Journal articles: 'Biochemical compartmentalization'

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Diekmann, Yoan, and José B. Pereira-Leal. "Evolution of intracellular compartmentalization." Biochemical Journal 449, no. 2 (December 14, 2012): 319–31. http://dx.doi.org/10.1042/bj20120957.

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Cells compartmentalize their biochemical functions in a variety of ways, notably by creating physical barriers that separate a compartment via membranes or proteins. Eukaryotes have a wide diversity of membrane-based compartments, many that are lineage- or tissue-specific. In recent years, it has become increasingly evident that membrane-based compartmentalization of the cytosolic space is observed in multiple prokaryotic lineages, giving rise to several types of distinct prokaryotic organelles. Endosymbionts, previously believed to be a hallmark of eukaryotes, have been described in several bacteria. Protein-based compartments, frequent in bacteria, are also found in eukaryotes. In the present review, we focus on selected intracellular compartments from each of these three categories, membrane-based, endosymbiotic and protein-based, in both prokaryotes and eukaryotes. We review their diversity and the current theories and controversies regarding the evolutionary origins. Furthermore, we discuss the evolutionary processes acting on the genetic basis of intracellular compartments and how those differ across the domains of life. We conclude that the distinction between eukaryotes and prokaryotes no longer lies in the existence of a compartmentalized cell plan, but rather in its complexity.

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Wassef, Marion, Jean Pierre Zanetta, Arlette Brehier, and Constantino Sotelo. "Transient biochemical compartmentalization of Purkinje cells during early cerebellar development." Developmental Biology 111, no. 1 (September 1985): 129–37. http://dx.doi.org/10.1016/0012-1606(85)90441-5.

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Duso, Lorenzo, and Christoph Zechner. "Stochastic reaction networks in dynamic compartment populations." Proceedings of the National Academy of Sciences 117, no. 37 (August 31, 2020): 22674–83. http://dx.doi.org/10.1073/pnas.2003734117.

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Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and typically very challenging to analyze computationally. Recent studies have made progress toward addressing this problem in the context of specific biological systems, but a general and sufficiently effective approach remains lacking. In this work, we propose a mathematical framework based on counting processes that allows us to study dynamic compartment populations with arbitrary interactions and internal biochemistry. We derive an efficient description of the dynamics in terms of differential equations which capture the statistics of the population. We demonstrate the relevance of our approach by analyzing models inspired by different biological processes, including subcellular compartmentalization and tissue homeostasis.

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Gartshteyn, Yevgeniya, Anca D. Askanase, Ruijiang Song, Shoiab Bukhari, Matthew Dragovich, Kieran Adam, and Adam Mor. "SLAMF6 compartmentalization enhances T cell functions." Life Science Alliance 6, no. 2 (December 8, 2022): e202201533. http://dx.doi.org/10.26508/lsa.202201533.

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Signaling lymphocyte activation molecule family member 6 (SLAMF6) is a T cell co-receptor. Previously, we showed that SLAMF6 clustering was required for T cell activation. To better understand the relationship between SLAMF6 location and function and to evaluate the role of SLAMF6 as a therapeutic target, we investigated how its compartmentalization on the cell surface affects T cell functions. We used biochemical and co-culture assays to show that T cell activity is enhanced when SLAMF6 colocalizes with the CD3 complex. Mechanistically, co-immunoprecipitation analysis revealed the SLAMF6-interacting proteins to be those essential for signaling downstream of T cell receptor, suggesting the two receptors share downstream signaling pathways. Bispecific anti-CD3/SLAMF6 antibodies, designed to promote SLAMF6 clustering with CD3, enhanced T cell activation. Meanwhile, anti-CD45/SLAMF6 antibodies inhibited SLAMF6 clustering with T cell receptor, likely because of the steric hindrance, but nevertheless enhanced T cell activation. We conclude that SLAMF6 bispecific antibodies have a role in modulating T cell responses, and future work will evaluate the therapeutic potential in tumor models.

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Scott, JD, and DW Carr. "Subcellular Localization of the Type II cAMP-Dependent Protein Kinase." Physiology 7, no. 4 (August 1, 1992): 143–48. http://dx.doi.org/10.1152/physiologyonline.1992.7.4.143.

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Diverse biochemical effects of different neurotransmitters or hormones that stimulate cAMP production may occur through activation of compartmentalized pools of cAMP-dependent protein kinase (PKA). Evidence suggests that compartmentalization of type II PKA is maintained through protein-protein interactions between the regulatory subunit and specific anchoring proteins.

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Koch, C., and A. Zador. "The function of dendritic spines: devices subserving biochemical rather than electrical compartmentalization." Journal of Neuroscience 13, no. 2 (February 1, 1993): 413–22. http://dx.doi.org/10.1523/jneurosci.13-02-00413.1993.

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Martin, William. "Evolutionary origins of metabolic compartmentalization in eukaryotes." Philosophical Transactions of the Royal Society B: Biological Sciences 365, no. 1541 (March 12, 2010): 847–55. http://dx.doi.org/10.1098/rstb.2009.0252.

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Many genes in eukaryotes are acquisitions from the free-living antecedents of chloroplasts and mitochondria. But there is no evolutionary ‘homing device’ that automatically directs the protein product of a transferred gene back to the organelle of its provenance. Instead, the products of genes acquired from endosymbionts can explore all targeting possibilities within the cell. They often replace pre-existing host genes, or even whole pathways. But the transfer of an enzymatic pathway from one compartment to another poses severe problems: over evolutionary time, the enzymes of the pathway acquire their targeting signals for the new compartment individually, not in unison. Until the whole pathway is established in the new compartment, newly routed individual enzymes are useless, and their genes will be lost through mutation. Here it is suggested that pathways attain novel compartmentation variants via a ‘minor mistargeting’ mechanism. If protein targeting in eukaryotic cells possesses enough imperfection such that small amounts of entire pathways continuously enter novel compartments, selectable units of biochemical function would exist in new compartments, and the genes could become selected. Dual-targeting of proteins is indeed very common within eukaryotic cells, suggesting that targeting variation required for this minor mistargeting mechanism to operate exists in nature.

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Lee, Kevin F. H., Cary Soares, and Jean-Claude Béïque. "Examining Form and Function of Dendritic Spines." Neural Plasticity 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/704103.

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The majority of fast excitatory synaptic transmission in the central nervous system takes place at protrusions along dendrites called spines. Dendritic spines are highly heterogeneous, both morphologically and functionally. Not surprisingly, there has been much speculation and debate on the relationship between spine structure and function. The advent of multi-photon laser-scanning microscopy has greatly improved our ability to investigate the dynamic interplay between spine form and function. Regulated structural changes occur at spines undergoing plasticity, offering a mechanism to account for the well-described correlation between spine size and synapse strength. In turn, spine structure can influence the degree of biochemical and perhaps electrical compartmentalization at individual synapses. Here, we review the relationship between dendritic spine morphology, features of spine compartmentalization and synaptic plasticity. We highlight emerging molecular mechanisms that link structural and functional changes in spines during plasticity, and also consider circumstances that underscore some divergence from a tight structure-function coupling. Because of the intricate influence of spine structure on biochemical and electrical signalling, activity-dependent changes in spine morphology alone may thus contribute to the metaplastic potential of synapses. This possibility asserts a role for structural dynamics in neuronal information storage and aligns well with current computational models.

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Adamkov, Marian, Sandra Hurta Csizmar, Veronika Mestanova, Desanka Vybohova, and Bibiana Krajnakova. "IS SURVIVIN LEVEL IDENTICAL BETWEEN ADENOMAS OF PROXIMAL AND DISTAL COLON?" Revista Argentina de Anatomía Clínica 14, no. 2 (July 29, 2022): 58–64. http://dx.doi.org/10.31051/1852.8023.v14.n2.37625.

