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Journal articles on the topic 'Biochemical interactions'

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Published: 10 December 2022
Last updated: 28 January 2023

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1

Taylor, K. "Immune–biochemical interactions in schizophrenia." Schizophrenia Research 44, no. 3 (September 2000): 245–46. http://dx.doi.org/10.1016/s0920-9964(99)00194-2.

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2

Netter, K. J. "Chronopharmacology — Cellular and biochemical interactions." Toxicology 61, no. 2 (April 1990): 211. http://dx.doi.org/10.1016/0300-483x(90)90022-9.

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3

Thomas, Brian F. "Interactions of Cannabinoids With Biochemical Substrates." Substance Abuse: Research and Treatment 11 (January 1, 2017): 117822181771141. http://dx.doi.org/10.1177/1178221817711418.

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Recent decades have seen much progress in the identification and characterization of cannabinoid receptors and the elucidation of the mechanisms by which derivatives of the Cannabis sativa plant bind to receptors and produce their physiological and psychological effects. The information generated in this process has enabled better understanding of the fundamental physiological and psychological processes controlled by the central and peripheral nervous systems and has fostered the development of natural and synthetic cannabinoids as therapeutic agents. A negative aspect of this decades-long effort is the proliferation of clandestinely synthesized analogs as recreational street drugs with dangerous effects. Currently, the interactions of cannabinoids with their biochemical substrates are extensively but inadequately understood, and the clinical application of derived and synthetic receptor ligands remains quite limited. The wide anatomical distribution and functional complexity of the cannabinoid system continue to indicate potential for both therapeutic and side effects, which offers challenges and opportunities for medicinal chemists involved in drug discovery and development.
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4

Kirkpatrick, Laura L., Martin M. Matzuk, D'Nette C. Dodds, and Mark S. Perin. "Biochemical Interactions of the Neuronal Pentraxins." Journal of Biological Chemistry 275, no. 23 (March 28, 2000): 17786–92. http://dx.doi.org/10.1074/jbc.m002254200.

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5

Simionescu, Maya. "Biochemical Interactions at the Endothelium.Anthony Cryer." Quarterly Review of Biology 60, no. 1 (March 1985): 73. http://dx.doi.org/10.1086/414203.

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6

Seidensticker, Martin J., and Jürgen Behrens. "Biochemical interactions in the wnt pathway." Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1495, no. 2 (February 2000): 168–82. http://dx.doi.org/10.1016/s0167-4889(99)00158-5.

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7

Mills, E. N. Clare, Marcos J. C. Alcocer, and Michael R. A. Morgan. "Biochemical interactions of food-derived peptides." Trends in Food Science & Technology 3 (January 1992): 64–68. http://dx.doi.org/10.1016/0924-2244(92)90132-g.

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8

Belak, Zachery R., Andrew Ficzycz, and Nick Ovsenek. "Biochemical characterization of Yin Yang 1 – RNA complexes." Biochemistry and Cell Biology 86, no. 1 (February 2008): 31–36. http://dx.doi.org/10.1139/o07-155.

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YY1 (Yin Yang 1) is present in the Xenopus oocyte cytoplasm as a constituent of messenger ribonucleoprotein complexes (mRNPs). Association of YY1 with mRNPs requires direct RNA-binding activity. Previously, we have shown YY1 has a high affinity for U-rich RNA; however, potential interactions with plausible in vivo targets have not been investigated. Here we report a biochemical characterization of the YY1–RNA interaction including an investigation of the stability, potential 5′-methylguanosine affinity, and specificity for target RNAs. The formation of YY1–RNA complexes in vitro was highly resistant to thermal, ionic, and detergent disruption. The endogenous oocyte YY1–mRNA interactions were also found to be highly stable. Specific YY1–RNA interactions were observed with selected mRNA and 5S RNA probes. The affinity of YY1 for these substrates was within an order of magnitude of that for its cognate DNA element. Experiments aimed at determining the potential role of the 7-methylguanosine cap on RNA-binding reveal no significant difference in the affinity of YY1 for capped or uncapped mRNA. Taken together, the results show that the YY1–RNA interaction is highly stable, and that YY1 possesses the ability to interact with structurally divergent RNA substrates. These data are the first to specifically document the interaction between YY1 and potential in vivo targets.
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9

Giese, M., M. Albrecht, and K. Rissanen. "Experimental investigation of anion–π interactions – applications and biochemical relevance." Chemical Communications 52, no. 9 (2016): 1778–95. http://dx.doi.org/10.1039/c5cc09072e.

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10

Wright, Gavin J., Stephen Martin, K. Mark Bushell, and Christian Söllner. "High-throughput identification of transient extracellular protein interactions." Biochemical Society Transactions 38, no. 4 (July 26, 2010): 919–22. http://dx.doi.org/10.1042/bst0380919.

