species. At present, there is no commercial vaccine available to prevent VNN in fish. The general goal of this research was to develop oral fish vaccines in yeast and red microalgae (Porphyridium sp.) against the RGNNV genotype. To achieve this, we planned to clone and sequence the coat protein gene of RGNNV, express the coat protein gene of RGNNV in yeast and red microalgae and evaluate the immune response in fish fed with recombinantVLPs antigens produced in yeast and algae. The collaboration between the Israeli group and the US group, having wide experience in red microalgae biochemistry, molecular genetics and large-scale cultivation, and the development of viral vaccines and eukaryotic protein expression systems, respectively, was synergistic to produce a vaccine for fish that would be cost-effective and efficacious against the betanodavirus infection.
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Minz, Dror, Stefan J. Green, Noa Sela, Yitzhak Hadar, Janet Jansson, and Steven Lindow. Soil and rhizosphere microbiome response to treated waste water irrigation. United States Department of Agriculture, January 2013. http://dx.doi.org/10.32747/2013.7598153.bard.
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Research objectives : Identify genetic potential and community structure of soil and rhizosphere microbial community structure as affected by treated wastewater (TWW) irrigation. This objective was achieved through the examination soil and rhizosphere microbial communities of plants irrigated with fresh water (FW) and TWW. Genomic DNA extracted from soil and rhizosphere samples (Minz laboratory) was processed for DNA-based shotgun metagenome sequencing (Green laboratory). High-throughput bioinformatics was performed to compare both taxonomic and functional gene (and pathway) differences between sample types (treatment and location). Identify metabolic pathways induced or repressed by TWW irrigation. To accomplish this objective, shotgun metatranscriptome (RNA-based) sequencing was performed. Expressed genes and pathways were compared to identify significantly differentially expressed features between rhizosphere communities of plants irrigated with FW and TWW. Identify microbial gene functions and pathways affected by TWW irrigation*. To accomplish this objective, we will perform a metaproteome comparison between rhizosphere communities of plants irrigated with FW and TWW and selected soil microbial activities. Integration and evaluation of microbial community function in relation to its structure and genetic potential, and to infer the in situ physiology and function of microbial communities in soil and rhizospere under FW and TWW irrigation regimes. This objective is ongoing due to the need for extensive bioinformatics analysis. As a result of the capabilities of the new PI, we have also been characterizing the transcriptome of the plant roots as affected by the TWW irrigation and comparing the function of the plants to that of the microbiome. *This original objective was not achieved in the course of this study due to technical issues, especially the need to replace the American PIs during the project. However, the fact we were able to analyze more than one plant system as a result of the abilities of the new American PI strengthened the power of the conclusions derived from studies for the 1ˢᵗ and 2ⁿᵈ objectives. Background: As the world population grows, more urban waste is discharged to the environment, and fresh water sources are being polluted. Developing and industrial countries are increasing the use of wastewater and treated wastewater (TWW) for agriculture practice, thus turning the waste product into a valuable resource. Wastewater supplies a year- round reliable source of nutrient-rich water. Despite continuing enhancements in TWW quality, TWW irrigation can still result in unexplained and undesirable effects on crops. In part, these undesirable effects may be attributed to, among other factors, to the effects of TWW on the plant microbiome. Previous studies, including our own, have presented the TWW effect on soil microbial activity and community composition. To the best of our knowledge, however, no comprehensive study yet has been conducted on the microbial population associated BARD Report - Project 4662 Page 2 of 16 BARD Report - Project 4662 Page 3 of 16 with plant roots irrigated with TWW – a critical information gap. In this work, we characterize the effect of TWW irrigation on root-associated microbial community structure and function by using the most innovative tools available in analyzing bacterial community- a combination of microbial marker gene amplicon sequencing, microbial shotunmetagenomics (DNA-based total community and gene content characterization), microbial metatranscriptomics (RNA-based total community and gene content characterization), and plant host transcriptome response. At the core of this research, a mesocosm experiment was conducted to study and characterize the effect of TWW irrigation on tomato and lettuce plants. A focus of this study was on the plant roots, their associated microbial communities, and on the functional activities of plant root-associated microbial communities. We have found that TWW irrigation changes both the soil and root microbial community composition, and that the shift in the plant root microbiome associated with different irrigation was as significant as the changes caused by the plant host or soil type. The change in microbial community structure was accompanied by changes in the microbial community-wide functional potential (i.e., gene content of the entire microbial