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Objectives: Considerable differences are known between proximal and distal colon, these include embryological, anatomical, histological, biochemical, and physiological characteristics. Above mentioned distinctions may influence development of variable clinico-morphological entities. Multifunctional antiapoptotic protein survivin participates in regulation of cell cycle, apoptotic cascades, and stimulates angiogenesis. Material and methods: We assessed immunohistochemically expression pattern of antiapoptotic protein survivin in a panel of 243 colon adenomas to determine its association with colon localization. In each section, subcellular compartmentalization of survivin and intensity of immunoreaction were evaluated. Results: Survivin was expressed in 190 cases (78.2%). Statistical analysis confirmed a significant correlation of subcellular survivin compartmentalization and intensity of immunoreaction with colon localization of adenomas. Conclusions: Taking into account unique features of survivin, its expression pattern in proximally sided adenomas, and distinctions between left and right colon, we suppose that survivin level may contribute to higher proliferative phenotype of proximal adenomas.

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Vallés, Ana Sofía, and Francisco J. Barrantes. "Nanoscale Sub-Compartmentalization of the Dendritic Spine Compartment." Biomolecules 11, no. 11 (November 15, 2021): 1697. http://dx.doi.org/10.3390/biom11111697.

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Compartmentalization of the membrane is essential for cells to perform highly specific tasks and spatially constrained biochemical functions in topographically defined areas. These membrane lateral heterogeneities range from nanoscopic dimensions, often involving only a few molecular constituents, to micron-sized mesoscopic domains resulting from the coalescence of nanodomains. Short-lived domains lasting for a few milliseconds coexist with more stable platforms lasting from minutes to days. This panoply of lateral domains subserves the great variety of demands of cell physiology, particularly high for those implicated in signaling. The dendritic spine, a subcellular structure of neurons at the receiving (postsynaptic) end of central nervous system excitatory synapses, exploits this compartmentalization principle. In its most frequent adult morphology, the mushroom-shaped spine harbors neurotransmitter receptors, enzymes, and scaffolding proteins tightly packed in a volume of a few femtoliters. In addition to constituting a mesoscopic lateral heterogeneity of the dendritic arborization, the dendritic spine postsynaptic membrane is further compartmentalized into spatially delimited nanodomains that execute separate functions in the synapse. This review discusses the functional relevance of compartmentalization and nanodomain organization in synaptic transmission and plasticity and exemplifies the importance of this parcelization in various neurotransmitter signaling systems operating at dendritic spines, using two fast ligand-gated ionotropic receptors, the nicotinic acetylcholine receptor and the glutamatergic receptor, and a second-messenger G-protein coupled receptor, the cannabinoid receptor, as paradigmatic examples.

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Reifenrath, Mara, Mislav Oreb, Eckhard Boles, and Joanna Tripp. "Artificial ER-Derived Vesicles as Synthetic Organelles for in Vivo Compartmentalization of Biochemical Pathways." ACS Synthetic Biology 9, no. 11 (October 19, 2020): 2909–16. http://dx.doi.org/10.1021/acssynbio.0c00241.

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Schuster, Benjamin S., Matthew C. Good, and Daniel A. Hammer. "Controllable Protein Phase Separation and Modular Recruitment to Investigate Biochemical Compartmentalization in Membraneless Organelles." Biophysical Journal 114, no. 3 (February 2018): 80a. http://dx.doi.org/10.1016/j.bpj.2017.11.482.

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Himiyama, Tomoki, and Yasunori Okamoto. "Artificial Metalloenzymes: From Selective Chemical Transformations to Biochemical Applications." Molecules 25, no. 13 (June 30, 2020): 2989. http://dx.doi.org/10.3390/molecules25132989.

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Artificial metalloenzymes (ArMs) comprise a synthetic metal complex in a protein scaffold. ArMs display performances combining those of both homogeneous catalysts and biocatalysts. Specifically, ArMs selectively catalyze non-natural reactions and reactions inspired by nature in water under mild conditions. In the past few years, the construction of ArMs that possess a genetically incorporated unnatural amino acid and the directed evolution of ArMs have become of great interest in the field. Additionally, biochemical applications of ArMs have steadily increased, owing to the fact that compartmentalization within a protein scaffold allows the synthetic metal complex to remain functional in a sea of inactivating biomolecules. In this review, we present updates on: (1) the newly reported ArMs, according to their type of reaction, and (2) the unique biochemical applications of ArMs, including chemoenzymatic cascades and intracellular/in vivo catalysis. We believe that ArMs have great potential as catalysts for organic synthesis and as chemical biology tools for pharmaceutical applications.

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Yamada, Ayako, Renaud Renault, Aleksandra Chikina, Bastien Venzac, Iago Pereiro, Sylvie Coscoy, Marine Verhulsel, et al. "Transient microfluidic compartmentalization using actionable microfilaments for biochemical assays, cell culture and organs-on-chip." Lab on a Chip 16, no. 24 (2016): 4691–701. http://dx.doi.org/10.1039/c6lc01143h.

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Laos, Roberto, and Steven Benner. "Fluorinated oil-surfactant mixtures with the density of water: Artificial cells for synthetic biology." PLOS ONE 17, no. 1 (January 20, 2022): e0252361. http://dx.doi.org/10.1371/journal.pone.0252361.

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There is a rising interest in biotechnology for the compartmentalization of biochemical reactions in water droplets. Several applications, such as the widely used digital PCR, seek to encapsulate a single molecule in a droplet to be amplified. Directed evolution, another technology with growing popularity, seeks to replicate what happens in nature by encapsulating a single gene and the protein encoded by this gene, linking genotype with phenotype. Compartmentalizing reactions in droplets also allows the experimentalist to run millions of different reactions in parallel. Compartmentalization requires a fluid that is immiscible with water and a surfactant to stabilize the droplets. While there are fluids and surfactants on the market that have been used to accomplish encapsulation, there are reported concerns with these. Span® 80, for example, a commonly used surfactant, has contaminants that interfere with various biochemical reactions. Similarly, synthetic fluids distributed by the cosmetic industry allow some researchers to produce experimental results that can be published, but then other researchers fail to reproduce some of these protocols due to the unreliable nature of these products, which are not manufactured with the intent of being used in biotechnology. The most reliable fluids, immiscible with water and suitable for biochemical reactions, are fluorinated fluids. Fluorinated compounds have the peculiar characteristic of being immiscible with water while at the same time not mixing with hydrophobic molecules. This peculiar characteristic has made fluorinated fluids attractive because it seems to be the basis of their being biologically inert. However, commercially available fluorinated fluids have densities between 1.4 to 1.6 g/mL. The higher-than-water density of fluorinated oils complicates handling of the droplets since these would float on the fluid since the water droplets would be less dense. This can cause aggregation and coalescence of the droplets. Here, we report the synthesis, characterization, and use of fluorinated polysiloxane oils that have densities similar to the one of water at room temperature, and when mixed with non-ionic fluorinated surfactants, can produce droplets encapsulating biochemical reactions. We show how droplets in these emulsions can host many biological processes, including PCR, DNA origami, rolling circle amplification (RCA), and Taqman® assays. Some of these use unnatural DNA built from an Artificially Expanded Genetic Information System (AEGIS) with six nucleotide "letters".

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Miyazaki, T., M. Yamasaki, K. Hashimoto, M. Yamazaki, M. Abe, H. Usui, M. Kano, K. Sakimura, and M. Watanabe. "Cav2.1 in Cerebellar Purkinje Cells Regulates Competitive Excitatory Synaptic Wiring, Cell Survival, and Cerebellar Biochemical Compartmentalization." Journal of Neuroscience 32, no. 4 (January 25, 2012): 1311–28. http://dx.doi.org/10.1523/jneurosci.2755-11.2012.

