Journal articles: 'Gain molecules'

1

Amato, I. "Shiny Molecules Gain New Luster." Science 259, no. 5098 (February 19, 1993): 1122. http://dx.doi.org/10.1126/science.259.5098.1122.

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Philippidis, Alex. "Large Molecules Continue to Gain Favor." Genetic Engineering & Biotechnology News 32, no. 10 (May 15, 2012): 10–11. http://dx.doi.org/10.1089/gen.32.10.04.

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Scotognella, Francesco. "Multilayer plasmonic photonic structures embedding photochromic molecules or optical gain molecules." Physica E: Low-dimensional Systems and Nanostructures 120 (June 2020): 114081. http://dx.doi.org/10.1016/j.physe.2020.114081.

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Hengel, H., K. Burke, D. Kyburz, R. M. Zinkernagel, and U. H. Koszinowski. "Peptides control the gain and loss of allele specificity by mutated MHC class I molecules." Journal of Immunology 154, no. 9 (May 1, 1995): 4557–64. http://dx.doi.org/10.4049/jimmunol.154.9.4557.

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Abstract To analyze the molecular basis of MHC class I allele-restricted peptide recognition, a set of eight Ld/Lq mutants was constructed and tested for peptide recognition by allele-restricted and peptide-specific CTL. The MHC molecules H-2Ld and H-2Lq differ at six amino acid positions (95, 97, 107, 116, 155, 157) located within the alpha 2 domain of the molecule. Both molecules present the lymphocytic choriomeningitis virus (LCMV) nucleoprotein-derived peptide RPQASGVYM and the murine cytomegalovirus (MCMV) pp89-derived peptide YPHFMPTNL to the respective virus-specific CD8+ CTL is a strictly allele-restricted fashion. All mutated MHC class I molecules did still bind the LCMV peptide and seven of eight mutants retained MCMV peptide binding. The exchange Arg-->Trp at position 97 of Lq in pocket C of the peptide binding groove prevented binding of the MCMV ligand and this loss was compensated by the additional exchange of Ile-->Leu in position 95 (pocket F). Within the Lq molecule, single mutations at either position 97 on the floor of the groove or position 155 of the wall sufficed for a gain of LCMV peptide recognition by Ld-restricted CTL. Altogether, six of eight mutants resulted in a gain of recognition by CTL specific for the other allele. Thus, six of the eight mutants lost MHC-restricted recognition and were accepted by both Ld- as well as Lq-restricted CTL when presenting the LCMV peptide. Only one case of simultaneous recognition of the MCMV peptide by both Ld- as well as Lq-restricted CTL was noted. In other mutations, a gain of recognition by Ld-restricted CTL was associated with a loss of recognition of Lq-restricted CTL. Analysis of extracted MCMV peptide from mutant molecules excluded quantitative differences in presented MCMV peptide as a reason for the lack of CTL recognition. Altogether, the results show that, rather than aminoacids at certain residue positions, individual peptides govern MHC allele specificity of CTL recognition.

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STARIKOV, E. B. "WHY DNA ELECTRICAL PROPERTIES CHANGE ON MOLECULAR OXYGEN DOPING: A QUANTUM-CHEMICAL STUDY." Modern Physics Letters B 18, no. 16 (July 10, 2004): 785–90. http://dx.doi.org/10.1142/s0217984904007311.

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A detailed semiempirical quantum-chemical study is reported on homogeneous adenosine-thymidine and guanosine-cytidine base pair steps, both pure ones and their complexes with oxygen molecules. The results of this study help gain detailed insight into physico-chemical mechanisms of electrical conduction control in DNA molecules when doping them with molecular oxygen or related molecules.

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Bethanis, Kostas, Elias Christoforides, Athena Andreou, and Elias Eliopoulos. "Molecular Symmetry of Permethylated β-Cyclodextrins upon Complexation." Symmetry 14, no. 10 (October 20, 2022): 2214. http://dx.doi.org/10.3390/sym14102214.

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The Cn molecular symmetry implicated by the schemes with which cyclodextrins (CDs), the well-known cyclic oligosaccharides, are introduced in the literature, is not valid. Numerous studies have shown that CDs are rather flexible with their macrocycle adopting various conformations that enable the inclusion complexation of guest molecules of various shapes. In this work, the loss and gain of the C7 symmetry of the heptakis (2, 3, 6-tri-O-methyl)-β-CD (TM-β-CD) is investigated by means of its conformation geometrical features in its hydrated form and upon complexation with molecules of different shapes. For this, the crystal structure of the inclusion complex of a bulky guest molecule (giberellic acid) in TM-β-CD is presented for the first time and compared with the previously determined crystal structures of monohydrated TM-β-CD and the inclusion complex of a linear monoterpenoid (geraniol) in TM-β-CD. The structural investigation was complemented by molecular dynamics simulations in an explicit solvent, based on the crystallographically determined models. The crucial role of the guest, in the symmetry gain of the host, reveals a pronounced induced-fit complexation mechanism for permethylated CDs.

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Nam, Ki Hyun. "Molecular Dynamics—From Small Molecules to Macromolecules." International Journal of Molecular Sciences 22, no. 7 (April 5, 2021): 3761. http://dx.doi.org/10.3390/ijms22073761.

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All molecular systems, from small molecules to macromolecules, exhibit specific characteristics for a specific environment and time. In order to gain an accurate understanding of the functions of all types of molecules, studies of their structure and dynamics are essential. Through dynamic studies, using techniques such as spectroscopy, structure determination, and computer analysis, it is possible to collect functional information on molecules at specific times and in specific environments. Such information not only reveals the properties and mechanisms of action of molecules but also provides insights that can be applied to various industries, such as the development of new materials and drugs. Herein, I discuss the importance of molecular dynamics studies, present the time scale of molecular motion, and review techniques for analyzing molecular dynamics.

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Balducci, G., G. Gigli, and G. Meloni. "Dissociation energies of the Ga2, In2, and GaIn molecules." Journal of Chemical Physics 109, no. 11 (September 15, 1998): 4384–88. http://dx.doi.org/10.1063/1.477041.

