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Georgiev V, Ivanov I, Pavlov A. Recent Progress in Amaryllidaceae Biotechnology. Molecules 2020; 25:E4670. [PMID: 33066212 PMCID: PMC7587388 DOI: 10.3390/molecules25204670] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/07/2020] [Accepted: 10/12/2020] [Indexed: 12/11/2022] Open
Abstract
Plants belonging to the monocotyledonous Amaryllidaceae family include about 1100 species divided among 75 genera. They are well known as medicinal and ornamental plants, producing pharmaceutically important alkaloids, the most intensively investigated of which are galanthamine and lycorine. Amaryllidaceae alkaloids possess various biological activities, the most important one being their anti-acetylcholinesterase activity, used for the treatment of Alzheimer's disease. Due to increased demand for Amaryllidaceae alkaloids (mainly galanthamine) and the limited availability of plant sources, in vitro culture technology has attracted the attention of researchers as a prospective alternative for their sustainable production. Plant in vitro systems have been extensively used for continuous, sustainable, and economically viable production of bioactive plant secondary metabolites. Over the past two decades, a significant success has been demonstrated in the development of in vitro systems synthesizing Amaryllidaceae alkaloids. The present review discusses the state of the art of in vitro Amaryllidaceae alkaloids production, summarizing recently documented plant in vitro systems producing them, as well as the authors' point of view on the development of biotechnological production processes with a focus on the future prospects of in vitro culture technology for the commercial production of these valuable alkaloids.
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Han H, Davidson LA, Fan Y, Goldsby JS, Yoon G, Jin U, Wright GA, Landrock KK, Weeks BR, Wright RC, Allred CD, Jayaraman A, Ivanov I, Roper J, Safe SH, Chapkin RS. Loss of aryl hydrocarbon receptor potentiates FoxM1 signaling to enhance self-renewal of colonic stem and progenitor cells. EMBO J 2020; 39:e104319. [PMID: 32915464 PMCID: PMC7527924 DOI: 10.15252/embj.2019104319] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/28/2020] [Accepted: 07/02/2020] [Indexed: 12/26/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR), a ligand-activated transcription factor that senses xenobiotics, diet, and gut microbial-derived metabolites, is increasingly recognized as a key regulator of intestinal biology. However, its effects on the function of colonic stem and progenitor cells remain largely unexplored. Here, we observed that inducible deletion of AhR in Lgr5+ stem cells increases the percentage of colonic stem cells and enhances organoid initiating capacity and growth of sorted stem and progenitor cells, while AhR activation has the opposite effect. Moreover, intestinal-specific AhR knockout increases basal stem cell and crypt injury-induced cell proliferation and promotes colon tumorigenesis in a preclinical colitis-associated tumor model by upregulating FoxM1 signaling. Mechanistically, AhR transcriptionally suppresses FoxM1 expression. Activation of AhR in human organoids recapitulates phenotypes observed in mice, such as reduction in the percentage of colonic stem cells, promotion of stem cell differentiation, and attenuation of FoxM1 signaling. These findings indicate that the AhR-FoxM1 axis, at least in part, mediates colonic stem/progenitor cell behavior.
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Levett J, Ivanov I, Moran T, Spaziano M. TCT CONNECT-190 A Novel Artificial Intelligence Algorithm for Dynamical Coronary Artery Segmentation. J Am Coll Cardiol 2020. [DOI: 10.1016/j.jacc.2020.09.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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79
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Tsvetkov D, Mazurin M, Ivanov I, Malyshkin D, Sereda V, Zuev A. Crucial Role of Water in the Mechanosynthesis of CsPbI
3
and Other ABX
3
Halides. Chemistry 2020; 26:12549-12552. [DOI: 10.1002/chem.202003067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/04/2020] [Indexed: 01/28/2023]
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80
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Kleineberg C, Wölfer C, Abbasnia A, Pischel D, Bednarz C, Ivanov I, Heitkamp T, Börsch M, Sundmacher K, Vidaković‐Koch T. Light-Driven ATP Regeneration in Diblock/Grafted Hybrid Vesicles. Chembiochem 2020; 21:2149-2160. [PMID: 32187828 PMCID: PMC7496644 DOI: 10.1002/cbic.201900774] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/02/2020] [Indexed: 01/19/2023]
Abstract
Light-driven ATP regeneration systems combining ATP synthase and bacteriorhodopsin have been proposed as an energy supply in the field of synthetic biology. Energy is required to power biochemical reactions within artificially created reaction compartments like protocells, which are typically based on either lipid or polymer membranes. The insertion of membrane proteins into different hybrid membranes is delicate, and studies comparing these systems with liposomes are needed. Here we present a detailed study of membrane protein functionality in different hybrid compartments made of graft polymer PDMS-g-PEO and diblock copolymer PBd-PEO. Activity of more than 90 % in lipid/polymer-based hybrid vesicles could prove an excellent biocompatibility. A significant enhancement of long-term stability (80 % remaining activity after 42 days) could be demonstrated in polymer/polymer-based hybrids.
