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1. Recent Progress of SERS Nanoprobe for pH Detecting and Its Application in Biological Imaging.

Author

Zhang L, Zhao Q, Jiang Z, Shen J, Wu W, Liu X, Fan Q, and Huang W

Subjects
Humans, Hydrogen-Ion Concentration, Spectrum Analysis, Raman
Abstract

As pH value almost affects the function of cells and organisms in all aspects, in biology, biochemical and many other research fields, it is necessary to apply simple, intuitive, sensitive, stable detection of pH and base characteristics inside and outside the cell. Therefore, many research groups have explored the design and application of pH probes based on surface enhanced Raman scattering (SERS). In this review article, we discussed the basic theoretical background of explaining the working mechanism of pH SERS sensors, and also briefly described the significance of cell pH measurement, and simply classified and summarized the factors that affected the performance of pH SERS probes. Some applications of pH probes based on surface enhanced Raman scattering in intracellular and extracellular pH imaging and the combination of other analytical detection techniques are described. Finally, the development prospect of this field is presented.

Published
2021
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2. Pretreatment-dependent surface chemistry of wood nanocellulose for pH-sensitive hydrogels.

Author

Chinga-Carrasco G and Syverud K

Subjects
Hydrogels, Microscopy, Atomic Force, Microscopy, Electron, Scanning, Cellulose, Hydrogen-Ion Concentration, Nanostructures, Wood
Abstract

Nanocellulose from wood is a promising material with potential in various technological areas. Within biomedical applications, nanocellulose has been proposed as a suitable nano-material for wound dressings. This is based on the capability of the material to self-assemble into 3D micro-porous structures, which among others have an excellent capacity of maintaining a moist environment. In addition, the surface chemistry of nanocellulose is suitable for various applications. First, OH-groups are abundant in nanocellulose materials, making the material strongly hydrophilic. Second, the surface chemistry can be modified, introducing aldehyde and carboxyl groups, which have major potential for surface functionalization. In this study, we demonstrate the production of nanocellulose with tailor-made surface chemistry, by pre-treating the raw cellulose fibres with carboxymethylation and periodate oxidation. The pre-treatments yielded a highly nanofibrillated material, with significant amounts of aldehyde and carboxyl groups. Importantly, the poly-anionic surface of the oxidized nanocellulose opens up for novel applications, i.e. micro-porous materials with pH-responsive characteristics. This is due to the swelling capacity of the 3D micro-porous structures, which have ionisable functional groups. In this study, we demonstrated that nanocellulose gels have a significantly higher swelling degree in neutral and alkaline conditions, compared to an acid environment (pH 3). Such a capability can potentially be applied in chronic wounds for controlled and intelligent release of antibacterial components into biofilms., (© The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.)

Published
2014
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3. Comparative study of lignins isolated by alkali and ultrasound-assisted alkali extractions from wheat straw.

Author

Sun R and Tomkinson J

Subjects
Kinetics, Solubility, Triticum chemistry, Ultrasonography, Hydrogen-Ion Concentration, Lignin chemistry
Abstract

Treatment of the dewaxed wheat straw with 0.5 M KOH at 35 degrees C for 2.5 h without ultrasonic irradiation and with ultrasound assistance for 5, 10, 15, 20, 25, 30, and 35 min resulted in a dissolution of 43.9%, 43.9%, 43.9%, 44.4%, 44.4%, 45.6%, 46.8%, and 49.1% of the original lignin, respectively. Much better results were achieved under the ultrasonic irradiation time for 35 min where nearly 50% of the original lignin was solubilized at 35 degrees C for 2.5 h. The purity of the lignin preparations isolated by alkali with ultrasound assistance was higher than that of the lignin fraction obtained by alkali without ultrasonic irradiation, and their purity increased with an increment of irradiation time between 5 and 35 min, in which the content of associated polysaccharides in the former lignin preparations (0.87-1.06%) was lower than that of the latter lignin fraction (1.16%). In addition, the lignins isolated by alkali with ultrasonic irradiation time between 5 and 30 min showed a slightly higher molecular weight and thermal stability than the lignin obtained by alkali without ultrasound assistance. No substantial differences in the main structure features between the lignin preparations isolated by alkali and ultrasound-assisted alkali extractions were found.

Published
2002
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4. Influence of pH on the balance between methanogenesis and iron reduction.

Author

Marquart, Kyle A., Haller, Ben R., Paper, Janet M., Flynn, Theodore M., Boyanov, Maxim I., Shodunke, Ganiyat, Gura, Colleen, Jin, Qusheng, and Kirk, Matthew F.