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Winata, Anggun. "Enhancing Students' Visual-Spatial Abilities through the Use of Bonat Berakal Media in Understanding Shapes of Molecules." Hydrogen: Jurnal Kependidikan Kimia 11, no. 1 (February 15, 2023): 40. http://dx.doi.org/10.33394/hjkk.v11i1.6911.

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Students in 10th grade often get low learning outcomes on one of the chemical concepts, the shapes of molecules. Based on the test results, it can be seen that most students have difficulty on understanding and drawing the shapes of molecules. Many students have difficulty drawing shapes of molecules because shapes of molecules cannot be observed directly using the sense of sight, so students cannot project molecular images on their minds. The inability of students to understand molecular drawings in predicting the shape of molecules may be related to spatial visual abilities. The study aimed to investigate the effectiveness of using Bonat berakal media in enhancing tenth-grade students' visual-spatial abilities in understanding shapes of molecules. The students from classes A, B, and C in academic year 2022/2023 at SMAN 1 Tuban participated in the study. The research design was one group pre-test post-test. The instruments used were a teaching module on shapes of molecules and a spatial visual test. The data was analyzed using N-Gain score. The results showed that the pre-test average of students' spatial visual abilities was low but improved to a high category post-test. The study concluded that the use of Bonat berakal media was effective in improving students' visual-spatial abilities in shapes of melecules concepts, as indicated by an N-Gain score of 0.620.

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Belloche, Arnaud. "Exploring molecular complexity in the Galactic Center with ALMA." Proceedings of the International Astronomical Union 13, S332 (March 2017): 383–94. http://dx.doi.org/10.1017/s1743921317007815.

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AbstractThe search for complex organic molecules (COMs) in the ISM has revealed chemical species of ever greater complexity. This search relies heavily on the progress made in the laboratory to characterize the rotational spectra of these molecules. Observationally, the advent of ALMA with its high angular resolution and sensitivity has allowed to reduce the spectral confusion and detect low-abundance molecules that could not be probed before. We present results of the EMoCA survey conducted with ALMA toward the star-forming region Sgr B2(N). This spectral line survey aims at deciphering the molecular content of Sgr B2(N) in order to test the predictions of astrochemical models and gain insight into the chemical processes at work in the ISM. We report on the tentative detection of N-methylformamide, on deuterated COMs, and on the detection of a branched alkyl molecule. Prospects for probing molecular complexity in the ISM even further are discussed at the end.

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Al-Khayri, Jameel M., Sakshi Dubey, Gopishankar Thirumoorthy, Praveen Nagella, Adel Abdel-Sabour Rezk, and Wael Fathi Shehata. "In Silico Identification of 1-DTP Inhibitors of Corynebacterium diphtheriae Using Phytochemicals from Andrographis paniculata." Molecules 28, no. 2 (January 16, 2023): 909. http://dx.doi.org/10.3390/molecules28020909.

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A number of phytochemicals have been identified as promising drug molecules against a variety of diseases using an in-silico approach. The current research uses this approach to identify the phyto-derived drugs from Andrographis paniculata (Burm. f.) Wall. ex Nees (AP) for the treatment of diphtheria. In the present study, 18 bioactive molecules from Andrographis paniculata (obtained from the PubChem database) were docked against the diphtheria toxin using the AutoDock vina tool. Visualization of the top four molecules with the best dockscore, namely bisandrographolide (−10.4), andrographiside (−9.5), isoandrographolide (−9.4), and neoandrographolide (−9.1), helps gain a better understanding of the molecular interactions. Further screening using molecular dynamics simulation studies led to the identification of bisandrographolide and andrographiside as hit compounds. Investigation of pharmacokinetic properties, mainly ADMET, along with Lipinski’s rule and binding affinity considerations, narrowed down the search for a potent drug to bisandrographolide, which was the only molecule to be negative for AMES toxicity. Thus, further modification of this compound followed by in vitro and in vivo studies can be used to examine itseffectiveness against diphtheria.

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Sun, Ruijin, Yongsheng Hu, Guangling Cheng, and Aixi Chen. "Gain-phase grating via double tunneling in quantum dot molecules." Laser Physics Letters 18, no. 9 (August 12, 2021): 095202. http://dx.doi.org/10.1088/1612-202x/ac1743.

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13

JUN, WOONG GI, HYUK YOON, SEUNG HWAN LEE, JAE HONG KIM, and DONG HOON CHOI. "INORGANIC–ORGANIC HYBRID PHOTOREFRACTIVE MATERIALS BEARING THE BIFUNCTIONAL CHROMOPHORE." Journal of Nonlinear Optical Physics & Materials 14, no. 04 (December 2005): 497–504. http://dx.doi.org/10.1142/s0218863505002943.

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We prepared the photorefractive composite based on organic–inorganic hybrid materials containing charge-transporting molecules, second-order nonlinear optical chromophore, photosensitizer, and plasticizer either as a side chain unit or a guest molecule. New chromophore was synthesized to contain nonlinear optical chromophore and carbazole in one molecule. The functional chromophores were reacted to isocyanatotriethoxysilane to provide the functional precursor molecules. 2,4,7-Trinitrofluorenone (TNF) was added into the sol-gel materials to induce a charge-transfer complex. We also compared the gain coefficient of the photorefractive samples with the change of the concentration of the plasticizer, determined by two-beam coupling technique.

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Overbaugh, Julie, A. Dusty Miller, and Maribeth V. Eiden. "Receptors and Entry Cofactors for Retroviruses Include Single and Multiple Transmembrane-Spanning Proteins as well as Newly Described Glycophosphatidylinositol-Anchored and Secreted Proteins." Microbiology and Molecular Biology Reviews 65, no. 3 (September 1, 2001): 371–89. http://dx.doi.org/10.1128/mmbr.65.3.371-389.2001.

