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Nardini R, Pacchiarotti G, Svicher V, Salpini R, Bellocchi MC, Conti R, Sala MG, La Rocca D, Carioti L, Cersini A, Manna G, Scicluna MT. First National Prevalence in Italian Horse Population and Phylogenesis Highlight a Fourth Sub-Type Candidate of Equine Hepacivirus. Viruses 2024; 16:616. [PMID: 38675957 PMCID: PMC11054338 DOI: 10.3390/v16040616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Equine hepacivirus (EqHV, Flaviviridae, hepacivirus) is a small, enveloped RNA virus generally causing sub-clinical hepatitis with occasional fatalities. EqHV is reported in equids worldwide, but for Italy data are limited. To address this, a survey study was set up to estimate prevalence at a national level and among different production categories (equestrian; competition; work and meat; reproduction) and national macro-regions (North, Central, South, and Islands). Data obtained testing 1801 horse serum samples by Real-Time RT PCR were compared within the categories and regions. The NS3 fragment of the PCR-positive samples was sequenced by Sanger protocol for phylogenetic and mutational analysis. The tertiary structure of the NS3 protein was also assessed. The estimated national prevalence was 4.27% [1.97-6.59, 95% CI] and no statistical differences were detected among production categories and macro-regions. The phylogenesis confirmed the distribution in Italy of the three known EqHV subtypes, also suggesting a possible fourth sub-type that, however, requires further confirmation. Mutational profiles that could also affect the NS3 binding affinity to the viral RNA were detected. The present paper demonstrates that EqHV should be included in diagnostic protocols when investigating causes of hepatitis, and in quality control protocols for blood derived products due to its parental transmission.
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Affiliation(s)
- Roberto Nardini
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (G.P.); (R.C.); (M.G.S.); (D.L.R.); (A.C.); (G.M.); (M.T.S.)
| | - Giulia Pacchiarotti
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (G.P.); (R.C.); (M.G.S.); (D.L.R.); (A.C.); (G.M.); (M.T.S.)
| | - Valentina Svicher
- Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy;
| | - Romina Salpini
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.)
| | - Maria Concetta Bellocchi
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.)
| | - Raffaella Conti
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (G.P.); (R.C.); (M.G.S.); (D.L.R.); (A.C.); (G.M.); (M.T.S.)
| | - Marcello Giovanni Sala
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (G.P.); (R.C.); (M.G.S.); (D.L.R.); (A.C.); (G.M.); (M.T.S.)
| | - Davide La Rocca
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (G.P.); (R.C.); (M.G.S.); (D.L.R.); (A.C.); (G.M.); (M.T.S.)
| | - Luca Carioti
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy; (R.S.); (M.C.B.); (L.C.)
| | - Antonella Cersini
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (G.P.); (R.C.); (M.G.S.); (D.L.R.); (A.C.); (G.M.); (M.T.S.)
| | - Giuseppe Manna
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (G.P.); (R.C.); (M.G.S.); (D.L.R.); (A.C.); (G.M.); (M.T.S.)
| | | | - Maria Teresa Scicluna
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana “M. Aleandri”, 00178 Rome, Italy; (G.P.); (R.C.); (M.G.S.); (D.L.R.); (A.C.); (G.M.); (M.T.S.)
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Franzo G, Faustini G, Tucciarone CM, Pasotto D, Legnardi M, Cecchinato M. Conflicting Evidence between Clinical Perception and Molecular Epidemiology: The Case of Fowl Adenovirus D. Animals (Basel) 2023; 13:3851. [PMID: 38136888 PMCID: PMC10741239 DOI: 10.3390/ani13243851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/08/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Fowl adenoviruses (FAdVs, species FAdV-A/-E) are responsible for several clinical syndromes reported with increasing frequency in poultry farms in the last decades. In the present study, a phylodynamic analysis was performed on a group of FAdV-D Hexon sequences with adequate available metadata. The obtained results demonstrated the long-term circulation of this species, at least several decades before the first identification of the disease. After a period of progressive increase, the viral population showed a high-level circulation from approximately the 1960s to the beginning of the new millennium, mirroring the expansion of intensive poultry production and animal trade. At the same time, strain migration occurred mainly from Europe to other continents, although other among-continent connections were estimated. Thereafter, the viral population declined progressively, likely due to the improved control measures, potentially including the development and application of FAdV vaccines. An increase in the viral evolutionary rate featured this phase. A role of vaccine-induced immunity in shaping viral evolution could thus be hypothesized. Accordingly, several sites of the Hexon, especially those targeted by the host response were proven under a significant pervasive or episodic diversifying selection. The present study results demonstrate the role of intensive poultry production and market globalization in the rise of FAdV. The applied control strategies, on the other hand, were effective in limiting viral circulation and shaping its evolution.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health, University of Padua, Viale dell’Università, 16, 35020 Legnaro, Italy; (G.F.); (C.M.T.); (D.P.); (M.L.); (M.C.)
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Goekoop R, de Kleijn R. Hierarchical network structure as the source of hierarchical dynamics (power-law frequency spectra) in living and non-living systems: How state-trait continua (body plans, personalities) emerge from first principles in biophysics. Neurosci Biobehav Rev 2023; 154:105402. [PMID: 37741517 DOI: 10.1016/j.neubiorev.2023.105402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 09/25/2023]
Abstract
Living systems are hierarchical control systems that display a small world network structure. In such structures, many smaller clusters are nested within fewer larger ones, producing a fractal-like structure with a 'power-law' cluster size distribution (a mereology). Just like their structure, the dynamics of living systems shows fractal-like qualities: the timeseries of inner message passing and overt behavior contain high frequencies or 'states' (treble) that are nested within lower frequencies or 'traits' (bass), producing a power-law frequency spectrum that is known as a 'state-trait continuum' in the behavioral sciences. Here, we argue that the power-law dynamics of living systems results from their power-law network structure: organisms 'vertically encode' the deep spatiotemporal structure of their (anticipated) environments, to the effect that many small clusters near the base of the hierarchy produce high frequency signal changes and fewer larger clusters at its top produce ultra-low frequencies. Such ultra-low frequencies exert a tonic regulatory pressure that produces morphological as well as behavioral traits (i.e., body plans and personalities). Nested-modular structure causes higher frequencies to be embedded within lower frequencies, producing a power-law state-trait continuum. At the heart of such dynamics lies the need for efficient energy dissipation through networks of coupled oscillators, which also governs the dynamics of non-living systems (e.q., earthquakes, stock market fluctuations). Since hierarchical structure produces hierarchical dynamics, the development and collapse of hierarchical structure (e.g., during maturation and disease) should leave specific traces in system dynamics (shifts in lower frequencies, i.e. morphological and behavioral traits) that may serve as early warning signs to system failure. The applications of this idea range from (bio)physics and phylogenesis to ontogenesis and clinical medicine.
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Affiliation(s)
- R Goekoop
- Free University Amsterdam, Department of Behavioral and Movement Sciences, Parnassia Academy, Parnassia Group, PsyQ, Department of Anxiety Disorders, Early Detection and Intervention Team (EDIT), Lijnbaan 4, 2512VA The Hague, the Netherlands.
| | - R de Kleijn
- Faculty of Social and Behavioral Sciences, Department of Cognitive Psychology, Pieter de la Courtgebouw, Postbus 9555, 2300 RB Leiden, the Netherlands
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Chen YP, Huang CW, Lee F. Complete coding sequence of Tembusu virus isolated from geese in Taiwan in 2020. Microbiol Resour Announc 2023; 12:e0025623. [PMID: 37712679 PMCID: PMC10586138 DOI: 10.1128/mra.00256-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/04/2023] [Indexed: 09/16/2023] Open
Abstract
We reported the complete coding sequence of a Tembusu virus (TMUV) isolated from sick geese in Taiwan in 2020. The nucleotide sequence of the 20120008 isolate was most closely related to the strain TP1906 isolated from mosquitoes in Taiwan and clustered within a subgroup of Cluster 4 of the Tembusu virus.
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Affiliation(s)
- Yen-Ping Chen
- Veterinary Research Institute, Ministry of Agriculture, New Taipei City, Taiwan
| | - Chih-Wei Huang
- Veterinary Research Institute, Ministry of Agriculture, New Taipei City, Taiwan
| | - Fan Lee
- Veterinary Research Institute, Ministry of Agriculture, New Taipei City, Taiwan
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Tripodi P. Application of High-Resolution Melting and DNA Barcoding for Discrimination and Taxonomy Definition of Rocket Salad ( Diplotaxis spp.) Species. Genes (Basel) 2023; 14:1594. [PMID: 37628645 PMCID: PMC10454437 DOI: 10.3390/genes14081594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/04/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Nuclear and cytoplasmic DNA barcoding regions are useful for plant identification, breeding, and phylogenesis. In this study, the genetic diversity of 17 Diplotaxis species, was investigated with 5 barcode markers. The allelic variation was based on the sequences of chloroplast DNA markers including the spacer between trnL and trnF and tRNA-Phe gene (trnL-F), the rubisco (rbcl), the maturase K (matk), as well as the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA. A highly polymorphic marker (HRM500) derived from a comparison of cytoplasmic genome sequences in Brassicaceae, was also included. Subsequently, a real-time PCR method coupled with HRM analysis was implemented to better resolve taxonomic relationships and identify assays suitable for species identification. Integration of the five barcode regions revealed a grouping of the species according to the common chromosomal set number. Clusters including species with n = 11 (D. duveryrieriana or cretacea, D. tenuifolia, D. simplex and D. acris), n = 8 (D. ibicensis, D. brevisiliqua and D. ilorcitana), and n = 9 (D. brachycarpa, D. virgata, D. assurgens, and D. berthautii) chromosomes were identified. Both phylogenetic analysis and the genetic structure of the collection identified D. siifolia as the most distant species. Previous studies emphasized this species' extremely high glucosinolate content, particularly for glucobrassicin. High-resolution melting analysis showed specific curve patterns useful for the discrimination of the species, thus determining ITS1 as the best barcode for fingerprinting. Findings demonstrate that the approach used in this study is effective for taxa investigations and genetic diversity studies.
