Journal articles on the topic 'Compartmentalized reactions'
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1
Rodier, Bradley J., Al de Leon, Christina Hemmingsen, and Emily Pentzer. "Polymerizations in oil-in-oil emulsions using 2D nanoparticle surfactants." Polymer Chemistry 9, no. 13 (2018): 1547–50. http://dx.doi.org/10.1039/c7py01819c.
2
Simon, David, Franziska Obst, Sebastian Haefner, Toni Heroldt, Martin Peiter, Frank Simon, Andreas Richter, Brigitte Voit, and Dietmar Appelhans. "Hydrogel/enzyme dots as adaptable tool for non-compartmentalized multi-enzymatic reactions in microfluidic devices." Reaction Chemistry & Engineering 4, no. 1 (2019): 67–77. http://dx.doi.org/10.1039/c8re00180d.
3
Huttanus, Herbert M., and Ryan S. Senger. "A synthetic biosensor to detect peroxisomal acetyl-CoA concentration for compartmentalized metabolic engineering." PeerJ 8 (September 8, 2020): e9805. http://dx.doi.org/10.7717/peerj.9805.
Abstract:
Background Sub-cellular compartmentalization is used by cells to create favorable microenvironments for various metabolic reactions. These compartments concentrate enzymes, separate competing metabolic reactions, and isolate toxic intermediates. Such advantages have been recently harnessed by metabolic engineers to improve the production of various high-value chemicals via compartmentalized metabolic engineering. However, measuring sub-cellular concentrations of key metabolites represents a grand challenge for compartmentalized metabolic engineering. Methods To this end, we developed a synthetic biosensor to measure a key metabolite, acetyl-CoA, in a representative compartment of yeast, the peroxisome. This synthetic biosensor uses enzyme re-localization via PTS1 signal peptides to construct a metabolic pathway in the peroxisome which converts acetyl-CoA to polyhydroxybutyrate (PHB) via three enzymes. The PHB is then quantified by HPLC. Results The biosensor demonstrated the difference in relative peroxisomal acetyl-CoA availability under various culture conditions and was also applied to screening a library of single knockout yeast mutants. The screening identified several mutants with drastically reduced peroxisomal acetyl-CoA and one with potentially increased levels. We expect our synthetic biosensors can be widely used to investigate sub-cellular metabolism and facilitate the “design-build-test” cycle of compartmentalized metabolic engineering.
4
Punyasu, Nattharat, Saowalak Kalapanulak, and Treenut Saithong. "Development of a compartmentalized model for insight into the structured metabolic pathway of carbon metabolism in cassava leaves." APRIL 2019 13, (04) 2019 (April 20, 2019): 605–15. http://dx.doi.org/10.21475/ajcs.19.13.04.p1639.
Abstract:
In silico metabolic modeling has enabled systematic study of complicated metabolic processes underlying phenotypes of organisms. Modeling of plant metabolism is often hampered by the network complexity and lack of adequate knowledge. The existing metabolic networks of cassava only cover broad metabolism and are not compartmentalized to truly represent metabolism in photosynthetic tissues. To address the aforementioned limitations and develop a robust metabolic network, physiological and genomic data derived from cassava and leaf models of Arabidopsis and rice were to extend the scope of the existing model. The proposed compartmentalized network of metabolism in photosynthetic tissues of cassava, ph-MeRecon (photosynthetic-Manihot esculenta Metabolic Pathway Reconstruction) was developed based on the information resulting of the comparative study of multiple model plants and cassava genome. The ph-MeRecon covers primary carbon metabolism and comprises 461 metabolites, 550 reactions, and 1,037 metabolic genes. Enzymatic genes on the network were validated using RNA-expression data, and the reactions and pathways were compartmentalized into cytoplasm, chloroplast, mitochondria, and peroxisome. To ensure network connectivity, metabolic gaps were filled using gap reactions obtained from literature and metabolic pathway omnibus. In addition, information on plant physiology, including photosynthetic light-dependent reactions, carboxylase and oxygenase activity of RuBisCO enzyme, and phosphoenolpyruvate carboxylase enzyme activity was incorporated into ph-MeRecon to mimic cellular metabolism in cassava leaves. Thus, ph-MeRecon offers a multi-level platform for system analysis of cellular mechanisms underlying phenotypes of interest in cassava. The ph-MeRecon metabolic model is available at http://bml.sbi.kmutt.ac.th/ph-MeRecon/.
5
Kato, Shuzo, David Garenne, Vincent Noireaux, and Yusuke T. Maeda. "Phase Separation and Protein Partitioning in Compartmentalized Cell-Free Expression Reactions." Biomacromolecules 22, no. 8 (July 14, 2021): 3451–59. http://dx.doi.org/10.1021/acs.biomac.1c00546.
6
Baier, Gerold, and Sven Sahle. "Spatio-temporal patterns with hyperchaotic dynamics in diffusively coupled biochemical oscillators." Discrete Dynamics in Nature and Society 1, no. 2 (1997): 161–67. http://dx.doi.org/10.1155/s1026022697000162.
Abstract:
We present three examples how complex spatio-temporal patterns can be linked to hyperchaotic attractors in dynamical systems consisting of nonlinear biochemical oscillators coupled linearly with diffusion terms. The systems involved are: (a) a two-variable oscillator with two consecutive autocatalytic reactions derived from the Lotka–Volterra scheme; (b) a minimal two-variable oscillator with one first-order autocatalytic reaction; (c) a three-variable oscillator with first-order feedback lacking autocatalysis. The dynamics of a finite number of coupled biochemical oscillators may account for complex patterns in compartmentalized living systems like cells or tissue, and may be tested experimentally in coupled microreactors.
7
Daddaoua, Abdelali, Tino Krell, Carlos Alfonso, Bertrand Morel, and Juan-Luis Ramos. "Compartmentalized Glucose Metabolism in Pseudomonas putida Is Controlled by the PtxS Repressor." Journal of Bacteriology 192, no. 17 (June 25, 2010): 4357–66. http://dx.doi.org/10.1128/jb.00520-10.
Abstract:
ABSTRACT Metabolic flux analysis revealed that in Pseudomonas putida KT2440 about 50% of glucose taken up by the cells is channeled through the 2-ketogluconate peripheral pathway. This pathway is characterized by being compartmentalized in the cells. In fact, initial metabolism of glucose to 2-ketogluconate takes place in the periplasm through a set of reactions catalyzed by glucose dehydrogenase and gluconate dehydrogenase to yield 2-ketogluconate. This metabolite is subsequently transported to the cytoplasm, where two reactions are carried out, giving rise to 6-phosphogluconate, which enters the Entner-Doudoroff pathway. The genes for the periplasmic and cytoplasmic set of reactions are clustered in the host chromosome and grouped within two independent operons that are under the control of the PtxS regulator, which also modulates its own synthesis. Here, we show that although the two catabolic operons are induced in vivo by glucose, ketogluconate, and 2-ketogluconate, in vitro we found that only 2-ketogluconate binds to the regulator with an apparent KD (equilibrium dissociation constant) of 15 μM, as determined using isothermal titration calorimetry assays. PtxS is made of two domains, a helix-turn-helix DNA-binding domain located at the N terminus and a C-terminal domain that binds the effector. Differential scanning calorimetry assays revealed that PtxS unfolds via two events characterized by melting points of 48.1°C and 57.6°C and that, in the presence of 2-ketogluconate, the unfolding of the effector binding domain occurs at a higher temperature, providing further evidence for 2-ketogluconate-PtxS interactions. Purified PtxS is a dimer that binds to the target promoters with affinities in the range of 1 to 3 μM. Footprint analysis revealed that PtxS binds to an almost perfect palindrome that is present within the three promoters and whose consensus sequence is 5′-TGAAACCGGTTTCA-3′. This palindrome overlaps with the RNA polymerase binding site.
8
Di Bernardo, Salvatore, Romana Fato, and Giorgio Lenaz. "Redox Reactions in Lipid Membranes as a Model for Primordial Energy-Conserving Systems." International Astronomical Union Colloquium 161 (January 1997): 437–42. http://dx.doi.org/10.1017/s0252921100014950.
Abstract:
AbstractOne of the peculiar aspects of living systems is the production and conservation of energy. This aspect is provided by specialized organelles, such as the mitochondria and chloroplasts, in developed living organisms. In primordial systems lacking specialized enzymatic complexes the energy supply was probably bound to the generation and maintenance of an asymmetric distribution of charged molecules in compartmentalized systems. On the basis of experimental evidence, we suggest that lipophilic quinones were involved in the generation of this asymmetrical distribution of charges through vectorial redox reactions across lipid membranes.
