Editor’s Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

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35 pages, 1443 KiB  
Review
The Pathophysiology and Treatment of Essential Tremor: The Role of Adenosine and Dopamine Receptors in Animal Models
by Barbara Kosmowska and Jadwiga Wardas
Biomolecules 2021, 11(12), 1813; https://doi.org/10.3390/biom11121813 - 2 Dec 2021
Cited by 15 | Viewed by 7663
Abstract
Essential tremor (ET) is one of the most common neurological disorders that often affects people in the prime of their lives, leading to a significant reduction in their quality of life, gradually making them unable to independently perform the simplest activities. Here we [...] Read more.
Essential tremor (ET) is one of the most common neurological disorders that often affects people in the prime of their lives, leading to a significant reduction in their quality of life, gradually making them unable to independently perform the simplest activities. Here we show that current ET pharmacotherapy often does not sufficiently alleviate disease symptoms and is completely ineffective in more than 30% of patients. At present, deep brain stimulation of the motor thalamus is the most effective ET treatment. However, like any brain surgery, it can cause many undesirable side effects; thus, it is only performed in patients with an advanced disease who are not responsive to drugs. Therefore, it seems extremely important to look for new strategies for treating ET. The purpose of this review is to summarize the current knowledge on the pathomechanism of ET based on studies in animal models of the disease, as well as to present and discuss the results of research available to date on various substances affecting dopamine (mainly D3) or adenosine A1 receptors, which, due to their ability to modulate harmaline-induced tremor, may provide the basis for the development of new potential therapies for ET in the future. Full article
(This article belongs to the Collection Feature Papers in Section 'Molecular Medicine')
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16 pages, 1437 KiB  
Review
The Use of Fluorescent Anti-CEA Antibodies to Label, Resect and Treat Cancers: A Review
by Michael A. Turner, Thinzar M. Lwin, Siamak Amirfakhri, Hiroto Nishino, Robert M. Hoffman, Paul J. Yazaki and Michael Bouvet
Biomolecules 2021, 11(12), 1819; https://doi.org/10.3390/biom11121819 - 2 Dec 2021
Cited by 19 | Viewed by 3498
Abstract
A major barrier to the diagnosis and effective treatment of solid-tumor cancers is the difficulty in detection and visualization of tumor margins in primary and metastatic disease. The use of fluorescence can augment the surgeon’s ability to detect cancer and aid in its [...] Read more.
A major barrier to the diagnosis and effective treatment of solid-tumor cancers is the difficulty in detection and visualization of tumor margins in primary and metastatic disease. The use of fluorescence can augment the surgeon’s ability to detect cancer and aid in its resection. Several cancer types express carcinoembryonic antigen (CEA) including colorectal, pancreatic and gastric cancer. Antibodies to CEA have been developed and tagged with near-infrared fluorescent dyes. This review article surveyed the use of CEA antibodies conjugated to fluorescent probes for in vivo studies since 1990. PubMed and Google Scholar databases were queried, and 900 titles and abstracts were screened. Fifty-nine entries were identified as possibly meeting inclusion/exclusion criteria and were reviewed in full. Forty articles were included in the review and their citations were screened for additional entries. A total of 44 articles were included in the final review. The use of fluorescent anti-CEA antibodies has been shown to improve detection and resection of tumors in both murine models and clinically. The cumulative results indicate that fluorescent-conjugated anti-CEA antibodies have important potential to improve cancer diagnosis and surgery. In an emerging technology, anti-CEA fluorescent antibodies have also been successfully used for photoimmunotherapy treatment for cancer. Full article
(This article belongs to the Special Issue Feature Paper from Biomolecules Journal Reviewers)
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13 pages, 3905 KiB  
Article
Hydrogen Bond Arrangement Is Shown to Differ in Coexisting Phases of Aqueous Two-Phase Systems
by Pedro P. Madeira, Amber R. Titus, Luisa A. Ferreira, Alexander I. Belgovskiy, Elizabeth K. Mann, Jay Adin Mann, Jr., William V. Meyer, Anthony E. Smart, Vladimir N. Uversky and Boris Y. Zaslavsky
Biomolecules 2021, 11(12), 1787; https://doi.org/10.3390/biom11121787 - 30 Nov 2021
Cited by 8 | Viewed by 2494
Abstract
Analysis by attenuated total reflection–Fourier transform infrared spectroscopy shows that each coexisting phase in aqueous two-phase systems has a different arrangement of hydrogen bonds. Specific arrangements vary for systems formed by different solutes. The hydrogen bond arrangement is shown to correlate with differences [...] Read more.
Analysis by attenuated total reflection–Fourier transform infrared spectroscopy shows that each coexisting phase in aqueous two-phase systems has a different arrangement of hydrogen bonds. Specific arrangements vary for systems formed by different solutes. The hydrogen bond arrangement is shown to correlate with differences in hydrophobic and electrostatic properties of the different phases of five specific systems, four formed by two polymers and one by a single polymer and salt. The results presented here suggest that the arrangement of hydrogen bonds may be an important factor in phase separation. Full article
(This article belongs to the Special Issue The Physicochemical Basis of Intracellular Phase Separation)
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28 pages, 6362 KiB  
Article
A Combination of Structural, Genetic, Phenotypic and Enzymatic Analyses Reveals the Importance of a Predicted Fucosyltransferase to Protein O-Glycosylation in the Bacteroidetes
by Markus B. Tomek, Bettina Janesch, Matthias L. Braun, Manfred Taschner, Rudolf Figl, Clemens Grünwald-Gruber, Michael J. Coyne, Markus Blaukopf, Friedrich Altmann, Paul Kosma, Hanspeter Kählig, Laurie E. Comstock and Christina Schäffer
Biomolecules 2021, 11(12), 1795; https://doi.org/10.3390/biom11121795 - 30 Nov 2021
Cited by 9 | Viewed by 3558
Abstract
Diverse members of the Bacteroidetes phylum have general protein O-glycosylation systems that are essential for processes such as host colonization and pathogenesis. Here, we analyzed the function of a putative fucosyltransferase (FucT) family that is widely encoded in Bacteroidetes protein O-glycosylation [...] Read more.
Diverse members of the Bacteroidetes phylum have general protein O-glycosylation systems that are essential for processes such as host colonization and pathogenesis. Here, we analyzed the function of a putative fucosyltransferase (FucT) family that is widely encoded in Bacteroidetes protein O-glycosylation genetic loci. We studied the FucT orthologs of three Bacteroidetes species—Tannerella forsythia, Bacteroides fragilis, and Pedobacter heparinus. To identify the linkage created by the FucT of B. fragilis, we elucidated the full structure of its nine-sugar O-glycan and found that l-fucose is linked β1,4 to glucose. Of the two fucose residues in the T. forsythia O-glycan, the fucose linked to the reducing-end galactose was shown by mutational analysis to be l-fucose. Despite the transfer of l-fucose to distinct hexose sugars in the B. fragilis and T. forsythia O-glycans, the FucT orthologs from B. fragilis, T. forsythia, and P. heparinus each cross-complement the B. fragilis ΔBF4306 and T. forsythia ΔTanf_01305 FucT mutants. In vitro enzymatic analyses showed relaxed acceptor specificity of the three enzymes, transferring l-fucose to various pNP-α-hexoses. Further, glycan structural analysis together with fucosidase assays indicated that the T. forsythia FucT links l-fucose α1,6 to galactose. Given the biological importance of fucosylated carbohydrates, these FucTs are promising candidates for synthetic glycobiology. Full article
(This article belongs to the Special Issue Glycosylation—The Most Diverse Post-Translational Modification)
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21 pages, 1857 KiB  
Review
New Insights into the Role of Cysteine Cathepsins in Neuroinflammation
by Anja Pišlar, Lara Bolčina and Janko Kos
Biomolecules 2021, 11(12), 1796; https://doi.org/10.3390/biom11121796 - 30 Nov 2021
Cited by 15 | Viewed by 4153
Abstract
Neuroinflammation, which is mediated by microglia and astrocytes, is associated with the progression of neurodegenerative diseases. Increasing evidence shows that activated microglia induce the expression and secretion of various lysosomal cathepsins, particularly during the early stage of neuroinflammation. This trigger signaling cascade that [...] Read more.
Neuroinflammation, which is mediated by microglia and astrocytes, is associated with the progression of neurodegenerative diseases. Increasing evidence shows that activated microglia induce the expression and secretion of various lysosomal cathepsins, particularly during the early stage of neuroinflammation. This trigger signaling cascade that aggravate neurodegeneration. To date, most research on neuroinflammation has focused on the role of cysteine cathepsins, the largest cathepsin family. Cysteine cathepsins are primarily responsible for protein degradation in lysosomes; however, they also play a role in regulating a number of other important physiological and pathological processes. This review focuses on the functional roles of cysteine cathepsins in the central nervous system during neuroinflammation, with an emphasis on their roles in the polarization of microglia and neuroinflammation signaling, which in turn causes neuronal death and thus neurodegeneration. Full article
(This article belongs to the Special Issue Molecular and Cellular Mechanisms of Neuroinflammation)
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18 pages, 2536 KiB  
Article
Structural and Functional Characterization of Legionella pneumophila Effector MavL
by Kevin Voth, Shivani Pasricha, Ivy Yeuk Wah Chung, Rachelia R. Wibawa, Engku Nuraishah Huda E. Zainudin, Elizabeth L. Hartland and Miroslaw Cygler
Biomolecules 2021, 11(12), 1802; https://doi.org/10.3390/biom11121802 - 30 Nov 2021
Cited by 10 | Viewed by 3411
Abstract
Legionella pneumophila is a Gram-negative intracellular pathogen that causes Legionnaires’ disease in elderly or immunocompromised individuals. This bacterium relies on the Dot/Icm (Defective in organelle trafficking/Intracellular multiplication) Type IV Secretion System (T4SS) and a large (>330) set of effector proteins to colonize the [...] Read more.
Legionella pneumophila is a Gram-negative intracellular pathogen that causes Legionnaires’ disease in elderly or immunocompromised individuals. This bacterium relies on the Dot/Icm (Defective in organelle trafficking/Intracellular multiplication) Type IV Secretion System (T4SS) and a large (>330) set of effector proteins to colonize the host cell. The structural variability of these effectors allows them to disrupt many host processes. Herein, we report the crystal structure of MavL to 2.65 Å resolution. MavL adopts an ADP-ribosyltransferase (ART) fold and contains the distinctive ligand-binding cleft of ART proteins. Indeed, MavL binds ADP-ribose with Kd of 13 µM. Structural overlay of MavL with poly-(ADP-ribose) glycohydrolases (PARGs) revealed a pair of aspartate residues in MavL that align with the catalytic glutamates in PARGs. MavL also aligns with ADP-ribose “reader” proteins (proteins that recognize ADP-ribose). Since no glycohydrolase activity was observed when incubated in the presence of ADP-ribosylated PARP1, MavL may play a role as a signaling protein that binds ADP-ribose. An interaction between MavL and the mammalian ubiquitin-conjugating enzyme UBE2Q1 was revealed by yeast two-hybrid and co-immunoprecipitation experiments. This work provides structural and molecular insights to guide biochemical studies aimed at elucidating the function of MavL. Our findings support the notion that ubiquitination and ADP-ribosylation are global modifications exploited by L. pneumophila. Full article
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12 pages, 649 KiB  
Review
Role of Intestinal Alkaline Phosphatase in Innate Immunity
by Sudha B. Singh and Henry C. Lin
Biomolecules 2021, 11(12), 1784; https://doi.org/10.3390/biom11121784 - 29 Nov 2021
Cited by 30 | Viewed by 6387
Abstract
Intestinal alkaline phosphatase (IAP) is a multi-functional protein that has been demonstrated to primarily protect the gut. The role of IAP in maintaining intestinal homeostasis is underscored by the observation that IAP expression is defective in many gastrointestinal-related disorders such as inflammatory bowel [...] Read more.