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Dittrich, Marcus, Ingvild Birschmann, Christiane Stuhlfelder, Albert Sickmann, Sabine Herterich, Bernhard Nieswandt, Ulrich Walter, and Thomas Dandekar. "Understanding platelets." Thrombosis and Haemostasis 94, no. 11 (2005): 916–25. http://dx.doi.org/10.1160/th05-02-0121.

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SummaryNew large-scale analysis techniques such as bioinformatics, mass spectrometry and SAGE data analysis will allow a new framework for understanding platelets. This review analyses some important options and tasks for these tools and examines an outline of the new, refined picture of the platelet outlined by these new techniques. Looking at the platelet-specific building blocks of genome, (active) transcriptome and proteome (notably secretome and phospho-proteome), we summarize current bioinformatical and biochemical approaches, tasks as well as their limitations. Understanding the surprisingly complex platelet regarding compartmentalization, key cascades, and pathways including clinical implications will remain an exciting and hopefully fruitful challenge for the future.

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Anand-Ivell, Ravinder, and Richard Ivell. "The special systems biology of the sperm." Biochemical Journal 436, no. 3 (May 27, 2011): e3-e5. http://dx.doi.org/10.1042/bj20110766.

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Spermatozoa represent a highly specialized cell type, with a minimalist structure designed to fulfil a single principal function: the transport of an intact single-copy haploid genome to the site of fertilization in the oviduct, and consequent zygote formation. They have lost most of their original cytoplasm, and remaining organelles are extremely modified. One result of this is that biochemical dynamics are restricted by a lack of cytoplasmic diffusion and a dramatic compartmentalization, with an increased emphasis on the physicochemical modulation of membranes. This is also reflected in a truncated apoptotic pathway, described in this issue of the Biochemical Journal in an article by Koppers et al., which leads to a so-called ‘silent response’ in the female tract, whereby unused sperm are removed without inflammatory consequences that might otherwise be detrimental to the new embryo. This new study shows that sperm have not simply jettisoned unwanted cellular components, but have evolved a very appropriate systems biology adapted to the specialist role they have to perform.

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Seaver, Samuel M. D., Filipe Liu, Qizhi Zhang, James Jeffryes, José P. Faria, Janaka N. Edirisinghe, Michael Mundy, et al. "The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes." Nucleic Acids Research 49, no. D1 (September 28, 2020): D575—D588. http://dx.doi.org/10.1093/nar/gkaa746.

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Abstract For over 10 years, ModelSEED has been a primary resource for the construction of draft genome-scale metabolic models based on annotated microbial or plant genomes. Now being released, the biochemistry database serves as the foundation of biochemical data underlying ModelSEED and KBase. The biochemistry database embodies several properties that, taken together, distinguish it from other published biochemistry resources by: (i) including compartmentalization, transport reactions, charged molecules and proton balancing on reactions; (ii) being extensible by the user community, with all data stored in GitHub; and (iii) design as a biochemical ‘Rosetta Stone’ to facilitate comparison and integration of annotations from many different tools and databases. The database was constructed by combining chemical data from many resources, applying standard transformations, identifying redundancies and computing thermodynamic properties. The ModelSEED biochemistry is continually tested using flux balance analysis to ensure the biochemical network is modeling-ready and capable of simulating diverse phenotypes. Ontologies can be designed to aid in comparing and reconciling metabolic reconstructions that differ in how they represent various metabolic pathways. ModelSEED now includes 33,978 compounds and 36,645 reactions, available as a set of extensible files on GitHub, and available to search at https://modelseed.org/biochem and KBase.

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Kambe, Taiho, Tokuji Tsuji, Ayako Hashimoto, and Naoya Itsumura. "The Physiological, Biochemical, and Molecular Roles of Zinc Transporters in Zinc Homeostasis and Metabolism." Physiological Reviews 95, no. 3 (July 2015): 749–84. http://dx.doi.org/10.1152/physrev.00035.2014.

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Zinc is involved in a variety of biological processes, as a structural, catalytic, and intracellular and intercellular signaling component. Thus zinc homeostasis is tightly controlled at the whole body, tissue, cellular, and subcellular levels by a number of proteins, with zinc transporters being particularly important. In metazoan, two zinc transporter families, Zn transporters (ZnT) and Zrt-, Irt-related proteins (ZIP) function in zinc mobilization of influx, efflux, and compartmentalization/sequestration across biological membranes. During the last two decades, significant progress has been made in understanding the molecular properties, expression, regulation, and cellular and physiological roles of ZnT and ZIP transporters, which underpin the multifarious functions of zinc. Moreover, growing evidence indicates that malfunctioning zinc homeostasis due to zinc transporter dysfunction results in the onset and progression of a variety of diseases. This review summarizes current progress in our understanding of each ZnT and ZIP transporter from the perspective of zinc physiology and pathogenesis, discussing challenging issues in their structure and zinc transport mechanisms.

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Nagata, Toshihiko, Atsuko Kawahara, Chika Kasahara, Mika Yokota, Seiji Nishikawa, Yoichi Wakano, Hiroshi Ishida, and Toshihiko Nagata. "Biochemical study on the tissue compartmentalization of phosphophoryn, osteopontin and bone sialoprotein (BSP) in rat incisor dentin." Journal of Bone and Mineral Metabolism 12, S2 (December 1994): 7–13. http://dx.doi.org/10.1007/bf02383380.

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Quraishe, S., A. Asuni, W. C. Boelens, V. O'Connor, and A. Wyttenbach. "Expression of the small heat shock protein family in the mouse CNS: Differential anatomical and biochemical compartmentalization." Neuroscience 153, no. 2 (May 2008): 483–91. http://dx.doi.org/10.1016/j.neuroscience.2008.01.058.

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Pintér, Panka, and Alán Alpár. "The Role of Extracellular Matrix in Human Neurodegenerative Diseases." International Journal of Molecular Sciences 23, no. 19 (September 21, 2022): 11085. http://dx.doi.org/10.3390/ijms231911085.

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The dense neuropil of the central nervous system leaves only limited space for extracellular substances free. The advent of immunohistochemistry, soon followed by advanced diagnostic tools, enabled us to explore the biochemical heterogeneity and compartmentalization of the brain extracellular matrix in exploratory and clinical research alike. The composition of the extracellular matrix is critical to shape neuronal function; changes in its assembly trigger or reflect brain/spinal cord malfunction. In this study, we focus on extracellular matrix changes in neurodegenerative disorders. We summarize its phenotypic appearance and biochemical characteristics, as well as the major enzymes which regulate and remodel matrix establishment in disease. The specifically built basement membrane of the central nervous system, perineuronal nets and perisynaptic axonal coats can protect neurons from toxic agents, and biochemical analysis revealed how the individual glycosaminoglycan and proteoglycan components interact with these molecules. Depending on the site, type and progress of the disease, select matrix components can either proactively trigger the formation of disease-specific harmful products, or reactively accumulate, likely to reduce tissue breakdown and neuronal loss. We review the diagnostic use and the increasing importance of medical screening of extracellular matrix components, especially enzymes, which informs us about disease status and, better yet, allows us to forecast illness.

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Oses, Camila, Martin Stortz, Paula Verneri, Alejandra Guberman, and Valeria Levi. "Pluripotency transcription factors at the focus: the phase separation paradigm in stem cells." Biochemical Society Transactions 49, no. 6 (November 23, 2021): 2871–78. http://dx.doi.org/10.1042/bst20210856.