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Protein interactions are highly diverse in their biochemical nature, varying in affinity and are often dependent on the surrounding biochemical environment. Given this heterogeneity, it seems unlikely that any one method, and particularly those capable of screening for many protein interactions in parallel, will be able to detect all functionally relevant interactions that occur within a living cell. One major class of interactions that are not detected by current popular high-throughput methods are those that occur in the extracellular environment, especially those made by membrane-embedded receptor proteins. In the present article, we discuss some of our recent research in the development of a scalable assay to identify this class of protein interaction and some of the findings from its application in the construction of extracellular protein interaction networks.
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11

Miernyk, Jan A., and Jay J. Thelen. "Biochemical approaches for discovering protein-protein interactions." Plant Journal 53, no. 4 (February 4, 2008): 597–609. http://dx.doi.org/10.1111/j.1365-313x.2007.03316.x.

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12

Gates, Alexander J., Rion Brattig Correia, Xuan Wang, and Luis M. Rocha. "The effective graph reveals redundancy, canalization, and control pathways in biochemical regulation and signaling." Proceedings of the National Academy of Sciences 118, no. 12 (March 18, 2021): e2022598118. http://dx.doi.org/10.1073/pnas.2022598118.

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The ability to map causal interactions underlying genetic control and cellular signaling has led to increasingly accurate models of the complex biochemical networks that regulate cellular function. These network models provide deep insights into the organization, dynamics, and function of biochemical systems: for example, by revealing genetic control pathways involved in disease. However, the traditional representation of biochemical networks as binary interaction graphs fails to accurately represent an important dynamical feature of these multivariate systems: some pathways propagate control signals much more effectively than do others. Such heterogeneity of interactions reflects canalization—the system is robust to dynamical interventions in redundant pathways but responsive to interventions in effective pathways. Here, we introduce the effective graph, a weighted graph that captures the nonlinear logical redundancy present in biochemical network regulation, signaling, and control. Using 78 experimentally validated models derived from systems biology, we demonstrate that 1) redundant pathways are prevalent in biological models of biochemical regulation, 2) the effective graph provides a probabilistic but precise characterization of multivariate dynamics in a causal graph form, and 3) the effective graph provides an accurate explanation of how dynamical perturbation and control signals, such as those induced by cancer drug therapies, propagate in biochemical pathways. Overall, our results indicate that the effective graph provides an enriched description of the structure and dynamics of networked multivariate causal interactions. We demonstrate that it improves explainability, prediction, and control of complex dynamical systems in general and biochemical regulation in particular.
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13

Kumagait, Y., J. M. Fukuto, and A. K. Cho. "The Biochemical Disposition of Methylenedioxyphenyl Compounds." Current Medicinal Chemistry 1, no. 3 (October 1994): 254–61. http://dx.doi.org/10.2174/092986730103220214164602.

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Abstract: This review summarizes the interactions of the methylene­ dioxyphenyl or benzodioxole function with cytochrome P450 and their toxicological and pharmacokinetic implications. The methylenedioxy group is a common group in natural and synth,etic medicinal compounds and provides an electronegative function that •is relatively unreactive and non polar. The function is oxidized by cytochrome P450 to form a catechol and T formate or carbon monooxide or alternatively, forms a complex with the heme iron of cytochrome P450. This complex, characterized by its absorption in the 455 nm range, can be very stable and inhibits the catalytic cycle of the enzyme. This inhibitory action has been used to enhance the actions of insecticides and has been the basis for pharmacokinetic drug interactions, The catechol product of benzodioxole ring cleavage is redox active and can participate in quinone­ reactive oxygen based toxicity. The chemical basis for these interactions are proposed together with experimental ob ervations reported in the recent literature. Examples of pharmacokinetic drug interactions are also included.
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14

Newbery, D. McC, and A. C. Thompson. "The Chemistry of Alleopathy: Biochemical Interactions Among Plants." Journal of Applied Ecology 22, no. 3 (December 1985): 1016. http://dx.doi.org/10.2307/2403254.

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15

Richardson, P. Mick, and Alonzo C. Thompson. "The Chemistry of Allelopathy: Biochemical Interactions Among Plants." Brittonia 37, no. 3 (July 1985): 251. http://dx.doi.org/10.2307/2806071.

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16

Basauri, Arantza, Cristina González-Fernández, Marcos Fallanza, Eugenio Bringas, Raúl Fernandez-Lopez, Laura Giner, Gabriel Moncalián, Fernando de la Cruz, and Inmaculada Ortiz. "Biochemical interactions between LPS and LPS-binding molecules." Critical Reviews in Biotechnology 40, no. 3 (January 13, 2020): 292–305. http://dx.doi.org/10.1080/07388551.2019.1709797.

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17

McNabb, David S., and Leonard Guarente. "Genetic and biochemical probes for protein—protein interactions." Current Opinion in Biotechnology 7, no. 5 (October 1996): 554–59. http://dx.doi.org/10.1016/s0958-1669(96)80061-9.

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18

Bohr, V. A., M. Cooper, D. Orren, A. Machwe, J. Piotrowski, J. Sommers, P. Karmakar, and R. Brosh. "Werner syndrome protein: biochemical properties and functional interactions." Experimental Gerontology 35, no. 6-7 (September 2000): 695–702. http://dx.doi.org/10.1016/s0531-5565(00)00145-5.

