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Journal articles on the topic 'Compartmentalized reactions'

Author: Grafiati

Published: 25 May 2024

Last updated: 19 July 2025

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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.

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Simon, David, Franziska Obst, Sebastian Haefner, et al. "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.

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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.

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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 synthet

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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 (2019): 605–15. http://dx.doi.org/10.21475/ajcs.19.13.04.p1639.

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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 ex

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Fernández, Laia L., Julio Bastos-Arrieta, Dietmar Appelhans, et al. "Multi-compartmentalized electrochemical sensing platforms for monitoring cascade enzymatic reactions." Microchemical Journal 204 (September 2024): 111071. http://dx.doi.org/10.1016/j.microc.2024.111071.

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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 (2021): 3451–59. http://dx.doi.org/10.1021/acs.biomac.1c00546.

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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.

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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

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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 (2010): 4357–66. http://dx.doi.org/10.1128/jb.00520-10.

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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

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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.

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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 v

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Obst, Franziska, Anthony Beck, Chayan Bishayee, et al. "Hydrogel Microvalves as Control Elements for Parallelized Enzymatic Cascade Reactions in Microfluidics." Micromachines 11, no. 2 (2020): 167. http://dx.doi.org/10.3390/mi11020167.

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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-gla

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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 (2021): 168–86. http://dx.doi.org/10.3390/polysaccharides2010012.

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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

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Obst, Franziska, David Simon, Philipp J. Mehner, et al. "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.

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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.

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Siau, Jia Wei, Samuel Nonis, Sharon Chee, et al. "Directed co-evolution of interacting protein–peptide pairs by compartmentalized two-hybrid replication (C2HR)." Nucleic Acids Research 48, no. 22 (2020): e128-e128. http://dx.doi.org/10.1093/nar/gkaa933.

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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 interac

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Dujesiefken, Dirk, Andreas Rhaesa, Dieter Eckstein, and Horst Stobbe. "Tree Wound Reactions of Differently Treated Boreholes." Arboriculture & Urban Forestry 25, no. 3 (1999): 113–23. http://dx.doi.org/10.48044/jauf.1999.017.

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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 dif

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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 (2021): eabf9000. http://dx.doi.org/10.1126/sciadv.abf9000.

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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 phys

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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 (2021): 4703. http://dx.doi.org/10.3390/molecules26154703.

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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 sam

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Backlund, Michael, Frank Stein, Mandy Rettel, et al. "Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins." Nucleic Acids Research 48, no. 9 (2020): 4725–40. http://dx.doi.org/10.1093/nar/gkaa256.

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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 RN

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Cuomo, Francesca, Andrea Ceglie, Antonella De Leonardis, and Francesco Lopez. "Polymer Capsules for Enzymatic Catalysis in Confined Environments." Catalysts 9, no. 1 (2018): 1. http://dx.doi.org/10.3390/catal9010001.

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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 o

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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 (1996): 1131–43. http://dx.doi.org/10.1139/m96-145.

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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

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Malatini, Camilla, Carlos Carbajales, Mariángel Luna, et al. "3D-Printing of Capsule Devices as Compartmentalization Tools for Supported Reagents in the Search of Antiproliferative Isatins." Pharmaceuticals 16, no. 2 (2023): 310. http://dx.doi.org/10.3390/ph16020310.

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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 d

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Hopp, Grüter, and Hottiger. "Regulation of Glucose Metabolism by NAD+ and ADP-Ribosylation." Cells 8, no. 8 (2019): 890. http://dx.doi.org/10.3390/cells8080890.

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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 describ

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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.

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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

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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 (2023): 77–91. http://dx.doi.org/10.5709/ce.1897-9254.500.

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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 s

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Xie, Ganhua, Joe Forth, Shipei Zhu, et al. "Hanging droplets from liquid surfaces." Proceedings of the National Academy of Sciences 117, no. 15 (2020): 8360–65. http://dx.doi.org/10.1073/pnas.1922045117.