Subjects
HYDROGEN-ion concentration, IRON, FERRIC oxide, GOETHITE, METHANE, GEOBACTER
Abstract

Methanogenesis and iron reduction play major roles in determining global fluxes of greenhouse gases. Despite their importance, environmental factors that influence their interactions are poorly known. Here, we present evidence that pH significantly influences the balance between each reaction in anoxic environments that contain ferric (oxyhydr)oxide minerals. In sediment bioreactors that contained goethite as a source of ferric iron, both iron reduction and methanogenesis occurred but the balance between them varied significantly with pH. Compared to bioreactors receiving acidic media (pH 6), electron donor oxidation was 85% lower for iron reduction and 61% higher for methanogenesis in bioreactors receiving alkaline media (pH 7.5). Thus, methanogenesis displaced iron reduction considerably at alkaline pH. Geochemistry data collected from U.S. aquifers demonstrate that a similar pattern also exists on a broad spatial scale in natural settings. In contrast, in bioreactors that were not augmented with goethite, clay minerals served as the source of ferric iron and the balance between each reaction did not vary significantly with pH. We therefore conclude that pH can regulate the relative contributions of microbial iron reduction and methanogenesis to carbon fluxes from terrestrial environments. We further propose that the availability of ferric (oxyhydr)oxide minerals influences the extent to which the balance between each reaction is sensitive to pH. The results of this study advance our understanding of environmental controls on microbial methane generation and provide a basis for using pH and the occurrence of ferric minerals to refine predictions of greenhouse gas fluxes. [ABSTRACT FROM AUTHOR]

Published
2019
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5. Nanoarchaeum equitans and Ignicoccus hospitalis: New Insights into a Unique, Intimate Association of Two Archaea▿

Author

Martin Gallenberger, Wolfgang Eisenreich, Benjamin Junglas, Reinhard Rachel, Harald Huber, Karl O. Stetter, Ulrike Jahn, and Walter Paper

Subjects
Magnetic Resonance Spectroscopy, Ignicoccus, Sodium Chloride, Microbiology, Microbial Cell Biology, RNA, Ribosomal, 16S, Nanoarchaeota, Sulfites, Nanoarchaeum equitans, Amino Acids, Molecular Biology, Mutual influence, biology, Desulfurococcaceae, Temperature, Hydrogen-Ion Concentration, Commensalism, biology.organism_classification, Microscopy, Electron, DNA, Archaeal, Biochemistry, Stationary phase, Fermentation, Bacteria, Cell Division, Archaea
Abstract

Nanoarchaeum equitansandIgnicoccus hospitalisrepresent a unique, intimate association of two archaea. Both form a stable coculture which is mandatory forN.equitansbut not for the hostI.hospitalis. Here, we investigated interactions and mutual influence between these microorganisms. Fermentation studies revealed that during exponential growth only about 25% ofI.hospitaliscells are occupied byN.equitanscells (one to three cells). The latter strongly proliferate in the stationary phase ofI.hospitalis, until 80 to 90% of theI.hospitaliscells carry around 10N.equitanscells. Furthermore, the expulsion of H2S, the major metabolic end product ofI.hospitalis, by strong gas stripping yields huge amounts of freeN.equitanscells.N.equitanshad no influence on the doubling times, final cell concentrations, and growth temperature, pH, or salt concentration ranges or optima ofI.hospitalis. However, isolation studies using optical tweezers revealed that infection withN.equitansinhibited the proliferation of individualI.hospitaliscells. This inhibition might be caused by deprivation of the host of cell components like amino acids, as demonstrated by13C-labeling studies. The strong dependence ofN.equitansonI.hospitaliswas affirmed by live-dead staining and electron microscopic analyses, which indicated a tight physiological and structural connection between the two microorganisms. No alternative hosts, including otherIgnicoccusspecies, were accepted byN.equitans. In summary, the data show a highly specialized association ofN.equitansandI.hospitaliswhich so far cannot be assigned to a classical symbiosis, commensalism, or parasitism.