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19

Manzanares, Jorge, Javier Corchero, Julian Romero, Javier J. Fernández-Ruiz, José A. Ramos, and José A. Fuentes. "Pharmacological and biochemical interactions between opioids and cannabinoids." Trends in Pharmacological Sciences 20, no. 7 (July 1999): 287–94. http://dx.doi.org/10.1016/s0165-6147(99)01339-5.

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20

Richardson, M. A., L. Read, M. Reilly, R. Suckow, D. Casey, and I. Bitter. "Significant interactions: Gender, movement disorders, and biochemical variables." Schizophrenia Research 15, no. 1-2 (April 1995): 209. http://dx.doi.org/10.1016/0920-9964(95)95643-n.

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21

Saeho, Chong, and Fung Ho-leung. "Biochemical and pharmacological interactions between nitroglycerin and thiols." Biochemical Pharmacology 42, no. 7 (September 1991): 1433–39. http://dx.doi.org/10.1016/0006-2952(91)90456-f.

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22

Chu, X., K. Bleasby, GH Chan, I. Nunes, and R. Evers. "Transporters affecting biochemical test results: Creatinine-drug interactions." Clinical Pharmacology & Therapeutics 100, no. 5 (September 15, 2016): 437–40. http://dx.doi.org/10.1002/cpt.445.

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23

Duncan, R. R. "Fluorescence lifetime imaging microscopy (FLIM) to quantify protein–protein interactions inside cells." Biochemical Society Transactions 34, no. 5 (October 1, 2006): 679–82. http://dx.doi.org/10.1042/bst0340679.

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Recent developments in cellular imaging spectroscopy now permit the minimally invasive study of protein dynamics inside living cells. These advances are of interest to cell biologists, as proteins rarely act in isolation, but rather in concert with others in forming cellular machinery. Until recently, all protein interactions had to be determined in vitro using biochemical approaches: this biochemical legacy has provided cell biologists with the basis to test defined protein–protein interactions not only inside cells, but now also with high spatial resolution. These techniques can detect and quantify protein behaviours down to the single-molecule level, all inside living cells. More recent developments in TCSPC (time-correlated single-photon counting) imaging are now also driving towards being able to determine protein interaction rates with similar spatial resolution, and together, these experimental advances allow investigators to perform biochemical experiments inside living cells.
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24

Nezammahalleh, Hassan, Faezeh Ghanati, Shima Rezaei, Mohsin Ali Badshah, Joobee Park, Naseem Abbas, and Ahsan Ali. "Biochemical Interactions through Microscopic Techniques: Structural and Molecular Characterization." Polymers 14, no. 14 (July 13, 2022): 2853. http://dx.doi.org/10.3390/polym14142853.

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Many researchers and scientists have contributed significantly to provide structural and molecular characterizations of biochemical interactions using microscopic techniques in the recent decade, as these biochemical interactions play a crucial role in the production of diverse biomaterials and the organization of biological systems. The properties, activities, and functionalities of the biomaterials and biological systems need to be identified and modified for different purposes in both the material and life sciences. The present study aimed to review the advantages and disadvantages of three main branches of microscopy techniques (optical microscopy, electron microscopy, and scanning probe microscopy) developed for the characterization of these interactions. First, we explain the basic concepts of microscopy and then the breadth of their applicability to different fields of research. This work could be useful for future research works on biochemical self-assembly, biochemical aggregation and localization, biological functionalities, cell viability, live-cell imaging, material stability, and membrane permeability, among others. This understanding is of high importance in rapid, inexpensive, and accurate analysis of biochemical interactions.
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25

Zhao, Hongxia, and Pekka Lappalainen. "A simple guide to biochemical approaches for analyzing protein–lipid interactions." Molecular Biology of the Cell 23, no. 15 (August 2012): 2823–30. http://dx.doi.org/10.1091/mbc.e11-07-0645.

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Eukaryotic cells contain many different membrane compartments with characteristic shapes, lipid compositions, and dynamics. A large fraction of cytoplasmic proteins associate with these membrane compartments. Such protein–lipid interactions, which regulate the subcellular localizations and activities of peripheral membrane proteins, are fundamentally important for a variety of cell biological processes ranging from cytoskeletal dynamics and membrane trafficking to intracellular signaling. Reciprocally, many membrane-associated proteins can modulate the shape, lipid composition, and dynamics of cellular membranes. Determining the exact mechanisms by which these proteins interact with membranes will be essential to understanding their biological functions. In this Technical Perspective, we provide a brief introduction to selected biochemical methods that can be applied to study protein–lipid interactions. We also discuss how important it is to choose proper lipid composition, type of model membrane, and biochemical assay to obtain reliable and informative data from the lipid-interaction mechanism of a protein of interest.
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26

Hancock, C. Nathan, Katsuhiko Kondo, Brian Beecher, and Bruce McClure. "The S –locus and unilateral incompatibility." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 358, no. 1434 (June 29, 2003): 1133–40. http://dx.doi.org/10.1098/rstb.2003.1284.