Intestinal alkaline phosphatase (IAP) is a multi-functional protein that has been demonstrated to primarily protect the gut. The role of IAP in maintaining intestinal homeostasis is underscored by the observation that IAP expression is defective in many gastrointestinal-related disorders such as inflammatory bowel disease IBD, necrotizing enterocolitis, and metabolic syndrome and that exogenous IAP supplementation improves the outcomes associated with these disorders. Additionally, studies using transgenic IAP-knock out (IAP-KO) mouse models further support the importance of the defensive role of IAP in the intestine. Supplementation of exogenous IAP and cellular overexpression of IAP have also been used in vitro to dissect out the downstream mechanisms of this protein in mammalian cell lines. Some of the innate immune functions of IAP include lipopolysaccharide (LPS) detoxification, protection of gut barrier integrity, regulation of gut microbial communities and its anti-inflammatory roles. A novel function of IAP recently identified is the induction of autophagy. Due to its critical role in the gut physiology and its excellent safety profile, IAP has been used in phase 2a clinical trials for treating conditions such as sepsis-associated acute kidney injury. Many excellent reviews discuss the role of IAP in physiology and pathophysiology and here we extend these to include recent updates on this important host defense protein and discuss its role in innate immunity via its effects on bacteria as well as on host cells. We will also discuss the relationship between IAP and autophagy and how these two pathways may act in concert to protect the gut. Full article
(This article belongs to the Special Issue Exogenous and Endogenous Alkaline Phosphatase in Health and Disease)
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25 pages, 2446 KiB  
Review
Role of Store-Operated Ca2+ Entry in the Pulmonary Vascular Remodeling Occurring in Pulmonary Arterial Hypertension
by Bastien Masson, David Montani, Marc Humbert, Véronique Capuano and Fabrice Antigny
Biomolecules 2021, 11(12), 1781; https://doi.org/10.3390/biom11121781 - 27 Nov 2021
Cited by 20 | Viewed by 4244
Abstract
Pulmonary arterial hypertension (PAH) is a severe and multifactorial disease. PAH pathogenesis mostly involves pulmonary arterial endothelial and pulmonary arterial smooth muscle cell (PASMC) dysfunction, leading to alterations in pulmonary arterial tone and distal pulmonary vessel obstruction and remodeling. Unfortunately, current PAH therapies [...] Read more.
Pulmonary arterial hypertension (PAH) is a severe and multifactorial disease. PAH pathogenesis mostly involves pulmonary arterial endothelial and pulmonary arterial smooth muscle cell (PASMC) dysfunction, leading to alterations in pulmonary arterial tone and distal pulmonary vessel obstruction and remodeling. Unfortunately, current PAH therapies are not curative, and therapeutic approaches mostly target endothelial dysfunction, while PASMC dysfunction is under investigation. In PAH, modifications in intracellular Ca2+ homoeostasis could partly explain PASMC dysfunction. One of the most crucial actors regulating Ca2+ homeostasis is store-operated Ca2+ channels, which mediate store-operated Ca2+ entry (SOCE). This review focuses on the main actors of SOCE in human and experimental PASMC, their contribution to PAH pathogenesis, and their therapeutic potential in PAH. Full article
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34 pages, 2512 KiB  
Review
The ANXA2/S100A10 Complex—Regulation of the Oncogenic Plasminogen Receptor
by Alamelu G. Bharadwaj, Emma Kempster and David M. Waisman
Biomolecules 2021, 11(12), 1772; https://doi.org/10.3390/biom11121772 - 26 Nov 2021
Cited by 19 | Viewed by 4887
Abstract
The generation of the serine protease plasmin is initiated by the binding of its zymogenic precursor, plasminogen, to cell surface receptors. The proteolytic activity of plasmin, generated at the cell surface, plays a crucial role in several physiological processes, including fibrinolysis, angiogenesis, wound [...] Read more.
The generation of the serine protease plasmin is initiated by the binding of its zymogenic precursor, plasminogen, to cell surface receptors. The proteolytic activity of plasmin, generated at the cell surface, plays a crucial role in several physiological processes, including fibrinolysis, angiogenesis, wound healing, and the invasion of cells through both the basement membrane and extracellular matrix. The seminal observation by Albert Fischer that cancer cells, but not normal cells in culture, produce large amounts of plasmin formed the basis of current-day observations that plasmin generation can be hijacked by cancer cells to allow tumor development, progression, and metastasis. Thus, the cell surface plasminogen-binding receptor proteins are critical to generating plasmin proteolytic activity at the cell surface. This review focuses on one of the twelve well-described plasminogen receptors, S100A10, which, when in complex with its regulatory partner, annexin A2 (ANXA2), forms the ANXA2/S100A10 heterotetrameric complex referred to as AIIt. We present the theme that AIIt is the quintessential cellular plasminogen receptor since it regulates the formation and the destruction of plasmin. We also introduce the term oncogenic plasminogen receptor to define those plasminogen receptors directly activated during cancer progression. We then discuss the research establishing AIIt as an oncogenic plasminogen receptor-regulated during EMT and activated by oncogenes such as SRC, RAS, HIF1α, and PML-RAR and epigenetically by DNA methylation. We further discuss the evidence derived from animal models supporting the role of S100A10 in tumor progression and oncogenesis. Lastly, we describe the potential of S100A10 as a biomarker for cancer diagnosis and prognosis. Full article
(This article belongs to the Special Issue Plasminogen, Plasminogen Receptors and Binding Mechanisms in Cancer)
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12 pages, 6838 KiB  
Article
Selective Biological Effects of Selenium-Enriched Polysaccharide (Se-Le-30) Isolated from Lentinula edodes Mycelium on Human Immune Cells
by Beata Kaleta, Aleksander Roszczyk, Michał Zych, Monika Kniotek, Radosław Zagożdżon, Marzenna Klimaszewska, Eliza Malinowska, Michał Pac and Jadwiga Turło
Biomolecules 2021, 11(12), 1777; https://doi.org/10.3390/biom11121777 - 26 Nov 2021
Cited by 18 | Viewed by 2960
Abstract
A common edible mushroom Lentinula edodes, is an important source of numerous biologically active substances, including polysaccharides, with immunomodulatory and antitumor properties. In the present work, the biological activity of the crude, homogenous (Se)-enriched fraction (named Se-Le-30), which has been isolated from L. [...] Read more.
A common edible mushroom Lentinula edodes, is an important source of numerous biologically active substances, including polysaccharides, with immunomodulatory and antitumor properties. In the present work, the biological activity of the crude, homogenous (Se)-enriched fraction (named Se-Le-30), which has been isolated from L. edodes mycelium by a modified Chihara method towards human peripheral blood mononuclear cells (PBMCs) and peripheral granulocytes, was investigated. The Se-Le-30 fraction, an analog of lentinan, significantly inhibited the proliferation of human PBMCs stimulated with anti-CD3 antibodies or allostimulated, and down-regulated the production of tumor necrosis factor (TNF)-α by CD3+ T cells. Moreover, it was found that Se-Le-30 significantly reduced the cytotoxic activity of human natural killer (NK) cells. The results suggested the selective immunosuppressive activity of this fraction, which is non-typical for mushroom derived polysaccharides. Full article
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14 pages, 1977 KiB  
Article
CRISPR/dCas9 Transcriptional Activation of Endogenous Apolipoprotein AI and Paraoxonase 1 in Enterocytes Alleviates Endothelial Cell Dysfunction
by Laura Toma, Teodora Barbălată, Gabriela M. Sanda, Loredan S. Niculescu, Anca V. Sima and Camelia S. Stancu
Biomolecules 2021, 11(12), 1769; https://doi.org/10.3390/biom11121769 - 25 Nov 2021
Cited by 4 | Viewed by 2868
Abstract
Atherosclerosis is the main cause of cardiovascular diseases with high prevalence worldwide. A promising therapeutic strategy to reverse atherosclerotic process is to improve the athero-protective potential of high-density lipoproteins (HDL). Since the small intestine is a source of HDL, we aimed to activate [...] Read more.
Atherosclerosis is the main cause of cardiovascular diseases with high prevalence worldwide. A promising therapeutic strategy to reverse atherosclerotic process is to improve the athero-protective potential of high-density lipoproteins (HDL). Since the small intestine is a source of HDL, we aimed to activate transcription of the endogenous HDL major proteins, apolipoprotein AI (ApoAI) and paraoxonase 1 (PON1), in enterocytes, and to evaluate their potential to correct the pro-inflammatory status of endothelial cells (EC). Caco-2 enterocytes were transfected with CRISPR activation plasmids targeting ApoAI or PON1, and their gene and protein expression were measured in cells and conditioned medium (CM). ATP binding cassette A1 and G8 transporters (ABCA1, ABCG8), scavenger receptor BI (SR-BI), and transcription regulators peroxisome proliferator-activated receptor γ (PPARγ), liver X receptors (LXRs), and sirtuin-1 (SIRT1) were assessed. Anti-inflammatory effects of CM from transfected enterocytes were estimated through its ability to inhibit tumor necrosis factor α (TNFα) activation of EC. Transcriptional activation of ApoAI or PON1 in enterocytes induces: (i) increase of their gene and protein expression, and secretion in CM; (ii) stimulation of ABCA1/G8 and SR-BI; (iii) upregulation of PPARγ, LXRs, and SIRT1. CM from transfected enterocytes attenuated the TNFα-induced inflammatory and oxidative stress in EC, by decreasing TNF receptor 1, monocyte chemoattractant protein-1, and p22phox. In conclusion, transcriptional activation of endogenous ApoAI or PON1 in enterocytes by CRISPR/dCas9 system is a realistic approach to stimulate biogenesis and function of major HDL proteins which can regulate cholesterol efflux transporters and reduce the inflammatory stress in activated EC. Full article
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10 pages, 3723 KiB  
Article
Planar Boronic Graphene and Nitrogenized Graphene Heterostructure for Protein Stretch and Confinement
by Xuchang Su, Zhi He, Lijun Meng, Hong Liang and Ruhong Zhou
Biomolecules 2021, 11(12), 1756; https://doi.org/10.3390/biom11121756 - 24 Nov 2021
Cited by 1 | Viewed by 2341
Abstract
Single-molecule techniques such as electron tunneling and atomic force microscopy have attracted growing interests in protein sequencing. For these methods, it is critical to refine and stabilize the protein sample to a “suitable mode” before applying a high-fidelity measurement. Here, we show that [...] Read more.
Single-molecule techniques such as electron tunneling and atomic force microscopy have attracted growing interests in protein sequencing. For these methods, it is critical to refine and stabilize the protein sample to a “suitable mode” before applying a high-fidelity measurement. Here, we show that a planar heterostructure comprising boronic graphene (BC3) and nitrogenized graphene (C3N) sandwiched stripe (BC3/C3N/BC3) is capable of the effective stretching and confinement of three types of intrinsically disordered proteins (IDPs), including amyloid-β (1–42), polyglutamine (Q42), and α-Synuclein (61–95). Our molecular dynamics simulations demonstrate that the protein molecules interact more strongly with the C3N stripe than the BC3 one, which leads to their capture, elongation, and confinement along the center C3N stripe of the heterostructure. The conformational fluctuations of IDPs are substantially reduced after being stretched. This design may serve as a platform for single-molecule protein analysis with reduced thermal noise. Full article
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16 pages, 2832 KiB  
Article
MmpA, a Conserved Membrane Protein Required for Efficient Surface Transport of Trehalose Lipids in Corynebacterineae
by Tamaryn J. Cashmore, Stephan Klatt, Rajini Brammananth, Arek K. Rainczuk, Paul K. Crellin, Malcolm J. McConville and Ross L. Coppel
Biomolecules 2021, 11(12), 1760; https://doi.org/10.3390/biom11121760 - 24 Nov 2021
Cited by 5 | Viewed by 3092
Abstract
Cell walls of bacteria of the genera Mycobacterium and Corynebacterium contain high levels of (coryno)mycolic acids. These very long chain fatty acids are synthesized on the cytoplasmic leaflet of the inner membrane (IM) prior to conjugation to the disaccharide, trehalose, and transport to [...] Read more.