community, as determined through shotgun metagenome sequencing). The relative abundance of many genes was significantly different in TWW irrigated root microbiome relative to FW-irrigated root microbial communities. For example, the relative abundance of genes encoding for transporters increased in TWW-irrigated roots increased relative to FW-irrigated roots. Similarly, the relative abundance of genes linked to potassium efflux, respiratory systems and nitrogen metabolism were elevated in TWW irrigated roots when compared to FW-irrigated roots. The increased relative abundance of denitrifying genes in TWW systems relative FW systems, suggests that TWW-irrigated roots are more anaerobic compare to FW irrigated root. These gene functional data are consistent with geochemical measurements made from these systems. Specifically, the TWW irrigated soils had higher pH, total organic compound (TOC), sodium, potassium and electric conductivity values in comparison to FW soils. Thus, the root microbiome genetic functional potential can be correlated with pH, TOC and EC values and these factors must take part in the shaping the root microbiome. The expressed functions, as found by the metatranscriptome analysis, revealed many genes that increase in TWW-irrigated plant root microbial population relative to those in the FW-irrigated plants. The most substantial (and significant) were sodium-proton antiporters and Na(+)-translocatingNADH-quinoneoxidoreductase (NQR). The latter protein uses the cell respiratory machinery to harness redox force and convert the energy for efflux of sodium. As the roots and their microbiomes are exposed to the same environmental conditions, it was previously hypothesized that understanding the soil and rhizospheremicrobiome response will shed light on natural processes in these niches. This study demonstrate how newly available tools can better define complex processes and their downstream consequences, such as irrigation with water from different qualities, and to identify primary cues sensed by the plant host irrigated with TWW. From an agricultural perspective, many common practices are complicated processes with many ‘moving parts’, and are hard to characterize and predict. Multiple edaphic and microbial factors are involved, and these can react to many environmental cues. These complex systems are in turn affected by plant growth and exudation, and associated features such as irrigation, fertilization and use of pesticides. However, the combination of shotgun metagenomics, microbial shotgun metatranscriptomics, plant transcriptomics, and physical measurement of soil characteristics provides a mechanism for integrating data from highly complex agricultural systems to eventually provide for plant physiological response prediction and monitoring. BARD Report
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Coplin, David L., Shulamit Manulis, and Isaac Barash. roles Hrp-dependent effector proteins and hrp gene regulation as determinants of virulence and host-specificity in Erwinia stewartii and E. herbicola pvs. gypsophilae and betae. United States Department of Agriculture, June 2005. http://dx.doi.org/10.32747/2005.7587216.bard.
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Gram-negative plant pathogenic bacteria employ specialized type-III secretion systems (TTSS) to deliver an arsenal of pathogenicity proteins directly into host cells. These secretion systems are encoded by hrp genes (for hypersensitive response and pathogenicity) and the effector proteins by so-called dsp or avr genes. The functions of effectors are to enable bacterial multiplication by damaging host cells and/or by blocking host defenses. We characterized essential hrp gene clusters in the Stewart's Wilt of maize pathogen, Pantoea stewartii subsp. stewartii (Pnss; formerly Erwinia stewartii) and the gall-forming bacterium, Pantoea agglomerans (formerly Erwinia herbicola) pvs. gypsophilae (Pag) and betae (Pab). We proposed that the virulence and host specificity of these pathogens is a function of a) the perception of specific host signals resulting in bacterial hrp gene expression and b) the action of specialized signal proteins (i.e. Hrp effectors) delivered into the plant cell. The specific objectives of the proposal were: 1) How is the expression of the hrp and effector genes regulated in response to host cell contact and the apoplastic environment? 2) What additional effector proteins are involved in pathogenicity? 3) Do the presently known Pantoea effector proteins enter host cells? 4) What host proteins interact with these effectors? We characterized the components of the hrp regulatory cascade (HrpXY ->7 HrpS ->7 HrpL ->7 hrp promoters), showed that they are conserved in both Pnss and Fag, and discovered that the regulation of the hrpS promoter (hrpSp) may be a key point in integrating apoplastic signals. We also analyzed the promoters recognized by HrpL and demonstrated the relationship between their composition and efficiency. Moreover, we showed that promoter strength can influence disease expression. In Pnss, we found that the HrpXY two-component signal system may sense the metabolic status of the bacterium and is required for full hrp gene expression in planta. In both species, acyl-homoserine lactone-mediated quorum sensing may also regulate epiphytic fitness and/or pathogenicity. A common Hrp effector protein, DspE/WtsE, is conserved and required for virulence of both species. When introduced into corn cells, Pnss WtsE protein caused water-soaked lesions. In other plants, it either caused cell death or acted as an Avr determinant. Using a yeast- two-hybrid