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Plants have many ways to regulate the type of pollen that arrives on the stigma surface. Once there, further control mechanisms regulate compatibility. The latter controls are largely based on biochemical interactions that support compatible pollination and prevent incompatible matings. S–RNase–based self–incompatibility (SI) systems are the most phylogenetically widespread mechanisms for controlling pollination. Studies of Nicotiana establish a firm link between SI and unilateral interspecific incompatibility. Although implicated in both inter– and intraspecific compatibility, S–RNase operates through at least three distinct genetic mechanisms that differ in their dependence on non–S–RNase factors. Identification and characterization of these non–S–RNase factors is currently an area of active research. Searching for genetic and biochemical interactions with S–RNase can identify candidate non–S–RNase factors. HT–protein is one factor that is required for S –allele–specific pollen rejection in the Solanaceae. Major style arabinogalactan proteins such as TTS interact biochemically with S–RNase. These glycoproteins are known to interact with compatible pollen tubes and have long been suggested as possible recognition molecules. Their binding to S–RNase implies a link between stylar systems for compatibility and incompatibility. Thus, genetic and biochemical studies suggest a highly networked picture of pollen–pistil interactions.
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27

ZHANG, Jin-Bi, Zeng-Xiang PAN, Fei LIN, Xue-Shan MA, and Hong-Lin LIU. "Biochemical methods for the analysis of DNA-protein interactions." Hereditas (Beijing) 31, no. 3 (May 7, 2009): 325–36. http://dx.doi.org/10.3724/sp.j.1005.2009.00325.

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28

Brouwer, M., W. Chamulitrat, G. Ferruzzi, DL Sauls, and JB Weinberg. "Nitric oxide interactions with cobalamins: biochemical and functional consequences." Blood 88, no. 5 (September 1, 1996): 1857–64. http://dx.doi.org/10.1182/blood.v88.5.1857.1857.

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Abstract Nitric oxide (NO) is a paramagnetic gas that has been implicated in a wide range of biologic functions. The common pathway to evoke the functional response frequently involves the formation of an iron- nitrosyl complex in a target (heme) protein. In this study, we report on the interactions between NO and cobalt-containing vitamin B12 derivatives. Absorption spectroscopy showed that of the four Co(III) derivatives (cyanocobalamin [CN-Cbl], aquocobalamin [H2O-Cbl], adenosylcobalamin [Ado-Cbl], and methylcobalamin [MeCbl]), only the H2O- Cbl combined with NO. In addition, electron paramagnetic resonance spectroscopy of H2O-Cbl preparations showed the presence of a small amount of Cob-(II)alamin that was capable of combining with NO. The Co(III)-NO complex was very stable, but could transfer its NO moiety to hemoglobin (Hb). The transfer was accompanied by a reduction of the Co(III) to Co(II), indicating that NO+ (nitrosonium) was the leaving group. In accordance with this, the NO did not combine with the Hb Fe(II)-heme, but most likely with the Hb cysteine-thiolate. Similarly, the Co(III)-NO complex was capable of transferring its NO to glutathione. Ado-Cbl and Me-Cbl were susceptible to photolysis, but CN- Cbl and H2O-Cbl were not. The homolytic cleavage of the Co(III)-Ado or Co(III)-Me bond resulted in the reduction of the metal. When photolysis was performed in the presence of NO, formation of NO-Co(II) was observed. Co(II)-nitrosyl oxidized slowly to form Co(III)-nitrosyl. The capability of aquocobalamin to combine with NO had functional consequences. We found that nitrosylcobalamin had diminished ability to serve as a cofactor for the enzyme methionine synthase, and that aquocobalamin could quench NO-mediated inhibition of cell proliferation. Our in vitro studies therefore suggest that interactions between NO and cobalamins may have important consequences in vivo.
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29

Brouwer, M., W. Chamulitrat, G. Ferruzzi, DL Sauls, and JB Weinberg. "Nitric oxide interactions with cobalamins: biochemical and functional consequences." Blood 88, no. 5 (September 1, 1996): 1857–64. http://dx.doi.org/10.1182/blood.v88.5.1857.bloodjournal8851857.

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Nitric oxide (NO) is a paramagnetic gas that has been implicated in a wide range of biologic functions. The common pathway to evoke the functional response frequently involves the formation of an iron- nitrosyl complex in a target (heme) protein. In this study, we report on the interactions between NO and cobalt-containing vitamin B12 derivatives. Absorption spectroscopy showed that of the four Co(III) derivatives (cyanocobalamin [CN-Cbl], aquocobalamin [H2O-Cbl], adenosylcobalamin [Ado-Cbl], and methylcobalamin [MeCbl]), only the H2O- Cbl combined with NO. In addition, electron paramagnetic resonance spectroscopy of H2O-Cbl preparations showed the presence of a small amount of Cob-(II)alamin that was capable of combining with NO. The Co(III)-NO complex was very stable, but could transfer its NO moiety to hemoglobin (Hb). The transfer was accompanied by a reduction of the Co(III) to Co(II), indicating that NO+ (nitrosonium) was the leaving group. In accordance with this, the NO did not combine with the Hb Fe(II)-heme, but most likely with the Hb cysteine-thiolate. Similarly, the Co(III)-NO complex was capable of transferring its NO to glutathione. Ado-Cbl and Me-Cbl were susceptible to photolysis, but CN- Cbl and H2O-Cbl were not. The homolytic cleavage of the Co(III)-Ado or Co(III)-Me bond resulted in the reduction of the metal. When photolysis was performed in the presence of NO, formation of NO-Co(II) was observed. Co(II)-nitrosyl oxidized slowly to form Co(III)-nitrosyl. The capability of aquocobalamin to combine with NO had functional consequences. We found that nitrosylcobalamin had diminished ability to serve as a cofactor for the enzyme methionine synthase, and that aquocobalamin could quench NO-mediated inhibition of cell proliferation. Our in vitro studies therefore suggest that interactions between NO and cobalamins may have important consequences in vivo.
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30