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Kleineberg C, Wölfer C, Abbasnia A, Pischel D, Bednarz C, Ivanov I, Heitkamp T, Börsch M, Sundmacher K, Vidaković‐Koch T. Cover Feature: Light‐Driven ATP Regeneration in Diblock/Grafted Hybrid Vesicles (ChemBioChem 15/2020). Chembiochem 2020. [DOI: 10.1002/cbic.202000427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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82
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Krachmarova E, Ivanov I, Nacheva G. Nucleic acids in inclusion bodies obtained from E. coli cells expressing human interferon-gamma. Microb Cell Fact 2020; 19:139. [PMID: 32652996 PMCID: PMC7353671 DOI: 10.1186/s12934-020-01400-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/07/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inclusion bodies (IBs) are protein aggregates in recombinant bacterial cells containing mainly the target recombinant protein. Although it has been shown that IBs contain functional proteins along with protein aggregates, their direct application as pharmaceuticals is hindered by their heterogeneity and hazardous contaminants with bacterial origin. Therefore, together with the production of soluble species, IBs remain the main source for manufacture of recombinant proteins with medical application. The quality and composition of the IBs affect the refolding yield and further purification of the recombinant protein. The knowledge whether nucleic acids are genuine components or concomitant impurities of the IBs is a prerequisite for the understanding of the IBs formation and for development of optimized protocols for recombinant protein refolding and purification. IBs isolated from Escherichia coli overexpressing human interferon-gamma (hIFNγ), a protein with therapeutic application, were used as a model. RESULTS IBs were isolated from E. coli LE392 cells transformed with a hIFNγ expressing plasmid under standard conditions and further purified by centrifugation on a sucrose cushion, followed by several steps of sonication and washings with non-denaturing concentrations of urea. The efficiency of the purification was estimated by SDS-PAGE gel electrophoresis and parallel microbiological testing for the presence of residual intact bacteria. Phenol/chloroform extraction showed that the highly purified IBs contain both DNA and RNA. The latter were studied by UV spectroscopy and agarose gel electrophoresis combined with enzymatic treatment and hybridization. DNA was observed as a diffuse fraction mainly in the range of 250 to 1000 bp. RNA isolated by TRIzol® also demonstrated a substantial molecular heterogeneity. Hybridization with 32P-labelled oligonucleotides showed that the IBs contain rRNA and are enriched of hIFNγ mRNA. CONCLUSIONS The results presented in this study indicate that the nucleic acids might be intrinsic components rather than co-precipitated impurities in the IBs. We assume that the nucleic acids are active participants in the aggregation of recombinant proteins and formation of the IBs that originate from the transcription and translation machinery of the microbial cell factory. Further studies are needed to ascertain this notion.
