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Zhang B, Anderson PSL. Investigation of the rate-mediated form-function relationship in biological puncture. Sci Rep 2023; 13:12097. [PMID: 37495672 PMCID: PMC10372153 DOI: 10.1038/s41598-023-39092-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/20/2023] [Indexed: 07/28/2023] Open
Abstract
Puncture is a vital mechanism for survival in a wide range of organisms across phyla, serving biological functions such as prey capture, defense, and reproduction. Understanding how the shape of the puncture tool affects its functional performance is crucial to uncovering the mechanics underlying the diversity and evolution of puncture-based systems. However, such form-function relationships are often complicated by the dynamic nature of living systems. Puncture systems in particular operate over a wide range of speeds to penetrate biological tissues. Current studies on puncture biomechanics lack systematic characterization of the complex, rate-mediated, interaction between tool and material across this dynamic range. To fill this knowledge gap, we establish a highly controlled experimental framework for dynamic puncture to investigate the relationship between the puncture performance (characterized by the depth of puncture) and the tool sharpness (characterized by the cusp angle) across a wide range of bio-relevant puncture speeds (from quasi-static to [Formula: see text] 50 m/s). Our results show that the sensitivity of puncture performance to variations in tool sharpness reduces at higher puncture speeds. This trend is likely due to rate-based viscoelastic and inertial effects arising from how materials respond to dynamic loads. The rate-dependent form-function relationship has important biological implications: While passive/low-speed puncture organisms likely rely heavily on sharp puncture tools to successfully penetrate and maintain functionalities, higher-speed puncture systems may allow for greater variability in puncture tool shape due to the relatively geometric-insensitive puncture performance, allowing for higher adaptability during the evolutionary process to other mechanical factors.
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Affiliation(s)
- Bingyang Zhang
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Philip S L Anderson
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
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2
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Siebert HC, Eckert T, Bhunia A, Klatte N, Mohri M, Siebert S, Kozarova A, Hudson JW, Zhang R, Zhang N, Li L, Gousias K, Kanakis D, Yan M, Jiménez-Barbero J, Kožár T, Nifantiev NE, Vollmer C, Brandenburger T, Kindgen-Milles D, Haak T, Petridis AK. Blood pH Analysis in Combination with Molecular Medical Tools in Relation to COVID-19 Symptoms. Biomedicines 2023; 11:biomedicines11051421. [PMID: 37239092 DOI: 10.3390/biomedicines11051421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The global outbreak of SARS-CoV-2/COVID-19 provided the stage to accumulate an enormous biomedical data set and an opportunity as well as a challenge to test new concepts and strategies to combat the pandemic. New research and molecular medical protocols may be deployed in different scientific fields, e.g., glycobiology, nanopharmacology, or nanomedicine. We correlated clinical biomedical data derived from patients in intensive care units with structural biology and biophysical data from NMR and/or CAMM (computer-aided molecular modeling). Consequently, new diagnostic and therapeutic approaches against SARS-CoV-2 were evaluated. Specifically, we tested the suitability of incretin mimetics with one or two pH-sensitive amino acid residues as potential drugs to prevent or cure long-COVID symptoms. Blood pH values in correlation with temperature alterations in patient bodies were of clinical importance. The effects of biophysical parameters such as temperature and pH value variation in relation to physical-chemical membrane properties (e.g., glycosylation state, affinity of certain amino acid sequences to sialic acids as well as other carbohydrate residues and lipid structures) provided helpful hints in identifying a potential Achilles heel against long COVID. In silico CAMM methods and in vitro NMR experiments (including 31P NMR measurements) were applied to analyze the structural behavior of incretin mimetics and SARS-CoV fusion peptides interacting with dodecylphosphocholine (DPC) micelles. These supramolecular complexes were analyzed under physiological conditions by 1H and 31P NMR techniques. We were able to observe characteristic interaction states of incretin mimetics, SARS-CoV fusion peptides and DPC membranes. Novel interaction profiles (indicated, e.g., by 31P NMR signal splitting) were detected. Furthermore, we evaluated GM1 gangliosides and sialic acid-coated silica nanoparticles in complex with DPC micelles in order to create a simple virus host cell membrane model. This is a first step in exploring the structure-function relationship between the SARS-CoV-2 spike protein and incretin mimetics with conserved pH-sensitive histidine residues in their carbohydrate recognition domains as found in galectins. The applied methods were effective in identifying peptide sequences as well as certain carbohydrate moieties with the potential to protect the blood-brain barrier (BBB). These clinically relevant observations on low blood pH values in fatal COVID-19 cases open routes for new therapeutic approaches, especially against long-COVID symptoms.