Liotta, L. A., C. Nageswara Rao, and U. M. Wewer. "Biochemical Interactions of Tumor Cells with the Basement Membrane." Annual Review of Biochemistry 55, no. 1 (June 1986): 1037–57. http://dx.doi.org/10.1146/annurev.bi.55.070186.005133.

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31

ORLOFF, JOHN J., TERENCE L. WU, and ANDREW F. STEWART. "Parathyroid Hormone-Like Proteins: Biochemical Responses and Receptor Interactions*." Endocrine Reviews 10, no. 4 (November 1989): 476–95. http://dx.doi.org/10.1210/edrv-10-4-476.

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32

Artursson, Per, and John O'Mullane. "Cellular and biochemical interactions of macromolecular drug delivery systems." Advanced Drug Delivery Reviews 3, no. 2 (March 1989): 165–89. http://dx.doi.org/10.1016/0169-409x(89)90009-4.

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33

M�ller, H. G., and K. Kuschinsky. "Interactions of morphine with apomorphine: behavioural and biochemical studies." Naunyn-Schmiedeberg's Archives of Pharmacology 334, no. 4 (December 1986): 452–57. http://dx.doi.org/10.1007/bf00569385.

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34

Grodzinsky, A. M. "General and specific mechanisms of biochemical interactions between plants." Biologia Plantarum 31, no. 6 (November 1989): 448–57. http://dx.doi.org/10.1007/bf02876218.

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35

Asiegbu, F. O., M. Kacprzak, G. Daniel, M. Johansson, J. Stenlid, and M. Mañka. "Biochemical interactions of conifer seedling roots with Fusarium spp." Canadian Journal of Microbiology 45, no. 11 (November 1, 1999): 923–35. http://dx.doi.org/10.1139/w99-099.

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The importance of root and spore surface molecules in the interactions of Fusarium spp. with conifer roots, and cellular localization of proteins presumed to be involved in host defence, were investigated. For adhesion studies, using a combination of fluorescein isothiocyanate (FITC) labelled lectins and high perfomance liquid chromatography (HPLC), several sugars (pinitol, xylitol, galactose, mannose, and glucose) were detected in root surface mucilage. Both artificial substrata and detached living roots were used to evaluate the significance of selective removal of root or spore surface components on the adhesion process. The spores or roots were pretreated with either periodic acid, pronase E, potassium hydroxide or diethyl ether. Pretreatment of the spores with diethyl ether reduced significantly the level of spore adhesion, which suggests that the adhesive component is either a lipid, or is bound to lipid. Since oxidation of carbohydrate reactive sites with periodic acid on the root surface almost completely abolished the development of germ tubes by adherent spores, it was presumed that some of these periodate-sensitive substances serve as a nutrient source for the fungus. On inoculated roots, F. avenaceum and F. culmorum were significantly pathogenic to both Norway spruce and Scots pine seedlings. Cytochemical labelling of sites of accumulation of host defence molecules within infected root tissues using anti-peroxidase demonstrated increased peroxidase activity in host cell walls. With anti-chitinase and anti-glucanase, gold labelling was found mainly on pathogen hyphal walls.Key words: conifer seedlings, adhesion, Fusarium spp., PR proteins, immunolocalization, lectins.
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36

Müller-Navarra, Dörthe C. "Food Web Paradigms: The Biochemical View on Trophic Interactions." International Review of Hydrobiology 93, no. 4-5 (October 2008): 489–505. http://dx.doi.org/10.1002/iroh.200711046.

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37

Carpentier, Guillaume, Jérome Jaillet, Aude Pflieger, Jérémy Adet, Sylvaine Renault, and Corinne Augé-Gouillou. "Transposase–Transposase Interactions in MOS1 Complexes: A Biochemical Approach." Journal of Molecular Biology 405, no. 4 (January 2011): 892–908. http://dx.doi.org/10.1016/j.jmb.2010.11.032.

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38

Kothari, Priyanka, Vasudha Srivastava, Vasudha Aggarwal, Irina Tchernyshyov, Jennifer Van Eyk, Taekjip Ha, and Douglas N. Robinson. "Mapping the Biochemical Interactions of the Mechanoresponsive Contractility Controller." Biophysical Journal 116, no. 3 (February 2019): 119a—120a. http://dx.doi.org/10.1016/j.bpj.2018.11.669.