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Marušič N, Otrin L, Zhao Z, Lira RB, Kyrilis FL, Hamdi F, Kastritis PL, Vidaković-Koch T, Ivanov I, Sundmacher K, Dimova R. Constructing artificial respiratory chain in polymer compartments: Insights into the interplay between bo3 oxidase and the membrane. Proc Natl Acad Sci U S A 2020; 117:15006-15017. [PMID: 32554497 PMCID: PMC7334566 DOI: 10.1073/pnas.1919306117] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cytochrome bo3 ubiquinol oxidase is a transmembrane protein, which oxidizes ubiquinone and reduces oxygen, while pumping protons. Apart from its combination with F1Fo-ATPase to assemble a minimal ATP regeneration module, the utility of the proton pump can be extended to other applications in the context of synthetic cells such as transport, signaling, and control of enzymatic reactions. In parallel, polymers have been speculated to be phospholipid mimics with respect to their ability to self-assemble in compartments with increased stability. However, their usability as interfaces for complex membrane proteins has remained questionable. In the present work, we optimized a fusion/electroformation approach to reconstitute bo3 oxidase in giant unilamellar vesicles made of PDMS-g-PEO and/or phosphatidylcholine (PC). This enabled optical access, while microfluidic trapping allowed for online analysis of individual vesicles. The tight polymer membranes and the inward oriented enzyme caused 1 pH unit difference in 30 min, with an initial rate of 0.35 pH·min-1 To understand the interplay in these composite systems, we studied the relevant mechanical and rheological membrane properties. Remarkably, the proton permeability of polymer/lipid hybrids decreased after protein insertion, while the latter also led to a 20% increase of the polymer diffusion coefficient in polymersomes. In addition, PDMS-g-PEO increased the activity lifetime and the resistance to free radicals. These advantageous properties may open diverse applications, ranging from cell-free biotechnology to biomedicine. Furthermore, the presented study serves as a comprehensive road map for studying the interactions between membrane proteins and synthetic membranes, which will be fundamental for the successful engineering of such hybrid systems.
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Pacheva I, Ivanov I. Targeted Biomedical Treatment for Autism Spectrum Disorders. Curr Pharm Des 2020; 25:4430-4453. [PMID: 31801452 DOI: 10.2174/1381612825666191205091312] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 12/02/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND A diagnosis of autism spectrum disorders (ASD) represents presentations with impairment in communication and behaviour that vary considerably in their clinical manifestations and etiology as well as in their likely pathophysiology. A growing body of data indicates that the deleterious effect of oxidative stress, mitochondrial dysfunction, immune dysregulation and neuroinflammation, as well as their interconnections are important aspects of the pathophysiology of ASD. Glutathione deficiency decreases the mitochondrial protection against oxidants and tumor necrosis factor (TNF)-α; immune dysregulation and inflammation inhibit mitochondrial function through TNF-α; autoantibodies against the folate receptors underpin cerebral folate deficiency, resulting in disturbed methylation, and mitochondrial dysfunction. Such pathophysiological processes can arise from environmental and epigenetic factors as well as their combined interactions, such as environmental toxicant exposures in individuals with (epi)genetically impaired detoxification. The emerging evidence on biochemical alterations in ASD is forming the basis for treatments aimed to target its biological underpinnings, which is of some importance, given the uncertain and slow effects of the various educational interventions most commonly used. METHODS Literature-based review of the biomedical treatment options for ASD that are derived from established pathophysiological processes. RESULTS Most proposed biomedical treatments show significant clinical utility only in ASD subgroups, with specified pre-treatment biomarkers that are ameliorated by the specified treatment. For example, folinic acid supplementation has positive effects in ASD patients with identified folate receptor autoantibodies, whilst the clinical utility of methylcobalamine is apparent in ASD patients with impaired methylation capacity. Mitochondrial modulating cofactors should be considered when mitochondrial dysfunction is evident, although further research is required to identify the most appropriate single or combined treatment. Multivitamins/multiminerals formulas, as well as biotin, seem appropriate following the identification of metabolic abnormalities, with doses tapered to individual requirements. A promising area, requiring further investigations, is the utilization of antipurinergic therapies, such as low dose suramin. CONCLUSION The assessment and identification of relevant physiological alterations and targeted intervention are more likely to produce positive treatment outcomes. As such, current evidence indicates the utility of an approach based on personalized and evidence-based medicine, rather than treatment targeted to all that may not always be beneficial (primum non nocere).