Cell walls of bacteria of the genera Mycobacterium and Corynebacterium contain high levels of (coryno)mycolic acids. These very long chain fatty acids are synthesized on the cytoplasmic leaflet of the inner membrane (IM) prior to conjugation to the disaccharide, trehalose, and transport to the periplasm. Recent studies on Corynebacterium glutamicum have shown that acetylation of trehalose monohydroxycorynomycolate (hTMCM) promotes its transport across the inner membrane. Acetylation is mediated by the membrane acetyltransferase, TmaT, and is dependent on the presence of a putative methyltransferase, MtrP. Here, we identify a third protein that is required for the acetylation and membrane transport of hTMCM. Deletion of the C. glutamicum gene NCgl2761 (Rv0226c in Mycobacterium tuberculosis) abolished synthesis of acetylated hTMCM (AcTMCM), resulting in an accumulation of hTMCM in the inner membrane and reduced synthesis of trehalose dihydroxycorynomycolate (h2TDCM), a major outer membrane glycolipid. Complementation with the NCgl2761 gene, designated here as mmpA, restored the hTMCM:h2TDCM ratio. Comprehensive lipidomic analysis of the ΔtmaT, ΔmtrP and ΔmmpA mutants revealed strikingly similar global changes in overall membrane lipid composition. Our findings suggest that the acetylation and membrane transport of hTMCM is regulated by multiple proteins: MmpA, MtrP and TmaT, and that defects in this process lead to global, potentially compensatory changes in the composition of inner and outer membranes. Full article
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19 pages, 5080 KiB  
Article
Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families
by Stefania Pilati, Giulia Malacarne, David Navarro-Payá, Gabriele Tomè, Laura Riscica, Valter Cavecchia, José Tomás Matus, Claudio Moser and Enrico Blanzieri
Biomolecules 2021, 11(12), 1744; https://doi.org/10.3390/biom11121744 - 23 Nov 2021
Cited by 20 | Viewed by 5191
Abstract
The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof [...] Read more.
The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs. Full article
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22 pages, 4983 KiB  
Article
Quantitative Morphological Analysis of Filamentous Microorganisms in Cocultures and Monocultures: Aspergillus terreus and Streptomyces rimosus Warfare in Bioreactors
by Anna Ścigaczewska, Tomasz Boruta and Marcin Bizukojć
Biomolecules 2021, 11(11), 1740; https://doi.org/10.3390/biom11111740 - 22 Nov 2021
Cited by 7 | Viewed by 2388
Abstract
The aim of this study was to quantitatively characterize the morphology of the filamentous microorganisms Aspergillus terreus ATCC 20542 and Streptomyces rimosus ATCC 10970, cocultivated in stirred tank bioreactors, and to characterize their mutual influence with the use of quantitative image analysis. Three [...] Read more.
The aim of this study was to quantitatively characterize the morphology of the filamentous microorganisms Aspergillus terreus ATCC 20542 and Streptomyces rimosus ATCC 10970, cocultivated in stirred tank bioreactors, and to characterize their mutual influence with the use of quantitative image analysis. Three distinct coculture initiation strategies were applied: preculture versus preculture, spores versus spores and preculture versus preculture with time delay for one of the species. Bioreactor cocultures were accompanied by parallel monoculture controls. The results recorded for the mono- and cocultures were compared in order to investigate the effect of cocultivation on the morphological evolution of A. terreus and S. rimosus. Morphology-related observations were also confronted with the analysis of secondary metabolism. The morphology of the two studied filamentous species strictly depended on the applied coculture initiation strategy. In the cocultures initiated by the simultaneous inoculation, S. rimosus gained domination or advance over A. terreus. The latter microorganism dominated only in these experiments in which S. rimosus was introduced with a delay. Full article
(This article belongs to the Collection Feature Papers in Synthetic Biology and Bioengineering)
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20 pages, 3415 KiB  
Article
Emergence and Enhancement of Ultrasensitivity through Posttranslational Modulation of Protein Stability
by Carla M. Kumbale, Eberhard O. Voit and Qiang Zhang
Biomolecules 2021, 11(11), 1741; https://doi.org/10.3390/biom11111741 - 22 Nov 2021
Cited by 4 | Viewed by 2294
Abstract
Signal amplification in biomolecular networks converts a linear input to a steeply sigmoid output and is central to a number of cellular functions including proliferation, differentiation, homeostasis, adaptation, and biological rhythms. One canonical signal amplifying motif is zero-order ultrasensitivity that is mediated through [...] Read more.
Signal amplification in biomolecular networks converts a linear input to a steeply sigmoid output and is central to a number of cellular functions including proliferation, differentiation, homeostasis, adaptation, and biological rhythms. One canonical signal amplifying motif is zero-order ultrasensitivity that is mediated through the posttranslational modification (PTM) cycle of signaling proteins. The functionality of this signaling motif has been examined conventionally by supposing that the total amount of the protein substrates remains constant, as by the classical Koshland–Goldbeter model. However, covalent modification of signaling proteins often results in changes in their stability, which affects the abundance of the protein substrates. Here, we use mathematical models to explore the signal amplification properties in such scenarios and report some novel aspects. Our analyses indicate that PTM-induced protein stabilization brings the enzymes closer to saturation. As a result, ultrasensitivity may emerge or is greatly enhanced, with a steeper sigmoidal response, higher magnitude, and generally longer response time. In cases where PTM destabilizes the protein, ultrasensitivity can be regained through changes in the activities of the involved enzymes or from increased protein synthesis. Importantly, ultrasensitivity is not limited to modified or unmodified protein substrates—when protein turnover is considered, the total free protein substrate can also exhibit ultrasensitivity under several conditions. When full enzymatic reactions are used instead of Michaelis–Menten kinetics for the modeling, the total free protein substrate can even exhibit nonmonotonic dose–response patterns. It is conceivable that cells use inducible protein stabilization as a strategy in the signaling network to boost signal amplification while saving energy by keeping the protein substrate levels low at basal conditions. Full article
(This article belongs to the Special Issue Computational Approaches for the Study of Biomolecular Networks)
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18 pages, 2459 KiB  
Article
β-Dystroglycan Restoration and Pathology Progression in the Dystrophic mdx Mouse: Outcome and Implication of a Clinically Oriented Study with a Novel Oral Dasatinib Formulation
by Paola Mantuano, Brigida Boccanegra, Elena Conte, Michela De Bellis, Santa Cirmi, Francesca Sanarica, Ornella Cappellari, Ilaria Arduino, Annalisa Cutrignelli, Angela Assunta Lopedota, Antonietta Mele, Nunzio Denora and Annamaria De Luca
Biomolecules 2021, 11(11), 1742; https://doi.org/10.3390/biom11111742 - 22 Nov 2021
Cited by 16 | Viewed by 3333
Abstract
ROS-activated cSrc tyrosine kinase (TK) promotes the degradation of β-dystroglycan (β-DG), a dystrophin-glycoprotein complex component, which may reinforce damaging signals in Duchenne muscular dystrophy (DMD). Therefore, cSrc-TK represents a promising therapeutic target. In mdx mice, a 4-week subcutaneous treatment with dasatinib (DAS), a [...] Read more.
ROS-activated cSrc tyrosine kinase (TK) promotes the degradation of β-dystroglycan (β-DG), a dystrophin-glycoprotein complex component, which may reinforce damaging signals in Duchenne muscular dystrophy (DMD). Therefore, cSrc-TK represents a promising therapeutic target. In mdx mice, a 4-week subcutaneous treatment with dasatinib (DAS), a pan-Src-TKs inhibitor approved as anti-leukemic agent, increased muscle β-DG, with minimal amelioration of morphofunctional indices. To address possible dose/pharmacokinetic (PK) issues, a new oral DAS/hydroxypropyl(HP)-β-cyclodextrin(CD) complex was developed and chronically administered to mdx mice. The aim was to better assess the role of β-DG in pathology progression, meanwhile confirming DAS mechanism of action over the long-term, along with its efficacy and tolerability. The 4-week old mdx mice underwent a 12-week treatment with DAS/HP-β-CD10% dissolved in drinking water, at 10 or 20 mg/kg/day. The outcome was evaluated via in vivo/ex vivo disease-relevant readouts. Oral DAS/HP-β-CD efficiently distributed in mdx mice plasma and tissues in a dose-related fashion. The new DAS formulation confirmed its main upstream mechanism of action, by reducing β-DG phosphorylation and restoring its levels dose-dependently in both diaphragm and gastrocnemius muscle. However, it modestly improved in vivo neuromuscular function, ex vivo muscle force, and histopathology, although the partial recovery of muscle elasticity and the decrease of CK and LDH plasma levels suggest an increased sarcolemmal stability of dystrophic muscles. Our clinically oriented study supports the interest in this new, pediatric-suitable DAS formulation for proper exposure and safety and for enhancing β-DG expression. This latter mechanism is, however, not sufficient by itself to impact on pathology progression. In-depth analyses will be dedicated to elucidating the mechanism limiting DAS effectiveness in dystrophic settings, meanwhile assessing its potential synergy with dystrophin-based molecular therapies. Full article
(This article belongs to the Special Issue Molecular Basis of Neuromuscular Diseases)
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14 pages, 2047 KiB  
Article
Opposite Effects of Chronic Central Leptin Infusion on Activation of Insulin Signaling Pathways in Adipose Tissue and Liver Are Related to Changes in the Inflammatory Environment
by Vicente Barrios, Ana Campillo-Calatayud, Santiago Guerra-Cantera, Sandra Canelles, Álvaro Martín-Rivada, Laura M. Frago, Julie A. Chowen and Jesús Argente
Biomolecules 2021, 11(11), 1734; https://doi.org/10.3390/biom11111734 - 21 Nov 2021
Cited by 6 | Viewed by 2295
Abstract
Leptin modulates insulin signaling and this involves the Akt pathway, which is influenced by changes in the inflammatory environment and with leptin regulating cytokine synthesis. We evaluated the association between activation of the insulin-signaling pathway and alterations in pro- and anti-inflammatory cytokine levels [...] Read more.
Leptin modulates insulin signaling and this involves the Akt pathway, which is influenced by changes in the inflammatory environment and with leptin regulating cytokine synthesis. We evaluated the association between activation of the insulin-signaling pathway and alterations in pro- and anti-inflammatory cytokine levels in inguinal fat and liver of chronic central leptin infused (L), pair-fed (PF), and control rats. Signal transducer and activator of transcription 3 (STAT3) phosphorylation was increased in inguinal fat and reduced in liver of L rats. Phosphorylation of c-Jun N-terminal kinase (JNK) and nuclear factor kappa B (NFkB) was increased in inguinal fat of L rats, together with a pro-inflammatory cytokine profile, while in the liver activation of JNK and NFkB were reduced and an anti-inflammatory pattern was found. Phosphorylation of the insulin receptor, Akt and mechanistic target of rapamycin was decreased in inguinal fat and increased in liver of L rats. There was a direct relationship between pSTAT3 and JNK and a negative correlation of Akt with pSTAT3 and JNK in both tissues. These results indicate that the effects of chronically increased leptin on insulin-related signaling are tissue-specific and suggest that inflammation plays a relevant role in the crosstalk between leptin and insulin signaling. Full article
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25 pages, 4177 KiB  
Review
Piezoelectric Signals in Vascularized Bone Regeneration
by Delfo D’Alessandro, Claudio Ricci, Mario Milazzo, Giovanna Strangis, Francesca Forli, Gabriele Buda, Mario Petrini, Stefano Berrettini, Mohammed Jasim Uddin, Serena Danti and Paolo Parchi
Biomolecules 2021, 11(11), 1731; https://doi.org/10.3390/biom11111731 - 20 Nov 2021
Cited by 45 | Viewed by 7823
Abstract
The demand for bone substitutes is increasing in Western countries. Bone graft substitutes aim to provide reconstructive surgeons with off-the-shelf alternatives to the natural bone taken from humans or animal species. Under the tissue engineering paradigm, biomaterial scaffolds can be designed by incorporating [...] Read more.