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39

Chakraborty, Amit, Gui-Quan Sun, Laura Mustavich, Sheng-He Huang, and Bai-Lian Li. "Biochemical interactions between HIV-1 integrase and reverse transcriptase." FEBS Letters 587, no. 5 (December 25, 2012): 425–29. http://dx.doi.org/10.1016/j.febslet.2012.12.007.

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40

Siciliano, S. D., and J. J. Germida. "Mechanisms of phytoremediation: biochemical and ecological interactions between plants and bacteria." Environmental Reviews 6, no. 1 (March 1, 1998): 65–79. http://dx.doi.org/10.1139/a98-005.

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The use of plants to reduce contaminant levels in soil is a cost-effective method of reducing the risk to human and ecosystem health posed by contaminated soil sites. This review concentrates on plant-bacteria interactions that increase the degradation of hazardous organic compounds in soil. Plants and bacteria can form specific associations in which the plant provides the bacteria with a specific carbon source that induces the bacteria to reduce the phytotoxicity of the contaminated soil. Alternatively, plants and bacteria can form nonspecific associations in which normal plant processes stimulate the microbial community, which in the course of normal metabolic activity degrades contaminants in soil. Plants can provide carbon substrates and nutrients, as well as increase contaminant solubility. These biochemical mechanisms increase the degradative activity of bacteria associated with plant roots. In return, bacteria can augment the degradative capacity of plants or reduce the phytotoxicity of the contaminated soil. However, the specificity of the plant-bacteria interaction is dependent upon soil conditions, which can alter contaminant bioavailability, root exudate composition, and nutrient levels. In addition, the metabolic requirements for contaminant degradation may also dictate the form of the plant-bacteria interaction i.e., specific or nonspecific. No systematic framework that can predict plant-bacteria interactions in a contaminated soil has emerged, but it appears that the development of plant-bacteria associations that degrade contaminants in soil may be related to the presence of allelopathic chemicals in the rhizosphere. Therefore, investigations into plants that are resistant to or produce allelopathic chemicals is suggested as one possible method of identifying plant-bacteria associations that can degrade contaminants in soil.Key words: phytoremediation, mechanisms, rhizosphere, bacterial inoculants.
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41

Bowen, W. H. "Biochemical and Micro-Analytical Methods." Advances in Dental Research 1, no. 1 (December 1987): 88–91. http://dx.doi.org/10.1177/08959374870010012001.

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Because of the small amounts of material available for study, investigations of plaque, caries lesions in enamel, and antibodies in saliva pose difficult challenges for investigators. Sophisticated biochemical and fluorescence techniques can now be used to investigate the microbial composition of plaque, thereby avoiding the need for tedious culturing techniques from single sites on tooth surfaces. A range of microchemical methodologies is available which greatly facilitates the analysis of plaque fluid, thereby enhancing our understanding of tooth-plaque interactions. The application of a range of novel physiochemical techniques should help to clarify our knowledge of the interactions involved in pellicle formation and elucidate the phenomena involved in the formation of the early caries lesion. A range of techniques is now available for the study of antibodies in saliva. These include ELISA, RIA, and solid-phase immunoassay. The application of these methodologies to the investigation of oral diseases should facilitate our understanding of the pathogenesis of dental maladies at the molecular level.
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42

Kubrycht, Jaroslav, Karel Sigler, and Pavel Souček. "Virtual Interactomics of Proteins from Biochemical Standpoint." Molecular Biology International 2012 (August 8, 2012): 1–22. http://dx.doi.org/10.1155/2012/976385.

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Virtual interactomics represents a rapidly developing scientific area on the boundary line of bioinformatics and interactomics. Protein-related virtual interactomics then comprises instrumental tools for prediction, simulation, and networking of the majority of interactions important for structural and individual reproduction, differentiation, recognition, signaling, regulation, and metabolic pathways of cells and organisms. Here, we describe the main areas of virtual protein interactomics, that is, structurally based comparative analysis and prediction of functionally important interacting sites, mimotope-assisted and combined epitope prediction, molecular (protein) docking studies, and investigation of protein interaction networks. Detailed information about some interesting methodological approaches and online accessible programs or databases is displayed in our tables. Considerable part of the text deals with the searches for common conserved or functionally convergent protein regions and subgraphs of conserved interaction networks, new outstanding trends and clinically interesting results. In agreement with the presented data and relationships, virtual interactomic tools improve our scientific knowledge, help us to formulate working hypotheses, and they frequently also mediate variously important in silico simulations.
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43

Hoagland, Robert E. "Biochemical Interactions of Atrazine and Glyphosate in Soybean (Glycine max) Seedlings." Weed Science 37, no. 4 (July 1989): 491–97. http://dx.doi.org/10.1017/s0043174500072295.