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Arbizu S, Noratto G, Layosa M, Lage NN, Atienza L, Ivanov I, Talcott S, Chew BP. Chemopreventive Potential of DSC Anthocyanins and Total Phenolics Extracted from Dark Sweet Cherry (DSC) Through Modulation of MDA-MB-453 Breast Tumor Proteomic Profile. Curr Dev Nutr 2020. [DOI: 10.1093/cdn/nzaa044_004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Objectives
To investigate in vivo the chemopreventive activity of dark sweet cherry (DSC) extracted total phenolics (WE) or fractions enriched in anthocyanins (ACN) or proanthocyanidins (PCN) in athymic nude mice xenografted with MDA-MB-453 breast cancer cells.
Methods
MDA-MB-453 breast cancer cells (1 × 106 cells) were xenografted into athymic nude mice. Mice were gavaged with WE, ACN, or PCN extracts (150 mg/kg body weight/day) for 36 days followed by animal termination. Main organs and tumors were dissected for protein analyses following standard molecular biology techniques and high-resolution nano-HPLC tandem mass spectrometry.
Results
Tumor volume growth was suppressed at similar levels by WE, ACN, and PCN compared to controls (C) without signs of toxicity in main organs. Tumor protein analysis revealed ERK1/2 phosphorylation induced by WE, ACN, and PCN at similar levels, which may be linked to apoptosis induction by stress regulated ERK1/2 activation. Immunohistochemistry analysis showed decreased tumor cell proliferation and Ki-67 H-scores with potency WE ≥ ACN ≥ PCN. Differential quantitative proteomic analysis of tumor tissues from ACN and C groups revealed the identity of 71 proteins associated with poor breast cancer prognosis that were expressed only in C group (66 proteins), or upregulated in C group (5 proteins) compared to ACN group (p < 0.05).
Conclusions
These findings revealed the potential of DSC phenolics for breast cancer invasion and metastasis chemoprevention.
Funding Sources
This work was supported by the Northwest Cherry Growers, Washington State Fruit Commission.
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Noratto G, Layosa MA, Lage NN, Atienza L, Ivanov I, Mertens-Talcott SU, Chew BP. Antitumor potential of dark sweet cherry sweet (Prunus avium) phenolics in suppressing xenograft tumor growth of MDA-MB-453 breast cancer cells. J Nutr Biochem 2020; 84:108437. [PMID: 32615370 DOI: 10.1016/j.jnutbio.2020.108437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 12/26/2022]
Abstract
This study investigated in vivo the antitumor activity of dark sweet cherry (DSC) whole extracted phenolics (WE) and fractions enriched in anthocyanins (ACN) or proanthocyanidins (PCA) in athymic mice xenografted with MDA-MB-453 breast cancer cells. Mice were gavaged with WE, ACN or PCA extracts (150 mg/kg body weight/day) for 36 days. Results showed that tumor growth was suppressed at similar levels by WE, ACN and PCA compared to control group (C) without signs of toxicity or significant changes in mRNA oncogenic biomarkers in tumors or mRNA invasive biomarker in distant organs. Tumor protein analyses showed that WE, ACN and PCA induced at similar levels the stress-regulated ERK1/2 phosphorylation, known to be linked to apoptosis induction. However, ACN showed enhanced antitumor activity through down-regulation of total oncogenic and stress-related Akt, STAT3, p38, JNK and NF-kB proteins. In addition, immunohistochemistry analysis of Ki-67 revealed inhibition of tumor cell proliferation with potency WE ≥ ACN ≥ PCA. Differential quantitative proteomic high-resolution nano-HPLC tandem mass spectrometry analysis of tumors from ACN and C groups revealed the identity of 66 proteins associated with poor breast cancer prognosis that were expressed only in C group (61 proteins) or differentially up-regulated (P<.05) in C group (5 proteins). These findings revealed ACN-targeted proteins associated to tumor growth and invasion and the potential of DSC ACN for breast cancer treatment. Results lead to a follow-up study with highly immunodeficient mice/invasive cell line subtype and advanced tumor development to validate the anti-invasive activity of DSC anthocyanins.