The demand for bone substitutes is increasing in Western countries. Bone graft substitutes aim to provide reconstructive surgeons with off-the-shelf alternatives to the natural bone taken from humans or animal species. Under the tissue engineering paradigm, biomaterial scaffolds can be designed by incorporating bone stem cells to decrease the disadvantages of traditional tissue grafts. However, the effective clinical application of tissue-engineered bone is limited by insufficient neovascularization. As bone is a highly vascularized tissue, new strategies to promote both osteogenesis and vasculogenesis within the scaffolds need to be considered for a successful regeneration. It has been demonstrated that bone and blood vases are piezoelectric, namely, electric signals are locally produced upon mechanical stimulation of these tissues. The specific effects of electric charge generation on different cells are not fully understood, but a substantial amount of evidence has suggested their functional and physiological roles. This review summarizes the special contribution of piezoelectricity as a stimulatory signal for bone and vascular tissue regeneration, including osteogenesis, angiogenesis, vascular repair, and tissue engineering, by considering different stem cell sources entailed with osteogenic and angiogenic potential, aimed at collecting the key findings that may enable the development of successful vascularized bone replacements useful in orthopedic and otologic surgery. Full article
(This article belongs to the Special Issue New Insights into Stem Cell Regulation)
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15 pages, 2391 KiB  
Article
Assaying Paenibacillus alvei CsaB-Catalysed Ketalpyruvyltransfer to Saccharides by Measurement of Phosphate Release
by Fiona F. Hager-Mair, Cordula Stefanović, Charlie Lim, Katharina Webhofer, Simon Krauter, Markus Blaukopf, Roland Ludwig, Paul Kosma and Christina Schäffer
Biomolecules 2021, 11(11), 1732; https://doi.org/10.3390/biom11111732 - 20 Nov 2021
Cited by 2 | Viewed by 3036
Abstract
Ketalpyruvyltransferases belong to a widespread but little investigated class of enzymes, which utilise phosphoenolpyruvate (PEP) for the pyruvylation of saccharides. Pyruvylated saccharides play pivotal biological roles, ranging from protein binding to virulence. Limiting factors for the characterisation of ketalpyruvyltransferases are the availability of [...] Read more.
Ketalpyruvyltransferases belong to a widespread but little investigated class of enzymes, which utilise phosphoenolpyruvate (PEP) for the pyruvylation of saccharides. Pyruvylated saccharides play pivotal biological roles, ranging from protein binding to virulence. Limiting factors for the characterisation of ketalpyruvyltransferases are the availability of cognate acceptor substrates and a straightforward enzyme assay. We report on a fast ketalpyruvyltransferase assay based on the colorimetric detection of phosphate released during pyruvyltransfer from PEP onto the acceptor via complexation with Malachite Green and molybdate. To optimise the assay for the model 4,6-ketalpyruvyl::ManNAc-transferase CsaB from Paenibacillus alvei, a β-d-ManNAc-α-d-GlcNAc-diphosphoryl-11-phenoxyundecyl acceptor mimicking an intermediate of the bacterium’s cell wall glycopolymer biosynthesis pathway, upon which CsaB is naturally active, was produced chemo-enzymatically and used together with recombinant CsaB. Optimal assay conditions were 5 min reaction time at 37 °C and pH 7.5, followed by colour development for 1 h at 37 °C and measurement of absorbance at 620 nm. The structure of the generated pyruvylated product was confirmed by NMR spectroscopy. Using the established assay, the first kinetic constants of a 4,6-ketalpyuvyl::ManNAc-transferase could be determined; upon variation of the acceptor and PEP concentrations, a KM, PEP of 19.50 ± 3.50 µM and kcat, PEP of 0.21 ± 0.01 s−1 as well as a KM, Acceptor of 258 ± 38 µM and a kcat, Acceptor of 0.15 ± 0.01 s−1 were revealed. P. alvei CsaB was inactive on synthetic pNP-β-d-ManNAc and β-d-ManNAc-β-d-GlcNAc-1-OMe, supporting the necessity of a complex acceptor substrate. Full article
(This article belongs to the Special Issue Glycosylation—The Most Diverse Post-Translational Modification)
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15 pages, 1675 KiB  
Article
Dynamic DNA Methylation Changes in the COMT Gene Promoter Region in Response to Mental Stress and Its Modulation by Transcranial Direct Current Stimulation
by Ariane Wiegand, Arne Blickle, Christof Brückmann, Simone Weller, Vanessa Nieratschker and Christian Plewnia
Biomolecules 2021, 11(11), 1726; https://doi.org/10.3390/biom11111726 - 19 Nov 2021
Cited by 11 | Viewed by 3237
Abstract
Changes in epigenetic modifications present a mechanism how environmental factors, such as the experience of stress, can alter gene regulation. While stress-related disorders have consistently been associated with differential DNA methylation, little is known about the time scale in which these alterations emerge. [...] Read more.
Changes in epigenetic modifications present a mechanism how environmental factors, such as the experience of stress, can alter gene regulation. While stress-related disorders have consistently been associated with differential DNA methylation, little is known about the time scale in which these alterations emerge. We investigated dynamic DNA methylation changes in whole blood of 42 healthy male individuals in response to a stressful cognitive task, its association with concentration changes in cortisol, and its modulation by transcranial direct current stimulation (tDCS). We observed a continuous increase in COMT promotor DNA methylation which correlated with higher saliva cortisol levels and was still detectable one week later. However, this lasting effect was suppressed by concurrent activity-enhancing anodal tDCS to the dorsolateral prefrontal cortex. Our findings support the significance of gene-specific DNA methylation in whole blood as potential biomarkers for stress-related effects. Moreover, they suggest alternative molecular mechanisms possibly involved in lasting behavioral effects of tDCS. Full article
(This article belongs to the Special Issue Key Advances in Brain Stimulation)
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12 pages, 1373 KiB  
Article
Rhamnolipids as a Tool for Eradication of Trichosporon cutaneum Biofilm
by Olga Maťátková, Irena Kolouchová, Kristýna Lokočová, Jana Michailidu, Petr Jaroš, Markéta Kulišová, Tomáš Řezanka and Jan Masák
Biomolecules 2021, 11(11), 1727; https://doi.org/10.3390/biom11111727 - 19 Nov 2021
Cited by 5 | Viewed by 2296
Abstract
Microbial biofilms formed by pathogenic and antibiotic-resistant microorganisms represent a serious threat for public health in medicine and many industrial branches. Biofilms are involved in many persistent and chronic infections, the biofouling of water and food contamination. Therefore, current research is involved in [...] Read more.
Microbial biofilms formed by pathogenic and antibiotic-resistant microorganisms represent a serious threat for public health in medicine and many industrial branches. Biofilms are involved in many persistent and chronic infections, the biofouling of water and food contamination. Therefore, current research is involved in the development of new treatment strategies. Biofilm is a complex system, and thus all aspects of the measurement and monitoring of its growth and eradication in various conditions, including static and dynamic flow, are issues of great importance. The antibiofilm character of rhamnolipid mixtures produced by four Pseudomonas aeruginosa strains was studied under different conditions. For this purpose, the biofilm of opportunistic pathogen Trichosporon cutaneum was used and treated under static conditions (microscope glass coverslip in a Petri dish) and under dynamic conditions (a single-channel flow cell). The results show that the biological activity of rhamnolipids depends both on their properties and on the conditions of the biofilm formation. Therefore, this aspect must be taken into account when planning the experimental or application design. Full article
(This article belongs to the Collection Feature Papers in Lipids)
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13 pages, 1260 KiB  
Article
Late-Stage Functionalisation of Polycyclic (N-Hetero-) Aromatic Hydrocarbons by Detoxifying CYP5035S7 Monooxygenase of the White-Rot Fungus Polyporus arcularius
by Nico D. Fessner, Christopher Grimm, Wolfgang Kroutil and Anton Glieder
Biomolecules 2021, 11(11), 1708; https://doi.org/10.3390/biom11111708 - 17 Nov 2021
Cited by 5 | Viewed by 3729
Abstract
Functionalisation of polycyclic aromatic hydrocarbons (PAHs) and their N-heteroarene analogues (NPAHs) is a tedious synthetic endeavour that requires diverse bottom-up approaches. Cytochrome P450 enzymes of white-rot fungi were shown to participate in the fungal detoxification of xenobiotics and environmental hazards via hydroxylation [...] Read more.
Functionalisation of polycyclic aromatic hydrocarbons (PAHs) and their N-heteroarene analogues (NPAHs) is a tedious synthetic endeavour that requires diverse bottom-up approaches. Cytochrome P450 enzymes of white-rot fungi were shown to participate in the fungal detoxification of xenobiotics and environmental hazards via hydroxylation of PAH compounds. In this paper, the recently discovered activity of the monooxygenase CYP5035S7 towards (N)PAHs was investigated in detail, and products formed from the substrates azulene, acenaphthene, fluorene, anthracene, and phenanthrene by whole-cell biocatalysis were isolated and characterised. The observed regioselectivity of CYP5035S7 could be explained by a combination of the substrate’s electron density and steric factors influencing the substrate orientation giving insight into the active-site geometry of the enzyme. Full article
(This article belongs to the Special Issue Oxygenases: Exploiting Their Catalytic Power)
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18 pages, 958 KiB  
Review
Rare Does Not Mean Worthless: How Rare Diseases Have Shaped Neurodevelopment Research in the NGS Era
by Mattia Zaghi, Federica Banfi, Edoardo Bellini and Alessandro Sessa
Biomolecules 2021, 11(11), 1713; https://doi.org/10.3390/biom11111713 - 17 Nov 2021
Cited by 5 | Viewed by 3573
Abstract
The advent of next-generation sequencing (NGS) is heavily changing both the diagnosis of human conditions and basic biological research. It is now possible to dig deep inside the genome of hundreds of thousands or even millions of people and find both common and [...] Read more.
The advent of next-generation sequencing (NGS) is heavily changing both the diagnosis of human conditions and basic biological research. It is now possible to dig deep inside the genome of hundreds of thousands or even millions of people and find both common and rare genomic variants and to perform detailed phenotypic characterizations of both physiological organs and experimental models. Recent years have seen the introduction of multiple techniques using NGS to profile transcription, DNA and chromatin modifications, protein binding, etc., that are now allowing us to profile cells in bulk or even at a single-cell level. Although rare and ultra-rare diseases only affect a few people, each of these diseases represent scholarly cases from which a great deal can be learned about the pathological and physiological function of genes, pathways, and mechanisms. Therefore, for rare diseases, state-of-the-art investigations using NGS have double valence: their genomic cause (new variants) and the characterize the underlining the mechanisms associated with them (discovery of gene function) can be found. In a non-exhaustive manner, this review will outline the main usage of NGS-based techniques for the diagnosis and characterization of neurodevelopmental disorders (NDDs), under whose umbrella many rare and ultra-rare diseases fall. Full article
(This article belongs to the Special Issue Advance in Genomics of Rare Genetic Diseases)
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16 pages, 2524 KiB  
Article
Characterization of the Biomechanical Properties of Skin Using Vibrational Optical Coherence Tomography: Do Changes in the Biomechanical Properties of Skin Stroma Reflect Structural Changes in the Extracellular Matrix of Cancerous Lesions?
by Frederick H. Silver, Nikita Kelkar, Tanmay Deshmukh, Kelly Ritter, Nicole Ryan and Hari Nadiminti
Biomolecules 2021, 11(11), 1712; https://doi.org/10.3390/biom11111712 - 17 Nov 2021
Cited by 10 | Viewed by 3122
Abstract
Early detection of skin cancer is of critical importance since the five-year survival rate for early detected skin malignancies is 99% but drops to 27% for cancer that has spread to distant lymph nodes and other organs. Over 2.5 million benign skin biopsies [...] Read more.
Early detection of skin cancer is of critical importance since the five-year survival rate for early detected skin malignancies is 99% but drops to 27% for cancer that has spread to distant lymph nodes and other organs. Over 2.5 million benign skin biopsies (55% of the total) are performed each year in the US at an alarming cost of USD ~2.5 B. Therefore there is an unmet need for novel non-invasive diagnostic approaches to better differentiate between cancerous and non-cancerous lesions, especially in cases when there is a legitimate doubt that a biopsy may be required. The purpose of this study is to determine whether the differences in the extracellular matrices among normal skin, actinic keratosis (AK), basal cell carcinoma (BCC) and squamous cell carcinoma (SCC) can be assessed non-invasively using vibrational optical coherence tomography (VOCT). VOCT is a new diagnostic technology that uses infrared light and audible sound applied transversely to tissue to measure the resonant frequencies and elastic moduli of cells, dermal collagen, blood vessels and fibrous tissue in skin and lesion stroma without physically touching the skin. Our results indicate that the cellular, vascular and fibrotic resonant frequency peaks are altered in AK, BCC and SCC compared to those peaks observed in normal skin and can serve as physical biomarkers defining the differences between benign and cancerous skin lesions. The resonant frequency is increased from a value of 50 Hz in normal skin to a value of about 80 Hz in pre- and cancerous lesions. A new vascular peak is seen at 130 Hz in cancerous lesions that may reflect the formation of new tumor blood vessels. The peak at 260 Hz is similar to that seen in the skin of a subject with Scleroderma and skin wounds that have healed. The peak at 260 Hz appears to be associated with the deposition of large amounts of stiff fibrous collagen in the stroma surrounding cancerous lesions. Based on the results of this pilot study, VOCT can be used to non-invasively identify physical biomarkers that can help differentiate between benign and cancerous skin lesions. The appearance of new stiff cellular, fragile new vessels, and stiff fibrous material based on resonant frequency peaks and changes in the extracellular matrix can be used as a fingerprint of pre- and cancerous skin lesions. Full article
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20 pages, 10229 KiB  
Article
Three-Dimensional Virtual and Printed Prototypes in Complex Congenital and Pediatric Cardiac Surgery—A Multidisciplinary Team-Learning Experience
by Laszlo Kiraly, Nishant C. Shah, Osama Abdullah, Oraib Al-Ketan and Reza Rowshan
Biomolecules 2021, 11(11), 1703; https://doi.org/10.3390/biom11111703 - 16 Nov 2021
Cited by 15 | Viewed by 6948
Abstract
Three-dimensional (3D) virtual modeling and printing advances individualized medicine and surgery. In congenital cardiac surgery, 3D virtual models and printed prototypes offer advantages of better understanding of complex anatomy, hands-on preoperative surgical planning and emulation, and improved communication within the multidisciplinary team and [...] Read more.