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SUMMARY In the past few years, many retrovirus receptors, coreceptors, and cofactors have been identified. These molecules are important for some aspects of viral entry, although in some cases it remains to be determined whether they are required for binding or postbinding stages in entry, such as fusion. There are certain common features to the molecules that many retroviruses use to gain entry into the cell. For example, the receptors for most mammalian oncoretroviruses are multiple membrane-spanning transport proteins. However, avian retroviruses use single-pass membrane proteins, and a sheep retrovirus uses a glycosylphosphatidylinositol-anchored molecule as its receptor. For some retroviruses, particularly the lentiviruses, two cell surface molecules are required for efficient entry. More recently, a soluble protein that is required for viral entry has been identified for a feline oncoretrovirus. In this review, we will focus on the various strategies used by mammalian retroviruses to gain entry into the cell. The choice of receptors will also be discussed in light of pressures that drive viral evolution and persistence.

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Probstmeier, R., T. Fahrig, E. Spiess, and M. Schachner. "Interactions of the neural cell adhesion molecule and the myelin-associated glycoprotein with collagen type I: involvement in fibrillogenesis." Journal of Cell Biology 116, no. 4 (February 15, 1992): 1063–70. http://dx.doi.org/10.1083/jcb.116.4.1063.

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To gain insights into the functional role of the molecular association between neural adhesion molecules and extracellular matrix constituents, soluble forms of the myelin-associated glycoprotein (MAG) and the neural cell adhesion molecule (N-CAM), representing most of the extracellular domains of the molecules, were investigated in their ability to modify fibrillogenesis of collagen type I. MAG and N-CAM retarded the rate of fibril formation, as measured by changes in turbidity, and increased the diameter of the fibrils formed, but did not change the banding pattern when compared to collagen type I in the absence of adhesion molecules. Scatchard plot analysis of the binding of MAG and N-CAM to the fibril-forming collagen types I, II, III, and V suggest one binding site for N-CAM and two binding sites for MAG. Binding of MAG, but not of N-CAM, to collagen type I was decreased during fibril formation, probably due to a reduced accessibility of one binding site for MAG during fibrillogenesis. These results indicate that the neural adhesion molecules can influence the configuration of extracellular matrix constituents, thus, implicating them in the modulation of cell-substrate interactions.

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Webster, Paul. "Cryosections for Immunocytochemistry." Microscopy and Microanalysis 6, S2 (August 2000): 302–3. http://dx.doi.org/10.1017/s1431927600034000.

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Immunocytochemistry describes methods for visualization of specific intracellular molecules within cells. These methods use high affinity markers to specifically bind to target molecules in tissues or cells. For electron microscopy, the sites where these markers are bound are visualized using electron opaque probes. Successful immunocytochemistry depends upon immobilization of target molecules, retention of subcellular morphology, and upon total accessibility of affinity marker to the target molecules.Accessibility to extracellular molecules is not usually a problem, but for intracellular molecules, labeling protocols must be able to preserve subcellular morphology and allow the affinity markers to gain access to their target molecules. Currently, the best way to gain access to the inside of cells for electron microscopy (TEM) is to cut thin sections through them. In this way, morphology is retained and affinity markers can be applied to the cut face of the cells.

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Yin, Fan, Jianbo De, Han Huang, Yuan Li, Meihui Liu, Shuai Li, Chunling Gu, Jiannian Yao, Qing Liao, and Hongbing Fu. "Molecular engineering of excited-state process for multicolor microcrystalline lasers." Journal of Materials Chemistry C 10, no. 11 (2022): 4166–72. http://dx.doi.org/10.1039/d1tc05280b.

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We realize multicolor microcrystalline lasers by engineering the excited-state overlap between the stimulated emission and triplet absorption based on the organic molecular design. These molecules possessing both high gain and potential high carrier transport behaviors can be attractive candidates for the electrically pumped organic laser.

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Yamane, Junji, Naoki Ohyabu, Min Yao, Hiroshi Takemoto, and Isao Tanaka. "In-crystal chemical ligation for lead compound generation." Journal of Applied Crystallography 43, no. 6 (October 20, 2010): 1329–37. http://dx.doi.org/10.1107/s0021889810037222.

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A new fragment-based growth strategy for lead compound generation is proposed, which is based onin situchemical ligation and is operable in X-ray-based fragment screening format. The method involves two classes of bifunctional molecules, referred to as anchor molecules and tuning molecules. The anchor molecules are designed to form stable complexes with target proteins and to connect with the tuning molecules. The procedure begins with the introduction of the anchor molecule into the target protein, to which the tuning molecule is linked in the crystal. Proof-of-concept experiments using trypsin crystals charged withpara-aldehyde benzamidine showed that the crystals acted as a platform to select self-assembled ligation products. Furthermore, time-resolved crystallography allowed identification of the reaction field and direct visualization of the reaction pathway. The ability to rapidly gain an understanding of the relations between a set of chemical modifications and their interactions with target proteins would accelerate the hit-to-lead process. A potential crystallographic growth strategyviathe self-assembly technique and its biological implications are discussed.

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Zhou, Mengjie, Jiangyong He, Caiyun Li, Yan-Ge Liu, Yang Yue, Ruijin He, Siyu Chen, et al. "Oscillatory self-organization dynamics between soliton molecules induced by gain fluctuation." Optics Express 29, no. 11 (May 12, 2021): 16362. http://dx.doi.org/10.1364/oe.427549.

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Hwang, Inkyu, Jing-Feng Huang, Hidehiro Kishimoto, Anders Brunmark, Per A. Peterson, Michael R. Jackson, Charles D. Surh, Zeling Cai, and Jonathan Sprent. "T Cells Can Use Either T Cell Receptor or Cd28 Receptors to Absorb and Internalize Cell Surface Molecules Derived from Antigen-Presenting Cells." Journal of Experimental Medicine 191, no. 7 (March 27, 2000): 1137–48. http://dx.doi.org/10.1084/jem.191.7.1137.