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Affiliation(s)
- Hans-Christian Siebert
- RI-B-NT-Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Thomas Eckert
- Department of Chemistry and Biology, University of Applied Sciences Fresenius, Limburger Str. 2, 65510 Idstein, Germany
- RISCC-Research Institute for Scientific Computing and Consulting, Ludwig-Schunk-Str. 15, 35452 Heuchelheim, Germany
- Institut für Veterinärphysiologie und Biochemie, Fachbereich Veterinärmedizin, Justus-Liebig Universität Gießen, Frankfurter Str. 100, 35392 Gießen, Germany
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Nele Klatte
- Department of Chemistry and Biology, University of Applied Sciences Fresenius, Limburger Str. 2, 65510 Idstein, Germany
| | - Marzieh Mohri
- RI-B-NT-Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Simone Siebert
- RI-B-NT-Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Anna Kozarova
- Department of Biomedical Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - John W Hudson
- Department of Biomedical Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Ruiyan Zhang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Ning Zhang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Lan Li
- Klinik für Neurochirurgie, Alfried Krupp Krankenhaus, Rüttenscheid, Alfried-Krupp-Straße 21, 45131 Essen, Germany
| | - Konstantinos Gousias
- Klinik für Neurochirurgie, Klinikum Lünen, St.-Marien-Hospital, Akad. Lehrkrankenhaus der Westfälische Wilhelms-Universität Münster, 44534 Lünen, Germany
| | - Dimitrios Kanakis
- Institute of Pathology, University of Nicosia Medical School, 2408 Egkomi, Cyprus
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | | | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Jesenná 5, 04001 Košice, Slovakia
| | - Nikolay E Nifantiev
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia
| | - Christian Vollmer
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Timo Brandenburger
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Detlef Kindgen-Milles
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Thomas Haak
- Diabetes Klinik Bad Mergentheim, Theodor-Klotzbücher-Str. 12, 97980 Bad Mergentheim, Germany
| | - Athanasios K Petridis
- Medical School, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
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3
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Liu B, Zhang N, Yang J, Sun W, Zhang R, Zheng X, Wang Z, Siebert HC, Han J. Preparation, Characterization, Evaluation of Neuroprotective Effect, and Related Mechanisms of Phosphatidylserine Emulsion in 5- and 12-Week Old Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1852-1864. [PMID: 35107277 DOI: 10.1021/acs.jafc.1c07403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phosphatidylserine (PS) improves learning and memory capacity. In this study, PS formulation was optimized by a response surface methodology. Moreover, we found that PS not only functions as a biologically active component in food preparations but also improves the emulsion's physical stability. Our results showed that the PS emulsions are characterized by a smaller particle size, higher ζ-potential (negative), higher viscosity, and lower surface tension and centrifugal stability constants than the emulsion without PS. Furthermore, we explored the neuroprotective effects of PS emulsion and its underlying mechanisms. Treatment with 2% (w/w) PS emulsion for three months enhanced spatial learning and memory in 5- and 12-week old mice in the Morris water maze test. Western-blotting analysis displayed that the 2% (w/w) PS emulsion treated group upregulated BDNF, TrkB, PSD95, mTOR, MBP, and ErbB4 expression in the hippocampus of 5- and 12-week old mice. Reverse transcription polymerase chain reaction (RT-PCR) analysis revealed elevated Nrg-1 and ErbB4 mRNA expression in the 2% (w/w) PS emulsion treated groups, and high Nrg-1 and ErbB4 expression levels were associated with better myelination. In conclusion, we reported PS emulsions with high stability and high bioavailability. Meanwhile, 2% (w/w) PS emulsion enhances learning, memory, and myelination in mice by activating the BDNF/TrkB and Nrg-1/ErbB4 signaling.