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Affiliation(s)
- Pasquale Tripodi
- Research Centre for Vegetable and Ornamental Crops, Council for Agricultural Research and Economics (CREA), 84098 Pontecagnano Faiano, Italy
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Vargas-Castro I, Peletto S, Mattioda V, Goria M, Serracca L, Varello K, Sánchez-Vizcaíno JM, Puleio R, Nocera FD, Lucifora G, Acutis P, Casalone C, Grattarola C, Giorda F. Epidemiological and genetic analysis of Cetacean Morbillivirus circulating on the Italian coast between 2018 and 2021. Front Vet Sci 2023; 10:1216838. [PMID: 37583469 PMCID: PMC10424449 DOI: 10.3389/fvets.2023.1216838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/04/2023] [Indexed: 08/17/2023] Open
Abstract
Cetacean morbillivirus (CeMV) has caused several outbreaks, unusual mortality events, and interepidemic single-lethal disease episodes in the Mediterranean Sea. Since 2012, a new strain with a northeast (NE) Atlantic origin has been circulating among Mediterranean cetaceans, causing numerous deaths. The objective of this study was to determine the prevalence of CeMV in cetaceans stranded in Italy between 2018 and 2021 and characterize the strain of CeMV circulating. Out of the 354 stranded cetaceans along the Italian coastlines, 113 were CeMV-positive. This prevalence (31.9%) is one of the highest reported without an associated outbreak. All marine sectors along the Italian coastlines, except for the northern Adriatic coast, reported a positive molecular diagnosis of CeMV. In one-third of the CeMV-positive cetaceans submitted to a histological evaluation, a chronic form of the infection (detectable viral antigen, the absence of associated lesions, and concomitant coinfections) was suspected. Tissues from 24 animals were used to characterize the strain, obtaining 57 sequences from phosphoprotein, nucleocapsid, and fusion protein genes, which were submitted to GenBank. Our sequences showed the highest identity with NE-Atlantic strain sequences, and in the phylogenetic study, they clustered together with them. Regarding age and species, most of these individuals were adults (17/24, 70.83%) and striped dolphins (19/24, 79.16%). This study improves our understanding on the NE-Atlantic CeMV strain in the Italian waters, supporting the hypothesis of an endemic circulation of the virus in this area; however, additional studies are necessary to deeply comprehend the epidemiology of this strain in the Mediterranean Sea.
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Affiliation(s)
- Ignacio Vargas-Castro
- VISAVET Center and Animal Health Department, Veterinary School, Complutense University of Madrid, Madrid, Spain
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta - WOAH Collaborating Centre for the Health of Marine Mammals, Turin, Italy
| | - Virginia Mattioda
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta - WOAH Collaborating Centre for the Health of Marine Mammals, Turin, Italy
| | - Maria Goria
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta - WOAH Collaborating Centre for the Health of Marine Mammals, Turin, Italy
| | - Laura Serracca
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta - WOAH Collaborating Centre for the Health of Marine Mammals, Turin, Italy
| | - Katia Varello
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta - WOAH Collaborating Centre for the Health of Marine Mammals, Turin, Italy
| | | | - Roberto Puleio
- Istituto Zooprofilattico Sperimentale della Sicilia, Palermo, Italy
| | - Fabio Di Nocera
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Giuseppe Lucifora
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, Naples, Italy
| | - Pierluigi Acutis
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta - WOAH Collaborating Centre for the Health of Marine Mammals, Turin, Italy
| | - Cristina Casalone
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta - WOAH Collaborating Centre for the Health of Marine Mammals, Turin, Italy
| | - Carla Grattarola
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta - WOAH Collaborating Centre for the Health of Marine Mammals, Turin, Italy
| | - Federica Giorda
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta - WOAH Collaborating Centre for the Health of Marine Mammals, Turin, Italy
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Santucciu C, Bonelli P, Peruzzu A, Fancellu A, Farà A, Mastrandrea S, Drocchi G, Cossu A, Profili S, Porcu A, Masala G. Genetic Characterization of Echinococcus granulosus sensu stricto Isolated from Human Cysts from Sardinia, Italy. Diseases 2023; 11:91. [PMID: 37489443 PMCID: PMC10366878 DOI: 10.3390/diseases11030091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/26/2023] Open
Abstract
This study involved 20 patients affected by cystic echinococcosis (CE) who were referred to different hospitals of Sardinia (Italy) from 2017 to 2022. By means of a multidisciplinary approach, diagnosis was confirmed for CE in 18 patients and for different aetiologies in two subjects. Moreover, serology was positive for 15 subjects. Since multiple CE cysts were found in five patients, a total of 27 lesions were collected; however, only one for each patient was investigated for genetic characterization of E. granulosus s.s. DNA isolates. Our results included 15 fertile cysts that underwent DNA extraction and amplification by three different PCRs targeting nuclear (calreticulin) and mitochondrial genes (cox1 and nad5). DNA was sequenced, and by neighbour-joining phylogenetic trees we determined 10 G1 and five G3 genotypes previously reported in Sardinia. These sequences were used to construct a network, along with those circulating in Mediterranean areas. The haplotype network calculated on cox1 evidenced seven different haplotypes of the 15 isolates, with SAR2 the most represented, carried by seven cysts, and SAR17 never described in the Mediterranean area. Meanwhile, the nad5 sequences showed the most common haplotype as nd5SAR7, as well as two new haplotypes not previously described, nd5SAR13, isolated from a Sardinian patient, and nd5SAR14, isolated from a Romanian patient.
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Affiliation(s)
- Cinzia Santucciu
- WOAH and NRL for Echinococcosis, Animal Health, IZS della Sardegna, 07100 Sassari, Italy
| | - Piero Bonelli
- WOAH and NRL for Echinococcosis, Animal Health, IZS della Sardegna, 07100 Sassari, Italy
| | - Angela Peruzzu
- WOAH and NRL for Echinococcosis, Animal Health, IZS della Sardegna, 07100 Sassari, Italy
| | - Alessandro Fancellu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy
| | - Antonella Farà
- Department of Biomedical Sciences, Institute of Pathology, University of Sassari, 07100 Sassari, Italy
| | - Scilla Mastrandrea
- Unità Operativa Complessa di Malattie Infettive, Azienda Ospedaliero-Universitaria, 07100 Sassari, Italy
| | - Giovanni Drocchi
- Department of Surgical and Diagnostic Integrated Sciences (DISC), University of Genova, 16132 Genova, Italy
| | - Antonio Cossu
- Department of Biomedical Sciences, Institute of Pathology, University of Sassari, 07100 Sassari, Italy
| | - Stefano Profili
- Unità Operativa Complessa di Radiologia, Azienda Ospedaliero-Universitaria, 07100 Sassari, Italy
| | - Alberto Porcu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, 07100 Sassari, Italy
| | - Giovanna Masala
- WOAH and NRL for Echinococcosis, Animal Health, IZS della Sardegna, 07100 Sassari, Italy
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Lauriano ER, Alesci A, Aragona M, Pergolizzi S, Miller A, Zuwala K, Kuciel M, Zaccone G, Germanà A, Guerrera MC. Immunohistochemistry of the Gut-Associated Lymphoid Tissue (GALT) in African Bonytongue (Heterotis niloticus, Cuvier 1829). Int J Mol Sci 2023; 24. [PMID: 36768639 DOI: 10.3390/ijms24032316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Heterotis niloticus is a basal teleost, belonging to the Osteoglossidae family, which is widespread in many parts of Africa. The digestive tract of H. niloticus presents similar characteristics to those of higher vertebrates, exhibiting a gizzard-like stomach and lymphoid aggregates in the intestinal lamina propria. The adaptive immune system of teleost fish is linked with each of their mucosal body surfaces. In fish, the gut-associated lymphoid tissue (GALT) is generally a diffuse immune system that represents an important line of defense against those pathogens inhabiting the external environment that can enter through food. The GALT comprises intraepithelial lymphocytes, which reside in the epithelial layer, and lamina propria leukocytes, which consist of lymphocytes, macrophages, granulocytes, and dendritic-like cells. This study aims to characterize, for the first time, the leukocytes present in the GALT of H. niloticus, by confocal immuno- fluorescence techniques, using specific antibodies: toll-like receptor 2, major histocompatibility complex class II, S100 protein, serotonin, CD4, langerin, and inducible nitric oxide synthetase. Our results show massive aggregates of immune cells in the thickness of the submucosa, arranged in circumscribed oval-shaped structures that are morphologically similar to the isolated lymphoid follicles present in birds and mammals, thus expanding our knowledge about the intestinal immunity shown by this fish.
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Lo Presti A, Del Chierico F, Altomare A, Zorzi F, Monteleone G, Putignani L, Angeletti S, Cicala M, Guarino MPL, Ciccozzi M. Phylogenetic analysis of Prevotella copri from fecal and mucosal microbiota of IBS and IBD patients. Therap Adv Gastroenterol 2023; 16:17562848221136328. [PMID: 36644130 PMCID: PMC9837282 DOI: 10.1177/17562848221136328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/13/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Prevotella copri is the most abundant member of the genus Prevotella that inhabits the human large intestines. Evidences correlated the increase in Prevotella abundance to inflammatory disorders, suggesting a pathobiont role. OBJECTIVES The aim of this study was to investigate the phylogenetic dynamics of P. copri in patients with irritable bowel syndrome (IBS), inflammatory bowel diseases (IBDs) and in healthy volunteers (CTRL). DESIGN A phylogenetic approach was used to characterize 64 P. copri 16S rRNA sequences, selected from a metagenomic database of fecal and mucosal samples from 52 patients affected by IBD, 44 by IBS and 59 healthy. METHODS Phylogenetic reconstructions were carried out using the maximum likelihood (ML) and Bayesian methods. RESULTS Maximum likelihood phylogenetic tree applied onto reference and data sets, assigned all the reads to P. copri clade, in agreement with the taxonomic classification previously obtained. The longer mean genetic distances were observed for both the couples IBD and CTRL and IBD and IBS, respect to the distance between IBS and CTRL, for fecal samples. The intra-group mean genetic distance increased going from IBS to CTRLs to IBD, indicating elevated genetic variability within IBD of P. copri sequences. None clustering based on the tissue inflammation or on the disease status was evidenced, leading to infer that the variability seemed to not be influenced by concomitant diseases, disease phenotypes or tissue inflammation. Moreover, patients with IBS appeared colonized by different strains of P. copri. In IBS, a correlation between isolates and disease grading was observed. CONCLUSION The characterization of P. copri phylogeny is relevant to better understand the interactions between microbiota and pathophysiology of IBD and IBS, especially for future development of therapies based on microbes (e.g. probiotics and synbiotics), to restore the microbiota in these bowel diseases.
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Affiliation(s)
| | | | - Annamaria Altomare
- Research Unit of Gastroenterology, Department of Science and Technology for Humans and the Environment, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, Roma, Italy
| | - Francesca Zorzi
- Gastrointestinal Unit, Department of Systems Medicine, University Tor Vergata, Rome, Italy
| | - Giovanni Monteleone
- Gastrointestinal Unit, Department of Systems Medicine, University Tor Vergata, Rome, Italy
| | - Lorenza Putignani
- Department of Diagnostic and Laboratory Medicine, Unit of microbiology and diagnostic immunology, Unit of microbiomics and Multimodal Laboratory Medicine Research Area, Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico, Rome, Italy,Unit of Clinical Laboratory Fondazione Policlinico Universitario Campus Bio Medico, Rome, Italy
| | - Michele Cicala
- Research Unit of Gastroenterology, Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Via Alvaro del Portillo, Roma, Italy,Operative Research Unit of Gastroenterology, Fondazione Policlinico Universitario Campus Bio-Medico of Rome, Via Alvaro del Portillo, Roma, Italy
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Corsaro D. Acanthamoeba Mannose and Laminin Binding Proteins Variation across Species and Genotypes. Microorganisms 2022; 10:2162. [PMID: 36363753 PMCID: PMC9692275 DOI: 10.3390/microorganisms10112162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 10/26/2022] [Indexed: 11/26/2023] Open
Abstract
Acanthamoeba is a ubiquitous free-living amoeba capable of being an opportunistic pathogen in humans and animals. A critical step in infection is the adhesion of the amoeba to host cells and tissues, and two major parasite adhesins, mannose-binding protein (MBP) and laminin-binding protein (LBP), are known to recognize the cell surface glycoproteins and those of the extracellular matrix, respectively. In this study, the available genomes of Acanthamoeba were analysed to recover the sequences of MBP and LBP using previously published genetic data. Genes for both proteins were successfully obtained from strains belonging to various genotypes (T4A, T4D, T4G, T4F, T2, T5, T10, T22, T7 and T18), resulting in a single gene for LBP but identifying two types of MBP, MBP1 and MBP2. Phylogenetic analysis based on deduced amino acid sequences shows that both MBP and LBP have a branching pattern that is consistent with that based on 18S rDNA, indicating that changes in both proteins occurred during diversification of Acanthamoeba lines. Notably, all MBPs possess a conserved motif, shared with some bacterial C-type lectins, which could be the recognition site for mannose binding.