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Laboratory studies were conducted to evaluate possible interactions of atrazine and glyphosate on soybeans at the molecular level. Because these compounds alter the extractable activities of nitrate reductase (NR)3and phenylalanine ammonia-lyase (PAL), these enzymes were chosen as biochemical markers. Levels of anthocyanin, hydroxyphenolic compounds, and chlorophyll were also determined. Three-day-old dark-grown soybean seedlings, susceptible to both herbicides, were transferred to 2 mM CaSO4or CaSO4containing high-purity 10–4M atrazine, 10–4M glyphosate, or a combination of both herbicides at 10–4M each. Plants were placed in a growth chamber under continuous light (200 μE·m–2·s–1) at 25 C and harvested at 24-h intervals over a 96-h time course. Interactions of atrazine and glyphosate on hypocotyl elongation were detected after 96 h when the compounds were supplied simultaneously. Intermediate PAL levels were found in the atrazine + glyphosate treatment compared to the levels for each herbicide alone. At 96 h, anthocyanin content in hypocotyls in the atrazine + glyphosate treatment was twice that of the atrazine treatment, and hydroxyphenolic content was increased by 25% (per axis). Interactions of these herbicides were also apparent on NR activity; i.e., on a per organ basis the combination treatment resulted in levels 20% higher than glyphosate alone in roots and 16 times greater than glyphosate alone in leaves after 96 h. Total chlorophyll content in hypocotyls (μg/organ) was decreased by atrazine but not significantly by glyphosate after 96 h. Atrazine + glyphosate resulted in chlorophyll content equal to that of atrazine alone. Mathematical analyses showed that interactions on NR, PAL, anthocyanin levels, and hypocotyl elongation were antagonistic at 96 h. These data demonstrate interaction between atrazine and glyphosate in plant tissues that is related to some biochemical parameters associated with the secondary molecular mode of action of these herbicides.
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44

Vuong, Phu, Drew Bennion, Jeremy Mantei, Danielle Frost, and Rajeev Misra. "Analysis of YfgL and YaeT Interactions through Bioinformatics, Mutagenesis, and Biochemistry." Journal of Bacteriology 190, no. 5 (December 28, 2007): 1507–17. http://dx.doi.org/10.1128/jb.01477-07.

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ABSTRACT In Escherichia coli, YaeT, together with four lipoproteins, YfgL, YfiO, NlpB, and SmpA, forms a complex that is essential for β-barrel outer membrane protein biogenesis. Data suggest that YfgL and YfiO make direct but independent physical contacts with YaeT. Whereas the YaeT-YfiO interaction needs NlpB and SmpA for complex stabilization, the YaeT-YfgL interaction does not. Using bioinformatics, genetics, and biochemical approaches, we have identified three residues, L173, L175, and R176, in the mature YfgL protein that are critical for both function and interactions with YaeT. A single substitution at any of these sites produces no phenotypic defect, but two or three simultaneous alterations produce mild or yfgL-null phenotypes, respectively. Interestingly, biochemical data show that all YfgL variants, including those with single substitutions, have weakened in vivo YaeT-YfgL interaction. These defects are not due to mislocalization or low steady-state levels of YfgL. Cysteine-directed cross-linking data show that the region encompassing L173, L175, and R176 makes direct contact with YaeT. Using the same genetic and biochemical strategies, it was found that altering residues D227 and D229 in another region of YfgL from E221 to D229 resulted in defective YaeT bindings. In contrast, mutational analysis of conserved residues V319 to H328 of YfgL shows that they are important for YfgL biogenesis but not YfgL-YaeT interactions. The five YfgL mutants defective in YaeT associations and the yfgL background were used to show that SurA binds to YaeT (or another complex member) without going through YfgL.
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45

Cooley, Rachel, Neesha Kara, Ning Sze Hui, Jonathan Tart, Chloë Roustan, Roger George, David C. Hancock, et al. "Development of a cell-free split-luciferase biochemical assay as a tool for screening for inhibitors of challenging protein-protein interaction targets." Wellcome Open Research 5 (February 6, 2020): 20. http://dx.doi.org/10.12688/wellcomeopenres.15675.1.

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Targeting the interaction of proteins with weak binding affinities or low solubility represents a particular challenge for drug screening. The NanoLucâ ® Binary Technology (NanoBiTâ ®) was originally developed to detect protein-protein interactions in live mammalian cells. Here we report the successful translation of the NanoBit cellular assay into a biochemical, cell-free format using mammalian cell lysates. We show that the assay is suitable for the detection of both strong and weak protein interactions such as those involving the binding of RAS oncoproteins to either RAF or phosphoinositide 3-kinase (PI3K) effectors respectively, and that it is also effective for the study of poorly soluble protein domains such as the RAS binding domain of PI3K. Furthermore, the RAS interaction assay is sensitive and responds to both strong and weak RAS inhibitors. Our data show that the assay is robust, reproducible, cost-effective, and can be adapted for small and large-scale screening approaches. The NanoBit Biochemical Assay offers an attractive tool for drug screening against challenging protein-protein interaction targets, including the interaction of RAS with PI3K.
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46

Cooley, Rachel, Neesha Kara, Ning Sze Hui, Jonathan Tart, Chloë Roustan, Roger George, David C. Hancock, et al. "Development of a cell-free split-luciferase biochemical assay as a tool for screening for inhibitors of challenging protein-protein interaction targets." Wellcome Open Research 5 (June 2, 2020): 20. http://dx.doi.org/10.12688/wellcomeopenres.15675.2.