system, WtsE was shown to interact with a number of maize signal transduction proteins that are likely to have roles in either programmed cell death or disease resistance. In Pag and Pab, we have characterized the effector proteins HsvG, HsvB and PthG. HsvG and HsvB are homologous proteins that determine host specificity of Pag and Pab on gypsophila and beet, respectively. Both possess a transcriptional activation domain that functions in yeast. PthG was found to act as an Avr determinant on multiple beet species, but was required for virulence on gypsophila. In addition, we demonstrated that PthG acts within the host cell. Additional effector genes have been characterized on the pathogenicity plasmid, pPATHₚₐg, in Pag. A screen for HrpL- regulated genes in Pnsspointed up 18 candidate effector proteins and four of these were required for full virulence. It is now well established that the virulence of Gram-negative plant pathogenic bacteria is governed by Hrp-dependent effector proteins. However; the mode of action of many effectors is still unresolved. This BARD supported research will significantly contribute to the understanding of how Hrp effectors operate in Pantoea spp. and how they control host specificity and affect symptom production. This may lead to novel approaches for genetically engineering plants resistant to a wide range of bacterial pathogens by inactivating the Hrp effectors with "plantabodies" or modifying their receptors, thereby blocking the induction of the susceptible response. Alternatively, innovative technologies could be used to interfere with the Hrp regulatory cascade by blocking a critical step or mimicking plant or quorum sensing signals.
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Kirchhoff, Helmut, and Ziv Reich. Protection of the photosynthetic apparatus during desiccation in resurrection plants. United States Department of Agriculture, February 2014. http://dx.doi.org/10.32747/2014.7699861.bard.
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In this project, we studied the photosynthetic apparatus during dehydration and rehydration of the homoiochlorophyllous resurrection plant Craterostigmapumilum (retains most of the photosynthetic components during desiccation). Resurrection plants have the remarkable capability to withstand desiccation, being able to revive after prolonged severe water deficit in a few days upon rehydration. Homoiochlorophyllous resurrection plants are very efficient in protecting the photosynthetic machinery against damage by reactive oxygen production under drought. The main purpose of this BARD project was to unravel these largely unknown protection strategies for C. pumilum. In detail, the specific objectives were: (1) To determine the distribution and local organization of photosynthetic protein complexes and formation of inverted hexagonal phases within the thylakoid membranes at different dehydration/rehydration states. (2) To determine the 3D structure and characterize the geometry, topology, and mechanics of the thylakoid network at the different states. (3) Generation of molecular models for thylakoids at the different states and study the implications for diffusion within the thylakoid lumen. (4) Characterization of inter-system electron transport, quantum efficiencies, photosystem antenna sizes and distribution, NPQ, and photoinhibition at different hydration states. (5) Measuring the partition of photosynthetic reducing equivalents between the Calvin cycle, photorespiration, and the water-water cycle. At the beginning of the project, we decided to use C. pumilum instead of C. wilmsii because the former species was available from our collaborator Dr. Farrant. In addition to the original two dehydration states (40 relative water content=RWC and 5% RWC), we characterized a third state (15-20%) because some interesting changes occurs at this RWC. Furthermore, it was not possible to detect D1 protein levels by Western blot analysis because antibodies against other higher plants failed to detect D1 in C. pumilum. We developed growth conditions that allow reproducible generation of different dehydration and rehydration states for C. pumilum. Furthermore, advanced spectroscopy and microscopy for C. pumilum were established to obtain a detailed picture of structural and functional changes of the photosynthetic apparatus in different hydrated states. Main findings of our study are: 1. Anthocyan accumulation during desiccation alleviates the light pressure within the leaves (Fig. 1). 2. During desiccation, stomatal closure leads to drastic reductions in CO2 fixation and photorespiration. We could not identify alternative electron sinks as a solution to reduce ROS production. 3. On the supramolecular level, semicrystalline protein arrays were identified in thylakoid membranes in the desiccated state (see Fig. 3). On the electron transport level, a specific series of shut downs occur (summarized in Fig. 2). The main events include: Early shutdown of the ATPase activity, cessation of electron transport between cyt. bf complex and PSI (can reduce ROS formation at PSI); at higher dehydration levels uncoupling of LHCII from PSII and cessation of electron flow from PSII accompanied by crystal formation. The later could severe as a swift PSII reservoir during rehydration. The specific order of events in the course of dehydration and rehydration discovered in this project is indicative for regulated structural transitions specifically realized in resurrection plants. This detailed knowledge can serve as an interesting starting point for rationale genetic engineering of drought-tolerant crops.