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At the site of contact between T cells and antigen-presenting cells (APCs), T cell receptor (TCR)–peptide–major histocompatibility complex (MHC) interaction is intensified by interactions between other molecules, notably by CD28 and lymphocyte function-associated antigen 1 (LFA-1) on T cells interacting with B7 (B7-1 and B7-2), and intracellular adhesion molecule 1 (ICAM-1), respectively, on APCs. Here, we show that during T cell–APC interaction, T cells rapidly absorb various molecules from APCs onto the cell membrane and then internalize these molecules. This process is dictated by at least two receptors on T cells, namely CD28 and TCR molecules. The biological significance of T cell uptake of molecules from APCs is unclear. One possibility is that this process may allow activated T cells to move freely from one APC to another and eventually gain entry into the circulation.

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Hare, Stephanie R., and Dean J. Tantillo. "Post-transition state bifurcations gain momentum – current state of the field." Pure and Applied Chemistry 89, no. 6 (June 27, 2017): 679–98. http://dx.doi.org/10.1515/pac-2017-0104.

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AbstractThe existence of post-transition state bifurcations on potential energy surfaces for organic and biological reaction mechanisms has been known for decades, but recently, new reports of bifurcations have been occurring at a much higher rate. Beyond simply discovering bifurcations, computational chemists are developing techniques to understand what aspects of molecular structure and vibrations control the product selectivity in systems containing bifurcations. For example, the distribution of products seen in simulations has been found to be extremely sensitive to the local environment of the reacting system (i.e. the presence of a catalyst, enzyme, or explicit solvent molecules). The outlook for the future of this field is discussed, with an eye towards the application of the principles discussed here by experimental chemists to design a reaction setup to efficiently generate desired products.

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Ghahramani Seno, Mohammad M., Fuad G. Gwadry, Pingzhao Hu, and Stephen W. Scherer. "Neuregulin 1-alpha regulates phosphorylation, acetylation, and alternative splicing in lymphoblastoid cells." Genome 56, no. 10 (October 2013): 619–25. http://dx.doi.org/10.1139/gen-2013-0068.

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Neuregulins (NRGs) are signaling molecules involved in various cellular and developmental processes. Abnormal expression and (or) genomic variations of some of these molecules, such as NRG1, have been associated with disease conditions such as cancer and schizophrenia. To gain a comprehensive molecular insight into possible pathways/networks regulated by NRG1-alpha, we performed a global expression profiling analysis on lymphoblastoid cell lines exposed to NRG1-alpha. Our data show that this signaling molecule mainly regulates coordinated expression of genes involved in three processes: phosphorylation, acetylation, and alternative splicing. These processes have fundamental roles in proper development and function of various tissues including the central nervous system (CNS)—a fact that may explain conditions associated with NRG1 dysregulations such as schizophrenia. The data also suggest NRG1-alpha regulates genes (FBXO41) and miRNAs (miR-33) involved in cholesterol metabolism. Moreover, RPN2, a gene already shown to be dysregulated in breast cancer cells, is also differentially regulated by NRG1-alpha treatment.

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Kremer, Ran, Shira Roth, Avital Bross, Amos Danielli, and Yair Noam. "Using Temporally and Spatially Resolved Measurements to Improve the Sensitivity of Fluorescence-Based Immunoassays." Biosensors 14, no. 5 (April 28, 2024): 220. http://dx.doi.org/10.3390/bios14050220.

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Detecting low concentrations of biomarkers is essential in clinical laboratories. To improve analytical sensitivity, especially in identifying fluorescently labeled molecules, typical optical detection systems, consisting of a photodetector or camera, utilize time-resolved measurements. Taking a different approach, magnetic modulation biosensing (MMB) is a novel technology that combines fluorescently labeled probes and magnetic particles to create a sandwich assay with the target molecules. By concentrating the target molecules and then using time-resolved measurements, MMB provides the rapid and highly sensitive detection of various biomarkers. Here, we propose a novel signal-processing algorithm that enhances the detection and estimation of target molecules at low concentrations. By incorporating both temporally and spatially resolved measurements using human interleukin-8 as a target molecule, we show that the new algorithm provides a 2–4-fold improvement in the limit of detection and an ~25% gain in quantitative resolution.

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Haro Mares, Nadia B., Sonja C. Döller, Till Wissel, Markus Hoffmann, Michael Vogel, and Gerd Buntkowsky. "Structures and Dynamics of Complex Guest Molecules in Confinement, Revealed by Solid-State NMR, Molecular Dynamics, and Calorimetry." Molecules 29, no. 7 (April 8, 2024): 1669. http://dx.doi.org/10.3390/molecules29071669.

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This review gives an overview of current trends in the investigation of confined molecules such as water, small and higher alcohols, carbonic acids, ethylene glycol, and non-ionic surfactants, such as polyethylene glycol or Triton-X, as guest molecules in neat and functionalized mesoporous silica materials employing solid-state NMR spectroscopy, supported by calorimetry and molecular dynamics simulations. The combination of steric interactions, hydrogen bonds, and hydrophobic and hydrophilic interactions results in a fascinating phase behavior in the confinement. Combining solid-state NMR and relaxometry, DNP hyperpolarization, molecular dynamics simulations, and general physicochemical techniques, it is possible to monitor these confined molecules and gain deep insights into this phase behavior and the underlying molecular arrangements. In many cases, the competition between hydrogen bonding and electrostatic interactions between polar and non-polar moieties of the guests and the host leads to the formation of ordered structures, despite the cramped surroundings inside the pores.

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Morozov, Giora, Huaying Zhao, Michael Mage, Lisa Boyd, Peter Schuck, Kannan Natarajan, and David Margulies. "Tapasin-related protein TAPBPR interacts directly with peptide-free MHC-I/β2-microgolbulin complexes (APP3P.101)." Journal of Immunology 192, no. 1_Supplement (May 1, 2014): 111.2. http://dx.doi.org/10.4049/jimmunol.192.supp.111.2.