Published
2007

6. Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation

Author

Marc Delarue, Catherine Van Renterghem, Zaineb Fourati, Pierre-Jean Corringer, Ludovic Sauguet, Haidai Hu, Ákos Nemecz, Dynamique structurale des Macromolécules / Structural Dynamics of Macromolecules, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU), Récepteurs Canaux - Channel Receptors, Á.N. and Z.F. were supported by Agence Nationale de Recherches Grant 13-BSV8-0020 'Pentagate.' H.H. was sponsored by the China Scholarship Council and Institut Pasteur., We thank Anaïs Menny for sharing expertise on plasmid constructions, the staff of the Crystallography Platform (PF6) in the Institut Pasteur for initial crystal screens, Reinis Reinholds Ruza for help in data collection, Jérôme Loc’h for help during structural refinement and picture preparation, Stacy Gellenoncourt for help in purification and crystallization of the sTeLIC R86A mutant, the staff of synchrotron beamlines in Soleil (Orsay) and European Synchrotron Radiation Facility (Grenoble) for data collection, Pierre Legrand (Soleil synchrotron) for suggestions on refinement in Buster, and Marc Gielen for suggestions during the paper preparation, ANR-13-BSV8-0020,Pentagate,Mécanismes d'activation et de désensibilisation d'un récepteur-canal pentamérique(2013), and Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Gating, Crystallography, X-Ray, Divalent, 03 medical and health sciences, chemistry.chemical_compound, Allosteric Regulation, Bacterial Proteins, [CHIM.CRIS]Chemical Sciences/Cristallography, structural biology, Binding site, crystallography, Ion channel, Tetramethylammonium, chemistry.chemical_classification, Multidisciplinary, ligand-gated ion channel, druggable cavity, Hydrogen-Ion Concentration, Ligand-Gated Ion Channels, electrophysiology, Transmembrane protein, Quaternary Ammonium Compounds, 030104 developmental biology, chemistry, Structural biology, PNAS Plus, Biophysics, Ligand-gated ion channel, Gammaproteobacteria
Abstract

International audience; Pentameric ligand-gated ion channels (pLGICs) constitute a widespread class of ion channels, present in archaea, bacteria, and eukaryotes. Upon binding of their agonists in the extracellular domain, the transmembrane pore opens, allowing ions to go through, via a gating mechanism that can be modulated by a number of drugs. Even though high-resolution structural information on pLGICs has increased in a spectacular way in recent years, both in bacterial and in eukaryotic systems, the structure of the open channel conformation of some intensively studied receptors whose structures are known in a nonactive (closed) form, such as Erwinia chrysanthemi pLGIC (ELIC), is still lacking. Here we describe a gammaproteobacterial pLGIC from an endo-symbiont of Tevnia jerichonana (sTeLIC), whose sequence is closely related to the pLGIC from ELIC with 28% identity. We provide an X-ray crystallographic structure at 2.3 Å in an active conformation, where the pore is found to be more open than any current conformation found for pLGICs. In addition, two charged restriction rings are present in the vestibule. Functional characterization shows sTeLIC to be a cationic channel activated at alkaline pH. It is inhibited by divalent cations, but not by quaternary ammonium ions, such as tetramethylammonium. Additionally, we found that sTeLIC is allosterically potentiated by aromatic amino acids Phe and Trp, as well as their derivatives, such as 4-bromo-cinnamate, whose cocrystal structure reveals a vestibular binding site equivalent to, but more deeply buried than, the one already described for benzodiazepines in ELIC.

Published
2018

7. Secretory lipase from the human pathogen Leishmania major: Heterologous expression in the yeast Pichia pastoris and biochemical characterization

Author

Madiha Bou Ali, Youssef Gargouri, Saoussen Ben Ayed, Aymen Bali, Yassine Ben Ali, Dhafer Laouini, École Nationale d'Ingénieurs de Sfax | National School of Engineers of Sfax (ENIS), Université de Sfax - University of Sfax, Laboratoire de Transmission, Contrôle et Immunobiologie des Infections - Laboratory of Transmission, Control and Immunobiology of Infection (LR11IPT02), Institut Pasteur de Tunis, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), and The authors would like to thank Mr. Anouar Fendri, Professor of English, who kindly proofread this paper.

Subjects
0301 basic medicine, Models, Molecular, MESH: Leishmania major/genetics, MESH: Enzyme Stability, MESH: Hydrogen-Ion Concentration, Protein Conformation, Gene Expression, MESH: Amino Acid Sequence, MESH: Base Sequence, 01 natural sciences, Biochemistry, Pichia, MESH: Protein Conformation, Enzyme Stability, MESH: Pichia/genetics, Leishmania major, MESH: Lipase/antagonists & inhibitors, Cloning, Molecular, Enzyme Inhibitors, Leishmania, MESH: Lipase/metabolism, biology, Chemistry, Temperature, General Medicine, Hydrogen-Ion Concentration, MESH: Temperature, Parasite, MESH: Biocatalysis, MESH: Models, Molecular, MESH: Gene Expression, Leishmania donovani, Triacylglycerol lipase, MESH: Sequence Alignment, MESH: Leishmania major/enzymology, Pichia pastoris, 03 medical and health sciences, Humans, MESH: Cloning, Molecular, [SDV.MP.PAR]Life Sciences [q-bio]/Microbiology and Parasitology/Parasitology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Lipase, MESH: Humans, Base Sequence, MESH: Enzyme Inhibitors/pharmacology, 010401 analytical chemistry, MESH: Lipase/chemistry, biology.organism_classification, Yeast, 0104 chemical sciences, 030104 developmental biology, MESH: Lipase/genetics, biology.protein, Biocatalysis, Heterologous expression, Sequence Alignment
Abstract