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Corsaro D. Exploring LSU and ITS rDNA Sequences for Acanthamoeba Identification and Phylogeny. Microorganisms 2022; 10:1776. [PMID: 36144378 DOI: 10.3390/microorganisms10091776] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/22/2022] Open
Abstract
The identification and classification of strains of Acanthamoeba, a potentially pathogenic ubiquitous free-living amoeba, are largely based on the analysis of 18S rDNA sequences, currently delineating 23 genotypes, T1 to T23. In this study, the sequences of the ITS region, i.e., the 5.8S rDNA and the two internal transcribed spacers (ITS-1 and ITS-2), and those of the large subunit (LSU) rDNA of Acanthamoeba were recovered from amoeba genomes; the sequences are available in GenBank. The complete ITS–LSU sequences could be obtained for 15 strains belonging to 7 distinct lineages (T4A, T4D, T4F, T4G, T2, T5, and T18), and the site of the hidden break producing the 26Sα and 26Sβ was identified. For the other lines, either the LSU is partial (T2/T6, T7) or the ITS is fragmentary (T7, T10, T22). It is noteworthy that a number of sequences assigned to fungi turned out to actually be Acanthamoeba, only some of which could be affiliated with known genotypes. Analysis of the obtained sequences indicates that both ITS and LSU are promising for diagnostic and phylogenetic purposes.
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Kokhanyuk B, Vántus VB, Radnai B, Vámos E, Kajner G, Galbács G, Telek E, Mészáros M, Deli MA, Németh P, Engelmann P. Distinct Uptake Routes Participate in Silver Nanoparticle Engulfment by Earthworm and Human Immune Cells. Nanomaterials (Basel) 2022; 12:2818. [PMID: 36014683 PMCID: PMC9413649 DOI: 10.3390/nano12162818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
The consequences of engineered silver nanoparticle (AgNP) exposure and cellular interaction with the immune system are poorly understood. The immunocytes of the Eisenia andrei earthworm are frequently applied in ecotoxicological studies and possess functional similarity to vertebrate macrophages. Hence, we characterized and compared the endocytosis mechanisms for the uptake of 75 nm AgNPs by earthworm coelomocytes, human THP-1 monocytes, and differentiated THP-1 (macrophage-like) cells. Our results indicate that microtubule-dependent, scavenger-receptor, and PI3K signaling-mediated macropinocytosis are utilized during AgNP engulfment by human THP-1 and differentiated THP-1 cells. However, earthworm coelomocytes employ actin-dependent phagocytosis during AgNPs uptake. In both human and earthworm immunocytes, AgNPs were located in the cytoplasm, within the endo-/lysosomes. We detected that the internalization of AgNPs is TLR/MyD88-dependent, also involving the bactericidal/permeability-increasing protein (BPI) in the case of human immunocytes. The exposure led to decreased mitochondrial respiration in human immunocytes; however, in coelomocytes, it enhanced respiratory parameters. Our findings provide more data about NP trafficking as nano-carriers in the nanomedicine field, as well as contribute to an understanding of the ecotoxicological consequences of nanoparticle exposure.
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Affiliation(s)
- Bohdana Kokhanyuk
- Department of Immunology and Biotechnology, Clinical Center, Medical School, University of Pécs, H-7624 Pécs, Hungary
| | - Viola Bagóné Vántus
- Department of Biochemistry and Medicinal Chemistry, Medical School, University of Pécs, H-7624 Pécs, Hungary
| | - Balázs Radnai
- Department of Biochemistry and Medicinal Chemistry, Medical School, University of Pécs, H-7624 Pécs, Hungary
| | - Eszter Vámos
- Department of Biochemistry and Medicinal Chemistry, Medical School, University of Pécs, H-7624 Pécs, Hungary
| | - Gyula Kajner
- Department of Inorganic and Analytical Chemistry, Faculty of Science and Informatics, University of Szeged, H-6720 Szeged, Hungary
| | - Gábor Galbács
- Department of Inorganic and Analytical Chemistry, Faculty of Science and Informatics, University of Szeged, H-6720 Szeged, Hungary
| | - Elek Telek
- Department of Biophysics, Medical School, University of Pécs, H-7624 Pécs, Hungary
| | - Mária Mészáros
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary
| | - Mária A. Deli
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network, H-6726 Szeged, Hungary
| | - Péter Németh
- Department of Immunology and Biotechnology, Clinical Center, Medical School, University of Pécs, H-7624 Pécs, Hungary
| | - Péter Engelmann
- Department of Immunology and Biotechnology, Clinical Center, Medical School, University of Pécs, H-7624 Pécs, Hungary
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Pisaturo M, Di Fraia A, Occhiello L, Minichini C, Starace M, Iodice V, Farella N, Stanzione M, Coppola N. Genetic Variability in Patients with HCV-Related Hepatocellular Carcinoma. Infect Drug Resist 2021; 14:5199-5208. [PMID: 34908854 PMCID: PMC8665876 DOI: 10.2147/idr.s337647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/09/2021] [Indexed: 12/09/2022] Open
Abstract
Background The present paper evaluates the genetic variability of HCV in patients with hepatocellular carcinoma (HCC). Methods Amino acid substitutions (aas) in NS3, NS5A and core regions were analyzed in 17 patients with HCC (Cases) and 13 without HCC (Controls), all naïve to DAAs. For the Cases, a sample of neoplastic liver tissue, non-neoplastic liver tissue and a serum sample were collected; for the Controls, a sample of liver tissue was collected. Sanger sequencing of three regions was performed using homemade protocols. Results Phylogenetic trees showed that there was no difference in the virus populations in the three compartments analyzed for the three HCV regions in patients with HCC. Low variability and no difference between the Cases and Controls were observed in the core and NS5A regions; however, in the NS3 region, a higher variability was observed in the Cases. No difference was observed in the core region between Cases and Controls. In NS3, aa substitutions at positions 103 and 122 were more frequently found in Cases than Controls (in both cases 50% vs 9.1%, p<0.05); moreover, aas in positions 32, 44 (p=0.035 for both), 79 (p=0.008) and 121 (p=0.018) were observed in the Cases and absent in the Controls. Finally, considering the NS5A region, aa substitutions at positions 37 and 54 were more frequently identified in the Cases than the Controls, but without statistical significance. Conclusion These data may suggest a higher aa variability in patients with HCC than in those without, especially in the NS3 region.
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Affiliation(s)
- Mariantonietta Pisaturo
- Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Alessandra Di Fraia
- Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Laura Occhiello
- Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Carmine Minichini
- Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Mario Starace
- Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | | | - Nunzia Farella
- IX Infectious Disease Unit, AORN dei Colli, Naples, Italy
| | - Maria Stanzione
- Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania "L. Vanvitelli", Naples, Italy
| | - Nicola Coppola
- Infectious Diseases, Department of Mental Health and Public Medicine, University of Campania "L. Vanvitelli", Naples, Italy
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Bertelli A, D'Ursi P, Campisi G, Messali S, Milanesi M, Giovanetti M, Ciccozzi M, Caccuri F, Caruso A. Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket. Viruses 2021; 13:2511. [PMID: 34960779 DOI: 10.3390/v13122511] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Genotype screening was implemented in Italy and showed a significant prevalence of new SARS-CoV-2 mutants carrying Q675H mutation, near the furin cleavage site of spike protein. Currently, this mutation, which is expressed on different SARS-CoV-2 lineages circulating worldwide, has not been thoughtfully investigated. Therefore, we performed phylogenetic and biocomputational analysis to better understand SARS-CoV-2 Q675H mutants’ evolutionary relationships with other circulating lineages and Q675H function in its molecular context. Our studies reveal that Q675H spike mutation is the result of parallel evolution because it arose independently in separate evolutionary clades. In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region. This results in an optimized directionality of arginine residues involved in interaction of spike with the furin binding pocket, thus improving proteolytic exposure of the viral protein. Furin was predicted to have a greater affinity for Q675H than Q675 substrate conformations. As a consequence, Q675H mutation could confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. Interestingly, here we have shown that Q675H spike mutation is documented in all the VOCs. This finding highlights that VOCs are still evolving to enhance viral fitness and to adapt to the human host. At the same time, it may suggest Q675H spike mutation involvement in SARS-CoV-2 evolution.
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15
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Franzo G, Menandro ML, Tucciarone CM, Barbierato G, Crovato L, Mondin A, Libanora M, Obber F, Orusa R, Robetto S, Citterio C, Grassi L. Canine Circovirus in Foxes from Northern Italy: Where Did It All Begin? Pathogens 2021; 10:pathogens10081002. [PMID: 34451466 PMCID: PMC8400258 DOI: 10.3390/pathogens10081002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 01/26/2023] Open
Abstract
Canine circovirus (CanineCV) is a recently identified virus affecting both domestic and wild carnivores, including foxes, sometimes in presence of severe clinical signs. Its circulation in wild animals can thus represent a potential threat for endangered species conservation and an infection source for dogs. Nevertheless, no data were available on its circulation in the Alps region of Northern Italy. In the present study, samples collected from 186 foxes in the period 2009–2020 from Valle d’Aosta and Veneto regions were tested using a real-time PCR assay, demonstrating a viral circulation of approximatively 2–5%, depending on the considered regions. Two complete or almost complete genome sequences were obtained, highlighting that the detected strains were part of a so defined “fox only” clade, which suggests that, despite common contact opportunities, Alps foxes are not involved in frequent transmission events to domestic dogs. Such genetic isolation could be at least partially attributed to some sort of independent evolution occurred in the foxes, leading to species barrier. Additionally, CanineCV strains in foxes from Italy were unexpectedly related to those previously identified in foxes from the United Kingdom and Scandinavian area. Combining the history of fox distribution in Europe since the last glacial maximum (LGM) with the viral history allowed us to speculate a long-standing coexistence between European canine circovirus and this host, justifying the peculiar geographic distribution and evolutionary paths of the fox infecting clade.
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Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.M.); (C.M.T.); (G.B.); (L.C.); (A.M.); (L.G.)