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87
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Windberger U, Dibiasi C, Lotz EM, Scharbert G, Reinbacher-Koestinger A, Ivanov I, Ploszczanski L, Antonova N, Lichtenegger H. The effect of hematocrit, fibrinogen concentration and temperature on the kinetics of clot formation of whole blood. Clin Hemorheol Microcirc 2020; 75:431-445. [PMID: 32390608 DOI: 10.3233/ch-190799] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Dynamic mechanical analysis of blood clots can be used to detect the coagulability of blood. OBJECTIVE We investigated the kinetics of clot formation by changing several blood components, and we looked into the clot "signature" at its equilibrium state by using viscoelastic and dielectric protocols. METHODS Oscillating shear rheometry, ROTEM, and a dielectro-rheological device was used. RESULTS In fibrinogen- spiked samples we found the classical high clotting ability: shortened onset, faster rate of clotting, and higher plateau stiffness. Electron microscopy explained the gain of stiffness. Incorporated RBCs weakened the clots. Reduction of temperature during the clotting process supported the development of high moduli by providing more time for fiber assembly. But at low HCT, clot firmness could be increased by elevating the temperature from 32 to 37°C. In contrast, when the fibrinogen concentration was modified, acceleration of clotting via temperature always reduced clot stiffness, whatever the initial fibrinogen concentration. Electrical resistance increased continuously during clotting; loss tangent (D) (relaxation frequency 249 kHz) decreased when clots became denser: fewer dipoles contributed to the relaxation process. The relaxation peak (Dmax) shifted to lower frequencies at higher platelet count. CONCLUSION Increasing temperature accelerates clot formation but weakens clots. Rheometry and ROTEM correlate well.
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Abstract
Cross validation is often used to split input data into training and test set in Support vector machines. The two most commonly used cross validation versions are the tenfold and leave-one-out cross validation. Another commonly used resampling method is the random test/train split. The advantage of these methods is that they avoid overfitting in the model and perform model selection. They, however, can increase the computational time for fitting Support vector machines with the increase of the size of the dataset. In this research, we propose an alternative for fitting SVM, which we call the tenfold bootstrap for Support vector machines. This resampling procedure can significantly reduce execution time despite the big number of observations, while preserving model’s accuracy. With this finding, we propose a solution to the problem of slow execution time when fitting support vector machines on big datasets.
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Coleman MC, Whitfield-Cargile C, Cohen ND, Goldsby JL, Davidson L, Chamoun-Emanuelli AM, Ivanov I, Eades S, Ing N, Chapkin RS. Non-invasive evaluation of the equine gastrointestinal mucosal transcriptome. PLoS One 2020; 15:e0229797. [PMID: 32176710 PMCID: PMC7075554 DOI: 10.1371/journal.pone.0229797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/13/2020] [Indexed: 02/07/2023] Open
Abstract
Evaluating the health and function of the gastrointestinal tract can be challenging in all species, but is especially difficult in horses due to their size and length of the gastrointestinal (GI) tract. Isolation of mRNA of cells exfoliated from the GI mucosa into feces (i.e., the exfoliome) offers a novel means of non-invasively examining the gene expression profile of the GI mucosa. This approach has been utilized in people with colorectal cancer. Moreover, we have utilized this approach in a murine model of GI inflammation and demonstrated that the exfoliome reflects the tissue transcriptome. The ability of the equine exfoliome to provide non-invasive information regarding the health and function of the GI tract is not known. The objective of this study was to characterize the gene expression profile found in exfoliated intestinal epithelial cells from normal horses and compare the exfoliome data with the tissue mucosal transcriptome. Mucosal samples were collected from standardized locations along the GI tract (i.e. ileum, cecum, right dorsal colon, and rectum) from four healthy horses immediately following euthanasia. Voided feces were also collected. RNA isolation, library preparation, and RNA sequencing was performed on fecal and intestinal mucosal samples. Comparison of gene expression profiles from the tissue and exfoliome revealed correlation of gene expression. Moreover, the exfoliome contained reads representing the diverse array of cell types found in the GI mucosa suggesting the equine exfoliome serves as a non-invasive means of examining the global gene expression pattern of the equine GI tract.