9
Obst, Franziska, Anthony Beck, Chayan Bishayee, Philipp J. Mehner, Andreas Richter, Brigitte Voit, and Dietmar Appelhans. "Hydrogel Microvalves as Control Elements for Parallelized Enzymatic Cascade Reactions in Microfluidics." Micromachines 11, no. 2 (February 5, 2020): 167. http://dx.doi.org/10.3390/mi11020167.
Abstract:
Compartmentalized microfluidic devices with immobilized catalysts are a valuable tool for overcoming the incompatibility challenge in (bio) catalytic cascade reactions and high-throughput screening of multiple reaction parameters. To achieve flow control in microfluidics, stimuli-responsive hydrogel microvalves were previously introduced. However, an application of this valve concept for the control of multistep reactions was not yet shown. To fill this gap, we show the integration of thermoresponsive poly(N-isopropylacrylamide) (PNiPAAm) microvalves (diameter: 500 and 600 µm) into PDMS-on-glass microfluidic devices for the control of parallelized enzyme-catalyzed cascade reactions. As a proof-of-principle, the biocatalysts glucose oxidase (GOx), horseradish peroxidase (HRP) and myoglobin (Myo) were immobilized in photopatterned hydrogel dot arrays (diameter of the dots: 350 µm, amount of enzymes: 0.13–2.3 µg) within three compartments of the device. Switching of the microvalves was achieved within 4 to 6 s and thereby the fluid pathway of the enzyme substrate solution (5 mmol/L) in the device was determined. Consequently, either the enzyme cascade reaction GOx-HRP or GOx-Myo was performed and continuously quantified by ultraviolet-visible (UV-Vis) spectroscopy. The functionality of the microvalves was shown in four hourly switching cycles and visualized by the path-dependent substrate conversion.
10
Obst, Franziska, David Simon, Philipp J. Mehner, Jens W. Neubauer, Anthony Beck, Oleksandr Stroyuk, Andreas Richter, Brigitte Voit, and Dietmar Appelhans. "One-step photostructuring of multiple hydrogel arrays for compartmentalized enzyme reactions in microfluidic devices." Reaction Chemistry & Engineering 4, no. 12 (2019): 2141–55. http://dx.doi.org/10.1039/c9re00349e.
Abstract:
A moulding technique is presented for the simultaneous photostructuring on the μm scale of hydrogels with nanomaterials on one substrate, usable for the fabrication of microfluidic double-chamber reactors.
11
Vafakish, Bahareh, and Lee D. Wilson. "A Review on Recent Progress of Glycan-Based Surfactant Micelles as Nanoreactor Systems for Chemical Synthesis Applications." Polysaccharides 2, no. 1 (March 7, 2021): 168–86. http://dx.doi.org/10.3390/polysaccharides2010012.
Abstract:
The nanoreactor concept and its application as a modality to carry out chemical reactions in confined and compartmentalized structures continues to receive increasing attention. Micelle-based nanoreactors derived from various classes of surfactant demonstrate outstanding potential for chemical synthesis. Polysaccharide (glycan-based) surfactants are an emerging class of biodegradable, non-toxic, and sustainable alternatives over conventional surfactant systems. The unique structure of glycan-based surfactants and their micellar structures provide a nanoenvironment that differs from that of the bulk solution, and supported by chemical reactions with uniquely different reaction rates and mechanisms. In this review, the aggregation of glycan-based surfactants to afford micelles and their utility for the synthesis of selected classes of reactions by the nanoreactor technique is discussed. Glycan-based surfactants are ecofriendly and promising surfactants over conventional synthetic analogues. This contribution aims to highlight recent developments in the field of glycan-based surfactants that are relevant to nanoreactors, along with future opportunities for research. In turn, coverage of research for glycan-based surfactants in nanoreactor assemblies with tailored volume and functionality is anticipated to motivate advanced research for the synthesis of diverse chemical species.
12
Siau, Jia Wei, Samuel Nonis, Sharon Chee, Li Quan Koh, Fernando J. Ferrer, Christopher J. Brown, and Farid J. Ghadessy. "Directed co-evolution of interacting protein–peptide pairs by compartmentalized two-hybrid replication (C2HR)." Nucleic Acids Research 48, no. 22 (October 26, 2020): e128-e128. http://dx.doi.org/10.1093/nar/gkaa933.
Abstract:
Abstract Directed evolution methodologies benefit from read-outs quantitatively linking genotype to phenotype. We therefore devised a method that couples protein–peptide interactions to the dynamic read-out provided by an engineered DNA polymerase. Fusion of a processivity clamp protein to a thermostable nucleic acid polymerase enables polymerase activity and DNA amplification in otherwise prohibitive high-salt buffers. Here, we recapitulate this phenotype by indirectly coupling the Sso7d processivity clamp to Taq DNA polymerase via respective fusion to a high affinity and thermostable interacting protein–peptide pair. Escherichia coli cells co-expressing protein–peptide pairs can directly be used in polymerase chain reactions to determine relative interaction strengths by the measurement of amplicon yields. Conditional polymerase activity is further used to link genotype to phenotype of interacting protein–peptide pairs co-expressed in E. coli using the compartmentalized self-replication directed evolution platform. We validate this approach, termed compartmentalized two-hybrid replication, by selecting for high-affinity peptides that bind two model protein partners: SpyCatcher and the large fragment of NanoLuc luciferase. We further demonstrate directed co-evolution by randomizing both protein and peptide components of the SpyCatcher–SpyTag pair and co-selecting for functionally interacting variants.
13
Dujesiefken, Dirk, Andreas Rhaesa, Dieter Eckstein, and Horst Stobbe. "Tree Wound Reactions of Differently Treated Boreholes." Arboriculture & Urban Forestry 25, no. 3 (May 1, 1999): 113–23. http://dx.doi.org/10.48044/jauf.1999.017.
Abstract:
Holes from increment borings create wounds that lead to discoloration and may result in a colonization of the wood by fungi. There are various opinions about the damage caused by such borings and about the efficacy of wound dressings. For this reason, 78 differently treated boreholes in large-leaved lime (Jilia platyphyllos Scop.) and small-leaved lime (Tilia cordata Mill.), as well as in horsechestnut (Aesculus hippocastanum L.) and silver birch (Betula pendula Roth), were examined macroscopically and microscopically with regard to the wound reactions nearly 10 years after boring. Obvious differences in wound reactions were observed among the tree species. Both species of lime compartmentalized the wounds very effectively. Horsechestnut, on the other hand, revealed more extensive discoloration. Silver birch had the weakest compartmentalization, with discoloration up to 2 m (6.6 ft) in length. Cambial dieback around all borings, except for those plugged with creosote-impregnated wood dowels, was approximately the same for all species. Fungi occurred only within the discoloration. Cell wall disintegration was rarely observed. Treatment with LacBalsam® or polyurethane had little or no influence on the wound reactions. Boreholes sealed with impregnated wood dowels had far-reaching discoloration and cambial dieback as a result of the toxic effect of creosote.
14
Mu, Wenjing, Zhen Ji, Musen Zhou, Jianzhong Wu, Yiyang Lin, and Yan Qiao. "Membrane-confined liquid-liquid phase separation toward artificial organelles." Science Advances 7, no. 22 (May 2021): eabf9000. http://dx.doi.org/10.1126/sciadv.abf9000.
Abstract:
As the basic unit of life, cells are compartmentalized microreactors with molecularly crowded microenvironments. The quest to understand the cell origin inspires the design of synthetic analogs to mimic their functionality and structural complexity. In this work, we integrate membraneless coacervate microdroplets, a prototype of artificial organelles, into a proteinosome to build hierarchical protocells that may serve as a more realistic model of cellular organization. The protocell subcompartments can sense extracellular signals, take actions in response to these stimuli, and adapt their physicochemical behaviors. The tiered protocells are also capable of enriching biomolecular reactants within the confined organelles, thereby accelerating enzymatic reactions. The ability of signal processing inside protocells allows us to design the Boolean logic gates (NOR and NAND) using biochemical inputs. Our results highlight possible exploration of protocell-community signaling and render a flexible synthetic platform to study complex metabolic reaction networks and embodied chemical computation.