Three-dimensional (3D) virtual modeling and printing advances individualized medicine and surgery. In congenital cardiac surgery, 3D virtual models and printed prototypes offer advantages of better understanding of complex anatomy, hands-on preoperative surgical planning and emulation, and improved communication within the multidisciplinary team and to patients. We report our single center team-learning experience about the realization and validation of possible clinical benefits of 3D-printed models in surgical planning of complex congenital cardiac surgery. CT-angiography raw data were segmented into 3D-virtual models of the heart-great vessels. Prototypes were 3D-printed as rigid “blood-volume” and flexible “hollow”. The accuracy of the models was evaluated intraoperatively. Production steps were realized in the framework of a clinical/research partnership. We produced 3D prototypes of the heart-great vessels for 15 case scenarios (nine males, median age: 11 months) undergoing complex intracardiac repairs. Parity between 3D models and intraoperative structures was within 1 mm range. Models refined diagnostics in 13/15, provided new anatomic information in 9/15. As a team-learning experience, all complex staged redo-operations (13/15; Aristotle-score mean: 10.64 ± 1.95) were rehearsed on the 3D models preoperatively. 3D-printed prototypes significantly contributed to an improved/alternative operative plan on the surgical approach, modification of intracardiac repair in 13/15. No operative morbidity/mortality occurred. Our clinical/research partnership provided coverage for the extra time/labor and material/machinery not financed by insurance. 3D-printed models provided a team-learning experience and contributed to the safety of complex congenital cardiac surgeries. A clinical/research partnership may open avenues for bioprinting of patient-specific implants. Full article
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19 pages, 2572 KiB  
Review
Co-Evolution of Breast Milk Lipid Signaling and Thermogenic Adipose Tissue
by Tamás Röszer
Biomolecules 2021, 11(11), 1705; https://doi.org/10.3390/biom11111705 - 16 Nov 2021
Cited by 11 | Viewed by 4292
Abstract
Breastfeeding is a unique and defining behavior of mammals and has a fundamental role in nourishing offspring by supplying a lipid-rich product that is utilized to generate heat and metabolic fuel. Heat generation from lipids is a feature of newborn mammals and is [...] Read more.
Breastfeeding is a unique and defining behavior of mammals and has a fundamental role in nourishing offspring by supplying a lipid-rich product that is utilized to generate heat and metabolic fuel. Heat generation from lipids is a feature of newborn mammals and is mediated by the uncoupling of mitochondrial respiration in specific fat depots. Breastfeeding and thermogenic adipose tissue have a shared evolutionary history: both have evolved in the course of homeothermy evolution; breastfeeding mammals are termed “thermolipials”, meaning “animals with warm fat”. Beyond its heat-producing capacity, thermogenic adipose tissue is also necessary for proper lipid metabolism and determines adiposity in offspring. Recent advances have demonstrated that lipid metabolism in infants is orchestrated by breast milk lipid signals, which establish mother-to-child signaling and control metabolic development in the infant. Breastfeeding rates are declining worldwide, and are paralleled by an alarming increase in childhood obesity, which at least in part may have its roots in the impaired metabolic control by breast milk lipid signals. Full article
(This article belongs to the Special Issue Breast Milk-Derived Biomolecules in Human Health)
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22 pages, 2366 KiB  
Review
Expanding the Disorder-Function Paradigm in the C-Terminal Tails of Erbbs
by Louise Pinet, Nadine Assrir and Carine van Heijenoort
Biomolecules 2021, 11(11), 1690; https://doi.org/10.3390/biom11111690 - 14 Nov 2021
Cited by 3 | Viewed by 3093
Abstract
ErbBs are receptor tyrosine kinases involved not only in development, but also in a wide variety of diseases, particularly cancer. Their extracellular, transmembrane, juxtamembrane, and kinase folded domains were described extensively over the past 20 years, structurally and functionally. However, their whole C-terminal [...] Read more.
ErbBs are receptor tyrosine kinases involved not only in development, but also in a wide variety of diseases, particularly cancer. Their extracellular, transmembrane, juxtamembrane, and kinase folded domains were described extensively over the past 20 years, structurally and functionally. However, their whole C-terminal tails (CTs) following the kinase domain were only described at atomic resolution in the last 4 years. They were shown to be intrinsically disordered. The CTs are known to be tyrosine-phosphorylated when the activated homo- or hetero-dimers of ErbBs are formed. Their phosphorylation triggers interaction with phosphotyrosine binding (PTB) or Src Homology 2 (SH2) domains and activates several signaling pathways controling cellular motility, proliferation, adhesion, and apoptosis. Beyond this passive role of phosphorylated domain and site display for partners, recent structural and function studies unveiled active roles in regulation of phosphorylation and interaction: the CT regulates activity of the kinase domain; different phosphorylation states have different compaction levels, potentially modulating the succession of phosphorylation events; and prolines have an important role in structure, dynamics, and possibly regulatory interactions. Here, we review both the canonical role of the disordered CT domains of ErbBs as phosphotyrosine display domains and the recent findings that expand the known range of their regulation functions linked to specific structural and dynamic features. Full article
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11 pages, 1607 KiB  
Review
An Asp to Strike Out Cancer? Therapeutic Possibilities Arising from Aspartate’s Emerging Roles in Cell Proliferation and Survival
by Iiro Taneli Helenius, Hanumantha Rao Madala and Jing-Ruey Joanna Yeh
Biomolecules 2021, 11(11), 1666; https://doi.org/10.3390/biom11111666 - 10 Nov 2021
Cited by 26 | Viewed by 4459
Abstract
A better understanding of the metabolic constraints of a tumor may lead to more effective anticancer treatments. Evidence has emerged in recent years shedding light on a crucial aspartate dependency of many tumor types. As a precursor for nucleotide synthesis, aspartate is indispensable [...] Read more.
A better understanding of the metabolic constraints of a tumor may lead to more effective anticancer treatments. Evidence has emerged in recent years shedding light on a crucial aspartate dependency of many tumor types. As a precursor for nucleotide synthesis, aspartate is indispensable for cell proliferation. Moreover, the malate–aspartate shuttle plays a key role in redox balance, and a deficit in aspartate can lead to oxidative stress. It is now recognized that aspartate biosynthesis is largely governed by mitochondrial metabolism, including respiration and glutaminolysis in cancer cells. Therefore, under conditions that suppress mitochondrial metabolism, including mutations, hypoxia, or chemical inhibitors, aspartate can become a limiting factor for tumor growth and cancer cell survival. Notably, aspartate availability has been associated with sensitivity or resistance to various therapeutics that are presently in the clinic or in clinical trials, arguing for a critical need for more effective aspartate-targeting approaches. In this review, we present current knowledge of the metabolic roles of aspartate in cancer cells and describe how cancer cells maintain aspartate levels under different metabolic states. We also highlight several promising aspartate level-modulating agents that are currently under investigation. Full article
(This article belongs to the Special Issue Role of the Mitochondrial Stress Response in Human Cancer Progression)
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17 pages, 1711 KiB  
Article
Genetic and Metabolic Determinants of Atrial Fibrillation in a General Population Sample: The CHRIS Study
by David B. Emmert, Vladimir Vukovic, Nikola Dordevic, Christian X. Weichenberger, Chiara Losi, Yuri D’Elia, Claudia Volpato, Vinicius V. Hernandes, Martin Gögele, Luisa Foco, Giulia Pontali, Deborah Mascalzoni, Francisco S. Domingues, Rupert Paulmichl, Peter P. Pramstaller, Cristian Pattaro, Alessandra Rossini, Johannes Rainer, Christian Fuchsberger and Marzia De Bortoli
Biomolecules 2021, 11(11), 1663; https://doi.org/10.3390/biom11111663 - 9 Nov 2021
Cited by 12 | Viewed by 3485
Abstract
Atrial fibrillation (AF) is a supraventricular arrhythmia deriving from uncoordinated electrical activation with considerable associated morbidity and mortality. To expand the limited understanding of AF biological mechanisms, we performed two screenings, investigating the genetic and metabolic determinants of AF in the Cooperative Health [...] Read more.
Atrial fibrillation (AF) is a supraventricular arrhythmia deriving from uncoordinated electrical activation with considerable associated morbidity and mortality. To expand the limited understanding of AF biological mechanisms, we performed two screenings, investigating the genetic and metabolic determinants of AF in the Cooperative Health Research in South Tyrol study. We found 110 AF cases out of 10,509 general population individuals. A genome-wide association scan (GWAS) identified two novel loci (p-value < 5 × 10−8) around SNPs rs745582874, next to gene PBX1, and rs768476991, within gene PCCA, with genotype calling confirmed by Sanger sequencing. Risk alleles at both SNPs were enriched in a family detected through familial aggregation analysis of the phenotype, and both rare alleles co-segregated with AF. The metabolic screening of 175 metabolites, in a subset of individuals, revealed a 41% lower concentration of lysophosphatidylcholine lysoPC a C20:3 in AF cases compared to controls (p-adj = 0.005). The genetic findings, combined with previous evidence, indicate that the two identified GWAS loci may be considered novel genetic rare determinants for AF. Considering additionally the association of lysoPC a C20:3 with AF by metabolic screening, our results demonstrate the valuable contribution of the combined genomic and metabolomic approach in studying AF in large-scale population studies. Full article
(This article belongs to the Special Issue Advance in Genomics of Rare Genetic Diseases)
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12 pages, 2915 KiB  
Article
Data-Driven Analysis of Fluorination of Ligands of Aminergic G Protein Coupled Receptors
by Wojciech Pietruś, Rafał Kurczab, Dagmar Stumpfe, Andrzej J. Bojarski and Jürgen Bajorath
Biomolecules 2021, 11(11), 1647; https://doi.org/10.3390/biom11111647 - 8 Nov 2021
Cited by 2 | Viewed by 2318
Abstract
Currently, G protein-coupled receptors are the targets with the highest number of drugs in many therapeutic areas. Fluorination has become a common strategy in designing highly active biological compounds, as evidenced by the steadily increasing number of newly approved fluorine-containing drugs. Herein, we [...] Read more.