International audience; Leishmaniasis is a parasitic reticuloendotheliosis whose pathogen is a zooflagellate belonging to the genus Leishmania transmitted by the bite of an infected phlebotome. Recently, a unique secretory lipase from the human pathogen Leishmania donovani Ldlip3 has been identified and characterized. This lipase has a high identity with a putative triacylglycerol lipase of Leishmania major (Lmlip2). In the present study, Lmlip2 was expressed in the eukaryotic heterologous expression system Pichia pastoris as tagged enzyme of 308 amino acids. Maximal protein production was reached after 2 days of fermentation. Optimal Lmlip2 lipase activity was measured using the pH stat technique at pH 8 at 26 °C using vinyl esters and triacylglycerols (true lipids) as substrates. Moreover, biochemical characterization of Lmlip2 contained in culture supernatant, illustrates that L. major secreted lipase is active and stable at low temperatures especially 26°and prefer neutral pH; concerning substrate specificityLmlip2 presents a preference for short chains lipid substrates vinyl esters such as VC2, VC3 and VC4 likewise, it is capable to hydrolyze long chain triacylglycerols like olive oil. Metal ions and surfactants tested in this study decrease Lmlip2 activity. Further studies are needed to clarify the relation between the lipase activity and the virulence. Thus, it could lead to the identification of novel targets to block cutaneous Leishmaniasis in human hosts.

Published
2018

8. Helicobacter pylori Adapts to Chronic Infection and Gastric Disease via pH-Responsive BabA-Mediated Adherence

Author

Verena Königer, D. Scott Merrell, Roman Andriiovych Moskalenko, Rainer Haas, Thomas Borén, Sara Henriksson, Jafar Mahdavi, Abhijit Chowdhury, Johan Ögren, Anders Hofer, Jay V. Solnick, Dan Danielsson, Sara K. Lindén, Dag Ilver, Konstantinos S. Papadakos, Susanne Vikström, Jörgen Ådén, Jan Holgersson, Gerhard Gröbner, Alexej Schmidt, Jeanna Bugaytsova, Oscar Björnham, Göran O. Bylund, Rolf Sjöström, Stefan Oscarson, Dionyssios N. Sgouras, Lori M. Hansen, Yevgen A Chernov, Anders Esberg, Kristof Moonens, Christopher Aisenbrey, Charles Kelly, Ludmilla A. Morozova-Roche, Jeannette M. Whitmire, Beatriz Martinez-Gonzalez, Asish K. Mukhopadhyay, Angela Eldridge, Nicklas Strömberg, Robert H. Gilman, Andre Dubois, Lars Engstrand, Staffan Schedin, Brett A. Chromy, Justine Younson, Matthew Goldman, Anna Shevtsova, Macarena P. Quintana-Hayashi, Hui Liu, Magnus Unemo, Lena Rakhimova, Anna Åberg, Sebastian Suerbaum, Anna Arnqvist, Pär Gideonsson, Maréne Landström, Douglas E. Berg, Kristoffer Brännström, Anders Olofsson, Melissa Mendez, G. Balakrish Nair, Han Remaut, Umeå University, School of Life Sciences, University of Nottingham, UK (UON), Sahlgrenska Academy at University of Gothenburg [Göteborg], Université libre de Bruxelles (ULB), VIB-VUB Center for Structural Biology [Bruxelles], VIB [Belgium], Sumy State University, Max Von Pettenkofer Institute (MVP), Ludwig-Maximilians-Universität München (LMU), Uniformed Services University of the Health Sciences (USUHS), King‘s College London, Johns Hopkins Bloomberg School of Public Health [Baltimore], Johns Hopkins University (JHU), School of Digestive and Liver Diseases [Kolkata] (SDLD), National Institute of Cholera and Enteric Diseases, Translational Health Science and Technology Institute [Faridabad] (THSTI), Institut Pasteur Hellénique, Réseau International des Instituts Pasteur (RIIP), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Karolinska Institutet [Stockholm], Örebro University Hospital [Örebro, Sweden], Hannover Medical School [Hannover] (MHH), German Center for Infection Research - partner site Hannover-Braunschweig (DZIF), School of Chemistry and Chemical Biology (UCD), University College Dublin [Dublin] (UCD), University of California [Davis] (UC Davis), University of California, German Center for Infection Research, Partnersite Munich (DZIF), Département d'Informatique [Bruxelles] (ULB), Faculté des Sciences [Bruxelles] (ULB), Université libre de Bruxelles (ULB)-Université libre de Bruxelles (ULB), University of California [San Diego] (UC San Diego), This work was supported by grants from Vetenskapsrådet (VR/M) to T.B. and S.K.L., Cancerfonden to T.B. and A.A., VR/NT to A.A. and S. Schedin, Formas to S.K.L., the J.C. Kempe and Seth M. Kempe Memorial Foundation, the Knut and Alice Wallenberg Foundation (2012.0090) to T.B. and M.L., European Union Seventh Framework Program GastricGlycoExplorer ITN grant number 316929 to T.B. and Y.A.C., Magn. Bergvall’s Foundation to S. Schedin, DFG (SFB 900/A1) to S. Suerbaum, DFG (HA2697/16-1) to R.H., FP6 ANR-06-PATHO-00701 ERA-NET and Actions Concertées Inter-Pasteuriennes (ACIP) (2006) to D.N.S., NIH R01DK063041 to D.E.B., NIH CA082312 to D.S.M., NIH AI070803 and AI081037 to J.V.S., CSIR project, India (No. 37(1640)/14/EMR –II) to A.K.M., and VIB and FWO (grants: G033717N and 12H8416N) to K.M. and H.R., This paper is dedicated to the memory of our friend, collaborator, and co-author Dr. Andre Dubois, a great scientist who contributed importantly both intellectually and materially to this project. We thank S. Michopoulos and G. Mantzaris for H. pylori clinical isolates and Ö. Furberg (NoPolo.se), N. Ulander (softplanbangkok.com), S. Lindström, and M. Borén for the digital movie, tech, art, and figure work, respectively., Vrije Universiteit Brussel, Basic (bio-) Medical Sciences, Structural Biology Brussels, and Department of Bio-engineering Sciences