15
Costa, Marlene, Fátima Paiva-Martins, Sonia Losada-Barreiro, and Carlos Bravo-Díaz. "Modeling Chemical Reactivity at the Interfaces of Emulsions: Effects of Partitioning and Temperature." Molecules 26, no. 15 (August 3, 2021): 4703. http://dx.doi.org/10.3390/molecules26154703.
Abstract:
Bulk phase chemistry is hardly ever a reasonable approximation to interpret chemical reactivity in compartmentalized systems, because multiphasic systems may alter the course of chemical reactions by modifying the local concentrations and orientations of reactants and by modifying their physical properties (acid-base equilibria, redox potentials, etc.), making them—or inducing them—to react in a selective manner. Exploiting multiphasic systems as beneficial reaction media requires an understanding of their effects on chemical reactivity. Chemical reactions in multiphasic systems follow the same laws as in bulk solution, and the measured or observed rate constant of bimolecular reactions can be expressed, under dynamic equilibrium conditions, in terms of the product of the rate constant and of the concentrations of reactants. In emulsions, reactants distribute between the oil, water, and interfacial regions according to their polarity. However, determining the distributions of reactive components in intact emulsions is arduous because it is physically impossible to separate the interfacial region from the oil and aqueous ones without disrupting the existing equilibria and, therefore, need to be determined in the intact emulsions. The challenge is, thus, to develop models to correctly interpret chemical reactivity. Here, we will review the application of the pseudophase kinetic model to emulsions, which allows us to model chemical reactivity under a variety of experimental conditions and, by carrying out an appropriate kinetic analysis, will provide important kineticparameters.
16
Backlund, Michael, Frank Stein, Mandy Rettel, Thomas Schwarzl, Joel I. Perez-Perri, Annika Brosig, Yang Zhou, Gabriele Neu-Yilik, Matthias W. Hentze, and Andreas E. Kulozik. "Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins." Nucleic Acids Research 48, no. 9 (April 20, 2020): 4725–40. http://dx.doi.org/10.1093/nar/gkaa256.
Abstract:
Abstract Cellular stress causes multifaceted reactions to trigger adaptive responses to environmental cues at all levels of the gene expression pathway. RNA-binding proteins (RBP) are key contributors to stress-induced regulation of RNA fate and function. Here, we uncover the plasticity of the RNA interactome in stressed cells, differentiating between responses in the nucleus and in the cytoplasm. We applied enhanced RNA interactome capture (eRIC) analysis preceded by nucleo-cytoplasmic fractionation following arsenite-induced oxidative stress. The data reveal unexpectedly compartmentalized RNA interactomes and their responses to stress, including differential responses of RBPs in the nucleus versus the cytoplasm, which would have been missed by whole cell analyses.
17
Malatini, Camilla, Carlos Carbajales, Mariángel Luna, Osvaldo Beltrán, Manuel Amorín, Christian F. Masaguer, José M. Blanco, Silvia Barbosa, Pablo Taboada, and Alberto Coelho. "3D-Printing of Capsule Devices as Compartmentalization Tools for Supported Reagents in the Search of Antiproliferative Isatins." Pharmaceuticals 16, no. 2 (February 16, 2023): 310. http://dx.doi.org/10.3390/ph16020310.
Abstract:
The application of high throughput synthesis methodologies in the generation of active pharmaceutical ingredients (APIs) currently requires the use of automated and easily scalable systems, easy dispensing of supported reagents in solution phase organic synthesis (SPOS), and elimination of purification and extraction steps. The recyclability and recoverability of supported reagents and/or catalysts in a rapid and individualized manner is a challenge in the pharmaceutical industry. This objective can be achieved through a suitable compartmentalization of these pulverulent reagents in suitable devices for it. This work deals with the use of customized polypropylene permeable-capsule devices manufactured by 3D printing, using the fused deposition modeling (FDM) technique, adaptable to any type of flask or reactor. The capsules fabricated in this work were easily loaded “in one step” with polymeric reagents for use as scavengers of isocyanides in the work-up process of Ugi multicomponent reactions or as compartmentalized and reusable catalysts in copper-catalyzed cycloadditions (CuAAC) or Heck palladium catalyzed cross-coupling reactions (PCCCRs). The reaction products are different series of diversely substituted isatins, which were tested in cancerous cervical HeLa and murine 3T3 Balb fibroblast cells, obtaining potent antiproliferative activity. This work demonstrates the applicability of 3D printing in chemical processes to obtain anticancer APIs.
18
Cuomo, Francesca, Andrea Ceglie, Antonella De Leonardis, and Francesco Lopez. "Polymer Capsules for Enzymatic Catalysis in Confined Environments." Catalysts 9, no. 1 (December 20, 2018): 1. http://dx.doi.org/10.3390/catal9010001.
Abstract:
Catalysis is at the base of a series of biological and technological application processes. In recent years, the tendency has developed to carry out catalyzed reactions within confined structures, thus forming systems called micro or nanoreactors. Compartmentalized structures are cavities delimited by a wall where specific functions are introduced with a defined concentration and in the desired sites. These containers are generally referred to as nano or microcapsules, assuming the function of reactors in the presence of chemical reactions. Among the various types of existing structures, one of the most interesting is represented by systems made with polymers. This review aims to highlight some of the current advances in the use of functionalized structures that are useful for catalysis reactions, paying particular attention to polymer capsules and enzymes. The built-up methods used for the production of polymer capsules, as well as the aspects that influence membrane permeability and reactivity to environmental conditions, are discussed. Recent advances on biocatalysis confined in polymeric capsules are illustrated, and the strengths and weaknesses of the principal nanoreactors are considered.
19
Kpémoua, K., B. Boher, M. Nicole, P. Calatayud, and J. P. Geiger. "Cytochemistry of defense responses in cassava infected by Xanthomonas campestris pv. manihotis." Canadian Journal of Microbiology 42, no. 11 (November 1, 1996): 1131–43. http://dx.doi.org/10.1139/m96-145.
Abstract:
Stems of susceptible and resistant cassava plants have been cytologically investigated for their defense reactions to an aggressive strain of Xanthomonas campestris pv. manihotis. Histochemistry, in conjunction with gold cytochemistry, revealed that in susceptible and resistant plants, phloem and xylem parenchyma cells displayed a wide range of responses that limited the bacterial growth within the infected plants. Lignification and suberization associated with callose deposition were effective mechanisms that reinforced host barriers in the phloem. In the infected xylem, vessels were plugged by a material of pectic and (or) lignin-like origin. Flavonoids have been seen to be incorporated in secondary cell wall coatings. These reactions occurred at a higher intensity in the resistant plants. The number of phoem and xylem cells producing autofluorescent compounds was higher in infected resistant plants than in susceptible plants. Reactions have been observed in the resistant variety only, such as secretion of phenol-like molecules by tyloses and hyperplasic activity of phloem cells that compartmentalized bacterial lysis pockets, which are potent secondary inoculum sources.Key words: lignin, suberin, callose, phenol, tylose, flavonoid, pectin.
20
Hopp, Grüter, and Hottiger. "Regulation of Glucose Metabolism by NAD+ and ADP-Ribosylation." Cells 8, no. 8 (August 13, 2019): 890. http://dx.doi.org/10.3390/cells8080890.
Abstract:
Cells constantly adapt their metabolic pathways to meet their energy needs and respond to nutrient availability. During the last two decades, it has become increasingly clear that NAD+, a coenzyme in redox reactions, also mediates several ubiquitous cell signaling processes. Protein ADP-ribosylation is a post-translational modification that uses NAD+ as a substrate and is best known as part of the genotoxic stress response. However, there is increasing evidence that NAD+-dependent ADP-ribosylation regulates other cellular processes, including metabolic pathways. In this review, we will describe the compartmentalized regulation of NAD+ biosynthesis, consumption, and regeneration with a particular focus on the role of ADP-ribosylation in the regulation of glucose metabolism in different cellular compartments.
21
Chen, Chen. "Interaction Between Argonaute2 and RNA Molecules: AGO2 Molecular Structure and Different Regions in Nucleotide Chain." BIO Web of Conferences 59 (2023): 01001. http://dx.doi.org/10.1051/bioconf/20235901001.