Currently, G protein-coupled receptors are the targets with the highest number of drugs in many therapeutic areas. Fluorination has become a common strategy in designing highly active biological compounds, as evidenced by the steadily increasing number of newly approved fluorine-containing drugs. Herein, we identified in the ChEMBL database and analysed 1554 target-based FSAR sets (non-fluorinated compounds and their fluorinated analogues) comprising 966 unique non-fluorinated and 2457 unique fluorinated compounds active against 33 different aminergic GPCRs. Although a relatively small number of activity cliffs (defined as a pair of structurally similar compounds showing significant differences of activity −ΔpPot > 1.7) was found in FSAR sets, it is clear that appropriately introduced fluorine can increase ligand potency more than 50-fold. The analysis of matched molecular pairs (MMPs) networks indicated that the fluorination of the aromatic ring showed no clear trend towards a positive or negative effect on affinity; however, a favourable site for a positive potency effect of fluorination was the ortho position. Fluorination of aliphatic fragments more often led to a decrease in biological activity. The results may constitute the rules of thumb for fluorination of aminergic receptor ligands and provide insights into the role of fluorine substitutions in medicinal chemistry. Full article
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19 pages, 1175 KiB  
Review
miRNA as a Modulator of Immunotherapy and Immune Response in Melanoma
by Mai-Huong Thi Nguyen, Yueh-Hsia Luo, An-Lun Li, Jen-Chieh Tsai, Kun-Lin Wu, Pei-Jung Chung and Nianhan Ma
Biomolecules 2021, 11(11), 1648; https://doi.org/10.3390/biom11111648 - 8 Nov 2021
Cited by 22 | Viewed by 4102
Abstract
Immune checkpoint inhibitors are a promising therapy for the treatment of cancers, including melanoma, that improved benefit clinical outcomes. However, a subset of melanoma patients do not respond or acquire resistance to immunotherapy, which limits their clinical applicability. Recent studies have explored the [...] Read more.
Immune checkpoint inhibitors are a promising therapy for the treatment of cancers, including melanoma, that improved benefit clinical outcomes. However, a subset of melanoma patients do not respond or acquire resistance to immunotherapy, which limits their clinical applicability. Recent studies have explored the reasons related to the resistance of melanoma to immune checkpoint inhibitors. Of note, miRNAs are the regulators of not only cancer progression but also of the response between cancer cells and immune cells. Investigation of miRNA functions within the tumor microenvironment have suggested that miRNAs could be considered as key partners in immunotherapy. Here, we reviewed the known mechanism by which melanoma induces resistance to immunotherapy and the role of miRNAs in immune responses and the microenvironment. Full article
(This article belongs to the Special Issue MicroRNAs - Small Molecules with Great Potential in Tumorigenesis)
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12 pages, 1151 KiB  
Article
Metabolic Profiles, Bioactive Compounds, and Antioxidant Capacity in Lentinula edodes Cultivated on Log versus Sawdust Substrates
by Miso Nam, Ji Yeon Choi and Min-Sun Kim
Biomolecules 2021, 11(11), 1654; https://doi.org/10.3390/biom11111654 - 8 Nov 2021
Cited by 22 | Viewed by 3542
Abstract
Lentinula edodes (shiitake) is a popular nutritious edible mushroom with a desirable aroma and flavor. Traditional cultivation of L. edodes on beds of logs has been replaced by cultivation on sawdust, but the effects of cultivation changes on L. edodes mushrooms have not [...] Read more.
Lentinula edodes (shiitake) is a popular nutritious edible mushroom with a desirable aroma and flavor. Traditional cultivation of L. edodes on beds of logs has been replaced by cultivation on sawdust, but the effects of cultivation changes on L. edodes mushrooms have not been well characterized. We determined the metabolic profile, bioactive compounds, and antioxidant capacity in L. edodes grown on log or sawdust substrates. Metabolic profiles of L. edodes extracts were determined by 1H nuclear magnetic resonance (NMR) and ultra-performance liquid chromatography to quadrupole time-of-flight mass spectrometry. Principal component analysis score plots from 1H NMR analysis showed clear differences between samples. Concentrations of primary metabolites, especially amino acids, generally decreased in L. edodes grown on logs compared to sawdust. Phenolic compounds showed variations in concentration depending on the cultivation method. Bioactive compounds and their antioxidant capacity were analyzed spectrophotometrically. L. edodes cultivated on logs had high concentrations of bioactive compounds with strong antioxidant capacity compared to L. edodes cultivated on sawdust. Thus, the concentration of primary metabolites was high in L. edodes grown on sawdust, which produces a high growth rate. In contrast, log-cultivated L. edodes, which were similar to wild mushrooms, had high levels of bioactive compounds and high antioxidant capacity. This information is useful for determining optimal cultivation conditions for nutritional and medicinal uses of L. edodes mushrooms. Full article
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21 pages, 17965 KiB  
Review
The Synthesis and Biological Evaluation of D-Ring-Modified Vitamin D Analogues
by Fumihiro Kawagoe, Sayuri Mototani and Atsushi Kittaka
Biomolecules 2021, 11(11), 1639; https://doi.org/10.3390/biom11111639 - 4 Nov 2021
Cited by 9 | Viewed by 2976
Abstract
The vitamin D3 structure consists of the A-ring, a linker originating from the B-ring, C-ring, D-ring, and side-chain moieties. Each unit has its unique role in expressing the biological activities of vitamin D3. Many efforts have been made to date [...] Read more.
The vitamin D3 structure consists of the A-ring, a linker originating from the B-ring, C-ring, D-ring, and side-chain moieties. Each unit has its unique role in expressing the biological activities of vitamin D3. Many efforts have been made to date to assess the possible clinical use of vitamin D. Some organic chemists focused on the D-ring structure of vitamin D and synthesized D-ring-modified vitamin D analogues, and their biological activities were studied. This review summarizes the synthetic methodologies of D-ring-modified vitamin D analogues, except for seco-D, and their preliminary biological profiles. Full article
(This article belongs to the Special Issue Biochemistry and Molecular Biology of Vitamin D and Its Analog)
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15 pages, 1541 KiB  
Review
Revisiting the Large-Conductance Calcium-Activated Potassium (BKCa) Channels in the Pulmonary Circulation
by Divya Guntur, Horst Olschewski, Péter Enyedi, Réka Csáki, Andrea Olschewski and Chandran Nagaraj
Biomolecules 2021, 11(11), 1629; https://doi.org/10.3390/biom11111629 - 3 Nov 2021
Cited by 12 | Viewed by 4409
Abstract
Potassium ion concentrations, controlled by ion pumps and potassium channels, predominantly govern a cell′s membrane potential and the tone in the vessels. Calcium-activated potassium channels respond to two different stimuli-changes in voltage and/or changes in intracellular free calcium. Large conductance calcium-activated potassium (BKCa) [...] Read more.
Potassium ion concentrations, controlled by ion pumps and potassium channels, predominantly govern a cell′s membrane potential and the tone in the vessels. Calcium-activated potassium channels respond to two different stimuli-changes in voltage and/or changes in intracellular free calcium. Large conductance calcium-activated potassium (BKCa) channels assemble from pore forming and various modulatory and auxiliary subunits. They are of vital significance due to their very high unitary conductance and hence their ability to rapidly cause extreme changes in the membrane potential. The pathophysiology of lung diseases in general and pulmonary hypertension, in particular, show the implication of either decreased expression and partial inactivation of BKCa channel and its subunits or mutations in the genes encoding different subunits of the channel. Signaling molecules, circulating humoral molecules, vasorelaxant agents, etc., have an influence on the open probability of the channel in pulmonary arterial vascular cells. BKCa channel is a possible therapeutic target, aimed to cause vasodilation in constricted or chronically stiffened vessels, as shown in various animal models. This review is a comprehensive collation of studies on BKCa channels in the pulmonary circulation under hypoxia (hypoxic pulmonary vasoconstriction; HPV), lung pathology, and fetal to neonatal transition, emphasising pharmacological interventions as viable therapeutic options. Full article
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17 pages, 1300 KiB  
Review
KCNQ1OT1: An Oncogenic Long Noncoding RNA
by Patrice Cagle, Qi Qi, Suryakant Niture and Deepak Kumar
Biomolecules 2021, 11(11), 1602; https://doi.org/10.3390/biom11111602 - 29 Oct 2021
Cited by 47 | Viewed by 5360
Abstract
Long noncoding RNAs (lncRNAs) are transcripts greater than 200 nucleotides that do not code for proteins but regulate gene expression. Recent studies indicate that lncRNAs are involved in the modulation of biological functions in human disease. KCNQ1 Opposite Strand/Antisense Transcript 1 (KCNQ1OT1) encodes [...] Read more.
Long noncoding RNAs (lncRNAs) are transcripts greater than 200 nucleotides that do not code for proteins but regulate gene expression. Recent studies indicate that lncRNAs are involved in the modulation of biological functions in human disease. KCNQ1 Opposite Strand/Antisense Transcript 1 (KCNQ1OT1) encodes a lncRNA from the opposite strand of KCNQ1 in the CDKN1C/KCNQ1OT1 cluster that is reported to play a vital role in the development and progression of cancer. KCNQ1OT1 regulates cancer cell proliferation, cell cycle, migration and invasion, metastasis, glucose metabolism, and immune evasion. The aberrant expression of KCNQ1OT1 in cancer patients is associated with poor prognosis and decreased survival. This review summarizes recent literature related to the biological functions and molecular mechanisms of KCNQ1OT1 in various human cancers, including colorectal, bladder, breast, oral, melanoma, osteosarcoma, lung, glioma, ovarian, liver, acute myeloid leukemia, prostate, and gastric. We also discuss the role of KCNQ1OT1 as a promising diagnostic biomarker and a novel therapeutic target in human cancers. Full article
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19 pages, 5233 KiB  
Article
The Type III Effectome of the Symbiotic Bradyrhizobium vignae Strain ORS3257
by Nicolas Busset, Djamel Gully, Albin Teulet, Joël Fardoux, Alicia Camuel, David Cornu, Dany Severac, Eric Giraud and Peter Mergaert
Biomolecules 2021, 11(11), 1592; https://doi.org/10.3390/biom11111592 - 28 Oct 2021
Cited by 14 | Viewed by 4105
Abstract
Many Bradyrhizobium strains are able to establish a Nod factor-independent symbiosis with the leguminous plant Aeschynomene indica by the use of a type III secretion system (T3SS). Recently, an important advance in the understanding of the molecular factors supporting this symbiosis has been [...] Read more.
Many Bradyrhizobium strains are able to establish a Nod factor-independent symbiosis with the leguminous plant Aeschynomene indica by the use of a type III secretion system (T3SS). Recently, an important advance in the understanding of the molecular factors supporting this symbiosis has been achieved by the in silico identification and functional characterization of 27 putative T3SS effectors (T3Es) of Bradyrhizobium vignae ORS3257. In the present study, we experimentally extend this catalog of T3Es by using a multi-omics approach. Transcriptome analysis under non-inducing and inducing conditions in the ORS3257 wild-type strain and the ttsI mutant revealed that the expression of 18 out of the 27 putative effectors previously identified, is under the control of TtsI, the global transcriptional regulator of T3SS and T3Es. Quantitative shotgun proteome analysis of culture supernatant in the wild type and T3SS mutant strains confirmed that 15 of the previously determined candidate T3Es are secreted by the T3SS. Moreover, the combined approaches identified nine additional putative T3Es and one of them was experimentally validated as a novel effector. Our study underscores the power of combined proteome and transcriptome analyses to complement in silico predictions and produce nearly complete effector catalogs. The establishment of the ORS3257 effectome will form the basis for a full appraisal of the symbiotic properties of this strain during its interaction with various host legumes via different processes. Full article
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18 pages, 1045 KiB  
Review
Bioprinting Au Natural: The Biologics of Bioinks
by Kelsey Willson, Anthony Atala and James J. Yoo
Biomolecules 2021, 11(11), 1593; https://doi.org/10.3390/biom11111593 - 28 Oct 2021
Cited by 19 | Viewed by 3370
Abstract
The development of appropriate bioinks is a complex task, dependent on the mechanical and biochemical requirements of the final construct and the type of printer used for fabrication. The two most common tissue printers are micro-extrusion and digital light projection printers. Here we [...] Read more.
The development of appropriate bioinks is a complex task, dependent on the mechanical and biochemical requirements of the final construct and the type of printer used for fabrication. The two most common tissue printers are micro-extrusion and digital light projection printers. Here we briefly discuss the required characteristics of a bioink for each of these printing processes. However, physical printing is only a short window in the lifespan of a printed construct—the system must support and facilitate cellular development after it is printed. To that end, we provide a broad overview of some of the biological molecules currently used as bioinks. Each molecule has advantages for specific tissues/cells, and potential disadvantages are discussed, along with examples of their current use in the field. Notably, it is stressed that active researchers are trending towards the use of composite bioinks. Utilizing the strengths from multiple materials is highlighted as a key component of bioink development. Full article
(This article belongs to the Special Issue Biological Biomaterials for Regenerative Medicine)
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16 pages, 2882 KiB  
Article
Glycan Epitopes and Potential Glycoside Antagonists of DC-SIGN Involved in COVID-19: In Silico Study
by Meina Gao, Hui Li, Chenghao Ye, Kaixian Chen, Hualiang Jiang and Kunqian Yu
Biomolecules 2021, 11(11), 1586; https://doi.org/10.3390/biom11111586 - 27 Oct 2021
Cited by 4 | Viewed by 3750
Abstract
Glycosylation is an important post-translational modification that affects a wide variety of physiological functions. DC-SIGN (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin) is a protein expressed in antigen-presenting cells that recognizes a variety of glycan epitopes. Until now, the binding of DC-SIGN to SARS-CoV-2 [...] Read more.