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Affiliation(s)
- Bingyi Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Ning Zhang
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252059, China
- RI-B-NT - Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr.116, 24118 Kiel, Germany
| | - Junrong Yang
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Wei Sun
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Ruiyan Zhang
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252059, China
- RI-B-NT - Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr.116, 24118 Kiel, Germany
| | - Xuexing Zheng
- Department of Virology, School of Public Health, Shandong University, Jinan 250012, China
| | - Zhengping Wang
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252059, China
- Liaocheng High-Tech Biotechnology Co., Ltd., Liaocheng 252059, China
| | - Hans-Christian Siebert
- RI-B-NT - Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr.116, 24118 Kiel, Germany
| | - Jun Han
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng 252059, China
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4
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Guo Q, Whipps CM, Zhai Y, Li D, Gu Z. Quantitative Insights into the Contribution of Nematocysts to the Adaptive Success of Cnidarians Based on Proteomic Analysis. BIOLOGY 2022; 11:91. [PMID: 35053089 PMCID: PMC8773148 DOI: 10.3390/biology11010091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 12/13/2022]
Abstract
Nematocysts are secretory organelles in cnidarians that play important roles in predation, defense, locomotion, and host invasion. However, the extent to which nematocysts contribute to adaptation and the mechanisms underlying nematocyst evolution are unclear. Here, we investigated the role of the nematocyst in cnidarian evolution based on eight nematocyst proteomes and 110 cnidarian transcriptomes/genomes. We detected extensive species-specific adaptive mutations in nematocyst proteins (NEMs) and evidence for decentralized evolution, in which most evolutionary events involved non-core NEMs, reflecting the rapid diversification of NEMs in cnidarians. Moreover, there was a 33-55 million year macroevolutionary lag between nematocyst evolution and the main phases of cnidarian diversification, suggesting that the nematocyst can act as a driving force in evolution. Quantitative analysis revealed an excess of adaptive changes in NEMs and enrichment for positively selected conserved NEMs. Together, these findings suggest that nematocysts may be key to the adaptive success of cnidarians and provide a reference for quantitative analyses of the roles of phenotypic novelties in adaptation.
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Affiliation(s)
- Qingxiang Guo
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Christopher M Whipps
- SUNY-ESF, College of Environmental Science and Forestry, State University of New York, 246 Illick Hall, 1 Forestry Drive, Syracuse, NY 13210, USA
| | - Yanhua Zhai
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Dan Li
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
| | - Zemao Gu
- Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention, Wuhan 430070, China
- Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Wuhan 430070, China
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Eckert T, von Cosel J, Kamps B, Siebert HC, Zhang R, Zhang N, Gousias K, Petridis AK, Kanakis D, Falahati K. Evidence for Quantum Chemical Effects in Receptor-Ligand Binding Between Integrin and Collagen Fragments - A Computational Investigation With an Impact on Tissue Repair, Neurooncolgy and Glycobiology. Front Mol Biosci 2021; 8:756701. [PMID: 34869589 PMCID: PMC8637888 DOI: 10.3389/fmolb.2021.756701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/22/2021] [Indexed: 11/23/2022] Open
Abstract
The collagen-integrin interactions are mediated by the doubly charged Mg2+ cation. In nature this cation seems to have the optimal binding strength to stabilize this complex. It is essential that the binding is not too weak so that the complex becomes unstable, however, it is also of importance that the ligand-receptor binding is still labile enough so that the ligand can separate from the receptor in a suited environment. In the case of crystal growing for experimentally useful integrin-collagen fragment complexes it turned out that Co2+ cations are ideal mediators to form stable complexes for such experiments. Although, one can argue that Co2+ is in this context an artificial cation, however, it is now of special interest to test the impact of this cation in cell-culture experiments focusing on integrin-ligand interactions. In order to examine, in particular, the role cobalt ions we have studied a Co2+ based model system using quantum chemical calculations. Thereby, we have shown that hybrid and long-range corrected functional, which are approximations provide already a sufficient level of accuracy. It is of interest to study a potential impact of cations on the binding of collagen-fragments including collagens from