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The transcription factors (TFs) OCT4, SOX2 and NANOG are key players of the gene regulatory network of pluripotent stem cells. Evidence accumulated in recent years shows that even small imbalances in the expression levels or relative concentrations of these TFs affect both, the maintenance of pluripotency and cell fate decisions. In addition, many components of the transcriptional machinery including RNA polymerases, cofactors and TFs such as those required for pluripotency, do not distribute homogeneously in the nucleus but concentrate in multiple foci influencing the delivery of these molecules to their DNA-targets. How cells control strict levels of available pluripotency TFs in this heterogeneous space and the biological role of these foci remain elusive. In recent years, a wealth of evidence led to propose that many of the nuclear compartments are formed through a liquid–liquid phase separation process. This new paradigm early penetrated the stem cells field since many key players of the pluripotency circuitry seem to phase-separate. Overall, the formation of liquid compartments may modulate the kinetics of biochemical reactions and consequently regulate many nuclear processes. Here, we review the state-of-the-art knowledge of compartmentalization in the cell nucleus and the relevance of this process for transcriptional regulation, particularly in pluripotent stem cells. We also highlight the recent advances and new ideas in the field showing how compartmentalization may affect pluripotency preservation and cell fate decisions.

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Hoffman, David P., Gleb Shtengel, C. Shan Xu, Kirby R. Campbell, Melanie Freeman, Lei Wang, Daniel E. Milkie, et al. "Correlative three-dimensional super-resolution and block-face electron microscopy of whole vitreously frozen cells." Science 367, no. 6475 (January 16, 2020): eaaz5357. http://dx.doi.org/10.1126/science.aaz5357.

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Within cells, the spatial compartmentalization of thousands of distinct proteins serves a multitude of diverse biochemical needs. Correlative super-resolution (SR) fluorescence and electron microscopy (EM) can elucidate protein spatial relationships to global ultrastructure, but has suffered from tradeoffs of structure preservation, fluorescence retention, resolution, and field of view. We developed a platform for three-dimensional cryogenic SR and focused ion beam–milled block-face EM across entire vitreously frozen cells. The approach preserves ultrastructure while enabling independent SR and EM workflow optimization. We discovered unexpected protein-ultrastructure relationships in mammalian cells including intranuclear vesicles containing endoplasmic reticulum–associated proteins, web-like adhesions between cultured neurons, and chromatin domains subclassified on the basis of transcriptional activity. Our findings illustrate the value of a comprehensive multimodal view of ultrastructural variability across whole cells.

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Konishi, Hiroaki, Eiji Nakata, Futa Komatsubara, and Takashi Morii. "Controlled Assembly of Fluorophores inside a Nanoliposome." Molecules 28, no. 2 (January 16, 2023): 911. http://dx.doi.org/10.3390/molecules28020911.

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Cellular compartmentalization plays an essential role in organizing the complex and multiple biochemical reactions in the cell. An artificial compartment would provide powerful strategies to develop new biochemical tools for material production and diagnosis, but it is still a great challenge to synthesize the compartments that encapsulate materials of interest while controlling their accurate locations, numbers, and stoichiometry. In this study, we evaluated chemical characteristics of a liposome-encapsulated compartment, which has great potential to locate various materials of interest with precise control of their locations and numbers in the compartment. A nanoliposome was constructed inside a ring-shaped DNA origami skeleton according to the method of Yang et al., and further equipped with a double-stranded DNA platform to assemble molecules of interest in the nanoliposome. Upon formation of the nanoliposome, a pH-sensitive fluorophore on the bridged platform showed little or no response to the pH change of the outer buffer, ensuring that the molecules assembled on the platform are effectively shielded from the outer environment. The ring-shaped DNA skeleton equipped with a double-stranded DNA platform allows spatial assembly of several functional molecules inside the nanoliposome to isolate them from the outer environment.

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Sorkhabi-Abdolmaleki, S., A. Zibaee, H. Hoda, R. Hosseini, and M. Fazeli-Dinan. "Proteolytic compartmentalization and activity in the midgut of Andrallus spinidens Fabricius (Hemiptera: Pentatomidae)." Journal of Entomological and Acarological Research 45, no. 1 (April 23, 2013): 8. http://dx.doi.org/10.4081/jear.2013.e8.

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Digestive proteolytic activity in the alimentary canal of Andrallus spinidens, a potential biocontrol agent of lepidopteran larvae, was studied by considering enzyme compartmentalization and diversity. The alimentary canal of adults consists of a foregut, a four- sectioned midgut, namely V1 to V4 (ventriculus), and a hindgut. The optimal pH for general proteolytic activity was found to be at pH 8 with a small peak at pH 6. Results revealed that there are several specific proteases in the midgut of A. spinidens, including trypsin-like, chymotrypsin-like, and elastase as serine proteases, and cathepsins B, L and D as cysteine proteases, in addition to two exopeptidases of carboxy- and aminopetidases. Compartmentalization of digestive proteolytic activity showed that V3 is the main area of proteolytic secretion for both general and specific proteases and that V4 has the lowest enzymatic role, so that four out of the eight specific proteases found showed no activity in this section. The lowest and the highest proteolytic activity was found to be in the 1st and 4th nymphal instars, respectively. Using the specific inhibitors phenylmethylsulfonyl fluoride, Na-p-tosyl-L-lysine chloromethyl ketone, Ntosyl- L-phenylalanine chloromethyl ketone, L-trans-epoxysuccinyl-leucylamido-( 4-guanidino)-butane, cystatin, phenanthroline and ethylendiamidetetraacetic acid, we verified the presence of all specific proteases noted using both biochemical assays and sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Our findings demonstrated that A. spinidens could utilize several caterpillars because of the presence of various of proteases in its midgut.

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Kader, Adel A. "Ethylene-induced Senescence and Physiological Disorders in Harvested Horticultural Crops." HortScience 20, no. 1 (February 1985): 54–57. http://dx.doi.org/10.21273/hortsci.20.1.54.

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Abstract Ethylene plays a major role in plant senescence via its direct and indirect effects on the regulation of metabolism. The known physiological and biochemical effects of C2H4 on harvested horticultural crops include increased respiratory activity; increased activity of enzymes such as polygalacturonase, peroxidase, lipoxidase, alphaamylase, polyphenol oxidase, and phenylalanine ammonialyase (PAL); increased permeability and loss of cell compartmentalization; and alteration of auxin transport or metabolism (34). Nevertheless, the mechanism by which C2H4 promotes senescence remains unknown. Lieberman (21) stated that the action of C2H4 in accelerating senescence can be associated with interactions with auxins, gibberellins, cytokinins, and abscisic acid (ABA). The mechanisms involved in these interrelationships are not fully understood, but there is evidence to suggest that a general antagonism exists between the senescence promoters (C2H4 and ABA) and the senescence inhibitors (auxins, gibberellins, and cytokinins).

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Sharifloo, A., A. Zibaee, J. Jalali Sendi, and K. Talebi Jahroumi. "Biochemical characterization a digestive trypsin in the midgut of large cabbage white butterfly, Pieris brassicae L. (Lepidoptera: Pieridae)." Bulletin of Entomological Research 108, no. 4 (November 7, 2017): 501–9. http://dx.doi.org/10.1017/s0007485317001067.