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Abstract The molecular mechanism by which MHC-I molecules are loaded with peptides is crucial to fundamental aspects of antigen presentation relating to self-tolerance and CD8 T cell activation. To gain insight into the mechanism of MHC-I peptide loading we have studied human TAPBPR (TAP binding protein-related) protein, which is 22% identical to tapasin in amino acid sequence, widely expressed and IFN-γ inducible, but is not part of the peptide-loading complex (PLC). To understand the interaction of TAPBPR with MHC-I, we produced recombinant soluble TAPBPR and evaluated its interactions with MHC-I/β2m complexes in vitro. Using recombinant MHC-I molecules refolded with photolabile peptides, we show, by gel-shift analysis, size exclusion chromatography, and analytical ultracentrifugation that TAPBPR binds MHC-I/β2m after photolysis of the bound peptide, in a 1:1 molar ratio. MHC-I molecules loaded with low-affinity peptides also bind TAPBPR. The TAPBPR/MHC interaction is reversed by exposure to high-affinity peptides known to bind the MHC-I molecule, indicating a role of TAPBPR in stabilizing a peptide-receptive form of the MHC-I/β2m complex. Because of the predicted structural similarity of TAPBPR to tapasin, this system not only provides insight into the molecular details of TAPBPR/MHC-I binding, but may also elucidate tapasin interactions in the PLC that have previously eluded experimental interrogation.

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Sentrayan, K., L. Major, A. Michael, and V. Kushawaha. "Liquid nitrogen and room-temperature SRS gain coefficient in isotopic hydrogen molecules." Journal of Physics D: Applied Physics 25, no. 12 (December 14, 1992): 1697–701. http://dx.doi.org/10.1088/0022-3727/25/12/004.

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Platonenko, Viktor T., and M. K. Shayakhmetova. "Influence of forbidden transitions on the gain-band structure of XeCl molecules." Soviet Journal of Quantum Electronics 22, no. 4 (April 30, 1992): 334–36. http://dx.doi.org/10.1070/qe1992v022n04abeh003437.

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Tanwar, Garima, and Rituraj Purohit. "Gain of native conformation of Aurora A S155R mutant by small molecules." Journal of Cellular Biochemistry 120, no. 7 (February 11, 2019): 11104–14. http://dx.doi.org/10.1002/jcb.28387.

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Soldatov, V. S., T. V. Bezyazychnaya, and E. G. Kosandrovich. "Visualization of magnesium and rubidium ion hydration in sulfocationite using quantum chemical calculation." Doklady of the National Academy of Sciences of Belarus 65, no. 6 (December 26, 2021): 692–701. http://dx.doi.org/10.29235/1561-8323-2021-65-6-692-701.

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Based on the data of ab initio calculation of the structure of (RSO3)2Mg (H2O)18 and (RSO3Rb)2(H2O)16 clusters, which simulate the structure of swollen sulfostyrene ion exchangers in the corresponding ionic forms and a water cluster of comparable size, the numbers of water molecules directly bound to cations and their coordination numbers, including the oxygen atoms of the sulfonic groups linked to the cation, were calculated. It is shown that the first molecular layer around the magnesium ion is formed from water molecules with the highest binding energy with the cluster, and around the rubidium ion – from the molecules of the nearest environment with the lowest binding energies. This is explained by the fact that the transfer of water molecules from its volume to magnesium hydrate is energetically favorable, but not to rubidium hydrate. Therefore, the magnesium ion builds its hydrate mainly from water molecules with the highest binding energy in order to obtain the greatest energy gain, and the rubidium ion – from molecules with the lowest energy, which provides the smallest energy loss.

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Patti, Angela, and Claudia Sanfilippo. "Breaking Molecular Symmetry through Biocatalytic Reactions to Gain Access to Valuable Chiral Synthons." Symmetry 12, no. 9 (September 4, 2020): 1454. http://dx.doi.org/10.3390/sym12091454.

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In this review the recent reports of biocatalytic reactions applied to the desymmetrization of meso-compounds or symmetric prochiral molecules are summarized. The survey of literature from 2015 up to date reveals that lipases are still the most used enzymes for this goal, due to their large substrate tolerance, stability in different reaction conditions and commercial availability. However, a growing interest is focused on the use of other purified enzymes or microbial whole cells to expand the portfolio of exploitable reactions and the molecular diversity of substrates to be transformed. Biocatalyzed desymmetrization is nowadays recognized as a reliable and efficient approach for the preparation of pharmaceuticals or natural bioactive compounds and many processes have been scaled up for multigram preparative purposes, also in continuous-flow conditions.

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Pálinkás, G., and I. Bakó. "Excess Properties of Water-Methanol Mixtures as Studied by MD Simulations." Zeitschrift für Naturforschung A 46, no. 1-2 (February 1, 1991): 95–99. http://dx.doi.org/10.1515/zna-1991-1-215.

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AbstractMolecular dynamics simulations with pair interactions reproduce experimental excess properties of methanol-water mixtures. Water molecules lose, and methanol molecules gain neighbours in the mixtures as compared to the solvents. The water-methanol mixture with 0.25 mole fraction of methanol, resulting in extreme values for different excess properties, is characterized by the highest number of molecules with maximal number of H-bonded neighbours.

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Saponara, Enrica, Rong Chen, Theresia Reding, Richard Zuellig, Darren C. Henstridge, Rolf Graf, and Sabrina Sonda. "Single or combined ablation of peripheral serotonin and p21 limit adipose tissue expansion and metabolic alterations in early adulthood in mice fed a normocaloric diet." PLOS ONE 16, no. 8 (August 11, 2021): e0255687. http://dx.doi.org/10.1371/journal.pone.0255687.