various species because different integrins have numerous biological functions (e.g. Integrin - NCAM (Neural cell adhesion molecule) interactions) and are triggered by intact and degraded collagen fragments. Since integrin-carbohydrate interactions play a key role when bio-medical problems such as tumor cell adhesion and virus-host cell infections have to be addressed on a sub-molecular level it is essential to understand the interactions with heavy-metal ions also at the sub-atomic level. Our findings open new routes, especially, in the fields of tissue repair and neuro-oncology for example for cell-culture experiments with different ions. Since Co2+ ions seem to bind stronger to integrin than Mg2+ ions it should be feasible to exchange these cations in suited tumor tissues although different cations are present in other metalloproteins which are active in such tissues. Various staining methods can be applied to document the interactions of integrins with carbohydrate chains and other target structures. Thereby, it is possible to study a potential impact of these interactions on biological functions. It was therefore necessary to figure out first which histological-glycobiological experimental settings of tumor cells are suited for our purpose. Since the interactions of several metalloproteins (integrin, ADAM12) with polysialic acid and the HNK-1 epitope play a crucial role in tumor tissues selected staining methods are proper tools to obtain essential information about the impact of the metal ions under study.
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Affiliation(s)
- Thomas Eckert
- RISCC Research Institute for Scientific Computing and Consulting, Heuchelheim, Germany
- Institut für Veterinärphysiologie und Biochemie, Fachbereich Veterinärmedizin, Justus-Liebig- Universität Gießen, Gießen, Germany
- Fachbereich Biologie und Chemie, Hochschule Fresenius University of Applied Sciences, Idstein, Germany
| | - Jan von Cosel
- RISCC Research Institute for Scientific Computing and Consulting, Heuchelheim, Germany
| | - Benedict Kamps
- RISCC Research Institute for Scientific Computing and Consulting, Heuchelheim, Germany
- Fachbereich Biologie und Chemie, Hochschule Fresenius University of Applied Sciences, Idstein, Germany
| | | | - Ruiyan Zhang
- RI-B-NT Research Institute of Bioinformatics and Nanotechnology, Kiel, Germany
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng, China
| | - Ning Zhang
- RI-B-NT Research Institute of Bioinformatics and Nanotechnology, Kiel, Germany
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng, China
| | - Konstantinos Gousias
- Klinik für Neurochirurgie, Klinikum Lünen, St.-Marien-Hospital, Akad. Lehrkrankenhaus der Westf. Wilhelms-Universität Münster, Lünen, Germany
| | | | - Dimitrios Kanakis
- Institute of Pathology, University of Nicosia Medical School, Nicosia, Cyprus
| | - Konstantin Falahati
- RISCC Research Institute for Scientific Computing and Consulting, Heuchelheim, Germany
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Efficacy of Chondroprotective Food Supplements Based on Collagen Hydrolysate and Compounds Isolated from Marine Organisms. Mar Drugs 2021; 19:md19100542. [PMID: 34677442 PMCID: PMC8541357 DOI: 10.3390/md19100542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Osteoarthritis belongs to the most common joint diseases in humans and animals and shows increased incidence in older patients. The bioactivities of collagen hydrolysates, sulfated glucosamine and a special fatty acid enriched dog-food were tested in a dog patient study of 52 dogs as potential therapeutic treatment options in early osteoarthritis. Biophysical, biochemical, cell biological and molecular modeling methods support that these well-defined substances may act as effective nutraceuticals. Importantly, the applied collagen hydrolysates as well as sulfated glucosamine residues from marine organisms were strongly supported by both an animal model and molecular modeling of intermolecular interactions. Molecular modeling of predicted interaction dynamics was evaluated for the receptor proteins MMP-3 and ADAMTS-5. These proteins play a prominent role in the maintenance of cartilage health as well as innate and adapted immunity. Nutraceutical data were generated in a veterinary clinical study focusing on mobility and agility. Specifically, key clinical parameter (MMP-3 and TIMP-1) were obtained from blood probes of German shepherd dogs with early osteoarthritis symptoms fed with collagen hydrolysates. Collagen hydrolysate, a chondroprotective food supplement was examined by high resolution NMR experiments. Molecular modeling simulations were used to further characterize the interaction potency of collagen fragments and glucosamines with protein receptor structures. Potential beneficial effects of collagen hydrolysates, sulfated glycans (i.e., sulfated glucosamine from crabs and mussels) and lipids, especially, eicosapentaenoic acid (extracted from fish oil) on biochemical and physiological processes are discussed here in the context of human and veterinary medicine.