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Targeting the interaction of proteins with weak binding affinities or low solubility represents a particular challenge for drug screening. The NanoLuc ® Binary Technology (NanoBiT ®) was originally developed to detect protein-protein interactions in live mammalian cells. Here we report the successful translation of the NanoBit cellular assay into a biochemical, cell-free format using mammalian cell lysates. We show that the assay is suitable for the detection of both strong and weak protein interactions such as those involving the binding of RAS oncoproteins to either RAF or phosphoinositide 3-kinase (PI3K) effectors respectively, and that it is also effective for the study of poorly soluble protein domains such as the RAS binding domain of PI3K. Furthermore, the RAS interaction assay is sensitive and responds to both strong and weak RAS inhibitors. Our data show that the assay is robust, reproducible, cost-effective, and can be adapted for small and large-scale screening approaches. The NanoBit Biochemical Assay offers an attractive tool for drug screening against challenging protein-protein interaction targets, including the interaction of RAS with PI3K.
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47

Husain, Fasahath, Matthew Humbard, and Rajeev Misra. "Interaction between the TolC and AcrA Proteins of a Multidrug Efflux System of Escherichia coli." Journal of Bacteriology 186, no. 24 (December 15, 2004): 8533–36. http://dx.doi.org/10.1128/jb.186.24.8533-8536.2004.

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ABSTRACT This paper provides the biochemical evidence for physical interactions between the outer membrane component, TolC, and the membrane fusion protein component, AcrA, of the major antibiotic efflux pump of Escherichia coli. Cross-linking between TolC and AcrA was independent of the presence of any externally added substrate of the efflux pump or of the pump protein, AcrB. The biochemical demonstration of a TolC-AcrA interaction is consistent with genetic studies in which extragenic suppressors of a mutant TolC strain were found in the acrA gene.
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48

Wittenstein, Timon, Nava Leibovich, and Andreas Hilfinger. "Quantifying biochemical reaction rates from static population variability within incompletely observed complex networks." PLOS Computational Biology 18, no. 6 (June 22, 2022): e1010183. http://dx.doi.org/10.1371/journal.pcbi.1010183.

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Quantifying biochemical reaction rates within complex cellular processes remains a key challenge of systems biology even as high-throughput single-cell data have become available to characterize snapshots of population variability. That is because complex systems with stochastic and non-linear interactions are difficult to analyze when not all components can be observed simultaneously and systems cannot be followed over time. Instead of using descriptive statistical models, we show that incompletely specified mechanistic models can be used to translate qualitative knowledge of interactions into reaction rate functions from covariability data between pairs of components. This promises to turn a globally intractable problem into a sequence of solvable inference problems to quantify complex interaction networks from incomplete snapshots of their stochastic fluctuations.
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49

Rola-Pleszczynski, Marek, and Jana Stankova. "Cytokine-Leukotriene Receptor Interactions." Scientific World JOURNAL 7 (2007): 1348–58. http://dx.doi.org/10.1100/tsw.2007.183.

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Biochemical and pharmacological studies have identified the structure of leukotrienes, the pathways that lead to their synthesis, and the signaling events they trigger when they interact with their cognate receptors. A privileged interaction exists between these lipid mediators and another group of molecules essential for inflammation and immune modulation, namely, cytokines. Whereas leukotrienes can trigger the synthesis and release of selected cytokines in distinct cell populations, many cytokines can affect cellular responsiveness to leukotrienes by modulating leukotriene receptor expression. As we progressively begin to unravel these complex interactions, new areas of cell-cell communication and eventual therapeutic interventions will emerge.
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50

Albrecht, D. L., and R. J. Noelle. "Membrane Ig-cytoskeletal interactions. I. Flow cytofluorometric and biochemical analysis of membrane IgM-cytoskeletal interactions." Journal of Immunology 141, no. 11 (December 1, 1988): 3915–22. http://dx.doi.org/10.4049/jimmunol.141.11.3915.

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Abstract Membrane IgM (mIgM) and mIgD are the receptors for Ag on the surface of B lymphocytes, mIg is soluble in detergent; however, when mIg is cross-linked with anti-Ig, the mIg becomes associated with the cytoskeletal matrix and is rendered detergent-insoluble. By a novel flow cytofluorometric assay and by biochemical analysis, it has been shown that anti-isotype-specific antibodies induce mIgM and mIgD to associate with the cytoskeleton of B lymphocytes in an isotype-specific fashion. The detergent solubility of other prominent B lymphocyte surface proteins, such as class I and class II MHC proteins were unaffected by cross-linking of mIg. A panel of mu-specific mAb was analyzed for their ability to induce mIgM-cytoskeletal association. Although all mAb bound mIgM, only three out of seven rendered mIgM cytoskeletally associated. Further analysis revealed a strict correlation in the capacity of mu-specific mAb to induce capping and to induce the association of mIgM with the cytoskeleton.
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