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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 assemb

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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 (2020): 17783–90. http://dx.doi.org/10.1021/acssuschemeng.0c06325.

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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.

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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.

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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 abo

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Holthuis, Joost C. M., and Christian Ungermann. "Cellular microcompartments constitute general suborganellar functional units in cells." Biological Chemistry 394, no. 2 (2013): 151–61. http://dx.doi.org/10.1515/hsz-2012-0265.

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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 organizi

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Wu, Chueh-Yu, Mengxing Ouyang, Bao Wang, et al. "Monodisperse drops templated by 3D-structured microparticles." Science Advances 6, no. 45 (2020): eabb9023. http://dx.doi.org/10.1126/sciadv.abb9023.

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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

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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.

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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 dr

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Weyland, Mathias S., Harold Fellermann, Maik Hadorn, et al. "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.

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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 au

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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 (2014): 20130459. http://dx.doi.org/10.1098/rstb.2013.0459.

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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. Howeve

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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 (2013): 94–102. http://dx.doi.org/10.1515/jib-2013-223.

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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,

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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 (2018): 249–70. http://dx.doi.org/10.1146/annurev-genet-120417-031217.

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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 organell

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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 (2019): 164. http://dx.doi.org/10.3390/catal9020164.

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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

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Fellermann, Harold, and Luca Cardelli. "Programming chemistry in DNA-addressable bioreactors." Journal of The Royal Society Interface 11, no. 99 (2014): 20130987. http://dx.doi.org/10.1098/rsif.2013.0987.

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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 simp

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Albert, Pamela L. "Grief and Loss in the Workplace." Progress in Transplantation 11, no. 3 (2001): 169–73. http://dx.doi.org/10.1177/152692480101100304.

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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

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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 (2019): 404. http://dx.doi.org/10.3390/antiox8090404.

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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 transfer

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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.

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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 nico

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Song, Jianxing. "In the Beginning: Let Hydration Be Coded in Proteins for Manifestation and Modulation by Salts and Adenosine Triphosphate." International Journal of Molecular Sciences 25, no. 23 (2024): 12817. http://dx.doi.org/10.3390/ijms252312817.

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Water exists in the beginning and hydrates all matter. Life emerged in water, requiring three essential components in compartmentalized spaces: (1) universal energy sources driving biochemical reactions and processes, (2) molecules that store, encode, and transmit information, and (3) functional players carrying out biological activities and structural organization. Phosphorus has been selected to create adenosine triphosphate (ATP) as the universal energy currency, nucleic acids for genetic information storage and transmission, and phospholipids for cellular compartmentalization. Meanwhile, p

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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.

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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 intens

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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 (2018): 84. http://dx.doi.org/10.3390/metabo8040084.

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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

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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 (2020): 20200545. http://dx.doi.org/10.1098/rsif.2020.0545.

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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

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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 (2023): 4227–41. http://dx.doi.org/10.1113/jp282696.

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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 comp

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de Almeida, Naomi M., Sarah Neumann, Rob J. Mesman, et al. "Immunogold Localization of Key Metabolic Enzymes in the Anammoxosome and on the Tubule-Like Structures of Kuenenia stuttgartiensis." Journal of Bacteriology 197, no. 14 (2015): 2432–41. http://dx.doi.org/10.1128/jb.00186-15.

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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 esta

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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.

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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 n

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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 (2020): 1396. http://dx.doi.org/10.3390/microorganisms8091396.

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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 24

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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 (2015): 1144–50. http://dx.doi.org/10.1128/ec.00130-15.

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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 (SUL

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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 (1994): 615–25. http://dx.doi.org/10.1079/bjn19940167.

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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 toler

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Renoz, François, Jérôme Ambroise, Bertrand Bearzatto, et al. "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 (2022): 1360. http://dx.doi.org/10.3390/microorganisms10071360.

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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 c

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