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Ling AJW, Chang LS, Babji AS, Latip J, Koketsu M, Lim SJ. Review of sialic acid's biochemistry, sources, extraction and functions with special reference to edible bird's nest. Food Chem 2021; 367:130755. [PMID: 34390910 DOI: 10.1016/j.foodchem.2021.130755] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 07/24/2021] [Accepted: 08/02/2021] [Indexed: 12/12/2022]
Abstract
Sialic acids are a group of nine-carbon α-keto acids. Sialic acid exists in more than 50 forms, with the natural types discovered as N-acetylneuraminic acid (Neu5Ac), deaminoneuraminic acid (2-keto-3-deoxy-nonulononic acid or Kdn), and N-glycolylneuraminic acid (Neu5Gc). Sialic acid level varies depending on the source, where edible bird's nest (EBN), predominantly Neu5Ac, is among the major sources of sialic acid. Due to its high nutritive value and complexity, sialic acid has been studied extensively through acid, aqueous, and enzymatic extraction. Although detection by chromatographic methods or mass spectrometry is common, the isolation and recovery work remained limited. Sialic acid is well-recognised for its bioactivities, including brain and cognition development, immune-enhancing, anti-hypertensive, anticancer, and skin whitening properties. Therefore, sialic acid can be used as a functional ingredient in the various industries. This paper reviews the current trend in the biochemistry, sources, extraction, and functions of sialic acids with special reference to EBN.
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Affiliation(s)
- Alvin Jin Wei Ling
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Lee Sin Chang
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Abdul Salam Babji
- Innovation Centre for Confectionery Technology (MANIS), Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia; Centre for Innovation and Technology Transfer (INOVASI@UKM), Chancellery, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Jalifah Latip
- Department of Chemistry, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
| | - Mamoru Koketsu
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan.
| | - Seng Joe Lim
- Department of Food Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia; Innovation Centre for Confectionery Technology (MANIS), Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
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8
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Moneer J, Siebert S, Krebs S, Cazet J, Prexl A, Pan Q, Juliano C, Böttger A. Differential gene regulation in DAPT-treated Hydra reveals candidate direct Notch signalling targets. J Cell Sci 2021; 134:jcs258768. [PMID: 34346482 PMCID: PMC8353520 DOI: 10.1242/jcs.258768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/03/2021] [Indexed: 11/20/2022] Open
Abstract
In Hydra, Notch inhibition causes defects in head patterning and prevents differentiation of proliferating nematocyte progenitor cells into mature nematocytes. To understand the molecular mechanisms by which the Notch pathway regulates these processes, we performed RNA-seq and identified genes that are differentially regulated in response to 48 h of treating the animals with the Notch inhibitor DAPT. To identify candidate direct regulators of Notch signalling, we profiled gene expression changes that occur during subsequent restoration of Notch activity and performed promoter analyses to identify RBPJ transcription factor-binding sites in the regulatory regions of Notch-responsive genes. Interrogating the available single-cell sequencing data set revealed the gene expression patterns of Notch-regulated Hydra genes. Through these analyses, a comprehensive picture of the molecular pathways regulated by Notch signalling in head patterning and in interstitial cell differentiation in Hydra emerged. As prime candidates for direct Notch target genes, in addition to Hydra (Hy)Hes, we suggest Sp5 and HyAlx. They rapidly recovered their expression levels after DAPT removal and possess Notch-responsive RBPJ transcription factor-binding sites in their regulatory regions.