- Correspondence: ; Tel.: +39-049-827-2968
| | - Maria Luisa Menandro
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.M.); (C.M.T.); (G.B.); (L.C.); (A.M.); (L.G.)
| | - Claudia Maria Tucciarone
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.M.); (C.M.T.); (G.B.); (L.C.); (A.M.); (L.G.)
| | - Giacomo Barbierato
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.M.); (C.M.T.); (G.B.); (L.C.); (A.M.); (L.G.)
| | - Lorenzo Crovato
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.M.); (C.M.T.); (G.B.); (L.C.); (A.M.); (L.G.)
| | - Alessandra Mondin
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.M.); (C.M.T.); (G.B.); (L.C.); (A.M.); (L.G.)
| | - Martina Libanora
- O.U. of Ecopathology, SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 32100 Belluno, Italy; (M.L.); (F.O.); (C.C.)
| | - Federica Obber
- O.U. of Ecopathology, SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 32100 Belluno, Italy; (M.L.); (F.O.); (C.C.)
| | - Riccardo Orusa
- S.C. Valle d.’Aosta—National Reference Centre Wildlife Diseases, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZS PLV)—Ce.R.M.A.S., 11020 Quart, AO, Italy; (R.O.); (S.R.)
| | - Serena Robetto
- S.C. Valle d.’Aosta—National Reference Centre Wildlife Diseases, Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d’Aosta (IZS PLV)—Ce.R.M.A.S., 11020 Quart, AO, Italy; (R.O.); (S.R.)
| | - Carlo Citterio
- O.U. of Ecopathology, SCT2 Belluno, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), 32100 Belluno, Italy; (M.L.); (F.O.); (C.C.)
| | - Laura Grassi
- Department of Animal Medicine, Production and Health (MAPS), University of Padua, 35020 Legnaro, Italy; (M.L.M.); (C.M.T.); (G.B.); (L.C.); (A.M.); (L.G.)
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Gigliucci F, van Hoek AHAM, Chiani P, Knijn A, Minelli F, Scavia G, Franz E, Morabito S, Michelacci V. Genomic Characterization of hlyF-positive Shiga Toxin-Producing Escherichia coli, Italy and the Netherlands, 2000-2019. Emerg Infect Dis 2021; 27:853-861. [PMID: 33622476 PMCID: PMC7920663 DOI: 10.3201/eid2703.203110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Shiga toxin–producing Escherichia coli (STEC) O80:H2 has emerged in Europe as a cause of hemolytic uremic syndrome associated with bacteremia. STEC O80:H2 harbors the mosaic plasmid pR444_A, which combines several virulence genes, including hlyF and antimicrobial resistance genes. pR444_A is found in some extraintestinal pathogenic E. coli (ExPEC) strains. We identified and characterized 53 STEC strains with ExPEC-associated virulence genes isolated in Italy and the Netherlands during 2000–2019. The isolates belong to 2 major populations: 1 belongs to sequence type 301 and harbors diverse stx2 subtypes, the intimin variant eae-ξ, and pO157-like and pR444_A plasmids; 1 consists of strains belonging to various sequence types, some of which lack the pO157 plasmid, the locus of enterocyte effacement, and the antimicrobial resistance–encoding region. Our results showed that STEC strains harboring ExPEC-associated virulence genes can include multiple serotypes and that the pR444_A plasmid can be acquired and mobilized by STEC strains.
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Abstract
Lipocalins represent one of the most successful superfamilies of proteins. Most of them are extracellular carriers for hydrophobic ligands across aqueous media, but other functions have been reported. They are present in most living organisms including bacteria. In animals they have been identified in mammals, molluscs, and arthropods; sequences have also been reported for plants. A subgroup of lipocalins, referred to as odorant-binding proteins (OBPs), mediate chemical communication in mammals by ferrying specific pheromones to the vomeronasal organ. So far, these proteins have not been reported as carriers of semiochemicals in other living organisms; instead chemical communication in arthropods is mediated by other protein families structurally unrelated to lipocalins. A search in the databases has revealed extensive duplication and differentiation of lipocalin genes in some species of insects, crustaceans, and chelicerates. Their large numbers, ranging from a handful to few dozens in the same species, their wide divergence, both within and between species, and their expression in chemosensory organs suggest that such expansion may have occurred under environmental pressure, thus supporting the hypothesis that lipocalins may be involved in chemical communication in arthropods.
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Affiliation(s)
- Jiao Zhu
- Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria.,Faculty of Biology, Institute of Molecular Physiology, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Alessio Iannucci
- Departement of Biology, University of Firenze, Sesto Fiorentino, Italy
| | | | - Wolfgang Knoll
- Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria
| | - Paolo Pelosi
- Austrian Institute of Technology GmbH, Biosensor Technologies, Tulln, Austria
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18
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Roumani M, Besseau S, Gagneul D, Robin C, Larbat R. Phenolamides in plants: an update on their function, regulation, and origin of their biosynthetic enzymes. J Exp Bot 2021; 72:2334-2355. [PMID: 33315095 DOI: 10.1093/jxb/eraa582] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
Phenolamides represent a family of specialized metabolites, consisting of the association of hydroxycinnamic acid derivatives with aliphatic or aromatic amines. Since the discovery of the first phenolamide in the late 1940s, decades of phytochemical analyses have revealed a high structural diversity for this family and a wide distribution in the plant kingdom. The occurrence of structurally diverse phenolamides in almost all plant organs has led to early hypotheses on their involvement in floral initiation and fertility, as well as plant defense against biotic and abiotic stress. In the present work, we critically review the literature ascribing functional hypotheses to phenolamides and recent evidence on the control of their biosynthesis in response to biotic stress. We additionally provide a phylogenetic analysis of the numerous N-hydroxycinnamoyltransferases involved in the synthesis of phenolamides and discuss the potential role of other enzyme families in their diversification. The data presented suggest multiple evolutionary events that contributed to the extension of the taxonomic distribution and diversity of phenolamides.
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Affiliation(s)
- Marwa Roumani
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
| | - Sébastien Besseau
- EA 2106, Biomolécules et biotechnologies végétales (BBV), Université de Tours, Tours, France
| | - David Gagneul
- UMR 1158, BioEcoAgro, Université de Lille, INRAe, Université de Liège, UPJV, YNCREA, Université d'Artois, Université Littoral Côte d'Opale, Institut Charles Viollette (ICV), Lille, France
| | - Christophe Robin
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
| | - Romain Larbat
- UMR 1121, Laboratoire Agronomie et Environnement (LAE), Université de Lorraine- INRAe, Nancy, France
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Bednářová M, Karafiátová M, Hřibová E, Bartoš J. B Chromosomes in Genus Sorghum (Poaceae). Plants (Basel) 2021; 10:505. [PMID: 33803087 PMCID: PMC8001295 DOI: 10.3390/plants10030505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 12/30/2022]
Abstract
B chromosomes (Bs) are supernumerary dispensable genomic elements that have been reported in several thousand eukaryotic species. Since their discovery, Bs have been subjected to countless studies aiming at the clarification of their origin, composition, and influence on the carriers. Despite these efforts, we still have very limited knowledge of the processes that led to the emergence of Bs, the mechanisms of their transmission, and the effects of Bs on the hosts. In the last decade, sophisticated molecular methods, including next-generation sequencing, have provided powerful tool to help answer some of these questions, but not many species have received much attention yet. In this review, we summarize the currently available information about Bs in the genus Sorghum, which has so far been on the periphery of scientific interest. We present an overview of the occurrence and characteristics of Bs in various Sorghum species, discuss the possible mechanisms involved in their maintenance and elimination, and outline hypotheses of the origin of Bs in this genus.
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Affiliation(s)
| | | | | | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic; (M.B.); (M.K.); (E.H.)
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Grassi L, Franzo G, Martini M, Mondin A, Cassini R, Drigo M, Pasotto D, Vidorin E, Menandro ML. Ecotyping of Anaplasma phagocytophilum from Wild Ungulates and Ticks Shows Circulation of Zoonotic Strains in Northeastern Italy. Animals (Basel) 2021; 11:310. [PMID: 33530571 DOI: 10.3390/ani11020310] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Tick-borne infectious diseases represent a rising threat both for human and animal health, since they are emerging worldwide. Among the bacterial infections, Anaplasma phagocytophilum has been largely neglected in Europe. Despite its diffusion in ticks and animals, the ecoepidemiology of its genetic variants is not well understood. The latest studies identify four ecotypes of Anaplasma phagocytophilum in Europe, and only ecotype I has shown zoonotic potential. The aim of the present study was to investigate the genetic variants of Anaplasma phagocytophilum in wild ungulates, the leading reservoir species, and in feeding ticks, the main vector of infection. The analyzed samples were collected in northeastern Italy, the same area where the first Italian human cases of anaplasmosis in the country were reported. Using biomolecular tools and phylogenetic analysis, ecotypes I and II were detected in both ticks (Ixodes ricinus species) and wild ungulates. Specifically, ecotype II was mainly detected in roe deer and related ticks; and ecotype I, the potentially zoonotic variant, was detected in Ixodes ricinus ticks and also in roe deer, red deer, chamois, mouflon, and wild boar. These findings reveal not only the wide diffusion of Anaplasma phagocytophilum, but also the presence of zoonotic variants. Abstract Anaplasma phagocytophilum (A. phagocytophilum) is a tick-borne pathogen causing disease in both humans and animals. Human granulocytic anaplasmosis (HGA) is an emerging disease, but despite the remarkable prevalence in European ticks and wild animals, human infection appears underdiagnosed. Several genetic variants are circulating in Europe, including the zoonotic ecotype I. This study investigated A. phagocytophilum occurrence in wild ungulates and their ectoparasites in an area where HGA has been reported. Blood samples from wild ungulates and ectoparasites were screened by biomolecular methods targeting the mps2 gene. The groEL gene was amplified and sequenced to perform genetic characterization and phylogenetic analysis. A total of 188 blood samples were collected from different wild ungulates species showing an overall prevalence of 63.8% (88.7% in wild ruminants and 3.6% in wild boars). The prevalence of A. phagocytophilum DNA in ticks (manly Ixodes ricinus), and keds collected from wild ruminants was high, reflecting the high infection rates obtained in their hosts. Among ticks collected from wild boars (Hyalomma marginatum and Dermacentor marginatus) no DNA was detected. Phylogenetic analysis demonstrated the presence of ecotype I and II. To date, this is the first Italian report of ecotype I in alpine chamois, mouflon, and wild boar species. These findings suggest their role in HGA epidemiology, and the high prevalence detected in this study highlights that this human tick-borne disease deserves further attention.
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Paulo AJ, Wanderley MCDA, de Oliveira RJV, Vieira WADS, Alves LC, Viana Marques DDA, Converti A, Porto ALF. Production and partial purification by PEG/citrate ATPS of a β-galactosidase from the new promising isolate Cladosporium tenuissimum URM 7803. Prep Biochem Biotechnol 2020; 51:289-299. [PMID: 32907464 DOI: 10.1080/10826068.2020.1815054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
β-Galactosidase production, partial purification and characterization by a new fungal were investigated. Partial purification was performed by aqueous two-phase system (ATPS) using polyethylene glycol (PEG) molar mass, PEG concentration, citrate concentration and pH as the independent variables. Purification factor (PF), partition coefficient (K) and yield (Y) were the responses. After identification by rDNA sequencing and classification as Cladosporium tenuissimum URM 7803, this isolate achieved a maximum cell concentration and β-galactosidase activity of 0.48 g/L and 462.1 U/mL, respectively. β-Galactosidase partitioned preferentially for bottom salt-rich phase likely due to hydrophobicity and volume exclusion effect caused in the top phase by the high PEG concentration and molar mass. The highest value of PF (12.94) was obtained using 24% (w/w) PEG 8000 g/mol and 15% (w/w) citrate, while that of Y (79.76%) using 20% (w/w) PEG 400 g/mol and 25% (w/w) citrate, both at pH 6. The enzyme exhibited optimum temperature in crude and ATPS extracts in the ranges 35-50 °C and 40-55 °C, respectively, and optimum pH in the range 3.0-4.5, with a fall of enzyme activity under alkaline conditions. Some metal ions and detergents inhibited, while others stimulated enzyme activity. Finally, C. tenuissimum URM 7803 β-galactosidase showed a profile suitable for prebiotics production.