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AbstractA comprehensive study on digestive trypsin was undertaken in the larval midgut of Pieris brassicae L. Results of enzymatic compartmentalization showed a significantly higher activity of crude trypsin in the anterior larval midgut rather than posterior-midgut. Using Diethylaminoethyl cellulose fast flow column chromatography a purified trypsin was obtained by specific activity of 21 U mg−1 protein, recovery of 22%, purification fold of 28-fold and molecular weight of 25 kDa. This purified enzyme showed the highest activity at pH 8 and the corresponding temperature of 40°C. However, the specific inhibitors used including 4-(2-Aminoethyl) benzenesulfonyl fluroride hydrochloride, N-p-Tosyl-L-lysine methyl ester hydrochloride and Soybean Trypsin Inhibitor significantly lowered the activity of the purified enzyme in vitro. Moreover, the activity of trypsin and likewise the nutritional indices were significantly altered in the larval midgut feeding upon the leaves treated by 1 mM concentration of each inhibitor in comparison with control. Determination of enzymatic characteristics of insect trypsins is crucial in paving the path for controlling pests by potential natural compounds via transgenic plants.

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Ianeselli, Alan, Damla Tetiker, Julian Stein, Alexandra Kühnlein, Christof B. Mast, Dieter Braun, and T. Y. Dora Tang. "Non-equilibrium conditions inside rock pores drive fission, maintenance and selection of coacervate protocells." Nature Chemistry 14, no. 1 (December 6, 2021): 32–39. http://dx.doi.org/10.1038/s41557-021-00830-y.

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AbstractKey requirements for the first cells on Earth include the ability to compartmentalize and evolve. Compartmentalization spatially localizes biomolecules from a dilute pool and an evolving cell, which, as it grows and divides, permits mixing and propagation of information to daughter cells. Complex coacervate microdroplets are excellent candidates as primordial cells with the ability to partition and concentrate molecules into their core and support primitive and complex biochemical reactions. However, the evolution of coacervate protocells by fusion, growth and fission has not yet been demonstrated. In this work, a primordial environment initiated the evolution of coacervate-based protocells. Gas bubbles inside heated rock pores perturb the coacervate protocell distribution and drive the growth, fusion, division and selection of coacervate microdroplets. Our findings provide a compelling scenario for the evolution of membrane-free coacervate microdroplets on the early Earth, induced by common gas bubbles within heated rock pores.

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Hoenen, Antje, Wenjun Liu, Georg Kochs, Alexander A. Khromykh, and Jason M. Mackenzie. "West Nile virus-induced cytoplasmic membrane structures provide partial protection against the interferon-induced antiviral MxA protein." Journal of General Virology 88, no. 11 (November 1, 2007): 3013–17. http://dx.doi.org/10.1099/vir.0.83125-0.

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The human MxA protein is a type I and III interferon (IFN)-induced protein with proven antiviral activity against RNA viruses. In this study, we investigated the effect of MxA expression on the replication of West Nile Virus strain Kunjin (WNVKUN). Pretreatment of A549 cells with IFN-α lead to increased expression of MxA, which contributed to inhibition of WNVKUN replication and secretion. However, in Vero cells stably expressing the MxA protein, WNVKUN replication, maturation and secretion was not inhibited. Biochemical and subcellular localization studies of WNVKUN proteins and MxA suggest that the MxA activity was not compromised by a flavivirus-encoded antagonist. Instead, we show that characteristic membranous structures induced during WNVKUN replication provide partial protection from MxA, possibly by ‘hiding’ WNVKUN replication components. This distinct compartmentalization of viral replication and components of the cellular antiviral response may be an evolutionary mechanism by which flaviviruses can hide from host surveillance.

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Tian, Siran, Harrison A. Curnutte, and Tatjana Trcek. "RNA Granules: A View from the RNA Perspective." Molecules 25, no. 14 (July 8, 2020): 3130. http://dx.doi.org/10.3390/molecules25143130.

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RNA granules are ubiquitous. Composed of RNA-binding proteins and RNAs, they provide functional compartmentalization within cells. They are inextricably linked with RNA biology and as such are often referred to as the hubs for post-transcriptional regulation. Much of the attention has been given to the proteins that form these condensates and thus many fundamental questions about the biology of RNA granules remain poorly understood: How and which RNAs enrich in RNA granules, how are transcripts regulated in them, and how do granule-enriched mRNAs shape the biology of a cell? In this review, we discuss the imaging, genetic, and biochemical data, which have revealed that some aspects of the RNA biology within granules are carried out by the RNA itself rather than the granule proteins. Interestingly, the RNA structure has emerged as an important feature in the post-transcriptional control of granule transcripts. This review is part of the Special Issue in the Frontiers in RNA structure in the journal Molecules.

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Martínez-Bisbal, M. Carmen, Vicent Esteve, Beatriz Martínez-Granados, and Bernardo Celda. "Magnetic Resonance Microscopy Contribution to Interpret High-Resolution Magic Angle Spinning Metabolomic Data of Human Tumor Tissue." Journal of Biomedicine and Biotechnology 2011 (2011): 1–8. http://dx.doi.org/10.1155/2011/763684.

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HRMAS NMR is considered a valuable technique to obtain detailed metabolic profile of unprocessed tissues. To properly interpret the HRMAS metabolomic results, detailed information of the actual state of the sample inside the rotor is needed. MRM (Magnetic Resonance Microscopy) was applied for obtaining structural and spatially localized metabolic information of the samples inside the HRMAS rotors. The tissue was observed stuck to the rotor wall under the effect of HRMAS spinning. MRM spectroscopy showed a transference of metabolites from the tissue to the medium. The sample shape and the metabolite transfer after HRMAS indicated that tissue had undergone alterations and it can not be strictly considered as intact. This must be considered when HRMAS is used for metabolic tissue characterization, and it is expected to be highly dependent on the manipulation of the sample. The localized spectroscopic information of MRM reveals the biochemical compartmentalization on tissue samples hidden in the HRMAS spectrum.

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Cermakova, Katerina, and H. Hodges. "Next-Generation Drugs and Probes for Chromatin Biology: From Targeted Protein Degradation to Phase Separation." Molecules 23, no. 8 (August 6, 2018): 1958. http://dx.doi.org/10.3390/molecules23081958.

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Chromatin regulation is a critical aspect of nuclear function. Recent advances have provided detailed information about dynamic three-dimensional organization of chromatin and its regulatory factors. Mechanisms crucial for normal nuclear function and epigenetic control include compartmentalization of biochemical reactions by liquid-phase separated condensates and signal-dependent regulation of protein stability. Synthetic control of these phenomena by small molecules provides deep insight into essential activities such as histone modification, BAF (SWI/SNF) and PBAF remodeling, Polycomb repression, enhancer looping by cohesin and CTCF, as well as many other processes that contribute to transcription. As a result, a complete understanding of the spatiotemporal mechanisms that underlie chromatin regulation increasingly requires the use of fast-acting drugs and chemical probes. Here, we provide a comprehensive review of next-generation chemical biology tools to interrogate the chromatin regulatory landscape, including selective PROTAC E3 ubiquitin ligase degraders, degrons, fluorescent ligands, dimerizers, inhibitors, and other drugs. These small molecules provide important insights into the mechanisms that govern gene regulation, DNA repair, development, and diseases like cancer.

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Yang, Jingya, Lingxiong Li, Xiong Zhang, Shibo Wu, Xiaohui Han, Xiong Li, and Jianchu Xu. "Comparative Transcriptomics Analysis of Roots and Leaves under Cd Stress in Calotropis gigantea L." International Journal of Molecular Sciences 23, no. 6 (March 19, 2022): 3329. http://dx.doi.org/10.3390/ijms23063329.