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Affiliation(s)
- Jasmin Moneer
- Ludwig Maximilians-University Munich, Germany, Biocenter, 82152 Planegg-Martinsried, Großhaderner Str. 2, Germany
| | - Stefan Siebert
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Stefan Krebs
- Ludwig-Maximilians-University Munich, Gene Center Munich, Feodor-Lynen-Str. 25 81377 Munich, Germany
| | - Jack Cazet
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Andrea Prexl
- Ludwig Maximilians-University Munich, Germany, Biocenter, 82152 Planegg-Martinsried, Großhaderner Str. 2, Germany
| | - Qin Pan
- Ludwig Maximilians-University Munich, Germany, Biocenter, 82152 Planegg-Martinsried, Großhaderner Str. 2, Germany
| | - Celina Juliano
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Angelika Böttger
- Ludwig Maximilians-University Munich, Germany, Biocenter, 82152 Planegg-Martinsried, Großhaderner Str. 2, Germany
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9
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Jin L, Liu C, Zhang N, Zhang R, Yan M, Bhunia A, Zhang Q, Liu M, Han J, Siebert HC. Attenuation of Human Lysozyme Amyloid Fibrillation by ACE Inhibitor Captopril: A Combined Spectroscopy, Microscopy, Cytotoxicity, and Docking Study. Biomacromolecules 2021; 22:1910-1920. [PMID: 33844512 DOI: 10.1021/acs.biomac.0c01802] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Misfolding proteins could form oligomers or amyloid fibers, which can cause a variety of amyloid-associated diseases. Thus, the inhibition of protein misfolding and fibrillation is a promising way to prevent and treat these diseases. Captopril (CAP) is an angiotensin-converting enzyme inhibitor (ACEI) that is widely used to treat diseases such as hypertension and heart failure. In this study, we found that CAP inhibits human lysozyme (HL) fibrillation through the combination techniques of biophysics and biochemistry. The data obtained by thioflavin-T (ThT) and Congo red (CR) assays showed that CAP hindered the aggregation of HL amyloid fibrils by reducing the β-sheet structure of HL amyloid, with an IC50 value of 34.75 ± 1.23 μM. Meanwhile, the particle size of HL amyloid decreased sharply in a concentration-dependent approach after CAP treatment. According to the visualization of atomic force microscopy (AFM) and transmission electron microscopy (TEM), we verified that in the presence of CAP, the needle-like fibers of HL amyloid were significantly reduced. In addition, CAP incubation dramatically improved the cell survival rate exposed to HL fibers. Our studies also revealed that CAP could form hydrogen bonds with amino acid residues of Glu 35 and Ala 108 in the binding pocket of HL, which help in maintaining the α-helical structure of HL and then prevent the formation of amyloid fibrillation. It can be concluded that CAP has antiamyloidogenic activity and a protective effect on HL amyloid cytotoxicity.
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Affiliation(s)
- Li Jin
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Chunhong Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Ning Zhang
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Ruiyan Zhang
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, 1 University Avenue, Lowell, Massachusetts 01854, United States
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), 700054 Kolkata, India
| | - Qinxiu Zhang
- School of Pharmaceutical Sciences, Shandong University, 44 West Wenhua Road, Jinan, Shandong 250012, China
| | - Min Liu
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Jun Han
- Institute of Biopharmaceutical Research, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Hans-Christian Siebert
- RI-B-NT Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148 Kiel, Germany
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