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Affiliation(s)
- Anderson José Paulo
- Campus Tefé, Federal Institute of Education, Science and Technology of Amazon (IFAM), Tefé, Brazil
| | | | | | | | - Luiz Carlos Alves
- Institute Aggeu Magalhães-IAM/FIOCRUZ, Federal University of Pernambuco, Recife, Brazil
| | - Daniela de Araújo Viana Marques
- Laboratory of Biotechnology Applied to Infectious and Parasitic Diseases, Biological Science Institute, University of Pernambuco-ICB/UPE, Santo Amaro, Recife, Brazil
| | - Attilio Converti
- Department of Civil, Chemical and Environmental Engineering, Pole of Chemical Engineering, Genoa, Italy
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Colavita F, Lapa D, Carletti F, Lalle E, Messina F, Rueca M, Matusali G, Meschi S, Bordi L, Marsella P, Nicastri E, Marchioni L, Mariano A, Scorzolini L, Ascoli Bartoli T, Di Caro A, Ippolito G, Capobianchi MR, Castilletti C. Virological Characterization of the First 2 COVID-19 Patients Diagnosed in Italy: Phylogenetic Analysis, Virus Shedding Profile From Different Body Sites, and Antibody Response Kinetics. Open Forum Infect Dis 2020; 7:ofaa403. [PMID: 33527081 PMCID: PMC7499768 DOI: 10.1093/ofid/ofaa403] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/28/2020] [Indexed: 12/31/2022] Open
Abstract
Background The pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains unclear. We report the detection of viral RNA from different anatomical districts and the antibody profile in the first 2 COVID-19 cases diagnosed in Italy. Methods We tested for SARS-CoV-2 RNA clinical samples, either respiratory and nonrespiratory (ie, saliva, serum, urine, vomit, rectal, ocular, cutaneous, and cervico-vaginal swabs), longitudinally collected from both patients throughout the hospitalization. Serological analysis was carried out on serial serum samples to evaluate IgM, IgA, IgG, and neutralizing antibody levels. Results SARS-CoV-2 RNA was detected since the early phase of illness, lasting over 2 weeks in both upper and lower respiratory tract samples. Virus isolate was obtained from acute respiratory samples, while no infectious virus was rescued from late respiratory samples with low viral RNA load, collected when serum antibodies had been developed. Several other specimens came back positive, including saliva, vomit, rectal, cutaneous, cervico-vaginal, and ocular swabs. IgM, IgA, and IgG were detected within the first week of diagnosis, with IgG appearing earlier and at higher titers. Neutralizing antibodies developed during the second week, reaching high titers 32 days after diagnosis. Conclusions Our longitudinal analysis showed that SARS-CoV-2 RNA can be detected in different body samples, which may be associated with broad tropism and different spectra of clinical manifestations and modes of transmission. Profiling antibody response and neutralizing activity can assist in laboratory diagnosis and surveillance actions.
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Affiliation(s)
- Francesca Colavita
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Daniele Lapa
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Fabrizio Carletti
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Eleonora Lalle
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Francesco Messina
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Martina Rueca
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Giulia Matusali
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Silvia Meschi
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Licia Bordi
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Patrizia Marsella
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Emanuele Nicastri
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Luisa Marchioni
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Andrea Mariano
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Laura Scorzolini
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | | | - Antonino Di Caro
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Giuseppe Ippolito
- National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
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Cavadini P, Molinari S, Merzoni F, Vismarra A, Posautz A, Alzaga Gil V, Chiari M, Giannini F, Capucci L, Lavazza A. Widespread occurrence of the non-pathogenic hare calicivirus (HaCV Lagovirus GII.2) in captive-reared and free-living wild hares in Europe. Transbound Emerg Dis 2020; 68:509-518. [PMID: 32603021 PMCID: PMC8247275 DOI: 10.1111/tbed.13706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/01/2020] [Accepted: 06/23/2020] [Indexed: 12/25/2022]
Abstract
The Lagovirus genus comprises both pathogenic viruses as European brown hare syndrome virus (EBHSV- GII.1) and rabbit hemorrhagic disease viruses (RHDV-GI.1 and RHDV2-GI.2), that principally infect European brown hares (Lepus europeaus) and European rabbits (Oryctolagus cuniculus), respectively, causing severe necrotic hepatitis, spleen enlargement and disseminated haemorrhage. This genus includes also non-pathogenic agents, such as rabbit calicivirus (RCV-E1 - GI.3) and the non-pathogenic hare Lagovirus, provisionally named hare calicivirus (HaCV - GII.2). The latter had been identified for the first time in 2012 in the gut contents and faeces of healthy young hares raised in a breeding farm. In this study, we further investigated the presence of HaCV by testing the intestinal tract of 621 wild hares collected between 2010 and 2018 in Northern and Central Italy, and in 2011 in Austria, Germany and Spain. These wild hares were found dead for causes other than EBHS or were healthy hares shot during the hunting season. Forty-three out of 322 hare samples from Italy and 14 out of 299 samples from Austria and Germany were positive for HaCV-GII.2 by RT-PCR using universal primers for lagoviruses and primers specific for HaCV. Sequence analysis of the full capsid protein gene conducted on 12 strains representative of different years and locations indicated that these viruses belong to the same, single cluster as the prototype strain initially identified at the hares' farm (HaCV_Bs12_1). The relatively high level of genetic variation (88% nt identity) within this cluster suggests HaCVs may have been circulating widely in Europe for some time.
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Affiliation(s)
- Patrizia Cavadini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
| | - Stefano Molinari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
| | - Francesca Merzoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
| | - Alice Vismarra
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
| | - Annika Posautz
- Department of Interdisciplinary Life Sciences, Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
| | | | - Mario Chiari
- D.G. Welfare, Regional Health Authority of Lombardy, Milan, Italy
| | - Francesca Giannini
- Parco Nazionale Arcipelago Toscano, Portoferraio, Località-Enfola, Italy
| | - Lorenzo Capucci
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna and OIE Reference Laboratory for Rabbit Haemorrhagic Disease, Brescia, Italy
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Hermyt M, Janiszewska K, Rupik W. Squamate egg tooth development revisited using three-dimensional reconstructions of brown anole (Anolis sagrei, Squamata, Dactyloidae) dentition. J Anat 2020; 236:1004-1020. [PMID: 32056203 PMCID: PMC7219623 DOI: 10.1111/joa.13166] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 01/17/2020] [Accepted: 01/20/2020] [Indexed: 02/02/2023] Open
Abstract
The egg tooth is a hatching adaptation, characteristic of all squamates. In brown anole embryos, the first tooth that starts differentiating is the egg tooth. It develops from a single tooth germ and, similar to the regular dentition of all the other vertebrates, the differentiating egg tooth of the brown anole passes through classic morphological and developmental stages named according to the shape of the dental epithelium: epithelial thickening, dental lamina, tooth bud, cap and bell stages. The differentiating egg tooth consists of three parts: the enamel organ, hard tissues and dental pulp. Shortly before hatching, the egg tooth connects with the premaxilla. Attachment tissue of the egg tooth does not undergo mineralization, which makes it different from the other teeth of most squamates. After hatching, odontoclasts are involved in resorption of the egg tooth's remains. This study shows that the brown anole egg tooth does not completely conform to previous reports describing iguanomorph egg teeth and reveals a need to investigate its development in the context of squamate phylogeny.
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Affiliation(s)
- Mateusz Hermyt
- Faculty of Natural SciencesInstitute of Biology, Biotechnology and Environmental ProtectionUniversity of Silesia in KatowiceKatowicePoland
| | | | - Weronika Rupik
- Faculty of Natural SciencesInstitute of Biology, Biotechnology and Environmental ProtectionUniversity of Silesia in KatowiceKatowicePoland
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Milazzo G, Mercatelli D, Di Muzio G, Triboli L, De Rosa P, Perini G, Giorgi FM. Histone Deacetylases (HDACs): Evolution, Specificity, Role in Transcriptional Complexes, and Pharmacological Actionability. Genes (Basel) 2020; 11:E556. [PMID: 32429325 DOI: 10.3390/genes11050556] [Citation(s) in RCA: 158] [Impact Index Per Article: 39.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 02/06/2023] Open
Abstract
Histone deacetylases (HDACs) are evolutionary conserved enzymes which operate by removing acetyl groups from histones and other protein regulatory factors, with functional consequences on chromatin remodeling and gene expression profiles. We provide here a review on the recent knowledge accrued on the zinc-dependent HDAC protein family across different species, tissues, and human pathologies, specifically focusing on the role of HDAC inhibitors as anti-cancer agents. We will investigate the chemical specificity of different HDACs and discuss their role in the human interactome as members of chromatin-binding and regulatory complexes.
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26
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Dei Giudici S, Franzoni G, Bonelli P, Angioi PP, Zinellu S, Deriu V, Carta T, Sechi AM, Salis F, Balzano F, Oggiano A. Genetic Characterization of Porcine Circovirus 3 Strains Circulating in Sardinian Pigs and Wild Boars. Pathogens 2020; 9:E344. [PMID: 32370251 DOI: 10.3390/pathogens9050344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022] Open
Abstract
Porcine circovirus 3 (PCV3) is a recently discovered member of the Circoviridae family. So far, its presence has been reported in North America, Asia, South America, and Europe. In this study, blood and tissue samples from 189 Sardinian suids (34 domestic pigs, 115 feral free ranging pigs, and 39 wild boars) were used to genetically characterize the PCV3 strains from Sardinia. PCV3 infection in the animals was confirmed by real time PCR. The detection rate in the three groups analyzed was l7.64% in domestic pigs, 77.39% in free ranging pigs, and 61.54% in wild boars. Moreover, our results showed that co-infection of PCV3 with other viruses is quite a common occurrence. Molecular characterization of Sardinian PCV3 strains was performed by sequencing 6 complete genomes and 12 complete cap genes. Our results revealed that there is a high similarity between our strains and those identified in different countries, confirming the genetic stability of PCV3 regardless of geographical origin. Haplotype network analysis revealed the presence of 6 whole genomes or 12 unique ORF2 haplotypes and a nonsynonymous mutation in ORF2 that leads to an R14K amino acid substitution. Phylogenetic analysis of whole genome and ORF2 was also conducted. The Sardinian strains were allocated in three different clusters of phylogenetic trees of both complete genome and ORF2. With this study, we have provided a snapshot of PCV3 circulation in Sardinia. Our findings might help to achieve a deeper understanding of this emerging porcine virus.