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Calotropis gigantea is often found in mining areas with heavy metal pollution. However, little is known about the physiological and molecular response mechanism of C. gigantea to Cd stress. In the present study, Cd tolerance characteristic of C. gigantea and the potential mechanisms were explored. Seed germination test results showed that C. gigantea had a certain Cd tolerance capacity. Biochemical and transcriptomic analysis indicated that the roots and leaves of C. gigantea had different responses to early Cd stress. A total of 176 and 1618 DEGs were identified in the roots and leaves of C. gigantea treated with Cd compared to the control samples, respectively. Results indicated that oxidative stress was mainly initiated in the roots of C. gigantea, whereas the leaves activated several Cd detoxification processes to cope with Cd, including the upregulation of genes involved in Cd transport (i.e., absorption, efflux, or compartmentalization), cell wall remodeling, antioxidant system, and chelation. This study provides preliminary information to understand how C. gigantea respond to Cd stress, which is useful for evaluating the potential of C. gigantea in the remediation of Cd-contaminated soils.

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Pereira-Filho, Jurandir, Leonardo R. Rörig, Carlos A. F. Schettini, Mariana A. Soppa, Bruno L. Santana, and José Eduardo dos Santos. "Spatial changes in the water quality of Itajaí-Açú Fluvial-Estuarine System, Santa Catarina, Brazil." Anais da Academia Brasileira de Ciências 82, no. 4 (December 2010): 963–82. http://dx.doi.org/10.1590/s0001-37652010000400019.

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This study was carried out with the aim of evaluating the spatial variation of the water quality in the Itajaí-Açú River estuary. Seven stations along the estuary were monitored on a weekly basis, from October 2003 to December 2004, plus two stations in tributaries (Itajaí-Mirim River, the main tributary, and one reference station). This monitoring included measurements of salinity, pH, dissolved oxygen, temperature, nutrients(NH+4,NO3-2,NO-3,PO3-4,H4SiO4) Biochemical Oxygen Demand (BOD), total phosphorous and dissolved organic phosphorus (TP and DOP), particulate organic carbon (POC), suspended particulate matter (SPM) and chlorophyll-a (Cla). Multivariate analyses demonstrated the compartmentalization of the system based on the deterioration in water quality and marine influence. Urban development was the main factor responsible for the spatial variation of the monitored variables, resulting in increases in the indicators for organic matter and a progressive decrease in O2. Despite the effect of dilution by marine influence, there was an increase in ammonium, attributed to the influence of the municipal districts of Itajaí and Navegantes, close to the river mouth.

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Berliocchi, Laura, Daniele Bano, and Pierluigi Nicotera. "Ca 2+ signals and death programmes in neurons." Philosophical Transactions of the Royal Society B: Biological Sciences 360, no. 1464 (November 3, 2005): 2255–58. http://dx.doi.org/10.1098/rstb.2005.1765.

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Cell death programmes are generally defined by biochemical/genetic routines that are linked to their execution and by the appearance of more or less typical morphological features. However, in pathological settings death signals may engage complex and interacting lethal pathways, some of which are common to different cells, whereas others are linked to a specific tissue and differentiation pattern. In neurons, death programmes can be spatially and temporally segregated. Most importantly physiological Ca 2+ signals are essential for cell function and survival. On the other hand, Ca 2+ overload or perturbations of intracellular Ca 2+ compartmentalization can activate or enhance mechanisms leading to cell death. An imbalance between Ca 2+ influx and efflux from cells is the initial signal leading to Ca 2+ overload and death of ischaemic neurons or cardiomyocytes. Alterations of intracellular Ca 2+ storage can integrate with death signals that do not initially require Ca 2+ , to promote processing of cellular components and death by apoptosis or necrosis. Finally, Ca 2+ can directly activate catabolic enzymes such as proteases, phospholipases and nucleases that directly cause cell demise and tissue damage.

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Majewska, Ania, Edward Brown, Jonathan Ross, and Rafael Yuste. "Mechanisms of Calcium Decay Kinetics in Hippocampal Spines: Role of Spine Calcium Pumps and Calcium Diffusion through the Spine Neck in Biochemical Compartmentalization." Journal of Neuroscience 20, no. 5 (March 1, 2000): 1722–34. http://dx.doi.org/10.1523/jneurosci.20-05-01722.2000.

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Verbitskaia, A. A., A. S. Egorova, E. A. Tsarkova, and A. K. Gaponenko. "Studying the effect of the OsGATA rice transcription factor on salt stress tolerance in wheat." Proceedings on applied botany, genetics and breeding 183, no. 3 (October 2, 2022): 9–16. http://dx.doi.org/10.30901/2227-8834-2022-3-9-16.

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This study shows the possibility of using the OsGATA rice transcription factor in transgenic lines of high-yielding wheat cultivars to increase their tolerance to salinity, which was confirmed using physiological and biochemical methods according to standard protocols. Wheat plants were grown in an artificial climate under optimal growing conditions. Genetic transformation methods were used to introduce the GATA gene into the genome of the used wheat genotypes. Transgenic lines were selected on selective media under in vitro conditions.The results of the experimental work showed that the expression of the GATA gene under salt stress may be responsible for the increased compartmentalization of Na+ in the vacuole, which provides improved salt tolerance. As a result of the experiment, collections of T1 transgenic wheat lines from cvs. ‘Zlata’, ‘Emir’ and ‘Agata’ expressing the GATA gene were obtained and studied for salt tolerance. Lines Zl.01, Zl.02, Zl.03 and Ag.02 were selected with PCR. Under NaCl salinity conditions, some of the transgenic lines showed a statistically significant increase in salinity resistance. The results of the study laid the foundation for studying GATA genes in wheat and for producing salinity-tolerant lines without growth defects or reduced productivity.

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Sönnichsen, Birte, Stefano De Renzis, Erik Nielsen, Jens Rietdorf, and Marino Zerial. "Distinct Membrane Domains on Endosomes in the Recycling Pathway Visualized by Multicolor Imaging of Rab4, Rab5, and Rab11." Journal of Cell Biology 149, no. 4 (May 15, 2000): 901–14. http://dx.doi.org/10.1083/jcb.149.4.901.

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Two endosome populations involved in recycling of membranes and receptors to the plasma membrane have been described, the early and the recycling endosome. However, this distinction is mainly based on the flow of cargo molecules and the spatial distribution of these membranes within the cell. To get insights into the membrane organization of the recycling pathway, we have studied Rab4, Rab5, and Rab11, three regulatory components of the transport machinery. Following transferrin as cargo molecule and GFP-tagged Rab proteins we could show that cargo moves through distinct domains on endosomes. These domains are occupied by different Rab proteins, revealing compartmentalization within the same continuous membrane. Endosomes are comprised of multiple combinations of Rab4, Rab5, and Rab11 domains that are dynamic but do not significantly intermix over time. Three major populations were observed: one that contains only Rab5, a second with Rab4 and Rab5, and a third containing Rab4 and Rab11. These membrane domains display differential pharmacological sensitivity, reflecting their biochemical and functional diversity. We propose that endosomes are organized as a mosaic of different Rab domains created through the recruitment of specific effector proteins, which cooperatively act to generate a restricted environment on the membrane.

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Guo, Zhigang, Limin Qian, Ren Liu, Huifang Dai, Mian Zhou, Li Zheng, and Binghui Shen. "Nucleolar Localization and Dynamic Roles of Flap Endonuclease 1 in Ribosomal DNA Replication and Damage Repair." Molecular and Cellular Biology 28, no. 13 (April 28, 2008): 4310–19. http://dx.doi.org/10.1128/mcb.00200-08.