Glycosylation is an important post-translational modification that affects a wide variety of physiological functions. DC-SIGN (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Non-integrin) is a protein expressed in antigen-presenting cells that recognizes a variety of glycan epitopes. Until now, the binding of DC-SIGN to SARS-CoV-2 Spike glycoprotein has been reported in various articles and is regarded to be a factor in systemic infection and cytokine storm. The mechanism of DC-SIGN recognition offers an alternative method for discovering new medication for COVID-19 treatment. Here, we discovered three potential pockets that hold different glycan epitopes by performing molecular dynamics simulations of previously reported oligosaccharides. The “EPN” motif, “NDD” motif, and Glu354 form the most critical pocket, which is known as the Core site. We proposed that the type of glycan epitopes, rather than the precise amino acid sequence, determines the recognition. Furthermore, we deduced that oligosaccharides could occupy an additional site, which adds to their higher affinity than monosaccharides. Based on our findings and previously described glycoforms on the SARS-CoV-2 Spike, we predicted the potential glycan epitopes for DC-SIGN. It suggested that glycan epitopes could be recognized at multiple sites, not just Asn234, Asn149 and Asn343. Subsequently, we found that Saikosaponin A and Liquiritin, two plant glycosides, were promising DC-SIGN antagonists in silico. Full article
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18 pages, 727 KiB  
Review
Self-Attention-Based Models for the Extraction of Molecular Interactions from Biological Texts
by Prashant Srivastava, Saptarshi Bej, Kristina Yordanova and Olaf Wolkenhauer
Biomolecules 2021, 11(11), 1591; https://doi.org/10.3390/biom11111591 - 27 Oct 2021
Cited by 15 | Viewed by 3934
Abstract
For any molecule, network, or process of interest, keeping up with new publications on these is becoming increasingly difficult. For many cellular processes, the amount molecules and their interactions that need to be considered can be very large. Automated mining of publications can [...] Read more.
For any molecule, network, or process of interest, keeping up with new publications on these is becoming increasingly difficult. For many cellular processes, the amount molecules and their interactions that need to be considered can be very large. Automated mining of publications can support large-scale molecular interaction maps and database curation. Text mining and Natural-Language-Processing (NLP)-based techniques are finding their applications in mining the biological literature, handling problems such as Named Entity Recognition (NER) and Relationship Extraction (RE). Both rule-based and Machine-Learning (ML)-based NLP approaches have been popular in this context, with multiple research and review articles examining the scope of such models in Biological Literature Mining (BLM). In this review article, we explore self-attention-based models, a special type of Neural-Network (NN)-based architecture that has recently revitalized the field of NLP, applied to biological texts. We cover self-attention models operating either at the sentence level or an abstract level, in the context of molecular interaction extraction, published from 2019 onwards. We conducted a comparative study of the models in terms of their architecture. Moreover, we also discuss some limitations in the field of BLM that identifies opportunities for the extraction of molecular interactions from biological text. Full article
(This article belongs to the Special Issue Computational Approaches for the Study of Biomolecular Networks)
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15 pages, 5447 KiB  
Article
Modeling Prostate Cancer Treatment Responses in the Organoid Era: 3D Environment Impacts Drug Testing
by Annelies Van Hemelryk, Lisanne Mout, Sigrun Erkens-Schulze, Pim J. French, Wytske M. van Weerden and Martin E. van Royen
Biomolecules 2021, 11(11), 1572; https://doi.org/10.3390/biom11111572 - 22 Oct 2021
Cited by 15 | Viewed by 4430
Abstract
Organoid-based studies have revolutionized in vitro preclinical research and hold great promise for the cancer research field, including prostate cancer (PCa). However, experimental variability in organoid drug testing complicates reproducibility. For example, we observed PCa organoids to be less affected by cabazitaxel, abiraterone [...] Read more.
Organoid-based studies have revolutionized in vitro preclinical research and hold great promise for the cancer research field, including prostate cancer (PCa). However, experimental variability in organoid drug testing complicates reproducibility. For example, we observed PCa organoids to be less affected by cabazitaxel, abiraterone and enzalutamide as compared to corresponding single cells prior to organoid assembly. We hypothesized that three-dimensional (3D) organoid organization and the use of various 3D scaffolds impact treatment efficacy. Live-cell imaging of androgen-induced androgen receptor (AR) nuclear translocation and taxane-induced tubulin stabilization was used to investigate the impact of 3D scaffolds, spatial organoid distribution and organoid size on treatment effect. Scaffolds delayed AR translocation and tubulin stabilization, with Matrigel causing a more pronounced delay than synthetic hydrogel as well as incomplete tubulin stabilization. Drug effect was further attenuated the more centrally organoids were located in the scaffold dome. Moreover, cells in the organoid core revealed a delayed treatment effect compared to cells in the organoid periphery, underscoring the impact of organoid size. These findings indicate that analysis of organoid drug responses needs careful interpretation and requires dedicated read-outs with consideration of underlying technical aspects. Full article
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15 pages, 2049 KiB  
Article
Phytochemical Profile, α-Glucosidase, and α-Amylase Inhibition Potential and Toxicity Evaluation of Extracts from Citrus aurantium (L) Peel, a Valuable By-Product from Northeastern Morocco
by Ouijdane Benayad, Mohamed Bouhrim, Salima Tiji, Loubna Kharchoufa, Mohamed Addi, Samantha Drouet, Christophe Hano, Jose Manuel Lorenzo, Hasnae Bendaha, Mohamed Bnouham and Mostafa Mimouni
Biomolecules 2021, 11(11), 1555; https://doi.org/10.3390/biom11111555 - 20 Oct 2021
Cited by 52 | Viewed by 5988
Abstract
Due to the high volume of peel produced, Citrus by-product processing could be a significant source of phenolic compounds, in addition to essential oil. Citrus fruit residues, which are usually dumped as waste in the environment, could be used as a source of [...] Read more.
Due to the high volume of peel produced, Citrus by-product processing could be a significant source of phenolic compounds, in addition to essential oil. Citrus fruit residues, which are usually dumped as waste in the environment, could be used as a source of nutraceuticals. Citrus aurantium (L), also known as sour or bitter orange, is a member of the Rutaceae family and is the result of interspecific hybridization between Citrus reticulata and Citrus maxima. The purpose of this study is to chemically and biologically evaluate the peel of C. aurantium, which is considered a solid waste destined for abandonment. To achieve more complete extraction of the phytochemicals, we used a sequential extraction process with Soxhlet using the increasing polarity of solvents (i.e., cyclohexane, chloroform, ethyl acetate, acetone, and ethanol–water mixture). Essential oil (EO) from the Citrus peel, which was present at 1.12%, was also prepared by hydrodistillation for comparison. Various phytochemical assays were used to determine the qualitative chemical composition, which was subsequently characterized using GC-MS and HPLC-DAD. The inhibitory effects of C. aurantium peel extract on two enzymes, intestinal α-glucosidase and pancreatic α-amylase, were measured in vitro to determine their potential hypoglycemic and antidiabetic actions. Each extract had a significantly different phytochemical composition. According to GC-MS analyses, which allow the identification of 19 compounds, d-limonene is the most abundant compound in both EO and cyclohexane extract, at 35.17% and 36.15% (w/w). This comparison with hydrodistillation shows the value of the sequential process in extracting this valuable terpene in large quantities while also allowing for the subsequent extraction of other bioactive substances. On the contrary, linoleic acid is abundant (54.35% (w/w)) in ethyl acetate extract (EAE) with a lower amount of d-limonene. HPLC-DAD analysis allows the identification of 11 phytochemicals, with naringenin being the most abundant flavanone, detected in acetone extract (ACE) (23.94% (w/w)), ethanol–water extract mixture (EWE) (28.71% (w/w)), and chloroform extract (CFE) (30.20% (w/w)). Several extracts significantly inhibited α-amylase and/or α-glycosidase in vitro. At a dose of 332 g/mL, ACE, CFE, and EWE inhibited the two enzymes by approximately 98%. There were strong significant correlations between naringenin and α-glucosidase inhibition and between gallic acid and α-amylase inhibition. Molecular docking experiments further verified this. Finally, oral administration of C. aurantium extracts at a dose of 2000 mg/kg did not cause any effect on mice mortality or signs of acute toxicity, indicating that it is non-toxic at these doses. These findings suggest that C. aurantium peels could be a valuable by-product by providing a rich source of non-toxic phytoconstituents, particularly those with potential antidiabetic action that needs to be confirmed in vivo. Full article
(This article belongs to the Special Issue Phytochemical Omics in Medicinal Plants 2.0)
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18 pages, 1424 KiB  
Review
CB2 Receptor Involvement in the Treatment of Substance Use Disorders
by Francisco Navarrete, María S. García-Gutiérrez, Ani Gasparyan, Daniela Navarro and Jorge Manzanares
Biomolecules 2021, 11(11), 1556; https://doi.org/10.3390/biom11111556 - 20 Oct 2021
Cited by 16 | Viewed by 3531
Abstract
The pharmacological modulation of the cannabinoid receptor 2 (CB2r) has emerged as a promising potential therapeutic option in addiction. The purpose of this review was to determine the functional involvement of CB2r in the effects produced by drugs of abuse at the central [...] Read more.
The pharmacological modulation of the cannabinoid receptor 2 (CB2r) has emerged as a promising potential therapeutic option in addiction. The purpose of this review was to determine the functional involvement of CB2r in the effects produced by drugs of abuse at the central nervous system (CNS) level by assessing evidence from preclinical and clinical studies. In rodents, several reports suggest the functional involvement of CB2r in the effects produced by drugs of abuse such as alcohol, cocaine, or nicotine. In addition, the discovery of CB2r in brain areas that are part of the reward system supports the relevance of CB2r in the field of addiction. Interestingly, animal studies support that the CB2r regulates anxiety and depression behavioral traits. Due to its frequent comorbidity with neuropsychiatric disorders, these pharmacological actions may be of great interest in managing SUD. Preliminary clinical trials are focused on exploring the therapeutic potential of modulating CB2r in treating addictive disorders. These promising results support the development of new pharmacological tools regulating the CB2r that may help to increase the therapeutic success in the management of SUD. Full article
(This article belongs to the Special Issue Translational Biomarkers in Addictive Disorders)
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15 pages, 31008 KiB  
Article
Angiogenic Potential of VEGF Mimetic Peptides for the Biofunctionalization of Collagen/Hydroxyapatite Composites
by Suya Wang, Felix Umrath, Wanjing Cen, Siegmar Reinert and Dorothea Alexander
Biomolecules 2021, 11(10), 1538; https://doi.org/10.3390/biom11101538 - 19 Oct 2021
Cited by 17 | Viewed by 4746
Abstract
Currently, the focus on bioinspired concepts for the development of tissue engineering constructs is increasing. For this purpose, the combination of collagen (Coll) and hydroxyapatite (HA) comes closest to the natural composition of the bone. In order to confer angiogenic properties to the [...] Read more.