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Gallina L, Savini F, Casà G, Bertoletti I, Bianchi A, Gibelli LR, Lelli D, Lavazza A, Scagliarini A. Epitheliotropic Infections in Wildlife Ruminants From the Central Alps and Stelvio National Park. Front Vet Sci 2020; 7:229. [PMID: 32426384 PMCID: PMC7203578 DOI: 10.3389/fvets.2020.00229] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/03/2020] [Indexed: 12/21/2022] Open
Abstract
The mountain chain of the Alps, represents the habitat of alpine fauna where the red deer (Cervus elaphus) population is the outmost numerous, followed by the chamois (Rupicapra rupicapra) and the alpine ibex (Capra ibex) at higher altitudes. Previous reports showed the circulation of epitheliotropic viruses, belonging to the families Papillomaviridae and Poxviridae, causing skin and mucosal lesions in wild ruminants of the Stelvio National Park, situated in the area. To deepen our knowledge on the natural dynamics of the infections, a passive surveillance on all the cases of proliferative skin and mucosal lesions in wild ruminants was performed. Twenty-seven samples (11 chamois, 10 red deer and 6 ibex) collected from 2008 to 2018 were analyzed by negative staining electron microscopy, histology, and PCR followed by genome sequencing and phylogenetic analyses. Results confirmed the spread of Parapoxvirus of Red Deer in New Zealand (PVNZ) in Italy, and its ability to cause severe lesions i.e., erosions and ulcers in the mouth. We showed for the first time a PVNZ/CePV1v (C. elaphus papillomavirus 1 variant) co-infection identified in one red deer. This result supports previous evidence on the ability of papillomavirus and parapoxvirus to mutually infect the same host tissue. Interestingly two ibex and one chamois showing orf virus (OV) skin lesions were shown to be co-infected with bovine papillomavirus type 1 and 2. The presence of bovine papillomavirus, in orf virus induced lesions of chamois and ibex raises the question of its pathogenetic role in these animal species. For the first time, OV/CePV1v co-infection was demonstrated in another chamois. CePV1v is sporadically reported in red deer throughout Europe and is considered species specific, its identification in a chamois suggests its ability of cross-infecting different animal species. Poxviruses and papillomavirus have been simultaneously detected also in the skin lesions of cattle, bird and human suggesting a possible advantageous interaction between these viruses. Taken together, our findings add further information on the epidemiology and pathogenetic role of epitheliotropic viruses in wild ruminants living in the central Alps and in Stelvio National Park.
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Affiliation(s)
- Laura Gallina
- Dipartimento di Scienze Mediche Veterinarie, Alma Mater Studiorum, Università di Bologna, Bologna, Italy
| | - Federica Savini
- Dipartimento di Scienze Mediche Veterinarie, Alma Mater Studiorum, Università di Bologna, Bologna, Italy
| | - Giovanni Casà
- Dipartimento di Scienze Mediche Veterinarie, Alma Mater Studiorum, Università di Bologna, Bologna, Italy
| | - Irene Bertoletti
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | - Alessandro Bianchi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | - Lucia Rita Gibelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | - Davide Lelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia-Romagna, Brescia, Italy
| | - Alessandra Scagliarini
- Dipartimento di Medicina Specialistica Diagnostica e Sperimentale, Alma Mater Studiorum, Università di Bologna, Bologna, Italy
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Mansour SMG, Mohamed FF, ElBakrey RM, Eid AAM, Mor SK, Goyal SM. Outbreaks of Duck Hepatitis A Virus in Egyptian Duckling Flocks. Avian Dis 2020; 63:68-74. [PMID: 31251521 DOI: 10.1637/11975-092118-reg.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/14/2018] [Indexed: 11/05/2022]
Abstract
During 2015, duck farms (n = 27) in Sharkia Province, Egypt, experienced several disease outbreaks leading to mortality and nervous manifestations. Upon necropsy, the affected ducklings showed liver lesions, such as hemorrhage or necrosis, suggestive of duck virus hepatitis (DVH). Reverse transcription-PCR (RT-PCR), on the basis of the 3D gene, found duck livers from 21 farms to be positive for duck hepatitis A virus serotype 1 (DHAV-1). All duck breeds (Pekin, Mallard, and Muscovy) were infected. The virus was isolated in embryonated chicken eggs, which showed embryonic mortality (40%-80%) within 5-7 days, stunting or dwarfing (69.6%), and necrotic liver foci (60.9%). The VP1 gene of 11 DHAV-1 strains was characterized by RT-PCR and Sanger sequencing. All study strains were clustered in a monophyletic branch within subclade B2 of Group 4 and were separated from the Egyptian vaccine strain. Several amino acid (aa) residues, such as V129, S142 (only in four strains), L181, G184, and K217, were related to virus attenuation. However, two aa residues (N193 and E205), found in virulent DHAV-1 strains, were also observed in our strains. This study confirms the circulation of DHAV-1 (subclade B2) in Lower Egypt and elucidates the phylogenetic characters of the VP1 genes, which will be useful in following the local trends of DHAV-1 infections. Further studies are indicated to determine the correlation between these mutations and the virulence of the Egyptian DHAV-1 isolates.
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Affiliation(s)
- Shimaa M G Mansour
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia 44511, Egypt
| | - Fakry F Mohamed
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia 44511, Egypt.,Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, MN 55108
| | - Reham M ElBakrey
- Department of Avian and Rabbit Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia 44511, Egypt
| | - Amal A M Eid
- Department of Avian and Rabbit Medicine, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Sharkia 44511, Egypt
| | - Sunil K Mor
- Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, MN 55108,
| | - Sagar M Goyal
- Department of Veterinary Population Medicine and Veterinary Diagnostic Laboratory, University of Minnesota, St. Paul, MN 55108
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29
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Banaszkiewicz S, Calland JK, Mourkas E, Sheppard SK, Pascoe B, Bania J. Genetic Diversity of Composite Enterotoxigenic Staphylococcus epidermidis Pathogenicity Islands. Genome Biol Evol 2020; 11:3498-3509. [PMID: 31769803 PMCID: PMC6931896 DOI: 10.1093/gbe/evz259] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2019] [Indexed: 02/07/2023] Open
Abstract
The only known elements encoding enterotoxins in coagulase-negative staphylococci are composite Staphylococcus epidermidis pathogenicity islands (SePIs), including SePI and S. epidermidis composite insertion (SeCI) regions. We investigated 1545 Staphylococcus spp. genomes using whole-genome MLST, and queried them for genes of staphylococcal enterotoxin family and for 29 ORFs identified in prototype SePI from S. epidermidis FRI909. Enterotoxin-encoding genes were identified in 97% of Staphylococcus aureus genomes, in one Staphylococcus argenteus genome and in nine S. epidermidis genomes. All enterotoxigenic S. epidermidis strains carried composite SePI, encoding sec and sel enterotoxin genes, and were assigned to a discrete wgMLST cluster also containing genomes with incomplete islands located in the same region as complete SePI in enterotoxigenic strains. Staphylococcus epidermidis strains without SeCI and SePI genes, and strains with complete SeCI and no SePI genes were identified but no strains were found to carry only SePI and not SeCI genes. The systematic differences between SePI and SeCI regions imply a lineage-specific pattern of inheritance and support independent acquisition of the two elements in S. epidermidis. We provided evidence of reticulate evolution of mobile elements that contain elements with different putative ancestry, including composite SePI that contains genes found in other coagulase-negative staphylococci (SeCI), as well as in S. aureus (SePI-like elements). We conclude that SePI-associated elements present in nonenterotoxigenic S. epidermidis represent a scaffold associated with acquisition of virulence-associated genes. Gene exchange between S. aureus and S. epidermidis may promote emergence of new pathogenic S. epidermidis clones.
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Affiliation(s)
- Sylwia Banaszkiewicz
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Poland
| | | | | | | | - Ben Pascoe
- The Milner Centre for Evolution, University of Bath, United Kingdom
| | - Jacek Bania
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Poland
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Affiliation(s)
- Marco Ciotti
- Laboratory of Microbiology and Virology, Polyclinic Tor Vergata Foundation, Viale Oxford 81, 00133 Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy
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31
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Lo Presti A, Del Chierico F, Altomare A, Zorzi F, Cella E, Putignani L, Guarino MPL, Monteleone G, Cicala M, Angeletti S, Ciccozzi M. Exploring the genetic diversity of the 16S rRNA gene of Akkermansia muciniphila in IBD and IBS. Future Microbiol 2019; 14:1497-1509. [PMID: 31850811 DOI: 10.2217/fmb-2019-0175] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: The human gastrointestinal tract harbors diverse, abundant microbiota and Akkermansia muciniphila is involved in this community. The aim of this study is to characterize 16 new A. muciniphila 16S ribosomal RNA sequences selected from a metagenomic database from stools of patients with irritable bowel syndrome (IBS), inflammatory bowel diseases and control (CTRLs) subjects by a phylogenetic approach. Materials & methods: A phylogenetic approach was used to study the genetic diversity and SNPs in 16 A. muciniphila 16S ribosomal RNA sequences from stools of 107 individuals, 36 of which were patients affected by IBS, 30 by inflammatory bowel disease and 41 were CTRLs. Results: Phylogenetic analysis confirmed the subdivision into different supported clusters. An increase of variability in IBS has been identified. Conclusion: The genetic variation combined to the relative abundance, contribute to the protective role of A. muciniphila. Phylogenesis represent an additional approach to investigate genetic variability.
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Affiliation(s)
| | | | | | - Francesca Zorzi
- Gastrointestinal Unit, Department of Systems Medicine, University Tor Vergata, Rome, Italy
| | - Eleonora Cella
- Unit of Medical Statistics & Molecular Epidemiology, University Campus Bio-Medico, Rome, Italy
| | - Lorenza Putignani
- Unit of Parasitology and Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Giovanni Monteleone
- Gastrointestinal Unit, Department of Systems Medicine, University Tor Vergata, Rome, Italy
| | - Michele Cicala
- Unit of Digestive Disease, Campus Bio-Medico University, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics & Molecular Epidemiology, University Campus Bio-Medico, Rome, Italy
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Titov VN, Sazhina NN, Evteeva NМ. [Ozone oxidizes oleic fatty acid with the highest rate constant and does not oxidize palmitic acid. Different physicochemical parameters of substrates and their role in phylogenesis.]. Klin Lab Diagn 2019; 64:132-139. [PMID: 31012550 DOI: 10.18821/0869-2084-2019-64-3-132-139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 03/01/2019] [Indexed: 11/17/2022]
Abstract
Physicochemical differences between О3 oxidation parameters for palmitic and oleic fatty acids (FA) during phylogenesis (evolution) are fundamental for а) production of palmitoleic monounsaturated fatty (MFA), b) formation of carnitine palmitoyltransferase as a FA transporter to mitochondria, and c) in vivo production of oleic MFA under humoral regulatory effect of insulin. In the strive for the best kinetic parameters of biological organisms without a possibility of modifying physicochemical and biochemical reactions in the mitochondrial matrix, the mitochondria can be provided with a substrate that increases energy production efficiency and the amount of ATP. Physicochemical parameters of oleic MFA has become the standard of an oxidation substrate for in vivo energy production; this MFA was synthesized in organisms for millions of years. Environmental influences are the second factor which determines kinetic perfection of biological organisms during phylogenesis. Are these influences always beneficial? Mostly, they are not. However, they largely stimulate adaptive functions of the organism, including the biological function of locomotion, cognitive function and the function of positioning in the environment. Biological, energy and kinetic perfection formed in vivo can be easily destroyed if phylogenetically herbivorous Homo sapiens abuses the diet of carnivorous animals (meat) which was not consumed by him and his ancestors during phylogenesis. This abuse is the major cause of metabolic pandemias in human population. They are: insulin resistance, atherosclerosis and atheromatosis, obesity and nonalcoholic liver disease. The most effective measures preventing metabolic pandemias, cardiac heart disease and myocardial infarction are extremely simple. People should remain herbivorous.