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Shani, Uri, Lynn Dudley, Alon Ben-Gal, Menachem Moshelion, and Yajun Wu. Root Conductance, Root-soil Interface Water Potential, Water and Ion Channel Function, and Tissue Expression Profile as Affected by Environmental Conditions. United States Department of Agriculture, October 2007. http://dx.doi.org/10.32747/2007.7592119.bard.
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Constraints on water resources and the environment necessitate more efficient use of water. The key to efficient management is an understanding of the physical and physiological processes occurring in the soil-root hydraulic continuum.While both soil and plant leaf water potentials are well understood, modeled and measured, the root-soil interface where actual uptake processes occur has not been sufficiently studied. The water potential at the root-soil interface (yᵣₒₒₜ), determined by environmental conditions and by soil and plant hydraulic properties, serves as a boundary value in soil and plant uptake equations. In this work, we propose to 1) refine and implement a method for measuring yᵣₒₒₜ; 2) measure yᵣₒₒₜ, water uptake and root hydraulic conductivity for wild type tomato and Arabidopsis under varied q, K⁺, Na⁺ and Cl⁻ levels in the root zone; 3) verify the role of MIPs and ion channels response to q, K⁺ and Na⁺ levels in Arabidopsis and tomato; 4) study the relationships between yᵣₒₒₜ and root hydraulic conductivity for various crops representing important botanical and agricultural species, under conditions of varying soil types, water contents and salinity; and 5) integrate the above to water uptake term(s) to be implemented in models. We have made significant progress toward establishing the efficacy of the emittensiometer and on the molecular biology studies. We have added an additional method for measuring ψᵣₒₒₜ. High-frequency water application through the water source while the plant emerges and becomes established encourages roots to develop towards and into the water source itself. The yᵣₒₒₜ and yₛₒᵢₗ values reflected wetting and drying processes in the rhizosphere and in the bulk soil. Thus, yᵣₒₒₜ can be manipulated by changing irrigation level and frequency. An important and surprising finding resulting from the current research is the obtained yᵣₒₒₜ value. The yᵣₒₒₜ measured using the three different methods: emittensiometer, micro-tensiometer and MRI imaging in both sunflower, tomato and corn plants fell in the same range and were higher by one to three orders of magnitude from the values of -600 to -15,000 cm suggested in the literature. We have added additional information on the regulation of aquaporins and transporters at the transcript and protein levels, particularly under stress. Our preliminary results show that overexpression of one aquaporin gene in tomato dramatically increases its transpiration level (unpublished results). Based on this information, we started screening mutants for other aquaporin genes. During the feasibility testing year, we identified homozygous mutants for eight aquaporin genes, including six mutants for five of the PIP2 genes. Including the homozygous mutants directly available at the ABRC seed stock center, we now have mutants for 11 of the 19 aquaporin genes of interest. Currently, we are screening mutants for other aquaporin genes and ion transporter genes. Understanding plant water uptake under stress is essential for the further advancement of molecular plant stress tolerance work as well as for efficient use of water in agriculture. Virtually all of Israel’s agriculture and about 40% of US agriculture is made possible by irrigation. Both countries face increasing risk of water shortages as urban requirements grow. Both countries will have to find methods of protecting the soil resource while conserving water resources—goals that appear to be in direct conflict. The climate-plant-soil-water system is nonlinear with many feedback mechanisms. Conceptual plant uptake and growth models and mechanism-based computer-simulation models will be valuable tools in developing irrigation regimes and methods that maximize the efficiency of agricultural water. This proposal will contribute to the development of these models by providing critical information on water extraction by the plant that will result in improved predictions of both water requirements and crop yields. Plant water use and plant response to environmental conditions cannot possibly be understood by using the tools and language of a single scientific discipline. This proposal links the disciplines of soil physics and soil physical chemistry with plant physiology and molecular biology in order to correctly treat and understand the soil-plant interface in terms of integrated comprehension. Results from the project will contribute to a mechanistic understanding of the SPAC and will inspire continued multidisciplinary research.