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Identifying the fundamental molecular factors that drive weight gain even in the absence of hypercaloric food intake, is crucial to enable development of novel treatments for the global pandemic of obesity. Here we investigated both adipose tissue-specific and systemic events that underlie the physiological weight gain occurring during early adulthood in mice fed a normocaloric diet. In addition, we used three different genetic models to identify molecular factors that promote physiological weight gain during normocaloric and hypercaloric diets. We demonstrated that normal physiological weight gain was accompanied by an increase in adipose tissue mass and the presence of cellular and metabolic signatures typically found during obesity, including adipocyte hypertrophy, macrophage recruitment into visceral fat and perturbed glucose metabolism. At the molecular level, this was associated with an increase in adipose tissue tryptophan hydroxylase 1 (Tph1) transcripts, the key enzyme responsible for the synthesis of peripheral serotonin. Genetic inactivation of Tph1 was sufficient to limit adipose tissue expansion and associated metabolic alterations. Mechanistically, we discovered that Tph1 inactivation resulted in down-regulation of cyclin-dependent kinase inhibitor p21Waf1/Cip1 expression. Single or double ablation of Tph1 and p21 were equally effective in preventing adipocyte expansion and systemic perturbation of glucose metabolism, upon both normocaloric and hypercaloric diets. Our results suggest that serotonin and p21 act as a central molecular determinant of weight gain and associated metabolic alterations, and highlights the potential of targeting these molecules as a pharmacologic approach to prevent the development of obesity.

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Baan, Willem A. "Megamasers in Young Active Galactic Nuclei." Symposium - International Astronomical Union 134 (1989): 402–3. http://dx.doi.org/10.1017/s0074180900141476.

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Megamaser emission provides new insights into the physics of active galactic nuclei. The megamaser phenomenon is consistent with a low-gain amplification model, where inverted foreground molecules amplify the radio continuum from the nucleus. The molecular gas seen in emission in the megamaser galaxies is located between 50 and 300 parsecs from the nucleus covering part of a possible NLR. Megamasers have been found for the molecules OH, H2CO and H2O. However, only OH megamasers form a clearly identifiable group of galaxies. They occur in prominent FIR galaxies and the FIR radiation field serves as a pumping agent for the OH molecules (Baan 1988). As a result only the ground state lines of OH are in emission, while the lines from excited states are in absorption (see Henkel, Güsten and Baan 1987).

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Irrera, Simona, and Nora H. de Leeuw. "A density functional theory study of the adsorption of uracil on the Au(100) surface." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 467, no. 2131 (February 23, 2011): 1959–69. http://dx.doi.org/10.1098/rspa.2010.0657.

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We have used plane-wave density functional theory methods to explore the adsorption modes and configurations of uracil molecules on a gold surface to gain insight into the rational design of surface functionalization. We have investigated at the molecular level, the interactions of the RNA pyrimidine base uracil molecule isolated on the single crystal (100) surface of the gold substrate to determine the structure of uracil and orientation. Our calculations have shown that the most stable adsorbate structure is the enol tautomer of uracil, which adsorbs flat onto the gold surface through one of its carbonyl atoms. This configuration, which is compatible with previous experimental findings, is thermodynamically preferred over the adsorbed keto structure by approximately 0.23 eV (22.2 kJ mol −1 ).

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Yampol'skaya, S. A., A. G. Yastremskiĭ, Yu N. Panchenko, and A. V. Puchikin. "Amplification of laser radiation at the edge of the KrF (B – X) spectral line." Quantum Electronics 52, no. 5 (May 1, 2022): 437–42. http://dx.doi.org/10.1070/qel18039.

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Abstract We report the results of experimental and numerical studies of the KrF electric discharge amplifier operating on a mixture of He – Kr – F2 gases. The possibility of expanding the short-wavelength spectral region of the induced radiation tuning at the B – X transition of the KrF molecule by removing the inverse population from the upper vibrational states of the electronic B level is shown. It is demonstrated that at the boundary of the active medium gain contour, the measured gain at a wavelength of 246.8 nm is 0.053 cm-1. Using the developed 1D model of the KrF electric discharge amplifier, it is shown that when the active medium is excited by a pump pulse with a specific peak power of ~10 MW cm-3, the gain in this spectral region is due to a longer relaxation time of the population of excimer molecules from the upper vibrational levels compared with the characteristic time of their production.

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TUKHVATULLIN, F. H., U. N. TASHKENBAEV, A. JUMABAEV, H. HUSHVAKTOV, A. ABSANOV, and G. SHARIFOV. "CALCULATIONS AND EXPERIMENTAL STUDIES OF THE AGGREGATION OF MOLECULES OF LIQUID ACETONE BY SPECTRA OF RAMAN SCATTERING." Journal of Nonlinear Optical Physics & Materials 22, no. 02 (June 2013): 1350022. http://dx.doi.org/10.1142/s0218863513500227.

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Experimental studies of the Raman scattering of the band of C = O vibrations of acetone (1710 cm–1) showed that the parallel and perpendicular polarized components have a large half-width (respectively, 11.6 and 18 cm–1) and also the bands' maxima of these components are shifted by ~5 cm–1. In the neutral solvent (heptane), the difference of the maxima position of the bands decreases. Calculations showed that the molecules of acetone can aggregate to form a dimer with the energy gain of 10.1 kJ/mole. In the dimer several hydrogen bonds are formed between the oxygen atom of one molecule and the hydrogen atoms of CH3 -group of another molecule. In an aqueous mixture of acetone, according to calculations, there is a possibility for formation of dimers and closed trimer aggregates with the energy gain, respectively, 19.1 and 45.8 kJ/mole. Calculation showed that symmetric and antisymmetric O–H vibrations of water are displaced in the interaction with acetone to lower frequencies, respectively, to 3808.4 and to 3931.8 –1.

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Xu, Baoyuan, Zhenhua Gao, Yanhui Wei, Yang Liu, Xun Sun, Weiguang Zhang, Xue Wang, Zifei Wang, and Xiangeng Meng. "Dynamically wavelength-tunable random lasers based on metal–organic framework particles." Nanoscale 12, no. 8 (2020): 4833–38. http://dx.doi.org/10.1039/c9nr09644b.

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Struckmeier, Jens. "Some Estimates on the Boltzmann Collision Operator." Mathematical Models and Methods in Applied Sciences 07, no. 07 (November 1997): 1023–33. http://dx.doi.org/10.1142/s0218202597000517.

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The paper presents some new estimates on the gain term of the Boltzmann collision operator. For Maxwellian molecules, it is shown that the L∞-norm of the gain term can be bounded in terms of the L1- and L∞-norm of the density function f. In the case of more general collision kernels, like the hard-sphere interaction potential, the gain term is estimated pointwise by the L∞-norm of the density function and the loss term of the Boltzmann collision operator.