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Affiliation(s)
- V N Titov
- National Medical Research Center for Cardiology Ministry of Health, 121552, Moscow, Russia
| | - N N Sazhina
- Emanuel Institute of Biochemical Physics, 119334, Moscow, Russia
| | - N М Evteeva
- Emanuel Institute of Biochemical Physics, 119334, Moscow, Russia
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Kolychev AP, Terpilovskii MA, Uversky VN. Sequential and Asynchronous Strengthening of the Influence of Temperature on the Endo- and Exocytosis of Insulin in the Isolated Vertebrata Hepatocytes: Summing up Previous Studies. Curr Protein Pept Sci 2019; 21:22-35. [PMID: 30907311 DOI: 10.2174/1389203720666190325101804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 02/19/2019] [Accepted: 03/11/2019] [Indexed: 11/22/2022]
Abstract
Insulin internalization and processing of the Insulin Receptor Complex (IRC) inside the cell are important components of the intracellular Mechanism of Insulin Action (MIA). They define the continuation of intracellular signaling of IRC and allow utilization of the parts of the complex after ligand dissociation. Traditionally, changes in the insulin regulatory system associated with the vertebrate phylogenesis have been evaluated by changes of its two elements: the hormone and its receptor. A hormone-competent cell was considered as an evolutionarily completed element of insulin regulatory system. However, previous studies of the isolated hepatocytes of four classes of vertebrates (lamprey, frog, chicken, and rat) revealed significant differences in the state of internalization of 125I-insulin and intracellular IRC processing. Radical differences were noted in the regulation of 125I-insulin internalization and the intracellular fate of the IRC. Here, cytosolic efficient insulin degradation and a complete lack of 125I-insulin exocytosis were observed in the cyclostome cells, whereas in amphibians the hormone underwent lysosomal degradation and showed low levels of exocytosis, while birds and mammals were characterized by high volumes of the excreted 125Iinsulin containing proteolytic 125I-insulin fragments. Despite the established recognition of the importance of the temperature factor, a complete understanding of the molecular mechanisms underlying the temperature effects on MIA is still missing. This poorly studied problem of the MIA temperature dependence can be behind the differences in the effect of temperature on the intracellular action of insulin and IGF-I. In fact, at different phylogenetic stages, successive changes were reported for the temperature dependence of the 125Iinsulin internalization and exocytosis. The following regularities were reported for the effect of temperature on the 125I-insulin internalization in isolated hepatocytes of different origin: complete lack of receptibility of the process to temperature in lampreys, receptibility of the process in a narrow range of low temperatures (0-5°C) in amphibians, and flexible regulation of 125I-insulin internalization in a wide temperature range (6- 37°C) in the cells from endothermic organisms. Reported data make it possible to observe three stages in the alteration of temperature regulation of 125I-insulin internalization (in cells of cyclostomes, amphibians, and endothermic organisms) and two stages of temperature regulation of 125I-insulin exocytosis in cells of amphibians, birds, and mammals. The data presented in this study reflect the specificity of the developmental reorganization of the intracellular MIA regulation and hormone utilization, and emphasize the central role of temperature in selective MIA formation during vertebrate phylogenesis.
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Affiliation(s)
- Alexander P Kolychev
- Laboratory of the Comparative Biochemistry of Enzymes, Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| | - Maxim A Terpilovskii
- Laboratory of the Comparative Biochemistry of Enzymes, Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, Saint-Petersburg, Russian Federation
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russian Federation
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Titov VN, Rozhkova ТА, Kaminnaya VА. [Biological role of insulin: transformation of carnivores leaving in the ocean into herbivores living on the dry land. Development of the biological function of locomotion and kinetic parameters of the body.]. Klin Lab Diagn 2019; 63:132-141. [PMID: 30673191 DOI: 10.18821/0869-2084-2018-63-3-132-141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 08/30/2017] [Indexed: 11/17/2022]
Abstract
Phylogenetic theory of general pathology draws researchers' attention to the following aspects of the biological effects of insulin. 1. Phylogenetically, in vivo insulin is primarily involved in the metabolism of fatty acids (FA) and only in the second turn in glucose metabolism; regulation of FA metabolism in cells started millions of years earlier than that of glucose metabolism. Phylogenetically late insulin blocks lipolysis only in phylogenetically late insulin-dependent subcutaneous adipocytes but not in phylogenetically early visceral fat cells of the omentum. 2. Biological role of insulin consists in the formation of the biological function of locomotion, i.e., movement arising from contraction of striated myocytes provided with substrates (FA and glucose) for energy production as macroergic ATP. 3. Biological destiny of phylogenetically late insulin is transformation of carnivorous (fish-eating) animals living in the ocean into herbivores living on the dry land. 4. Insulin has formed in vivo highly efficient oleic variant of FA metabolism instead of phylogenetically early less efficient palmitic variant. 5. Biologically, insulin is destined for providing cells with energy and perfection of physical activity and kinetic parameters of the organism. According to phylogenetic theory of general pathology and basic principles of endocrinology, clinical cases should be regarded as: 1. rare structurally-related insulindeficient type I diabetes mellitus, 2. rare structurally-related (receptor pathology) hyperinsulinemic type II diabetes mellitus, and 3. a great number of patients with functional disorders in the hormone activity, insulin resistance syndrome, metabolic syndrome and obesity. We believe that the food of herbivores should contain palmitic acid in the amounts that hepatocytes can esterify into oleic very low density lipoproteins and cells can internalize as ligand oleic by apoЕ/В-100 endocytosis without formation of low density lipoproteins.
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Affiliation(s)
- V N Titov
- National Medical Research Center of Cardiology of the Ministry of Health of Russia, Moscow, 121552
| | - Т А Rozhkova
- National Medical Research Center of Cardiology of the Ministry of Health of Russia, Moscow, 121552
| | - V А Kaminnaya
- National Medical Research Center of Cardiology of the Ministry of Health of Russia, Moscow, 121552
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Caragnano A, Foetisch A, Maneveldt GW, Millet L, Liu LC, Lin SM, Rodondi G, Payri CE. Revision of Corallinaceae (Corallinales, Rhodophyta): recognizing Dawsoniolithon gen. nov., Parvicellularium gen. nov. and Chamberlainoideae subfam. nov. containing Chamberlainium gen. nov. and Pneophyllum. J Phycol 2018; 54:391-409. [PMID: 29574890 DOI: 10.1111/jpy.12644] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/04/2018] [Indexed: 06/08/2023]
Abstract
A multi-gene (SSU, LSU, psbA, and COI) molecular phylogeny of the family Corallinaceae (excluding the subfamilies Lithophylloideae and Corallinoideae) showed a paraphyletic grouping of six monophyletic clades. Pneophyllum and Spongites were reassessed and recircumscribed using DNA sequence data integrated with morpho-anatomical comparisons of type material and recently collected specimens. We propose Chamberlainoideae subfam. nov., including the type genus Chamberlainium gen. nov., with C. tumidum comb. nov. as the generitype, and Pneophyllum. Chamberlainium is established to include several taxa previously ascribed to Spongites, the generitype of which currently resides in Neogoniolithoideae. Additionally we propose two new genera, Dawsoniolithon gen. nov. (Metagoniolithoideae), with D. conicum comb. nov. as the generitype and Parvicellularium gen. nov. (subfamily incertae sedis), with P. leonardi sp. nov. as the generitype. Chamberlainoideae has no diagnostic morpho-anatomical features that enable one to assign specimens to it without DNA sequence data, and it is the first subfamily to possess both Type 1 (Chamberlainium) and Type 2 (Pneophyllum) tetra/bisporangial conceptacle roof development. Two characters distinguish Chamberlainium from Spongites: tetra/biasporangial conceptacle chamber diameter (<300 μm in Chamberlainium vs. >300 μm in Spongites) and tetra/bisporangial conceptacle roof thickness (<8 cells in Chamberlainium vs. >8 cells in Spongites). Two characters also distinguish Pneophyllum from Dawsoniolithon: tetra/bisporangial conceptacle roof thickness (<8 cells in Pneophyllum vs. >8 cells in Dawsoniolithon) and thallus construction (dimerous in Pneophyllum vs. monomerous in Dawsoniolithon).
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Affiliation(s)
- Annalisa Caragnano
- Institut de Recherche pour le Développement, UMR ENTROPIE (IRD-Université de la Réunion-CNRS), BPA5, 98848, Nouméa, New Caledonia, France
| | - Alexandra Foetisch
- Institut de Recherche pour le Développement, UMR ENTROPIE (IRD-Université de la Réunion-CNRS), BPA5, 98848, Nouméa, New Caledonia, France
| | - Gavin W Maneveldt
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Bellville, 7535, South Africa
| | - Laurent Millet
- Institut de Recherche pour le Développement, UMR ENTROPIE (IRD-Université de la Réunion-CNRS), BPA5, 98848, Nouméa, New Caledonia, France
| | - Li-Chia Liu
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Showe-Mei Lin
- Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20224, Taiwan
| | - Graziella Rodondi
- Dip.to di Bioscienze, Università degli Studi di Milano, via G. Celoria 26, 20133, Milan, Italy
| | - Claude E Payri
- Institut de Recherche pour le Développement, UMR ENTROPIE (IRD-Université de la Réunion-CNRS), BPA5, 98848, Nouméa, New Caledonia, France
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Pfeffer CM, Ho BN, Singh ATK. The Evolution, Functions and Applications of the Breast Cancer Genes BRCA1 and BRCA2. Cancer Genomics Proteomics 2018; 14:293-298. [PMID: 28870997 DOI: 10.21873/cgp.20040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 07/26/2017] [Accepted: 08/02/2017] [Indexed: 12/17/2022] Open
Abstract
BRCA1 and BRCA2 are both tumor suppressors whose mutations are the cause of most hereditary breast cancers. Both genes are highly involved in ensuring genome stability. BRCA1 homologs are found in the plant and animal kingdoms while BRCA2 homologs are additionally found in the fungi kingdom. The initial origin of both genes remains unknown, however it is expected that the common ancestors originated around 1.6 billion years ago prior to the kingdoms diverging. There has been a great amount of divergence between homologs that is not observed in other tumor suppressors with only functionally important domains conserved. This divergence continues today with evidence of primate BRCA1/2 evolution. Cancer-associated mutations have been found to occur at conserved sites, indicating that conserved sites are important for function. In this study, we present a review on the phylogenesis of BRCA1 and BRCA2.