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Eneroth, Hanna, Hanna Karlsson Potter, and Elin Röös. Environmental impact of coffee, tea and cocoa – data collection for a consumer guide for plant-based foods. Department of Energy and Technology, Swedish University of Agricultural Sciences, 2022. http://dx.doi.org/10.54612/a.2n3m2d2pjl.
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In 2020, WWF launched a consumer guide on plant-based products targeting Swedish consumers. The development of the guide is described in a journal paper (Karlsson Potter & Röös, 2021) and the environmental impact of different plant based foods was published in a report (Karlsson Potter, Lundmark, & Röös, 2020). This report was prepared for WWF Sweden to provide scientific background information for complementing the consumer guide with information on coffee, tea and cocoa. This report includes quantitative estimations for several environmental categories (climate, land use, biodiversity and water use) of coffee (per L), tea (per L) and cocoa powder (per kg), building on the previously established methodology for the consumer guide. In addition, scenarios of consumption of coffee, tea and cocoa drink with milk/plant-based drinks and waste at household level, are presented. Tea, coffee and cacao beans have a lot in common. They are tropical perennial crops traditionally grown in the shade among other species, i.e. in agroforestry systems. Today, the production in intensive monocultures has negative impact on biodiversity. Re-introducing agroforestry practices may be part of the solution to improve biodiversity in these landscapes. Climate change will likely, due to changes in temperature, extreme weather events and increases in pests and disease, alter the areas where these crops can be grown in the future. A relatively high ratio of the global land used for coffee, tea and cocoa is certified according to sustainability standards, compared to other crops. Although research on the implications of voluntary standards on different outcomes is inconclusive, the literature supports that certifications have a role in incentivizing more sustainable farming. Coffee, tea and cocoa all contain caffeine and have a high content of bioactive compounds such as antioxidants, and they have all been associated with positive health outcomes. While there is a strong coffee culture in Sweden and coffee contributes substantially to the environmental impact of our diet, tea is a less consumed beverage. Cocoa powder is consumed as a beverage, but substantial amounts of our cocoa consumption is in the form of chocolate. Roasted ground coffee on the Swedish market had a climate impact of 4.0 kg CO2e per kg powder, while the climate impact of instant coffee powder was 11.5 kg CO2e per kg. Per litre, including the energy use for making the coffee, the total climate impact was estimated to 0.25 kg CO2e per L brewed coffee and 0.16 kg CO2e per L for instant coffee. Less green coffee beans are needed to produce the same amount of ready to drink coffee from instant coffee than from brewed coffee. Tea had a climate impact of approximately 6.3 kg CO2 e per kg dry leaves corresponding to an impact of 0.064 CO2e per L ready to drink tea. In the assessment of climate impact per cup, tea had the lowest impact with 0.013 kg CO2e, followed by black instant coffee (0.024 kg CO2e), black coffee (0.038 kg CO2e), and cocoa drink made with milk (0.33 kg CO2e). The climate impact of 1kg cocoa powder on the Swedish market was estimated to 2.8 kg CO2e. Adding milk to coffee or tea increases the climate impact substantially. The literature describes a high proportion of the total climate impact of coffee from the consumer stage due to the electricity used by the coffee machine. However, with the Nordic low-carbon energy mix, the brewing and heating of water and milk contributes to only a minor part of the climate impact of coffee. As in previous research, coffee also had a higher land use, water use and biodiversity impact than tea per L beverage. Another factor of interest at the consumer stage is the waste of prepared coffee. Waste of prepared coffee contributes to climate impact through the additional production costs and electricity for preparation, even though the latter was small in our calculations. The waste of coffee and tea at Summary household level is extensive and measures to reduce the amount of wasted coffee and tea could reduce the environmental impact of Swedish hot drink consumption. For the final evaluation of coffee and tea for the consumer guide, the boundary for the fruit and vegetable group was used. The functional unit for coffee and tea was 1 L prepared beverage without any added milk or sweetener. In the guide, the final evaluation of conventionally grown coffee is that it is ‘yellow’ (‘Consume sometimes’), and for organic produce, ‘light green’ (‘Please consume). The evaluation of conventionally grown tea is that it is ‘light green’, and for organic produce, ‘dark green’ (‘Preferably consume this’). For cocoa, the functional unit is 1 kg of cocoa powder and the boundary was taken from the protein group. The final evaluation of conventionally grown cocoa is that it is ‘orange’ (‘Be careful’), and for organically produced cocoa, ‘light green’.