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Garcia-Villatoro EL, DeLuca JAA, Callaway ES, Allred KF, Davidson LA, Hensel ME, Menon R, Ivanov I, Safe SH, Jayaraman A, Chapkin RS, Allred CD. Effects of high-fat diet and intestinal aryl hydrocarbon receptor deletion on colon carcinogenesis. Am J Physiol Gastrointest Liver Physiol 2020; 318:G451-G463. [PMID: 31905023 PMCID: PMC7137094 DOI: 10.1152/ajpgi.00268.2019] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Consumption of a high-fat diet has been associated with an increased risk of developing colorectal cancer (CRC). However, the effects of the interaction between dietary fat content and the aryl hydrocarbon receptor (AhR) on colorectal carcinogenesis remain unclear. Mainly known for its role in xenobiotic metabolism, AhR has been identified as an important regulator for maintaining intestinal epithelial homeostasis. Although previous research using whole body AhR knockout mice has revealed an increased incidence of colon and cecal tumors, the unique role of AhR activity in intestinal epithelial cells (IECs) and modifying effects of fat content in the diet at different stages of sporadic CRC development are yet to be elucidated. In the present study, we have examined the effects of a high-fat diet on IEC-specific AhR knockout mice in a model of sporadic CRC. Although loss of AhR activity in IECs significantly induced the development of premalignant lesions, in a separate experiment, no significant changes in colon mass incidence were observed. Moreover, consumption of a high-fat diet promoted cell proliferation in crypts at the premalignant colon cancer lesion stage and colon mass multiplicity as well as β-catenin expression and nuclear localization in actively proliferating cells in colon masses. Our data demonstrate the modifying effects of high-fat diet and AhR deletion in IECs on tumor initiation and progression.NEW & NOTEWORTHY Through the use of an intestinal-specific aryl hydrocarbon receptor (AhR) knockout mouse model, this study demonstrates that the expression of AhR in intestinal epithelial cells is required to reduce the formation of premalignant colon cancer lesions. Furthermore, consumption of a high-fat diet and the loss of AhR in intestinal epithelial cells influences the development of colorectal cancer at various stages.
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Abstract
Understanding how health-promoting microbiota are established and their beneficial interactions with the host is of critical biomedical importance. The current high throughput data acquisition technologies allow for integrating components of the gut ecosystem. The richness of data types and large number of measured variables involved underscores the critical importance of the appropriate choice of analytical and computational methods that can be used to model this complex ecosystem. This review outlines currently used approaches to perform analyses of data obtained as a result of interrogation of the gut-microbiota ecosystem and the challenges associated with these methodological and computational efforts. The problem of large dimensionality versus small numbers of samples is explained with discussions of clustering, dimensionality reduction, and statistical testing. Predictive modeling and data integration specific to the gut ecosystem are also discussed.
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92
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Ivanov I, Verhamme IM, Sun MF, Mohammed B, Cheng Q, Matafonov A, Dickeson SK, Joseph K, Kaplan AP, Gailani D. Protease activity in single-chain prekallikrein. Blood 2020; 135:558-567. [PMID: 31800958 PMCID: PMC7033373 DOI: 10.1182/blood.2019002224] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 11/19/2019] [Indexed: 12/23/2022] Open
Abstract
Prekallikrein (PK) is the precursor of the trypsin-like plasma protease kallikrein (PKa), which cleaves kininogens to release bradykinin and converts the protease precursor factor XII (FXII) to the enzyme FXIIa. PK and FXII undergo reciprocal conversion to their active forms (PKa and FXIIa) by a process that is accelerated by a variety of biological and artificial surfaces. The surface-mediated process is referred to as contact activation. Previously, we showed that FXII expresses a low level of proteolytic activity (independently of FXIIa) that may initiate reciprocal activation with PK. The current study was undertaken to determine whether PK expresses similar activity. Recombinant PK that cannot be converted to PKa was prepared by replacing Arg371 with alanine at the activation cleavage site (PK-R371A, or single-chain PK). Despite being constrained to the single-chain precursor form, PK-R371A cleaves high-molecular-weight kininogen (HK) to release bradykinin with a catalytic efficiency ∼1500-fold lower than that of kallikrein cleavage of HK. In the presence of a surface, PK-R371A converts FXII to FXIIa with a specific activity ∼4 orders of magnitude lower than for PKa cleavage of FXII. These results support the notion that activity intrinsic to PK and FXII can initiate reciprocal activation of FXII and PK in solution or on a surface. The findings are consistent with the hypothesis that the putative zymogens of many trypsin-like proteases are actually active proteases, explaining their capacity to undergo processes such as autoactivation and to initiate enzyme cascades.