Abstract:
Argonaute2 (AGO2) is an important protein connecting the construction of RNA-induced silencing complex (RISC) and micro-RNA (miRNA) biogenesis. This paper explores the mechanism during the function through previous studies which reveal the crystal structure and affinity comparisons. It is concluded that the AGO2 have compartmentalized domains for certain functions, which have both individual and cooperative role in the entire process. The characters of AGO2 and miRNA suggest a model of regiondifferent nucleotide chains in miRNA, which means its epigenetic information is based on base sequence and its special information. According to these findings, further studies are advised to monitor the reactions in a dynamical method, which would be a new potential entry point for clinical utilization.
22
Méndez-Suárez, Mariano, and Ignacio Danvila-del-Valle. "Negative Word of Mouth (NWOM) using Compartmental Epidemiological Models in Banking Digital Transformation." Contemporary Economics 17, no. 1 (March 31, 2023): 77–91. http://dx.doi.org/10.5709/ce.1897-9254.500.
Abstract:
Our article is among the first to model the reactions of customers to the digital transformation of European banks in a scenario of declining interest margins. Motivated by the hypothesis that customers’ feelings, perceptions and negative reactions towards digital transformation are channeled through the spread of negative word-of-mouth (NWOM) in a way analogous to the spread of a disease epidemic, we propose and analyze a compartmentalized mathematical model using data from a medium-sized Spanish commercial bank. To understand the NWOM phenomenon with an epidemiological approach we consider some realistic interactions in a social network and we formulate a novel application of the susceptible-exposed-infected-recovered-mortality (SEIRM) model. The results indicate that a better understanding of consumers’ negative reactions and their correct monitoring can help banks improve profitability when facing a digital transformation process. In summary, the research warns commercial bank managers about the need to carefully assess the effects of changes brought about by digital transformation and the development fee management strategies based on the behavior of customer groups, as well as the deployment of new churn risk management methods to deal with the most disengaged customers.
23
Cheng, Xiqing, Zhiping Zheng, Xirong Zhou, and Qin Kuang. "Metal–Organic Framework as a Compartmentalized Integrated Nanozyme Reactor to Enable High-Performance Cascade Reactions for Glucose Detection." ACS Sustainable Chemistry & Engineering 8, no. 48 (November 23, 2020): 17783–90. http://dx.doi.org/10.1021/acssuschemeng.0c06325.
24
Stano, Pasquale, Paolo Carrara, Yutetsu Kuruma, Tereza Pereira de Souza, and Pier Luigi Luisi. "Compartmentalized reactions as a case of soft-matter biotechnology: synthesis of proteins and nucleic acids inside lipid vesicles." Journal of Materials Chemistry 21, no. 47 (2011): 18887. http://dx.doi.org/10.1039/c1jm12298c.
25
Xie, Ganhua, Joe Forth, Shipei Zhu, Brett A. Helms, Paul D. Ashby, Ho Cheung Shum, and Thomas P. Russell. "Hanging droplets from liquid surfaces." Proceedings of the National Academy of Sciences 117, no. 15 (March 27, 2020): 8360–65. http://dx.doi.org/10.1073/pnas.1922045117.
Abstract:
Natural and man-made robotic systems use the interfacial tension between two fluids to support dense objects on liquid surfaces. Here, we show that coacervate-encased droplets of an aqueous polymer solution can be hung from the surface of a less dense aqueous polymer solution using surface tension. The forces acting on and the shapes of the hanging droplets can be controlled. Sacs with homogeneous and heterogeneous surfaces are hung from the surface and, by capillary forces, form well-ordered arrays. Locomotion and rotation can be achieved by embedding magnetic microparticles within the assemblies. Direct contact of the droplet with air enables in situ manipulation and compartmentalized cascading chemical reactions with selective transport. Applications including functional microreactors, motors, and biomimetic robots are evident.
26
Hussain, Hazrat, Elkin Amado, and Jörg Kressler. "Functional Polyether-based Amphiphilic Block Copolymers Synthesized by Atom-transfer Radical Polymerization." Australian Journal of Chemistry 64, no. 9 (2011): 1183. http://dx.doi.org/10.1071/ch11147.
Abstract:
This review deals with the synthesis, physical properties, and applications of amphiphilic block copolymers based on hydrophilic poly(ethylene oxide) (PEO) or hydrophobic poly(propylene oxide) (PPO). Oligomeric PEO and PPO are frequently functionalized by converting their OH end groups into macroinitiators for atom-transfer radical polymerization. They are then used to generate additional blocks as part of complex copolymer architectures. Adding hydrophobic and hydrophilic blocks, respectively, leads to polymers with amphiphilic character in water. They are surface active and form micelles above a critical micellization concentration. Together with recent developments in post-polymerization techniques through quantitative coupling reactions (‘click’ chemistry) a broad variety of tailored functionalities can be introduced to the amphiphilic block copolymers. Examples are outlined including stimuli responsiveness, membrane penetrating ability, formation of multi-compartmentalized micelles, etc.
27
Holthuis, Joost C. M., and Christian Ungermann. "Cellular microcompartments constitute general suborganellar functional units in cells." Biological Chemistry 394, no. 2 (February 1, 2013): 151–61. http://dx.doi.org/10.1515/hsz-2012-0265.
Abstract:
Abstract All cells are compartmentalized to facilitate enzymatic reactions or cellular dynamics. In eukaryotic cells, organelles differ in their protein/lipid repertoire, luminal ion composition, pH, and redox status. In addition, organelles contain specialized subcompartments even within the same membrane or within its lumen. Moreover, the bacterial plasma membrane reveals a remarkable degree of organization, which is recapitulated in eukaryotic cells and often linked to cell signaling. Finally, protein-based compartments are also known in the bacterial and eukaryotic cytosol. As the organizing principle of such cellular subcompartments is likely similar, previous definitions like rafts, microdomains, and all kinds of ‘-somes’ fall short as a general denominator to describe such suborganellar structures. Within this review, we will introduce the term cellular microcompartment as a general suborganellar functional unit and discuss its relevance to understand subcellular organization and function.
28
Wu, Chueh-Yu, Mengxing Ouyang, Bao Wang, Joseph de Rutte, Alexis Joo, Matthew Jacobs, Kyung Ha, Andrea L. Bertozzi, and Dino Di Carlo. "Monodisperse drops templated by 3D-structured microparticles." Science Advances 6, no. 45 (November 2020): eabb9023. http://dx.doi.org/10.1126/sciadv.abb9023.
Abstract:
The ability to create uniform subnanoliter compartments using microfluidic control has enabled new approaches for analysis of single cells and molecules. However, specialized instruments or expertise has been required, slowing the adoption of these cutting-edge applications. Here, we show that three dimensional–structured microparticles with sculpted surface chemistries template uniformly sized aqueous drops when simply mixed with two immiscible fluid phases. In contrast to traditional emulsions, particle-templated drops of a controlled volume occupy a minimum in the interfacial energy of the system, such that a stable monodisperse state results with simple and reproducible formation conditions. We describe techniques to manufacture microscale drop-carrier particles and show that emulsions created with these particles prevent molecular exchange, concentrating reactions within the drops, laying a foundation for sensitive compartmentalized molecular and cell-based assays with minimal instrumentation.
29
Gudmundsson, G., A. S. Oskarsdottir, and H. Einarsdottir. "Role of Lumbar Drainage as an Adjunct for controlling Intracranial pressure in Acute Bacterial Meningitis." Clinical Medicine Insights: Trauma and Intensive Medicine 4 (January 2013): CMTIM.S8440. http://dx.doi.org/10.4137/cmtim.s8440.
Abstract:
This case report describes a 16-year-old girl with fulminant bacterial meningitis in whom external ventricular drainage and intense volume-targeted therapy (the Lund protocol) was not sufficient to control intracranial pressure, but lumbar drainage on day 8 decreased the intracranial pressure immediately and led to a sustained low intracranial pressure level. The case is unusual and not fully understood, but the authors assume that due to inflammation and tissue reactions following aggressive infection, cerebrospinal fluid could not flow freely from the posterior fossa up to the ventricular drain. High pressure in the posterior compartment maintained the high intracranial pressure measured by the ventricular drain, and lumbar drain insertion caused an immediate fall in pressure. The lesson learned is that during an intracranial pressure crisis in a patient with open basal cisterns, a lumbar drain may be necessary because the cerebrospinal fluid space can be compartmentalized.
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Weyland, Mathias S., Harold Fellermann, Maik Hadorn, Daniel Sorek, Doron Lancet, Steen Rasmussen, and Rudolf M. Füchslin. "The MATCHIT Automaton: Exploiting Compartmentalization for the Synthesis of Branched Polymers." Computational and Mathematical Methods in Medicine 2013 (2013): 1–8. http://dx.doi.org/10.1155/2013/467428.