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Gretz, J. Elizabeth, Christopher C. Norbury, Arthur O. Anderson, Amanda E. I. Proudfoot, and Stephen Shaw. "Lymph-Borne Chemokines and Other Low Molecular Weight Molecules Reach High Endothelial Venules via Specialized Conduits While a Functional Barrier Limits Access to the Lymphocyte Microenvironments in Lymph Node Cortex." Journal of Experimental Medicine 192, no. 10 (November 13, 2000): 1425–40. http://dx.doi.org/10.1084/jem.192.10.1425.

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Lymph-borne, soluble factors (e.g., chemokines and others) influence lymphocyte recirculation and endothelial phenotype at high endothelial venules (HEVs) in lymph node cortex. Yet the route lymph-borne soluble molecules travel from the subcapsular sinus to the HEVs is unclear. Therefore, we injected subcutaneously into mice and rats a wide variety of fluorophore-labeled, soluble molecules and examined their distribution in the draining lymph nodes. Rather than percolating throughout the draining lymph node, all molecules, including microbial lipopolysaccharide, were very visible in the subcapsular and medullary sinuses but were largely excluded from the cortical lymphocyte microenvironments. Exclusion prevailed even during the acute lymph node enlargement accompanying viral infection. However, low molecular mass (MW) molecules, including chemokines, did gain entry into the cortex, but in a very defined manner. Low MW, fluorophore-labeled molecules highlighted the subcapsular sinus, the reticular fibers, and the abluminal and luminal surfaces of the associated HEVs. These low MW molecules were in the fibers of the reticular network, a meshwork of collagen fibers ensheathed by fibroblastic reticular cells that connects the subcapsular sinus floor and the HEVs by intertwining with their basement membranes. Thus, low MW, lymph-borne molecules, including chemokines, traveled rapidly from the subcapsular sinus to the HEVs using the reticular network as a conduit.

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Zaviyalov, Alexandr, Philippe Grelu, and Falk Lederer. "Impact of slow gain dynamics on soliton molecules in mode-locked fiber lasers." Optics Letters 37, no. 2 (January 12, 2012): 175. http://dx.doi.org/10.1364/ol.37.000175.

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Nilsen, TW, R. Getts, and M. Weinstein. "Single Molecule Detection of Fluorescently Labelled DNA Dendrimers." Microscopy and Microanalysis 6, S2 (August 2000): 856–57. http://dx.doi.org/10.1017/s1431927600036771.

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Single molecule detection has been achieved via many highly sophisticated microscopic techniques. Here we describe the detection of single molecules with conventional epifluorescent microscopy. The key to the technique is the use of DNA dendrimers DNA dendrimers have demonstrated utility in nucleic acid blots, Southerns, Northerns, etc. Typically DNA dendrimers yield 50-100 fold gain in signal over comparably labeled oligonucleotides. Immunodendrimers, DNA dendrimers conjugated to antibody molecules, have also been constructed and utilized in western blot assays. Individual, i.e. single molecule, 4- layer dendrimers, are readily detectable as point sources via conventional fluorescence microscopy and are useful for in situ hybridization and flow fluorescence quantitation.Nucleic acid hybridization is the underlying principle behind DNA dendrimer assembly. The “monomer” of DNA dendrimers consists of partially double stranded heteroduplexed DNA. Each monomer has an approximately 50 base double stranded “waist” surrounded by four approximately 30 base single stranded “arms”.

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Monachino, Enrico, Lisanne M. Spenkelink, and Antoine M. van Oijen. "Watching cellular machinery in action, one molecule at a time." Journal of Cell Biology 216, no. 1 (December 15, 2016): 41–51. http://dx.doi.org/10.1083/jcb.201610025.

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Single-molecule manipulation and imaging techniques have become important elements of the biologist’s toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components.

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Ozdemir, Resul, Donghee Choi, Mehmet Ozdemir, Guhyun Kwon, Hyekyoung Kim, Unal Sen, Choongik Kim, and Hakan Usta. "Ultralow bandgap molecular semiconductors for ambient-stable and solution-processable ambipolar organic field-effect transistors and inverters." Journal of Materials Chemistry C 5, no. 9 (2017): 2368–79. http://dx.doi.org/10.1039/c6tc05079d.

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Bersani, Francesca, Eunjung Lee, Peter V. Kharchenko, Andrew W. Xu, Mingzhu Liu, Kristina Xega, Olivia C. MacKenzie, et al. "Pericentromeric satellite repeat expansions through RNA-derived DNA intermediates in cancer." Proceedings of the National Academy of Sciences 112, no. 49 (November 2, 2015): 15148–53. http://dx.doi.org/10.1073/pnas.1518008112.

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Aberrant transcription of the pericentromeric human satellite II (HSATII) repeat is present in a wide variety of epithelial cancers. In deriving experimental systems to study its deregulation, we observed that HSATII expression is induced in colon cancer cells cultured as xenografts or under nonadherent conditions in vitro, but it is rapidly lost in standard 2D cultures. Unexpectedly, physiological induction of endogenous HSATII RNA, as well as introduction of synthetic HSATII transcripts, generated cDNA intermediates in the form of DNA/RNA hybrids. Single molecule sequencing of tumor xenografts showed that HSATII RNA-derived DNA (rdDNA) molecules are stably incorporated within pericentromeric loci. Suppression of RT activity using small molecule inhibitors reduced HSATII copy gain. Analysis of whole-genome sequencing data revealed that HSATII copy number gain is a common feature in primary human colon tumors and is associated with a lower overall survival. Together, our observations suggest that cancer-associated derepression of specific repetitive sequences can promote their RNA-driven genomic expansion, with potential implications on pericentromeric architecture.

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Graziano, Giuseppe. "Comment on “Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors” by A. Battisti, G. Ciasca, A. Grottesi and A. Tenenbaum, Phys. Chem. Chem. Phys., 2017, 19, 8435." Physical Chemistry Chemical Physics 20, no. 1 (2018): 690–93. http://dx.doi.org/10.1039/c7cp04546h.