Subjects
0301 basic medicine, MESH: Hydrogen-Ion Concentration, Gastric acidity, MESH: Helicobacter Infections/pathology, MESH: Helicobacter pylori/physiology, Disease, adaptation, Bacterial Adhesion, polymorphism, acid responsiveness, MESH: Bacterial Adhesion, Bacterial, Hydrogen-Ion Concentration, gastric acidity, Adhesins, 3. Good health, Cell and molecular biology, medicine.anatomical_structure, Infectious Diseases, MESH: Gastric Mucosa/microbiology, Medical Microbiology, 030106 microbiology, Immunology, Digestive Diseases - (Peptic Ulcer), Biology, blood group antigen-binding adhesion, Microbiology, Helicobacter Infections, diversity, Vaccine Related, 03 medical and health sciences, Virology, ABO blood group system, Biodefense, Gastric mucosa, medicine, MESH: Helicobacter Infections/microbiology, multimerization, Adhesins, Bacterial, subpopulations, Helicobacter pylori, Prevention, gastric cancer, MESH: Adhesins, Bacterial/metabolism, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, MESH: Gastric Mucosa/pathology, Bacterial adhesin, Chronic infection, 030104 developmental biology, Emerging Infectious Diseases, Gastric Mucosa, Parasitology, Digestive Diseases
Abstract

The BabA adhesin mediates high-affinity binding of Helicobacter pylori to the ABO blood group antigen-glycosylated gastric mucosa. Here we show that BabA is acid responsive-binding is reduced at low pH and restored by acid neutralization. Acid responsiveness differs among strains; often correlates with different intragastric regions and evolves during chronic infection and disease progression; and depends on pH sensor sequences in BabA and on pH reversible formation of high-affinity binding BabA multimers. We propose that BabA's extraordinary reversible acid responsiveness enables tight mucosal bacterial adherence while also allowing an effective escape from epithelial cells and mucus that are shed into the acidic bactericidal lumen andthat bio-selection and changes in BabA bindingproperties through mutation and recombination with babA-related genes are selected by differencesamong individuals and by changes in gastric acidity over time. These processes generate diverse H.pylori subpopulations, in which BabA's adaptive evolution contributes to H.pylori persistence and overt gastric disease.

Published
2017