Abstract:
We propose an automaton, a theoretical framework that demonstrates how to improve the yield of the synthesis of branched chemical polymer reactions. This is achieved by separating substeps of the path of synthesis into compartments. We use chemical containers (chemtainers) to carry the substances through a sequence of fixed successive compartments. We describe the automaton in mathematical terms and show how it can be configured automatically in order to synthesize a given branched polymer target. The algorithm we present finds an optimal path of synthesis in linear time. We discuss how the automaton models compartmentalized structures found in cells, such as the endoplasmic reticulum and the Golgi apparatus, and we show how this compartmentalization can be exploited for the synthesis of branched polymers such as oligosaccharides. Lastly, we show examples of artificial branched polymers and discuss how the automaton can be configured to synthesize them with maximal yield.
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Woodruff, Jeffrey B., Oliver Wueseke, and Anthony A. Hyman. "Pericentriolar material structure and dynamics." Philosophical Transactions of the Royal Society B: Biological Sciences 369, no. 1650 (September 5, 2014): 20130459. http://dx.doi.org/10.1098/rstb.2013.0459.
Abstract:
A centrosome consists of two barrel-shaped centrioles embedded in a matrix of proteins known as the pericentriolar material (PCM). The PCM serves as a platform for protein complexes that regulate organelle trafficking, protein degradation and spindle assembly. Perhaps most important for cell division, the PCM concentrates tubulin and serves as the primary organizing centre for microtubules in metazoan somatic cells. Thus, similar to other well-described organelles, such as the nucleus and mitochondria, the cell has compartmentalized a multitude of vital biochemical reactions in the PCM. However, unlike these other organelles, the PCM is not membrane bound, but rather a dynamic collection of protein complexes and nucleic acids that constitute the organelle's interior and determine its boundary. How is the complex biochemical machinery necessary for the myriad centrosome functions concentrated and maintained in the PCM? Recent advances in proteomics and RNAi screening have unveiled most of the key PCM components and hinted at their molecular interactions ( table 1 ). Now we must understand how the interactions between these molecules contribute to the mesoscale organization and the assembly of the centrosome. Among outstanding questions are the intrinsic mechanisms that determine PCM shape and size, and how it functions as a biochemical reaction hub.
32
Liu, Lili, Qian Mei, Zhenning Yu, Tianhao Sun, Zijun Zhang, and Ming Chen. "An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice." Journal of Integrative Bioinformatics 10, no. 2 (June 1, 2013): 94–102. http://dx.doi.org/10.1515/jib-2013-223.
Abstract:
Summary Understanding how metabolic reactions translate the genome of an organism into its phenotype is a grand challenge in biology. Genome-wide association studies (GWAS) statistically connect genotypes to phenotypes, without any recourse to known molecular interactions, whereas a molecular mechanistic description ties gene function to phenotype through gene regulatory networks (GRNs), protein-protein interactions (PPIs) and molecular pathways. Integration of different regulatory information levels of an organism is expected to provide a good way for mapping genotypes to phenotypes. However, the lack of curated metabolic model of rice is blocking the exploration of genome-scale multi-level network reconstruction. Here, we have merged GRNs, PPIs and genome-scale metabolic networks (GSMNs) approaches into a single framework for rice via omics’ regulatory information reconstruction and integration. Firstly, we reconstructed a genome-scale metabolic model, containing 4,462 function genes, 2,986 metabolites involved in 3,316 reactions, and compartmentalized into ten subcellular locations. Furthermore, 90,358 pairs of protein-protein interactions, 662,936 pairs of gene regulations and 1,763 microRNA-target interactions were integrated into the metabolic model. Eventually, a database was developped for systematically storing and retrieving the genome-scale multi-level network of rice. This provides a reference for understanding genotype-phenotype relationship of rice, and for analysis of its molecular regulatory network.
33
Sedelnikova, Olga V., Thomas E. Hughes, and Jane A. Langdale. "Understanding the Genetic Basis of C4 Kranz Anatomy with a View to Engineering C3 Crops." Annual Review of Genetics 52, no. 1 (November 23, 2018): 249–70. http://dx.doi.org/10.1146/annurev-genet-120417-031217.
Abstract:
One of the most remarkable examples of convergent evolution is the transition from C3 to C4 photosynthesis, an event that occurred on over 60 independent occasions. The evolution of C4 is particularly noteworthy because of the complexity of the developmental and metabolic changes that took place. In most cases, compartmentalized metabolic reactions were facilitated by the development of a distinct leaf anatomy known as Kranz. C4 Kranz anatomy differs from ancestral C3 anatomy with respect to vein spacing patterns across the leaf, cell-type specification around veins, and cell-specific organelle function. Here we review our current understanding of how Kranz anatomy evolved and how it develops, with a focus on studies that are dissecting the underlying genetic mechanisms. This research field has gained prominence in recent years because understanding the genetic regulation of Kranz may enable the C3-to-C4 transition to be engineered, an endeavor that would significantly enhance crop productivity.
34
Peschke, Theo, Patrick Bitterwolf, Silla Hansen, Jannis Gasmi, Kersten Rabe, and Christof Niemeyer. "Self-Immobilizing Biocatalysts Maximize Space–Time Yields in Flow Reactors." Catalysts 9, no. 2 (February 8, 2019): 164. http://dx.doi.org/10.3390/catal9020164.
Abstract:
Maximizing space–time yields (STY) of biocatalytic flow processes is essential for the establishment of a circular biobased economy. We present a comparative study in which different biocatalytic flow reactor concepts were tested with the same enzyme, the (R)-selective alcohol dehydrogenase from Lactobacillus brevis (LbADH), that was used for stereoselective reduction of 5-nitrononane-2,8-dione. The LbADH contained a genetically encoded streptavidin (STV)-binding peptide to enable self-immobilization on STV-coated surfaces. The purified enzyme was immobilized by physisorption or chemisorption as monolayers on the flow channel walls, on magnetic microbeads in a packed-bed format, or as self-assembled all-enzyme hydrogels. Moreover, a multilayer biofilm with cytosolic-expressed LbADH served as a whole-cell biocatalyst. To enable cross-platform comparison, STY values were determined for the various reactor modules. While mono- and multilayer coatings of the reactor surface led to STY < 10, higher productivity was achieved with packed-bed reactors (STY ≈ 100) and the densely packed hydrogels (STY > 450). The latter modules could be operated for prolonged times (>6 days). Given that our approach should be transferable to other enzymes, we anticipate that compartmentalized microfluidic reaction modules equipped with self-immobilizing biocatalysts would be of great utility for numerous biocatalytic and even chemo-enzymatic cascade reactions under continuous flow conditions.
35
Fellermann, Harold, and Luca Cardelli. "Programming chemistry in DNA-addressable bioreactors." Journal of The Royal Society Interface 11, no. 99 (October 6, 2014): 20130987. http://dx.doi.org/10.1098/rsif.2013.0987.
Abstract:
We present a formal calculus, termed the chemtainer calculus , able to capture the complexity of compartmentalized reaction systems such as populations of possibly nested vesicular compartments. Compartments contain molecular cargo as well as surface markers in the form of DNA single strands. These markers serve as compartment addresses and allow for their targeted transport and fusion, thereby enabling reactions of previously separated chemicals. The overall system organization allows for the set-up of programmable chemistry in microfluidic or other automated environments. We introduce a simple sequential programming language whose instructions are motivated by state-of-the-art microfluidic technology. Our approach integrates electronic control, chemical computing and material production in a unified formal framework that is able to mimic the integrated computational and constructive capabilities of the subcellular matrix. We provide a non-deterministic semantics of our programming language that enables us to analytically derive the computational and constructive power of our machinery. This semantics is used to derive the sets of all constructable chemicals and supermolecular structures that emerge from different underlying instruction sets. Because our proofs are constructive, they can be used to automatically infer control programs for the construction of target structures from a limited set of resource molecules. Finally, we present an example of our framework from the area of oligosaccharide synthesis.
36
Albert, Pamela L. "Grief and Loss in the Workplace." Progress in Transplantation 11, no. 3 (September 2001): 169–73. http://dx.doi.org/10.1177/152692480101100304.