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Coplin, David, Isaac Barash, and Shulamit Manulis. Role of Proteins Secreted by the Hrp-Pathways of Erwinia stewartii and E. herbicola pv. gypsophilae in Eliciting Water-Soaking Symptoms and Initiating Galls. United States Department of Agriculture, June 2001. http://dx.doi.org/10.32747/2001.7580675.bard.
Full textAbstract:
Many bacterial pathogens of plants can inject pathogenicity proteins into host cells using a specialized type III secretion system encoded by hrpgenes. This system deliver effector proteins, into plant cells that function in both susceptible and resistant interactions. We have found that the virulence of Erwinia stewartii(Es; syn. Pantoea stewartii) and Erwinia herbicola pv. gypsophilae (Ehg, syn. Pantoea agglomerans), which cause Stewart's wilt of corn and galls on Gypsophila, respectively, depends on hrpgenes. The major objectives of this project were: To increase expression of hrpgenes in order to identify secreted proteins; to identify genes for proteins secreted by the type-III systems and determine if they are required for pathogenicity; and to determine if the secreted proteins can function within eukaryotic cells. We found that transcription of the hrp and effector genes in Es and Ehg is controlled by at least four genes that constitute a regulatory cascade. Environmental and/or physiological signaling appears to be mediated by the HrpX/HrpY two component system, with HrpX functioning as a sensor-kinase and HrpY as a response regulator. HrpYupregulateshrpS, which encodes a transcriptional enhancer. HrpS then activates hrpL, which encodes an alternate sigma factor that recognizes "hrp boxes". All of the regulatory genes are essential for pathogenicity, except HrpX, which appears only to be required for induction of the HR in tobacco by Es. In elucidating this regulatory pathway in both species, we made a number of significant new discoveries. HrpX is unusual for a sensor-kinase because it is cytoplasmic and contains PAS domains, which may sense the redox state of the bacterium. In Es, a novel methyl-accepting protein may function upstream of hrpY and repress hrp gene expression in planta. The esaIR quorum sensing system in Es represses hrp gene expression in Es in response to cell-density. We have discovered six new type III effector proteins in these species, one of which (DspE in Ehg and WtsE in Es) is common to both pathogens. In addition, Es wtsG, which is a homolog of an avrPpiB from P. syringae pv. pisi, and an Ehg ORF, which is a homolog of P. syringae pv. phaseolicola AvrPphD, were both demonstrated to encode virulence proteins. Two plasmidborne, Ehg Hop proteins, HsvG and PthG, are required for infection of gypsophilia, but interestingly, PthG also acts as an Avr elicitor in beets. Using a calmodulin-dependent adenylate cyclase (cyaA) reporter gene, we were successful in demonstrating that an HsvG-CyaA fusion protein can be transferred into human HeLa cells by the type-III system of enteropathogenic E. coli. This is a highly significant accomplishment because it is the first direct demonstration that an effector protein from a plant pathogenic bacterium is capable of being translocated into a eukaryotic cell by a type-III secretion system. Ehg is considered a limiting factor in Gypsophila production in Israel and Stewart’s Wilt is a serious disease in the Eastern and North Central USA, especially on sweet corn in epidemic years. We believe that our basic research on the characterization of type III virulence effectors should enable future identification of their receptors in plant cells. This may lead to novel approaches for genetically engineering resistant plants by modifying their receptors or inactivating effectors and thus blocking the induction of the susceptible response. Alternatively, hrp gene regulation might also provide a target for plant produced compounds that interfere with recognition of the host by the pathogen. Such strategies would be broadly applicable to a wide range of serious bacterial diseases on many crops throughout the USA and Israel.