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ABSTRACT Despite the wealth of information available on the biochemical functions and our recent findings of its roles in genome stability and cancer avoidance of the structure-specific flap endonuclease 1 (FEN1), its cellular compartmentalization and dynamics corresponding to its involvement in various DNA metabolic pathways are not yet elucidated. Several years ago, we demonstrated that FEN1 migrates into the nucleus in response to DNA damage and under certain cell cycle conditions. In the current paper, we found that FEN1 is superaccumulated in the nucleolus and plays a role in the resolution of stalled DNA replication forks formed at the sites of natural replication fork barriers. In response to UV irradiation and upon phosphorylation, FEN1 migrates to nuclear plasma to participate in the resolution of UV cross-links on DNA, most likely employing its concerted action of exonuclease and gap-dependent endonuclease activities. Based on yeast complementation experiments, the mutation of Ser187Asp, mimicking constant phosphorylation, excludes FEN1 from nucleolar accumulation. The replacement of Ser187 by Ala, eliminating the only phosphorylation site, retains FEN1 in nucleoli. Both of the mutations cause UV sensitivity, impair cellular UV damage repair capacity, and decline overall cellular survivorship.

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Matilla, Angel J. "Auxin: Hormonal Signal Required for Seed Development and Dormancy." Plants 9, no. 6 (June 1, 2020): 705. http://dx.doi.org/10.3390/plants9060705.

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The production of viable seeds is a key event in the life cycle of higher plants. Historically, abscisic acid (ABA) and gibberellin (GAs) were considered the main hormones that regulate seed formation. However, auxin has recently emerged as an essential player that modulates, in conjunction with ABA, different cellular processes involved in seed development as well as the induction, regulation and maintenance of primary dormancy (PD). This review examines and discusses the key role of auxin as a signaling molecule that coordinates seed life. The cellular machinery involved in the synthesis and transport of auxin, as well as their cellular and tissue compartmentalization, is crucial for the development of the endosperm and seed-coat. Thus, auxin is an essential compound involved in integuments development, and its transport from endosperm is regulated by AGAMOUS-LIKE62 (AGL62) whose transcript is specifically expressed in the endosperm. In addition, recent biochemical and genetic evidence supports the involvement of auxins in PD. In this process, the participation of the transcriptional regulator ABA INSENSITIVE3 (ABI3) is critical, revealing a cross-talk between auxin and ABA signaling. Future experimental aimed at advancing knowledge of the role of auxins in seed development and PD are also discussed.

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Casaní-Galdón, Salvador, Cecile Pereira, and Ana Conesa. "Padhoc: a computational pipeline for pathway reconstruction on the fly." Bioinformatics 36, Supplement_2 (December 2020): i795—i803. http://dx.doi.org/10.1093/bioinformatics/btaa811.

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Abstract Motivation Molecular pathway databases represent cellular processes in a structured and standardized way. These databases support the community-wide utilization of pathway information in biological research and the computational analysis of high-throughput biochemical data. Although pathway databases are critical in genomics research, the fast progress of biomedical sciences prevents databases from staying up-to-date. Moreover, the compartmentalization of cellular reactions into defined pathways reflects arbitrary choices that might not always be aligned with the needs of the researcher. Today, no tool exists that allow the easy creation of user-defined pathway representations. Results Here we present Padhoc, a pipeline for pathway ad hoc reconstruction. Based on a set of user-provided keywords, Padhoc combines natural language processing, database knowledge extraction, orthology search and powerful graph algorithms to create navigable pathways tailored to the user’s needs. We validate Padhoc with a set of well-established Escherichia coli pathways and demonstrate usability to create not-yet-available pathways in model (human) and non-model (sweet orange) organisms. Availability and implementation Padhoc is freely available at https://github.com/ConesaLab/padhoc. Supplementary information Supplementary data are available at Bioinformatics online.

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Argentiere, Simona, Pietro Aleardo Siciliano, and Laura Blasi. "How Microgels Can Improve the Impact of Organ-on-Chip and Microfluidic Devices for 3D Culture: Compartmentalization, Single Cell Encapsulation and Control on Cell Fate." Polymers 13, no. 19 (September 23, 2021): 3216. http://dx.doi.org/10.3390/polym13193216.

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The Organ-on-chip (OOC) devices represent the new frontier in biomedical research to produce micro-organoids and tissues for drug testing and regenerative medicine. The development of such miniaturized models requires the 3D culture of multiple cell types in a highly controlled microenvironment, opening new challenges in reproducing the extracellular matrix (ECM) experienced by cells in vivo. In this regard, cell-laden microgels (CLMs) represent a promising tool for 3D cell culturing and on-chip generation of micro-organs. The engineering of hydrogel matrix with properly balanced biochemical and biophysical cues enables the formation of tunable 3D cellular microenvironments and long-term in vitro cultures. This focused review provides an overview of the most recent applications of CLMs in microfluidic devices for organoids formation, highlighting microgels’ roles in OOC development as well as insights into future research.

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Pettinger, W. A., S. Umemura, D. D. Smyth, and W. B. Jeffries. "Renal alpha 2-adrenoceptors and the adenylate cyclase-cAMP system: biochemical and physiological interactions." American Journal of Physiology-Renal Physiology 252, no. 2 (February 1, 1987): F199—F208. http://dx.doi.org/10.1152/ajprenal.1987.252.2.f199.

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alpha 2-Adrenoceptors were first described pharmacologically ten years ago. Within three years their capacity to inhibit adenylate cyclase had been demonstrated in many tissues. They were demonstrated biochemically in the kidneys in 1981 even before any renal physiological effects of their activation were known. They predominate numerically over alpha 1-adrenoceptors in renal membranes and their density is increased in genetic forms of rat hypertension. alpha 1-Adrenoceptors normally mediate the vasoconstriction and sodium- and water-retaining effects of sympathetic neuronally released norepinephrine. Norepinephrine or epinephrine must be infused to activate alpha 2-adrenoceptors, suggesting that renal alpha 2-adrenoceptors are extrajunctional, whereas alpha 1-adrenoceptors are postjunctional. When alpha 1-adrenoceptors are chronically blocked, renal alpha 2-adrenoceptor density increases and they assume a location at postjunctional sites, the otherwise exclusive domain of alpha 1-adrenoceptors. Results from microdissection studies have established that alpha 2-adrenoceptors are present on most segments of the nephron and that their activation can suppress adenosine 3,'5'-cyclic monophosphate (cAMP) accumulation induced by most renal hormones. However, failure of alpha 2-adrenoceptor activation to suppress cAMP accumulation in some tubular segments induced by certain hormones suggests compartmentalization of adenylate cyclase regulation that is hormone-function specific. In view of the potent inhibitory effects of alpha 2-adrenoceptor stimulation on hormone activated cAMP accumulation in several discrete areas of the nephron, we suggest that alpha 2-adrenoceptors fulfill important regulatory role(s) in renal function. To date, alpha 2-adrenoceptor activation has been shown to reverse vasopressin-induced sodium and water retention, and arachidonic acid- and furosemide-induced cAMP, sodium, and water excretion in the isolated perfused kidney. Thus the effects are qualitatively and quantitatively dependent in these studies on the hormone being infused and are therefore hormone-function specific. Physiological effects of alpha 2-adrenoceptor activation of thyrocalcitonin and on parathyroid hormone-induced effects have not been studied. alpha 2-Adrenoceptor activation can inhibit renin release in some model systems and can activate a sodium-hydrogen antiporter system in proximal tubules. The physiological roles of these actions are unknown.

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Basit, Farwa, Javaid Akhter Bhat, Jin Hu, Prashant Kaushik, Ajaz Ahmad, Yajing Guan, and Parvaiz Ahmad. "Brassinosteroid Supplementation Alleviates Chromium Toxicity in Soybean (Glycine max L.) via Reducing Its Translocation." Plants 11, no. 17 (September 1, 2022): 2292. http://dx.doi.org/10.3390/plants11172292.