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Furlan, Aurélien L., Yoann Laurin, Camille Botcazon, Nely Rodríguez-Moraga, Sonia Rippa, Magali Deleu, Laurence Lins, Catherine Sarazin, and Sébastien Buchoux. "Contributions and Limitations of Biophysical Approaches to Study of the Interactions between Amphiphilic Molecules and the Plant Plasma Membrane." Plants 9, no. 5 (May 20, 2020): 648. http://dx.doi.org/10.3390/plants9050648.

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Some amphiphilic molecules are able to interact with the lipid matrix of plant plasma membranes and trigger the immune response in plants. This original mode of perception is not yet fully understood and biophysical approaches could help to obtain molecular insights. In this review, we focus on such membrane-interacting molecules, and present biophysically grounded methods that are used and are particularly interesting in the investigation of this mode of perception. Rather than going into overly technical details, the aim of this review was to provide to readers with a plant biochemistry background a good overview of how biophysics can help to study molecular interactions between bioactive amphiphilic molecules and plant lipid membranes. In particular, we present the biomimetic membrane models typically used, solid-state nuclear magnetic resonance, molecular modeling, and fluorescence approaches, because they are especially suitable for this field of research. For each technique, we provide a brief description, a few case studies, and the inherent limitations, so non-specialists can gain a good grasp on how they could extend their toolbox and/or could apply new techniques to study amphiphilic bioactive compound and lipid interactions.

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SATO, KIMINORI, KAZUOMI NUMATA, and KOICHIRO FUJIMOTO. "TRANSIENT STRUCTURAL EVOLUTION UPON THERMAL DEHYDRATION IN LAYERED-HECTORITE NANOPARTICLES." International Journal of Nanoscience 11, no. 06 (December 2012): 1240033. http://dx.doi.org/10.1142/s0219581x12400339.

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To gain an insight into earthquake slip weakening due to thermal pressurization, microscopic molecular structures associated with water desorption are investigated for layered-hectorite nanoparticles by positronium (Ps) annihilation spectroscopy, thermogravimetry and differential thermal analysis (TG–DTA) and time-resolved length-change measurement with high resolution dilatometry. The large macroscopic length change of ~ 6% occurs simultaneously with the formation of open spaces with the size of ~ 7 Å when water molecules are desorbed from the interlayer spaces.

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Bouvier, Marlene, and Jie Fu. "A molecular understanding of how the immunomodulatory E3-19K protein from adenovirus interferes with the class I antigen presentation pathway (78.13)." Journal of Immunology 182, no. 1_Supplement (April 1, 2009): 78.13. http://dx.doi.org/10.4049/jimmunol.182.supp.78.13.

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Abstract Adenoviruses (Ads) cause persistent infections. The Ad E3-19K protein binds and retains class I MHC molecules in the endoplasmic reticulum (ER), suppressing the cell-surface presentation of viral peptides. The molecular mechanism of E3-19K-mediated class I retention is mostly uncharacterized. This knowledge is important to better understand Ad pathogenicity, and to gain insights into the susceptibility of the class I antigen presentation pathway to viral interferences. Using biophysical and cell-based approaches, we showed for the first time that E3-19K associates with immature (nascent) and mature (peptide-filled) class I molecules. We also showed that E3-19K does not compete with the class I assembly proteins for binding onto class I molecules. Importantly, immature class I sequestered by E3-19K can still bind peptides. Together, these results suggest that Ads have evolved to interfere with the early and late stages of the class I antigen presentation pathway. We also showed that E3-19K associates with HLA-A and -B molecules, but not HLA-C molecules. This locus specificity may provide a functional advantage to Ads by inactivating T-cell receptors, while avoiding activation of NK receptors. Finally, we showed that residue 56 in MHC and residue 93 in E3-19K are highly critical for class I association with E3-19K. Overall, our results provide a molecular understanding of Ad pathogenicity. Funded by NIH AI65943.

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Mun, Eundeok, Jason Wilcox, Jamie L. Manson, Brian Scott, Paul Tobash, and Vivien S. Zapf. "The Origin and Coupling Mechanism of the Magnetoelectric Effect inTMCl2-4SC(NH2)2(TM= Ni and Co)." Advances in Condensed Matter Physics 2014 (2014): 1–4. http://dx.doi.org/10.1155/2014/512621.

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Most research on multiferroics and magnetoelectric effects to date has focused on inorganic oxides. Molecule-based materials are a relatively new field in which to search for magnetoelectric multiferroics and to explore new coupling mechanisms between electric and magnetic order. We present magnetoelectric behavior in NiCl2-4SC(NH2)2(DTN) and CoCl2-4SC(NH2)2(DTC). These compounds form tetragonal structures where the transition metal ion (Ni or Co) is surrounded by four electrically polar thiourea molecules [SC(NH2)2]. By tracking the magnetic and electric properties of these compounds as a function of magnetic field, we gain insights into the coupling mechanism by observing that, in DTN, the electric polarization tracks the magnetic ordering, whereas in DTC it does not. For DTN, all electrically polar thiourea molecules tilt in the same direction along thec-axis, breaking spatial-inversion symmetry, whereas, for DTC, two thiourea molecules tilt up and two tilt down with respect toc-axis, perfectly canceling the net electrical polarization. Thus, the magnetoelectric coupling mechanism in DTN is likely a magnetostrictive adjustment of the thiourea molecule orientation in response to magnetic order.

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Oberhauser, Werner. "Advance in Selective Alcohol and Polyol Oxidation Catalysis." Catalysts 12, no. 2 (February 18, 2022): 229. http://dx.doi.org/10.3390/catal12020229.

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The aerobic oxidation of organic molecules and in particular alcohols and bio-derived poly alcohols to value-added commodity molecules is under continuous investigation, due to the importance of oxidation products (aldehydes, ketones carboxylic acids and esters) and the challenging nature of this chemical transformation, since rather harsh reaction conditions (T > 100 °C) are needed to gain a significant substrate conversion [...]

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Journal articles on the topic 'Gain molecules'

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