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Marušič N, Otrin L, Zhao Z, Lira RB, Vidaković-Koch T, Ivanov I, Dimova R, Sundmacher K. Reconstitution of Respiratory Enzymes in PDMS-g-PEO Polymer and Polymer/Lipid Hybrid Vesicles. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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94
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Bogoeva V, Petrova L, Bouckaert J, Yordanova A, Ivanov I, Vanderesse R, Frochot C. Dual function of lectins — new perspectives in targeted photodynamic therapy. J PORPHYR PHTHALOCYA 2020. [DOI: 10.1142/s1088424619300209] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Porphyrins and phthalocyanines are photosensitizers (PS) that are used in clinical imaging, detection of cancer cells and are particularly applied in photodynamic therapy (PDT). Many scientists have been focused on the design of different porphyrin compounds. However, similar to other anti-cancer agents, they cannot selectively recognize tumor tissues. Scientists are seeking new methods to overcome this problem and to find appropriate targeted delivery strategies. Plant lectins are especially suitable molecules for such targeting as they preferentially recognize specific antigens on the glycosylated cancer cells. This review will give more detailed information about the dual function of lectins and their interactions with PSs, which is a new perspective in targeted PDT. The implications and potential applications of such studies will also be discussed.
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Ivanov I, Kotev V. PERSONALITY CHARACTERISTICS AND CONFLICT PREDISPOSITIONS IN TEAMS MARITZA AND RAKOVSKI FROM BULGARIAN WOMEN’S NATIONAL VOLLEYBALL LEAGUE. JOURNAL OF APPLIED SPORTS SCIENCES 2019. [DOI: 10.37393/jass.2019.02.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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96
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Gerasimov I, Trifonov S, Marinova D, Todorov A, Vacheva I, Popovska S, Asparuhov A, Ivanov I. MORPHOLOGICAL CHANGES IN THE PROPRIOCEPTORS OF HUMAN ANTERIOR CRUCIATE LIGAMENT DURING DEGENERATIVE OSTEOARTHRITIS. JOURNAL OF IMAB 2019. [DOI: 10.5272/jimab.2019254.2847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Wang Y, Ivanov I, Smith SA, Gailani D, Morrissey JH. Polyphosphate, Zn 2+ and high molecular weight kininogen modulate individual reactions of the contact pathway of blood clotting. J Thromb Haemost 2019; 17:2131-2140. [PMID: 31420909 PMCID: PMC6893101 DOI: 10.1111/jth.14612] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/09/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Inorganic polyphosphate modulates the contact pathway of blood clotting, which is implicated in thrombosis and inflammation. Polyphosphate polymer lengths are highly variable, with shorter polymers (approximately 60-100 phosphates) secreted from human platelets, and longer polymers (up to thousands of phosphates) in microbes. We previously reported that optimal triggering of clotting via the contact pathway requires very long polyphosphates, although the impact of shorter polyphosphate polymers on individual proteolytic reactions of the contact pathway was not interrogated. OBJECTIVES AND METHODS We conducted in vitro measurements of enzyme kinetics to investigate the ability of varying polyphosphate sizes, together with high molecular weight kininogen and Zn2+ , to mediate four individual proteolytic reactions of the contact pathway: factor XII autoactivation, factor XII activation by kallikrein, prekallikrein activation by factor XIIa, and prekallikrein autoactivation. RESULTS The individual contact pathway reactions were differentially dependent on polyphosphate length. Very long-chain polyphosphate was required to support factor XII autoactivation, whereas platelet-size polyphosphate significantly accelerated the activation of factor XII by kallikrein, and the activation of prekallikrein by factor XIIa. Intriguingly, polyphosphate did not support prekallikrein autoactivation. We also report that high molecular weight kininogen was required only when kallikrein was the enzyme (ie, FXII activation by kallikrein), whereas Zn2+ was required only when FXII was the substrate (ie, FXII activation by either kallikrein or FXIIa). Activation of prekallikrein by FXIIa required neither Zn2+ nor high molecular weight kininogen. CONCLUSIONS Platelet polyphosphate and Zn2+ can promote subsets of the reactions of the contact pathway, with implications for a variety of disease states.