Abstract:
Throughout history, death and loss have given rise to social ceremonies and commemorative activities that note the death, recognize the place the person occupied in society, and assist the bereaved through the process of grief. Each culture faces death with its own definition of “appropriate” social-emotional reactions, and when death occurs, it provides the occasion for socially conditioned grief reactions and mourning practices. Historically, such practices have incorporated a set of interrelated people, the majority of whom were very knowledgeable of the customs and their purposes. In such a setting, it was possible for close kin, friends, distant kin, and acquaintances to come together to share their loss and grief. However, people may experience a loss that does not fit a socially recognized and sanctioned role. Grief for these people may have to remain private. Although they may have experienced an intense loss, personally or professionally, they may not be given time off from work or have the opportunity to talk about the meaning of their loss. In our modern, compartmentalized society, social ceremonies and commemorative activities tend to be limited primarily to a small circle of the “proper” bereaved individuals. This separation has helped to create a subset of grievers whose legitimacy may not be recognized by society as a whole and whose needs are often not addressed.
37
Fernando, Veani, Xunzhen Zheng, Yashna Walia, Vandana Sharma, Joshua Letson, and Saori Furuta. "S-Nitrosylation: An Emerging Paradigm of Redox Signaling." Antioxidants 8, no. 9 (September 17, 2019): 404. http://dx.doi.org/10.3390/antiox8090404.
Abstract:
Nitric oxide (NO) is a highly reactive molecule, generated through metabolism of L-arginine by NO synthase (NOS). Abnormal NO levels in mammalian cells are associated with multiple human diseases, including cancer. Recent studies have uncovered that the NO signaling is compartmentalized, owing to the localization of NOS and the nature of biochemical reactions of NO, including S-nitrosylation. S-nitrosylation is a selective covalent post-translational modification adding a nitrosyl group to the reactive thiol group of a cysteine to form S-nitrosothiol (SNO), which is a key mechanism in transferring NO-mediated signals. While S-nitrosylation occurs only at select cysteine thiols, such a spatial constraint is partially resolved by transnitrosylation, where the nitrosyl moiety is transferred between two interacting proteins to successively transfer the NO signal to a distant location. As NOS is present in various subcellular locales, a stress could trigger concerted S-nitrosylation and transnitrosylation of a large number of proteins involved in divergent signaling cascades. S-nitrosylation is an emerging paradigm of redox signaling by which cells confer protection against oxidative stress.
38
Williams, Adrian C., Lisa J. Hill, and David B. Ramsden. "Nicotinamide, NAD(P)(H), and Methyl-Group Homeostasis Evolved and Became a Determinant of Ageing Diseases: Hypotheses and Lessons from Pellagra." Current Gerontology and Geriatrics Research 2012 (2012): 1–24. http://dx.doi.org/10.1155/2012/302875.
Abstract:
Compartmentalized redox faults are common to ageing diseases. Dietary constituents are catabolized to NAD(H) donating electrons producing proton-based bioenergy in coevolved, cross-species and cross-organ networks. Nicotinamide and NAD deficiency from poor diet or high expenditure causes pellagra, an ageing and dementing disorder with lost robustness to infection and stress. Nicotinamide and stress induce Nicotinamide-N-methyltransferase (NNMT) improving choline retention but consume methyl groups. High NNMT activity is linked to Parkinson’s, cancers, and diseases of affluence. Optimising nicotinamide and choline/methyl group availability is important for brain development and increased during our evolution raising metabolic and methylome ceilings through dietary/metabolic symbiotic means but strict energy constraints remain and life-history tradeoffs are the rule. An optimal energy, NAD and methyl group supply, avoiding hypo and hyper-vitaminoses nicotinamide and choline, is important to healthy ageing and avoids utilising double-edged symbionts or uncontrolled autophagy or reversions to fermentation reactions in inflammatory and cancerous tissue that all redistribute NAD(P)(H), but incur high allostatic costs.
39
Cynober, Luc. "Metabolism of Dietary Glutamate in Adults." Annals of Nutrition and Metabolism 73, Suppl. 5 (2018): 5–14. http://dx.doi.org/10.1159/000494776.
Abstract:
Background: Glutamate is a non-essential amino acid at the crossroads of nitrogen and energy metabolism. Glutamate metabolism is characterized by reactions that may be anabolic or catabolic in nature depending on the tissue (i.e., glutamate dehydrogenase, transaminases), and it can also be either the precursor or the metabolite of glutamine. Unlike glutamine, which is the form of interorgan ammonia transport, glutamate metabolism is mostly compartmentalized within the cells, its interorgan exchanges being limited to a flux from liver to muscle. Summary: Glutamate catabolism is extremely intense in the splanchnic area, such that after a meal (rich in proteins) almost no glutamate appears in the systemic circulation. However, this process is saturable as after glutamate loading at a high dose level, glutamate appears dose-dependently in the circulation. This systemic glutamate appearance is blunted if glutamate is co-ingested with a carbohydrate source. Key Messages: The underlying reason for this highly specific metabolism is that glutamate plays a key role in nitrogen homeostasis, and the organism does all it can to limit the bioavailability of glutamate, which can be neurotoxic in excess. As glutamate is never eaten alone, its bioavailability will be limited if not negligible, and no adverse effects are to be expected in adult humans.
40
Klanchui, Amornpan, Sudarat Dulsawat, Kullapat Chaloemngam, Supapon Cheevadhanarak, Peerada Prommeenate, and Asawin Meechai. "An Improved Genome-Scale Metabolic Model of Arthrospira platensis C1 (iAK888) and Its Application in Glycogen Overproduction." Metabolites 8, no. 4 (November 26, 2018): 84. http://dx.doi.org/10.3390/metabo8040084.
Abstract:
Glycogen-enriched biomass of Arthrospira platensis has increasingly gained attention as a source for bioethanol production. To study the metabolic capabilities of glycogen production in A. platensis C1, a genome-scale metabolic model (GEM) could be a useful tool for predicting cellular behavior and suggesting strategies for glycogen overproduction. New experimentally validated GEM of A. platensis C1 namely iAK888, which has improved metabolic coverage and functionality was employed in this research. The iAK888 is a fully functional compartmentalized GEM consisting of 888 genes, 1,096 reactions, and 994 metabolites. This model was demonstrated to reasonably predict growth and glycogen fluxes under different growth conditions. In addition, iAK888 was further employed to predict the effect of deficiencies of NO3−, PO43−, or SO42− on the growth and glycogen production in A. platensis C1. The simulation results showed that these nutrient limitations led to a decrease in growth flux and an increase in glycogen flux. The experiment of A. platensis C1 confirmed the enhancement of glycogen fluxes after the cells being transferred from normal Zarrouk’s medium to either NO3−, PO43−, or SO42−-free Zarrouk’s media. Therefore, iAK888 could be served as a predictive model for glycogen overproduction and a valuable multidisciplinary tool for further studies of this important academic and industrial organism.
41
Gabora, Liane, and Mike Steel. "A model of the transition to behavioural and cognitive modernity using reflexively autocatalytic networks." Journal of The Royal Society Interface 17, no. 171 (October 2020): 20200545. http://dx.doi.org/10.1098/rsif.2020.0545.
Abstract:
This paper proposes a model of the cognitive mechanisms underlying the transition to behavioural and cognitive modernity in the Upper Palaeolithic using autocatalytic networks. These networks have been used to model life’s origins. More recently, they have been applied to the emergence of cognitive structure capable of undergoing cultural evolution. Mental representations of knowledge and experiences play the role of catalytic molecules, the interactions among them (e.g. the forging of new associations or affordances) play the role of reactions, and thought processes are modelled as chains of these interactions. We posit that one or more genetic mutations may have allowed thought to be spontaneously tailored to the situation by modulating the degree of (i) divergence (versus convergence), (ii) abstractness (versus concreteness), and (iii) context specificity. This culminated in persistent, unified autocatalytic semantic networks that bridged previously compartmentalized knowledge and experience. We explain the model using one of the oldest-known uncontested examples of figurative art: the carving of the Hohlenstein–Stadel Löwenmensch, or lion man. The approach keeps track of where in a cultural lineage each innovation appears, and models cumulative change step by step. It paves the way for a broad scientific framework for the origins of both biological and cultural evolutionary processes.
42
Posner, Clara, Sohum Mehta, and Jin Zhang. "Fluorescent biosensor imaging meets deterministic mathematical modelling: quantitative investigation of signalling compartmentalization." Journal of Physiology 601, no. 19 (September 25, 2023): 4227–41. http://dx.doi.org/10.1113/jp282696.