Currently, the focus on bioinspired concepts for the development of tissue engineering constructs is increasing. For this purpose, the combination of collagen (Coll) and hydroxyapatite (HA) comes closest to the natural composition of the bone. In order to confer angiogenic properties to the scaffold material, vascular endothelial growth factor (VEGF) is frequently used. In the present study, we used a VEGF mimetic peptide (QK) and a modified QK-peptide with a poly-glutamic acid tag (E7-QK) to enhance binding to HA, and analyzed in detail binding efficiency and angiogenic properties. We detected a significantly higher binding efficiency of E7-QK peptides to hydroxyapatite particles compared to the unmodified QK-peptide. Tube formation assays revealed similar angiogenic functions of E7-QK peptide (1µM) as induced by the entire VEGF protein. Analyses of gene expression of angiogenic factors and their receptors (FLT-1, KDR, HGF, MET, IL-8, HIF-1α, MMP-1, IGFBP-1, IGFBP-2, VCAM-1, and ANGPT-1) showed higher expression levels in HUVECs cultured in the presence of 1 µM E7-QK and VEGF compared to those detected in the negative control group without any angiogenic stimuli. In contrast, the expression of the anti-angiogenic gene TIMP-1 showed lower mRNA levels in HUVECs cultured with E7-QK and VEGF. Sprouting assays with HUVEC spheroids within Coll/HA/E7-QK scaffolds showed significantly longer sprouts compared to those induced within Coll/HA/QK or Coll/HA scaffolds. Our results demonstrate a significantly better functionality of the E7-QK peptide, electrostatically bound to hydroxyapatite particles compared to that of unmodified QK peptide. We conclude that the used E7-QK peptide represents an excellently suited biomolecule for the generation of collagen/hydroxyapatite composites with angiogenic properties. Full article
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13 pages, 1622 KiB  
Article
New Insights to Regulation of Fructose-1,6-bisphosphatase during Anoxia in Red-Eared Slider, Trachemys scripta elegans
by Aakriti Gupta, Anchal Varma and Kenneth B. Storey
Biomolecules 2021, 11(10), 1548; https://doi.org/10.3390/biom11101548 - 19 Oct 2021
Cited by 7 | Viewed by 7789
Abstract
The red-eared slider (Trachemys scripta elegans) undergoes numerous changes to its physiological and metabolic processes to survive without oxygen. During anoxic conditions, its metabolic rate drops drastically to minimize energy requirements. The alterations in the central metabolic pathways are often accomplished [...] Read more.
The red-eared slider (Trachemys scripta elegans) undergoes numerous changes to its physiological and metabolic processes to survive without oxygen. During anoxic conditions, its metabolic rate drops drastically to minimize energy requirements. The alterations in the central metabolic pathways are often accomplished by the regulation of key enzymes. The regulation of one such enzyme, fructose-1,6-bisphosphatase (FBPase; EC 3.1.3.11), was characterized in the present study during anoxia in liver. FBPase is a crucial enzyme of gluconeogenesis. The FBPase was purified from liver tissue in both control and anoxic conditions and subsequently assayed to determine the kinetic parameters of the enzyme. The study revealed the relative degree of post-translational modifications in the FBPase from control and anoxic turtles. Further, this study demonstrated a significant decrease in the maximal activity in anoxic FBPase and decreased sensitivity to its substrate Fructose-1,6-bisphosphate (FBP) when compared to the control. Immunoblotting demonstrated increased threonine phosphorylation (~1.4-fold) in the anoxic FBPase. Taken together, these results suggest that the phosphorylation of liver FBPase is an important step in suppressing FBPase activity, ultimately leading to the inhibition of gluconeogenesis in the liver of the red-eared slider during anaerobic conditions. Full article
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26 pages, 6249 KiB  
Article
Cdc42-Specific GTPase-Activating Protein Rga1 Squelches Crosstalk between the High-Osmolarity Glycerol (HOG) and Mating Pheromone Response MAPK Pathways
by Jesse C. Patterson, Louise S. Goupil and Jeremy Thorner
Biomolecules 2021, 11(10), 1530; https://doi.org/10.3390/biom11101530 - 17 Oct 2021
Cited by 5 | Viewed by 4623
Abstract
Eukaryotes utilize distinct mitogen/messenger-activated protein kinase (MAPK) pathways to evoke appropriate responses when confronted with different stimuli. In yeast, hyperosmotic stress activates MAPK Hog1, whereas mating pheromones activate MAPK Fus3 (and MAPK Kss1). Because these pathways share several upstream components, including the small [...] Read more.
Eukaryotes utilize distinct mitogen/messenger-activated protein kinase (MAPK) pathways to evoke appropriate responses when confronted with different stimuli. In yeast, hyperosmotic stress activates MAPK Hog1, whereas mating pheromones activate MAPK Fus3 (and MAPK Kss1). Because these pathways share several upstream components, including the small guanosine-5'-triphosphate phosphohydrolase (GTPase) cell-division-cycle-42 (Cdc42), mechanisms must exist to prevent inadvertent cross-pathway activation. Hog1 activity is required to prevent crosstalk to Fus3 and Kss1. To identify other factors required to maintain signaling fidelity during hypertonic stress, we devised an unbiased genetic selection for mutants unable to prevent such crosstalk even when active Hog1 is present. We repeatedly isolated truncated alleles of RGA1, a Cdc42-specific GTPase-activating protein (GAP), each lacking its C-terminal catalytic domain, that permit activation of the mating MAPKs under hyperosmotic conditions despite Hog1 being present. We show that Rga1 down-regulates Cdc42 within the high-osmolarity glycerol (HOG) pathway, but not the mating pathway. Because induction of mating pathway output via crosstalk from the HOG pathway takes significantly longer than induction of HOG pathway output, our findings suggest that, under normal conditions, Rga1 contributes to signal insulation by limiting availability of the GTP-bound Cdc42 pool generated by hypertonic stress. Thus, Rga1 action contributes to squelching crosstalk by imposing a type of “kinetic proofreading”. Although Rga1 is a Hog1 substrate in vitro, we eliminated the possibility that its direct Hog1-mediated phosphorylation is necessary for its function in vivo. Instead, we found first that, like its paralog Rga2, Rga1 is subject to inhibitory phosphorylation by the S. cerevisiae cyclin-dependent protein kinase 1 (Cdk1) ortholog Cdc28 and that hyperosmotic shock stimulates its dephosphorylation and thus Rga1 activation. Second, we found that Hog1 promotes Rga1 activation by blocking its Cdk1-mediated phosphorylation, thereby allowing its phosphoprotein phosphatase 2A (PP2A)-mediated dephosphorylation. These findings shed light on why Hog1 activity is required to prevent crosstalk from the HOG pathway to the mating pheromone response pathway. Full article
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16 pages, 999 KiB  
Review
MicroRNAs and Metabolism: Revisiting the Warburg Effect with Emphasis on Epigenetic Background and Clinical Applications
by Zsuzsanna Gaál
Biomolecules 2021, 11(10), 1531; https://doi.org/10.3390/biom11101531 - 17 Oct 2021
Cited by 5 | Viewed by 4726
Abstract
Since the well-known hallmarks of cancer were described by Hanahan and Weinberg, fundamental advances of molecular genomic technologies resulted in the discovery of novel puzzle pieces in the multistep pathogenesis of cancer. MicroRNAs are involved in the altered epigenetic pattern and metabolic phenotype [...] Read more.
Since the well-known hallmarks of cancer were described by Hanahan and Weinberg, fundamental advances of molecular genomic technologies resulted in the discovery of novel puzzle pieces in the multistep pathogenesis of cancer. MicroRNAs are involved in the altered epigenetic pattern and metabolic phenotype of malignantly transformed cells. They contribute to the initiation, progression and metastasis-formation of cancers, also interacting with oncogenes, tumor-suppressor genes and epigenetic modifiers. Metabolic reprogramming of cancer cells results from the dysregulation of a complex network, in which microRNAs are located at central hubs. MicroRNAs regulate the expression of several metabolic enzymes, including tumor-specific isoforms. Therefore, they have a direct impact on the levels of metabolites, also influencing epigenetic pattern due to the metabolite cofactors of chromatin modifiers. Targets of microRNAs include numerous epigenetic enzymes, such as sirtuins, which are key regulators of cellular metabolic homeostasis. A better understanding of reversible epigenetic and metabolic alterations opened up new horizons in the personalized treatment of cancer. MicroRNA expression levels can be utilized in differential diagnosis, prognosis stratification and prediction of chemoresistance. The therapeutic modulation of microRNA levels is an area of particular interest that provides a promising tool for restoring altered metabolism of cancer cells. Full article
(This article belongs to the Special Issue MicroRNAs - Small Molecules with Great Potential in Tumorigenesis)
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23 pages, 2779 KiB  
Review
Decoding Stem Cells: An Overview on Planarian Stem Cell Heterogeneity and Lineage Progression
by M. Dolores Molina and Francesc Cebrià
Biomolecules 2021, 11(10), 1532; https://doi.org/10.3390/biom11101532 - 17 Oct 2021
Cited by 21 | Viewed by 9284
Abstract
Planarians are flatworms capable of whole-body regeneration, able to regrow any missing body part after injury or amputation. The extraordinary regenerative capacity of planarians is based upon the presence in the adult of a large population of somatic pluripotent stem cells. These cells, [...] Read more.
Planarians are flatworms capable of whole-body regeneration, able to regrow any missing body part after injury or amputation. The extraordinary regenerative capacity of planarians is based upon the presence in the adult of a large population of somatic pluripotent stem cells. These cells, called neoblasts, offer a unique system to study the process of stem cell specification and differentiation in vivo. In recent years, FACS-based isolation of neoblasts, RNAi functional analyses as well as high-throughput approaches such as single-cell sequencing have allowed a rapid progress in our understanding of many different aspects of neoblast biology. Here, we summarize our current knowledge on the molecular signatures that define planarian neoblasts heterogeneity, which includes a percentage of truly pluripotent stem cells, and guide the commitment of pluripotent neoblasts into lineage-specific progenitor cells, as well as their differentiation into specific planarian cell types. Full article
(This article belongs to the Special Issue New Insights into Stem Cell Regulation)
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34 pages, 8749 KiB  
Review
Hyaluronic Acid: A Key Ingredient in the Therapy of Inflammation
by Andreia Marinho, Cláudia Nunes and Salette Reis
Biomolecules 2021, 11(10), 1518; https://doi.org/10.3390/biom11101518 - 15 Oct 2021
Cited by 272 | Viewed by 18911
Abstract
Hyaluronic acid (HA) is a natural polymer, produced endogenously by the human body, which has unique physicochemical and biological properties, exhibiting desirable biocompatibility and biodegradability. Therefore, it has been widely studied for possible applications in the area of inflammatory diseases. Although exogenous HA [...] Read more.
Hyaluronic acid (HA) is a natural polymer, produced endogenously by the human body, which has unique physicochemical and biological properties, exhibiting desirable biocompatibility and biodegradability. Therefore, it has been widely studied for possible applications in the area of inflammatory diseases. Although exogenous HA has been described as unable to restore or replace the properties and activities of endogenous HA, it can still provide satisfactory pain relief. This review aims to discuss the advances that have been achieved in the treatment of inflammatory diseases using hyaluronic acid as a key ingredient, essentially focusing on studies carried out between the years 2017 and 2021. Full article
(This article belongs to the Special Issue Hyaluronic Acid in Human Medicine)
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11 pages, 932 KiB  
Review
Hyperbaric Oxygen Treatment—From Mechanisms to Cognitive Improvement
by Irit Gottfried, Nofar Schottlender and Uri Ashery
Biomolecules 2021, 11(10), 1520; https://doi.org/10.3390/biom11101520 - 15 Oct 2021
Cited by 79 | Viewed by 13657
Abstract
Hyperbaric oxygen treatment (HBOT)—the medical use of oxygen at environmental pressure greater than one atmosphere absolute—is a very effective therapy for several approved clinical situations, such as carbon monoxide intoxication, incurable diabetes or radiation-injury wounds, and smoke inhalation. In recent years, it has [...] Read more.
Hyperbaric oxygen treatment (HBOT)—the medical use of oxygen at environmental pressure greater than one atmosphere absolute—is a very effective therapy for several approved clinical situations, such as carbon monoxide intoxication, incurable diabetes or radiation-injury wounds, and smoke inhalation. In recent years, it has also been used to improve cognition, neuro-wellness, and quality of life following brain trauma and stroke. This opens new avenues for the elderly, including the treatment of neurological and neurodegenerative diseases and improvement of cognition and brain metabolism in cases of mild cognitive impairment. Alongside its integration into clinics, basic research studies have elucidated HBOT’s mechanisms of action and its effects on cellular processes, transcription factors, mitochondrial function, oxidative stress, and inflammation. Therefore, HBOT is becoming a major player in 21st century research and clinical treatments. The following review will discuss the basic mechanisms of HBOT, and its effects on cellular processes, cognition, and brain disorders. Full article
(This article belongs to the Special Issue Oxygen Therapy)
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