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Shomer, Ilan, Ruth E. Stark, Victor Gaba, and James D. Batteas. Understanding the hardening syndrome of potato (Solanum tuberosum L.) tuber tissue to eliminate textural defects in fresh and fresh-peeled/cut products. United States Department of Agriculture, November 2002. http://dx.doi.org/10.32747/2002.7587238.bard.
Full textAbstract:
The project sought to understand factors and mechanisms involved in the hardening of potato tubers. This syndrome inhibits heat softening due to intercellular adhesion (ICA) strengthening, compromising the marketing of industrially processed potatoes, particularly fresh peeled-cut or frozen tubers. However, ICA strengthening occurs under conditions which are inconsistent with the current ideas that relate it to Ca-pectate following pectin methyl esterase (PME) activity or to formation of rhamnogalacturonan (RG)-II-borate. First, it was necessary to induce strengthening of the middle lamellar complex (MLX) and the ICA as a stress response in some plant parenchyma. As normally this syndrome does not occur uniformly enough to study it, we devised an efficient model in which ICA-strengthening is induced consistently under simulated stress by short-chain, linear, mono-carboxylic acid molecules (OAM), at 65 oC [appendix 1 (Shomer&Kaaber, 2006)]. This rapid strengthening was insufficient for allowing the involved agents assembly to be identifiable; but it enabled us to develop an efficient in vitro system on potato tuber parenchyma slices at 25 ºC for 7 days, whereas unified stress was reliably simulated by OAMs in all the tissue cells. Such consistent ICA-strengthening in vitro was found to be induced according to the unique physicochemical features of each OAM as related to its lipophilicity (Ko/w), pKa, protonated proportion, and carbon chain length by the following parameters: OAM dissociation constant (Kdiss), adsorption affinity constant (KA), number of adsorbed OAMs required for ICA response (cooperativity factor) and the water-induced ICA (ICAwater). Notably, ICA-strengthening is accompanied by cell sap leakage, reflecting cell membrane rupture. In vitro, stress simulation by OAMs at pH<pKa facilitated the consistent assembly of ICAstrengthening agents, which we were able to characterize for the first time at the molecular level within purified insoluble cell wall of ICA-strengthened tissue. (a) With solid-state NMR, we established the chemical structure and covalent binding to cell walls of suberin-like agents associated exclusively with ICA strengthening [appendix 3 (Yu et al., 2006)]; (b) Using proteomics, 8 isoforms of cell wall-bound patatin (a soluble vacuolar 42-kDa protein) were identified exclusively in ICA-strengthened tissue; (c) With light/electron microscopy, ultrastructural characterization, histochemistry and immunolabeling, we co-localized patatin and pectin in the primary cell wall and prominently in the MLX; (d) determination of cell wall composition (pectin, neutral sugars, Ca-pectate) yielded similar results in both controls and ICA-strengthened tissue, implicating factors other than PME activity, Ca2+ or borate ions; (e) X-ray powder diffraction experiments revealed that the cellulose crystallinity in the cell wall is masked by pectin and neutral sugars (mainly galactan), whereas heat or enzymatic pectin degradation exposed the crystalline cellulose structure. Thus, we found that exclusively in ICA-strengthened tissue, heat-resistant pectin is evident in the presence of patatin and suberinlike agents, where the cellulose crystallinity was more hidden than in fresh control tissue. Conclusions: Stress response ICA-strengthening is simulated consistently by OAMs at pH< pKa, although PME and formation of Ca-pectate and RG-II-borate are inhibited. By contrast, at pH>pKa and particularly at pH 7, ICA-strengthening is mostly inhibited, although PME activity and formation of Ca-pectate or RG-II-borate are known to be facilitated. We found that upon stress, vacuolar patatin is released with cell sap leakage, allowing the patatin to associate with the pectin in both the primary cell wall and the MLX. The stress response also includes formation of covalently bound suberin-like polyesters within the insoluble cell wall. The experiments validated the hypotheses, thus led to a novel picture of the structural and molecular alterations responsible for the textural behavior of potato tuber. These findings represent a breakthrough towards understanding of the hardening syndrome, laying the groundwork for potato-handling strategies that assure textural quality of industrially processed particularly in fresh peeled cut tubers, ready-to-prepare and frozen preserved products.