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Chromium (Cr) phytotoxicity severely inhibits plant growth and development which makes it a prerequisite to developing techniques that prevent Cr accumulation in food chains. However, little is explored related to the protective role of brassinosteroids (BRs) against Cr-induced stress in soybean plants. Herein, the morpho-physiological, biochemical, and molecular responses of soybean cultivars with/without foliar application of BRs under Cr toxicity were intensely investigated. Our outcomes deliberated that BRs application noticeably reduced Cr-induced phytotoxicity by lowering Cr uptake (37.7/43.63%), accumulation (63.92/81.73%), and translocation (26.23/38.14%) in XD-18/HD-19, plant tissues, respectively; besides, improved seed germination ratio, photosynthetic attributes, plant growth, and biomass, as well as prevented nutrient uptake inhibition under Cr stress, especially in HD-19 cultivar. Furthermore, BRs stimulated antioxidative defense systems, both enzymatic and non-enzymatic, the compartmentalization of ion chelation, diminished extra production of reactive oxygen species (ROS), and electrolyte leakage in response to Cr-induced toxicity, specifically in HD-19. In addition, BRs improved Cr stress tolerance in soybean seedlings by regulating the expression of stress-related genes involved in Cr accumulation, and translocation. Inclusively, by considering the above-mentioned biomarkers, foliar spray of BRs might be considered an effective inhibitor of Cr-induced damages in soybean cultivars, even in Cr polluted soil.

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Saumell-Esnaola, Miquel, Sergio Barrondo, Gontzal García del Caño, María Aranzazu Goicolea, Joan Sallés, Beat Lutz, and Krisztina Monory. "Subsynaptic Distribution, Lipid Raft Targeting and G Protein-Dependent Signalling of the Type 1 Cannabinoid Receptor in Synaptosomes from the Mouse Hippocampus and Frontal Cortex." Molecules 26, no. 22 (November 16, 2021): 6897. http://dx.doi.org/10.3390/molecules26226897.

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Numerous studies have investigated the roles of the type 1 cannabinoid receptor (CB1) in glutamatergic and GABAergic neurons. Here, we used the cell-type-specific CB1 rescue model in mice to gain insight into the organizational principles of plasma membrane targeting and Gαi/o protein signalling of the CB1 receptor at excitatory and inhibitory terminals of the frontal cortex and hippocampus. By applying biochemical fractionation techniques and Western blot analyses to synaptosomal membranes, we explored the subsynaptic distribution (pre-, post-, and extra-synaptic) and CB1 receptor compartmentalization into lipid and non-lipid raft plasma membrane microdomains and the signalling properties. These data infer that the plasma membrane partitioning of the CB1 receptor and its functional coupling to Gαi/o proteins are not biased towards the cell type of CB1 receptor rescue. The extent of the canonical Gαi/o protein-dependent CB1 receptor signalling correlated with the abundance of CB1 receptor in the respective cell type (glutamatergic versus GABAergic neurons) both in frontal cortical and hippocampal synaptosomes. In summary, our results provide an updated view of the functional coupling of the CB1 receptor to Gαi/o proteins at excitatory and inhibitory terminals and substantiate the utility of the CB1 rescue model in studying endocannabinoid physiology at the subcellular level.

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Stavridou, Evangelia, Richard J. Webster, and Paul R. H. Robson. "The Effects of Moderate and Severe Salinity on Composition and Physiology in the Biomass Crop Miscanthus × giganteus." Plants 9, no. 10 (September 25, 2020): 1266. http://dx.doi.org/10.3390/plants9101266.

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Saline land represents a growing resource that could be utilised for growing biomass crops, such as Miscanthus × giganteus (Greef et Deu.), for eliminating competition with staple food crops. However, the response mechanisms to different salinity regimes, in relation to the impact on quality of the harvested biomass and the combustion properties are largely unknown. Herein, the focus was on the salt-induced compositional changes of ion flux and compartmentalization in the rhizome, stems, and leaves in relation to their impact on salinity tolerance and the combustion quality through investigating the photophysiological, morphophysiological, and biochemical responses of M. × giganteus to moderate and a severe salinity. Severe salinity induced an immediate and sustained adverse response with a reduction in biomass yield, photoinhibition, and metabolic limitations in photosynthesis. Moderate salinity resulted in a slower cumulative response with low biomass losses. Biomass composition, variations in ion compartmentalisation and induction of proline were dependent on the severity and duration of salinity. Ash behaviour indices, including the base percentage and base-to-acid ratio, indicated lower corrosion potential and lower risk of slagging under salinity. Understanding the impact of salinity on the potential for growth on saline land may identify new targets for breeding salinity-tolerant bioenergy crops.

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Yu, Lan, Mervi Toriseva, Syeda Afshan, Mario Cangiano, Vidal Fey, Andrew Erickson, Heikki Seikkula, et al. "Increased Expression and Altered Cellular Localization of Fibroblast Growth Factor Receptor-Like 1 (FGFRL1) Are Associated with Prostate Cancer Progression." Cancers 14, no. 2 (January 7, 2022): 278. http://dx.doi.org/10.3390/cancers14020278.

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Fibroblast growth factor receptors (FGFRs) 1–4 are involved in prostate cancer (PCa) regulation, but the role of FGFR-like 1 (FGFRL1) in PCa is unclear. FGFRL1 expression was studied by qRT-PCR and immunohistochemistry of patient tissue microarrays (TMAs) and correlated with clinical patient data. The effects of FGFRL1 knockdown (KD) in PC3M were studied in in vitro culture models and in mouse xenograft tumors. Our results showed that FGFRL1 was significantly upregulated in PCa. The level of membranous FGFRL1 was negatively associated with high Gleason scores (GSs) and Ki67, while increased cytoplasmic and nuclear FGFRL1 showed a positive correlation. Cox regression analysis indicated that nuclear FGFRL1 was an independent prognostic marker for biochemical recurrence after radical prostatectomy. Functional studies indicated that FGFRL1-KD in PC3M cells increases FGFR signaling, whereas FGFRL1 overexpression attenuates it, supporting decoy receptor actions of membrane-localized FGFRL1. In accordance with clinical data, FGFRL1-KD markedly suppressed PC3M xenograft growth. Transcriptomics of FGFRL1-KD cells and xenografts revealed major changes in genes regulating differentiation, ECM turnover, and tumor–stromal interactions associated with decreased growth in FGFRL1-KD xenografts. Our results suggest that FGFRL1 upregulation and altered cellular compartmentalization contribute to PCa progression. The nuclear FGFRL1 could serve as a prognostic marker for PCa patients.

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Pohland, F. G., and J. C. Kim. "Microbially mediated attenuation potential of landfill bioreactor systems." Water Science and Technology 41, no. 3 (February 1, 2000): 247–54. http://dx.doi.org/10.2166/wst.2000.0078.

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The origin and fate of landfill leachate and gas constituents generated during the sequential phases of solid waste transformation and stabilization are emphasized within the perspective of the in situ processes of microbially mediated attenuation. The fundamental biochemical and physicochemical reaction mechanisms are presented in terms of their spatial and temporal dimensions and their significance for transformation of both nonhazardous and hazardous waste constituents. Supporting information from laboratory, pilot-scale and full-scale applications is used as a basis for interpretive analysis and for providing operational guidance and promoting future developments. The diversity, domains, and functional interdependence of the acidogenic, methanogenic, sulfate and nitrate reducing, nitrifying and denitrifying, and methanotrophic consortia are addressed in order to reveal opportunities for landfill process modifications and associated operational optimization. Controlled attenuation, linked with operational and regulatory realities, are used to suggest innovative landfill configurations involving prospective compartmentalization and integrated waste loading, dedicated treatment zones for in situ transformation of waste and leachate constituents with associated gas capture, control and utilization. Monitoring requirements are emphasized to provide guidance and feedback for operational control and environmental compliance. Finally, technology needs for establishing a more unified approach to the development and management of bioreactor landfills are presented.

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Journal articles on the topic 'Biochemical compartmentalization'

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