Abstract:
AbstractCells execute specific responses to diverse environmental cues by encoding information in distinctly compartmentalized biochemical signalling reactions. Genetically encoded fluorescent biosensors enable the spatial and temporal monitoring of signalling events in live cells. Temporal and spatiotemporal computational models can be used to interpret biosensor experiments in complex biochemical networks and to explore hypotheses that are difficult to test experimentally. In this review, we first provide brief discussions of the experimental toolkit of fluorescent biosensors as well as computational basics with a focus on temporal and spatiotemporal deterministic models. We then describe how we used this combined approach to identify and investigate a protein kinase A (PKA) – cAMP – Ca2+ oscillatory circuit in MIN6 β cells, a mouse pancreatic β cell system. We describe the application of this combined approach to interrogate how this oscillatory circuit is differentially regulated in a nano‐compartment formed at the plasma membrane by the scaffolding protein A kinase anchoring protein 79/150. We leveraged both temporal and spatiotemporal deterministic models to identify the key regulators of this oscillatory circuit, which we confirmed with further experiments. The powerful approach of combining live‐cell biosensor imaging with quantitative modelling, as discussed here, should find widespread use in the investigation of spatiotemporal regulation of cell signalling. image
43
de Almeida, Naomi M., Sarah Neumann, Rob J. Mesman, Christina Ferousi, Jan T. Keltjens, Mike S. M. Jetten, Boran Kartal, and Laura van Niftrik. "Immunogold Localization of Key Metabolic Enzymes in the Anammoxosome and on the Tubule-Like Structures of Kuenenia stuttgartiensis." Journal of Bacteriology 197, no. 14 (May 11, 2015): 2432–41. http://dx.doi.org/10.1128/jb.00186-15.
Abstract:
ABSTRACTAnaerobic ammonium-oxidizing (anammox) bacteria oxidize ammonium with nitrite as the terminal electron acceptor to form dinitrogen gas in the absence of oxygen. Anammox bacteria have a compartmentalized cell plan with a central membrane-bound “prokaryotic organelle” called the anammoxosome. The anammoxosome occupies most of the cell volume, has a curved membrane, and contains conspicuous tubule-like structures of unknown identity and function. It was suggested previously that the catalytic reactions of the anammox pathway occur in the anammoxosome, and that proton motive force was established across its membrane. Here, we used antibodies raised against five key enzymes of the anammox catabolism to determine their cellular location. The antibodies were raised against purified native hydroxylamine oxidoreductase-like protein kustc0458 with its redox partner kustc0457, hydrazine dehydrogenase (HDH; kustc0694), hydroxylamine oxidase (HOX; kustc1061), nitrite oxidoreductase (NXR; kustd1700/03/04), and hydrazine synthase (HZS; kuste2859-61) of the anammox bacteriumKuenenia stuttgartiensis. We determined that all five protein complexes were exclusively located inside the anammoxosome matrix. Four of the protein complexes did not appear to form higher-order protein organizations. However, the present data indicated for the first time that NXR is part of the tubule-like structures, which may stretch the whole length of the anammoxosome. These findings support the anammoxosome as the locus of catabolic reactions of the anammox pathway.IMPORTANCEAnammox bacteria are environmentally relevant microorganisms that contribute significantly to the release of fixed nitrogen in nature. Furthermore, the anammox process is applied for nitrogen removal from wastewater as an environment-friendly and cost-effective technology. These microorganisms feature a unique cellular organelle, the anammoxosome, which was proposed to contain the energy metabolism of the cell and tubule-like structures with hitherto unknown function. Here, we purified five native enzymes catalyzing key reactions in the anammox metabolism and raised antibodies against these in order to localize them within the cell. We showed that all enzymes were located within the anammoxosome, and nitrite oxidoreductase was located exclusively at the tubule-like structures, providing the first insights into the function of these subcellular structures.
44
López-González, Cristal, Sheila Juárez-Colunga, Norma Cecilia Morales-Elías, and Axel Tiessen. "Exploring regulatory networks in plants: transcription factors of starch metabolism." PeerJ 7 (July 9, 2019): e6841. http://dx.doi.org/10.7717/peerj.6841.
Abstract:
Biological networks are complex (non-linear), redundant (cyclic) and compartmentalized at the subcellular level. Rational manipulation of plant metabolism may have failed due to inherent difficulties of a comprehensive understanding of regulatory loops. We first need to identify key factors controlling the regulatory loops of primary metabolism. The paradigms of plant networks are revised in order to highlight the differences between metabolic and transcriptional networks. Comparison between animal and plant transcription factors (TFs) reveal some important differences. Plant transcriptional networks function at a lower hierarchy compared to animal regulatory networks. Plant genomes contain more TFs than animal genomes, but plant proteins are smaller and have less domains as animal proteins which are often multifunctional. We briefly summarize mutant analysis and co-expression results pinpointing some TFs regulating starch enzymes in plants. Detailed information is provided about biochemical reactions, TFs and cis regulatory motifs involved in sucrose-starch metabolism, in both source and sink tissues. Examples about coordinated responses to hormones and environmental cues in different tissues and species are listed. Further advancements require combined data from single-cell transcriptomic and metabolomic approaches. Cell fractionation and subcellular inspection may provide valuable insights. We propose that shuffling of promoter elements might be a promising strategy to improve in the near future starch content, crop yield or food quality.
45
Ahmad, Ahmad, Archana Tiwari, and Shireesh Srivastava. "A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism and Biotechnological Potential." Microorganisms 8, no. 9 (September 11, 2020): 1396. http://dx.doi.org/10.3390/microorganisms8091396.
Abstract:
Thalassiosira pseudonana is a transformable and biotechnologically promising model diatom with an ability to synthesise nutraceuticals such as fucoxanthin and store a significant amount of polyglucans and lipids including omega-3 fatty acids. While it was the first diatom to be sequenced, a systems-level analysis of its metabolism has not been done yet. This work presents first comprehensive, compartmentalized, and functional genome-scale metabolic model of the marine diatom Thalassiosira pseudonana CCMP 1335, which we have termed iThaps987. The model includes 987 genes, 2477 reactions, and 2456 metabolites. Comparison with the model of another diatom Phaeodactylum tricornutum revealed presence of 183 unique enzymes (belonging primarily to amino acid, carbohydrate, and lipid metabolism) in iThaps987. Model simulations showed a typical C3-type photosynthetic carbon fixation and suggested a preference of violaxanthin–diadinoxanthin pathway over violaxanthin–neoxanthin pathway for the production of fucoxanthin. Linear electron flow was found be active and cyclic electron flow was inactive under normal phototrophic conditions (unlike green algae and plants), validating the model predictions with previous reports. Investigation of the model for the potential of Thalassiosira pseudonana CCMP 1335 to produce other industrially useful compounds suggest iso-butanol as a foreign compound that can be synthesized by a single-gene addition. This work provides novel insights about the metabolism and potential of the organism and will be helpful to further investigate its metabolism and devise metabolic engineering strategies for the production of various compounds.
46
Mi-ichi, Fumika, Akira Nozawa, Hiroki Yoshida, Yuzuru Tozawa, and Tomoyoshi Nozaki. "Evidence that the Entamoeba histolytica Mitochondrial Carrier Family Links Mitosomal and Cytosolic Pathways through Exchange of 3′-Phosphoadenosine 5′-Phosphosulfate and ATP." Eukaryotic Cell 14, no. 11 (September 18, 2015): 1144–50. http://dx.doi.org/10.1128/ec.00130-15.
Abstract:
ABSTRACT Entamoeba histolytica , a microaerophilic protozoan parasite, possesses mitosomes. Mitosomes are mitochondrion-related organelles that have largely lost typical mitochondrial functions, such as those involved in the tricarboxylic acid cycle and oxidative phosphorylation. The biological roles of Entamoeba mitosomes have been a long-standing enigma. We previously demonstrated that sulfate activation, which is not generally compartmentalized to mitochondria, is a major function of E. histolytica mitosomes. Sulfate activation cooperates with cytosolic enzymes, i.e., sulfotransferases (SULTs), for the synthesis of sulfolipids, one of which is cholesteryl sulfate. Notably, cholesteryl sulfate plays an important role in encystation, an essential process in the Entamoeba life cycle. These findings identified a biological role for Entamoeba mitosomes; however, they simultaneously raised a new issue concerning how the reactions of the pathway, separated by the mitosomal membranes, cooperate. Here, we demonstrated that the E. histolytica mitochondrial carrier family (EhMCF) has the capacity to exchange 3′-phosphoadenosine 5′-phosphosulfate (PAPS) with ATP. We also confirmed the cytosolic localization of all the E. histolytica SULTs, suggesting that in Entamoeba , PAPS, which is produced through mitosomal sulfate activation, is translocated to the cytosol and becomes a substrate for SULTs. In contrast, ATP, which is produced through cytosolic pathways, is translocated into the mitosomes and is a necessary substrate for sulfate activation. Taking our findings collectively, we suggest that EhMCF functions as a PAPS/ATP antiporter and plays a crucial role in linking the mitosomal sulfate activation pathway to cytosolic SULTs for the production of sulfolipids.