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Kim E, Ivanov I, Dougherty ER. Quantifying the notions of canalizing and master genes in a gene regulatory network-a Boolean network modeling perspective. Bioinformatics 2019; 35:643-649. [PMID: 30052771 DOI: 10.1093/bioinformatics/bty665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 07/18/2018] [Accepted: 07/24/2018] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Canalizing genes enforce broad corrective actions on cellular processes for the purpose of biological robustness maintaining a constant phenotype to remain unchanged in spite of genetic mutations or environmental perturbations. Despite their central role in biological systems, the observation/detection of canalizing genes is often impeded because the behavior of affected genes is highly varied relative to the inactive canalizer. Therefore, the activity of canalizing genes is difficult to predict to any significant degree by their subject genes under normal cell conditions. RESULTS We investigate this question and present a quantitative framework that allows for the estimation of the power of canalizing genes in the context of Boolean Networks (BNs) with perturbation. This framework borrows tools from the Pattern Recognition theory and uses the coefficient of determination (CoD) to capture the capacity of the canalizing genes. The canalizing power (CP) of a gene is quantitatively characterized by two terms: regulation power (RP) and incapacitating power (IP). We base this assumption on the idea that canalizing power of a gene should be quantified by the extent of its regulation on the overall network and the extent of control that the gene takes over from other master genes when it is activated, which is equivalent to reduction of the control of other master genes upon its activation. Following this, the CP concept is illustrated with examples in which the goal is to provide preliminary evidence that CP can be used to characterize the ability of canalizing genes. AVAILABILITY AND IMPLEMENTATION A library of functions written in MATLAB for computing CP is available at http://github.com/eunjikim-angie/CanalizingPower.
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Krafft D, López Castellanos S, Lira RB, Dimova R, Ivanov I, Sundmacher K. Compartments for Synthetic Cells: Osmotically Assisted Separation of Oil from Double Emulsions in a Microfluidic Chip. Chembiochem 2019; 20:2604-2608. [PMID: 31090995 PMCID: PMC6852271 DOI: 10.1002/cbic.201900152] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/10/2019] [Indexed: 01/20/2023]
Abstract
Liposomes are used in synthetic biology as cell-like compartments and their microfluidic production through double emulsions allows for efficient encapsulation of various components. However, residual oil in the membrane remains a critical bottleneck for creating pristine phospholipid bilayers. It has been discovered that osmotically driven shrinking leads to detachment of the oil drop. Separation inside a microfluidic chip has been realized to automate the procedure, which allows for controlled continuous production of monodisperse liposomes.
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Selvaraj SA, Lee KE, Harrell M, Ivanov I, Allegranzi B. Infection Rates and Risk Factors for Infection Among Health Workers During Ebola and Marburg Virus Outbreaks: A Systematic Review. J Infect Dis 2019; 218:S679-S689. [PMID: 30202878 PMCID: PMC6249600 DOI: 10.1093/infdis/jiy435] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Infection in health workers (HWs) has characterized outbreaks of Ebola virus disease (EVD) and Marburg virus disease (MVD). We conducted a systematic review to investigate infection and mortality rates and common exposure risks in HWs in EVD and MVD outbreaks. Methods We searched the EMBASE and PubMed databases to identify articles posted before 27 December 2017, with no language restrictions. Data on the number, frequency, and mortality of HW infection and exposure risks were extracted. Results Ninety-four articles related to 22 outbreaks were included. HW infections composed 2%-100% of cases in EVD and 5%-50% of cases in MVD outbreaks. Among exposed HWs, 0.6%-92% developed EVD, and 1%-10% developed MVD. HW infection rates were consistent through outbreaks. The most common exposure risk situations were inadequate personal protective equipment and exposure to patients with unrecognized EVD/MVD. Similar risks were reported in past EVD/MVD outbreaks and in the recent outbreak in West Africa. Conclusions Many outbreaks reported high proportions of infected HWs. Similar HW infection rates and exposure risk factors in both past and recent EVD and MVD outbreaks emphasize the need to improve the implementation of appropriate infection control measures consistently across all healthcare settings.
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