47
Miller, B. G., C. T. Whittemore, C. R. Stokes, and E. Telemo. "The effect of delayed weaning on the development of oral tolerance to soya-bean protein in pigs." British Journal of Nutrition 71, no. 4 (April 1994): 615–25. http://dx.doi.org/10.1079/bjn19940167.
Abstract:
The antibody response to a dietary antigen (soya-bean protein) and the development of oral tolerance was studied in pigs in a family pen system where the piglets are left with their mothers and gradually wean themselves onto a soya-bean-based diet over a 12 week period. In the first experiment three groups of pigs (eight pigs/group) aged either 2, 8 or 13 weeks were immunized with soya-bean protein or ovalbumin (OvA; controls) intra-peritoneally (i.p.) in Quill A adjuvant and subsequently boosted 2 weeks later. All groups showed an IgG response to the injected antigens indicating lack of tolerance induction to the dietary antigen. Interestingly the groups injected with OvA showed an almost identical response to soya- bean protein as the groups injected with soya-bean protein. In a second experiment with a similar protocol, soya bean was withdrawn from the feed before immunization which resulted in lack of response to soya-bean protein in the groups injected with OvA and a lack of response to injected soya-bean protein in the 14-week-old group, indicating that systemic tolerance was established by 12 weeks of age. The results from the two experiments suggest a compartmentalized response to soya-bean protein i.e. local antibody production to dietary soya bean along with systemic tolerance to injected soya-bean protein. The work also suggests that delayed‘natural’weaning may avoid damaging hypersensitivity reactions associated with early weaning.
48
Renoz, François, Jérôme Ambroise, Bertrand Bearzatto, Samir Fakhour, Nicolas Parisot, Mélanie Ribeiro Lopes, Jean-Luc Gala, Federica Calevro, and Thierry Hance. "The Di-Symbiotic Systems in the Aphids Sipha maydis and Periphyllus lyropictus Provide a Contrasting Picture of Recent Co-Obligate Nutritional Endosymbiosis in Aphids." Microorganisms 10, no. 7 (July 6, 2022): 1360. http://dx.doi.org/10.3390/microorganisms10071360.
Abstract:
Dependence on multiple nutritional bacterial symbionts forming a metabolic unit has repeatedly evolved in many insect species that feed on nutritionally unbalanced diets such as plant sap. This is the case for aphids of the subfamilies Lachninae and Chaitophorinae, which have evolved di-symbiotic systems in which the ancient obligate nutritional symbiont Buchnera aphidicola is metabolically complemented by an additional nutritional symbiont acquired more recently. Deciphering how different symbionts integrate both metabolically and anatomically in such systems is crucial to understanding how complex nutritional symbiotic systems function and evolve. In this study, we sequenced and analyzed the genomes of the symbionts B. aphidicola and Serratia symbiotica associated with the Chaitophorinae aphids Sipha maydis and Periphyllus lyropictus. Our results show that, in these two species, B. aphidicola and S. symbiotica complement each other metabolically (and their hosts) for the biosynthesis of essential amino acids and vitamins, but with distinct metabolic reactions supported by each symbiont depending on the host species. Furthermore, the S. symbiotica symbiont associated with S. maydis appears to be strictly compartmentalized into the specialized host cells housing symbionts in aphids, the bacteriocytes, whereas the S. symbiotica symbiont associated with P. lyropictus exhibits a highly invasive phenotype, presumably because it is capable of expressing a larger set of virulence factors, including a complete flagellum for bacterial motility. Such contrasting levels of metabolic and anatomical integration for two S. symbiotica symbionts that were recently acquired as nutritional co-obligate partners reflect distinct coevolutionary processes specific to each association.
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Mensa-Wilmot, K., JH LeBowitz, KP Chang, A. al-Qahtani, BS McGwire, S. Tucker, and JC Morris. "A glycosylphosphatidylinositol (GPI)-negative phenotype produced in Leishmania major by GPI phospholipase C from Trypanosoma brucei: topography of two GPI pathways." Journal of Cell Biology 124, no. 6 (March 15, 1994): 935–47. http://dx.doi.org/10.1083/jcb.124.6.935.
Abstract:
The major surface macromolecules of the protozoan parasite Leishmania major, gp63 (a metalloprotease), and lipophosphoglycan (a polysaccharide), are glycosylphosphatidylinositol (GPI) anchored. We expressed a cytoplasmic glycosylphosphatidylinositol phospholipase C (GPI-PLC) in L. major in order to examine the topography of the protein-GPI and polysaccharide-GPI pathways. In L. major cells expressing GPI-PLC, cell-associated gp63 could not be detected in immunoblots. Pulse-chase analysis revealed that gp63 was secreted into the culture medium with a half-time of 5.5 h. Secreted gp63 lacked anti-cross reacting determinant epitopes, and was not metabolically labeled with [3H]ethanolamine, indicating that it never received a GPI anchor. Further, the quantity of putative protein-GPI intermediates decreased approximately 10-fold. In striking contrast, lipophosphoglycan levels were unaltered. However, GPI-PLC cleaved polysaccharide-GPI intermediates (glycoinositol phospholipids) in vitro. Thus, reactions specific to the polysaccharide-GPI pathway are compartmentalized in vivo within the endoplasmic reticulum, thereby sequestering polysaccharide-GPI intermediates from GPI-PLC cleavage. On the contrary, protein-GPI synthesis at least up to production of Man(1 alpha 6)Man(1 alpha 4)GlcN-(1 alpha 6)-myo-inositol-1-phospholipid is cytosolic. To our knowledge this represents the first use of a catabolic enzyme in vivo to elucidate the topography of biosynthetic pathways. GPI-PLC causes a protein-GPI-negative phenotype in L. major, even when genes for GPI biosynthesis are functional. This phenotype is remarkably similar to that of some GPI mutants of mammalian cells: implications for paroxysmal nocturnal hemoglobinuria and Thy-1-negative T-lymphoma are discussed.
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Miyachi, S., T. Izumi, N. Matsubara, T. Naito, K. Haraguchi, and T. Wakabayashi. "Mechanism of the Formation of Dural Arteriovenous Fistula — The Role of the Emissary Vein." Interventional Neuroradiology 17, no. 2 (June 2011): 195–202. http://dx.doi.org/10.1177/159101991101700209.
Abstract:
Dural arteriovenous fistula (DAVF) can be separated into two types: DAVF which drains through an affected sinus (sinus type) and DAVF with direct reflux to the cortical vein (non-sinus type). The present report attempted to clarify the mechanism of formation and development of DAVF focusing on the emissary vein (EV) hypothesis. First, inflammation occurs at the penetrating point of the EV on the dura due to idiopathic or secondary causes. Local inflammatory reactions induce vessel dilatation and neovascularization, and subsequently create arteriovenous (AV) connections on the arteriole level. Although EV communicating with dural arteries might play a role as draining routes at first, they start to degrade due to compression of enlarged emissary arteries or to a hemodynamic shift to the drainage pathway of least resistance. Following the occlusion of drainage pathway through EV into the sinus or cortical veins may form, resulting in clinically detectable DAVF. The AV shunt then expands to the surrounding dura associated with recruitment of feeders from distant sites induced by expression of angiogenetic factors and a shift in the hemodynamic balance. In sinus type DAVF, the sinus is progressively compartmentalized and finally occludes due to thrombogenesis with activated coagulopathy or to hemodynamic hypertrophy of the sinus wall. This progression results in the mature, aggressive DAVF with drainage impairments. Previous mechanistic hypotheses focusing on sinus hypertension and sinus thromboses cannot explain the pathogenesis of non-sinus type of DAVF. Although the etiology of DAVF may be concerned by the thrombo-occlusive change of sinus, the unique theory presented in this report may enable an understanding of the common etiology of both types of DAVF.