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Affiliation(s)
- Claire M Pfeffer
- Department of Biology, Division of Natural and Social Sciences, Carthage College, Kenosha, WI, U.S.A
| | - Benjamin N Ho
- Department of Biology, Division of Natural and Social Sciences, Carthage College, Kenosha, WI, U.S.A
| | - Amareshwar T K Singh
- Department of Biology, Division of Natural and Social Sciences, Carthage College, Kenosha, WI, U.S.A.
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Fanelli E, Troccoli A, Vovlas N, Scarcia G, Mincuzzi A, Sanzani SM, Ippolito A, De Luca F. Occurrence of Sheraphelenchus sucus (Nematoda: Aphelenchoidinae) and Panagrellus sp. (Rhabditida: Panagrolaimidae) Associated with Decaying Pomegranate Fruit in Italy. J Nematol 2017; 49:418-426. [PMID: 29353931 PMCID: PMC5770290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Indexed: 06/07/2023] Open
Abstract
Two different nematode species were recovered from pomegranate decaying fruit in two localities in Southern Italy: the mycetophagus nematode Sheraphelenchus sucus and a bacterial feeder nematode belonging to the Panagrolaimidae (Rhabditida) family. Morphometrics of the Italian population of S. sucus closely resemble that of the type population, whereas some differences were found when compared with another population from Iran. Molecular characterization of the Italian S. sucus using the 18S rRNA gene, D2-D3 expansion domains of the 28S rDNA, the ITS region, and the partial mitochondrial COI were carried out. Sequences of the 18S rRNA gene, the D2-D3 domains, and the ITS were analyzed using several methods for inferring phylogeny to reconstruct the relationships among Sheraphelenchus and Bursaphelenchus species. The bacterial feeder Panagrellus sp. was characterized at the molecular level only. The D2-D3 expansion domains and ITS sequences of this Italian panagrolaimid were determined. The D2-D3 sequences of the Italian panagrolaimid showed 99% similarity with the corresponding sequence of Panagrellus sp. associated with Rhynchophorus ferrugineus. This is the first report on the tritrophic association of S. sucus and Rhabditida that uses both insects and pomegranate fruit as hosts.
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Affiliation(s)
- Elena Fanelli
- CNR, Istituto per la Protezione Sostenibile delle Piante (IPSP), 70126 Bari, Italy
| | - Alberto Troccoli
- CNR, Istituto per la Protezione Sostenibile delle Piante (IPSP), 70126 Bari, Italy
| | - Nicola Vovlas
- CNR, Istituto per la Protezione Sostenibile delle Piante (IPSP), 70126 Bari, Italy
| | - Gianluca Scarcia
- CNR, Istituto per la Protezione Sostenibile delle Piante (IPSP), 70126 Bari, Italy
- DiSSPA, Università di Bari "Aldo Moro," 70126 Bari, Italy
| | | | | | | | - Francesca De Luca
- CNR, Istituto per la Protezione Sostenibile delle Piante (IPSP), 70126 Bari, Italy
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Thorpe RS. THE USE OF DNA DIVERGENCE TO HELP DETERMINE THE CORRELATES OF EVOLUTION OF MORPHOLOGICAL CHARACTERS. Evolution 2017; 50:524-531. [PMID: 28568945 DOI: 10.1111/j.1558-5646.1996.tb03865.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/1994] [Accepted: 03/08/1995] [Indexed: 11/28/2022]
Abstract
Even though, from Darwin onwards, interisland evolution has been a cornerstone of evolutionary theory it has not been possible to determine to what extent this geographic variation reflects the phylogeny (e.g., pattern of island colonization) or ecogenetic adaptation to different ecological conditions on each island. Using the morphology of western Canary Island lacertids (Gallotia galloti) as an example, a procedure is explored that gives a preliminary answer to this problem when there are a limited number of islands. The phylogenetic component (represented by patristic distances derived from 1005 mitochondrial DNA [mtDNA] base pairs) can be separated from two potential ecogenetic factors (environmental richness and climate) by partial Mantel tests. This reveals that, although these components interact, some characters are correlated primarily to biodiversity/paucity (e.g., size), others are correlated to wet and lush environments (e.g., dorsal pattern), and others are correlated primarily to the phylogeny (e.g., sexual leg markings). The former two correlations may be due to ecogenetic adaptation to current ecological conditions, wheras the latter reflects historical processes.
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Affiliation(s)
- Roger S Thorpe
- School of Biological Sciences, University of Wales, Bangor, Gwynedd, LL57 2UW, U.K
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Liao ZH, Kuo TC, Kao CH, Chou TM, Kao YH, Huang RN. Identification of the chitinase genes from the diamondback moth, Plutella xylostella. Bull Entomol Res 2016; 106:769-780. [PMID: 27417424 DOI: 10.1017/s0007485316000511] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chitinases have an indispensable function in chitin metabolism and are well characterized in numerous insect species. Although the diamondback moth (DBM) Plutella xylostella, which has a high reproductive potential, short generation time, and characteristic adaptation to adverse environments, has become one of the most serious pests of cruciferous plants worldwide, the information on the chitinases of the moth is presently limited. In the present study, using degenerated polymerase chain reaction (PCR) and rapid amplification of cDNA ends-PCR strategies, four chitinase genes of P. xylostella were cloned, and an exhaustive search was conducted for chitinase-like sequences from the P. xylostella genome and transcriptomic database. Based on the domain analysis of the deduced amino acid sequences and the phylogenetic analysis of the catalytic domain sequences, we identified 15 chitinase genes from P. xylostella. Two of the gut-specific chitinases did not cluster with any of the known phylogenetic groups of chitinases and might be in a new group of the chitinase family. Moreover, in our study, group VIII chitinase was not identified. The structures, classifications and expression patterns of the chitinases of P. xylostella were further delineated, and with this information, further investigations on the functions of chitinase genes in DBM could be facilitated.
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Affiliation(s)
- Z H Liao
- Department of Life Science,National Central University,Chung-Li,Taoyuan,Taiwan 320,ROC
| | - T C Kuo
- Department of Biochemistry,Taipei Medical University,250 Wu-Hsing Street,Taipei 110,Taiwan
| | - C H Kao
- Applied Zoology Division,Taiwan Agricultural Research Institute,Council of Agriculture,Executive Yua,Wufeng,Taichung 41362,Taiwan
| | - T M Chou
- Applied Zoology Division,Taiwan Agricultural Research Institute,Council of Agriculture,Executive Yua,Wufeng,Taichung 41362,Taiwan
| | - Y H Kao
- Department of Life Science,National Central University,Chung-Li,Taoyuan,Taiwan 320,ROC
| | - R N Huang
- Department of Entomology,College of Bioresources and Agriculture, National Taiwan University,Taipei 106,Taiwan
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Romano S, Fernàndez-Guerra A, Reen FJ, Glöckner FO, Crowley SP, O'Sullivan O, Cotter PD, Adams C, Dobson ADW, O'Gara F. Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus. Front Microbiol 2016; 7:387. [PMID: 27065959 PMCID: PMC4811931 DOI: 10.3389/fmicb.2016.00387] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/11/2016] [Indexed: 01/15/2023] Open
Abstract
Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage. Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus. Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche within its microbiota. Our data suggest the presence of a sponge-specific lineage of Pseudovibrio. The reduction in genome size and the loss of some systems potentially used to successfully enter the host, leads to the hypothesis that P. axinellae strain AD2 may be a lineage that presents an ancient association with the host and that may be vertically transmitted to the progeny.
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Affiliation(s)
- Stefano Romano
- BIOMERIT Research Centre, University College Cork Cork, Ireland
| | - Antonio Fernàndez-Guerra
- Oxford e-Research Centre, University of OxfordOxford, UK; Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - F Jerry Reen
- BIOMERIT Research Centre, University College Cork Cork, Ireland
| | - Frank O Glöckner
- Microbial Genomics and Bioinformatics Research Group, Max Planck Institute for Marine MicrobiologyBremen, Germany; Jacobs University Bremen gGmbHBremen, Germany
| | | | - Orla O'Sullivan
- Teagasc Food Research CentreFermoy, Ireland; APC Microbiome InstituteCork, Ireland
| | - Paul D Cotter
- Teagasc Food Research CentreFermoy, Ireland; APC Microbiome InstituteCork, Ireland
| | - Claire Adams
- BIOMERIT Research Centre, University College Cork Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College CorkCork, Ireland; Environmental Research Institute, University College CorkCork, Ireland
| | - Fergal O'Gara
- BIOMERIT Research Centre, University College CorkCork, Ireland; School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin UniversityPerth, WA, Australia
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Michelacci V, Orsini M, Knijn A, Delannoy S, Fach P, Caprioli A, Morabito S. Development of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC). Front Microbiol 2016; 7:202. [PMID: 26941726 PMCID: PMC4763077 DOI: 10.3389/fmicb.2016.00202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/05/2016] [Indexed: 11/13/2022] Open
Abstract
Shiga-toxin producing Escherichia coli (STEC) strains possess a large accessory genome composed of virulence genes existing in multiple allelic variants, which sometimes segregate with specific STEC subpopulations. We analyzed the allelic variability of 91 virulence genes of STEC by Real Time PCR followed by melting curves analysis in 713 E. coli strains including 358 STEC. The 91 genes investigated were located on the locus of enterocyte effacement (LEE), OI-57, and OI-122 pathogenicity islands and displayed a total of 476 alleles in the study population. The combinations of the 91 alleles of each strain were termed allelic signatures and used to perform cluster analyses. We termed such an approach High Resolution Virulence Allelic Profiling (HReVAP) and used it to investigate the phylogeny of STEC of multiple serogroups. The dendrograms obtained identified groups of STEC segregating approximately with the serogroups and allowed the identification of subpopulations within the single groups. The study of the allelic signatures provided further evidence of the coevolution of the LEE and OI-122, reflecting the occurrence of their acquisition through a single event. The HReVAP analysis represents a sensitive tool for studying the evolution of LEE-positive STEC.
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Affiliation(s)
- Valeria Michelacci
- European Reference Laboratory for Escherichia coli, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità Rome, Italy
| | - Massimiliano Orsini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise G. Caporale Teramo, Italy
| | - Arnold Knijn
- Servizio Informatico, Documentazione, Biblioteca e Attività Editoriali, Istituto Superiore di Sanità Rome, Italy
| | - Sabine Delannoy
- Platform IdentyPath, Food Safety Laboratory, ANSES, Université Paris-Est Maisons-Alfort, France
| | - Patrick Fach
- Platform IdentyPath, Food Safety Laboratory, ANSES, Université Paris-Est Maisons-Alfort, France
| | - Alfredo Caprioli
- European Reference Laboratory for Escherichia coli, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità Rome, Italy
| | - Stefano Morabito
- European Reference Laboratory for Escherichia coli, Dipartimento di Sanità Pubblica Veterinaria e Sicurezza Alimentare, Istituto Superiore di Sanità Rome, Italy
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Wojtkowska M, Buczek D, Stobienia O, Karachitos A, Antoniewicz M, Slocinska M, Makałowski W, Kmita H. The TOM Complex of Amoebozoans: the Cases of the Amoeba Acanthamoeba castellanii and the Slime Mold Dictyostelium discoideum. Protist 2015; 166:349-62. [PMID: 26074248 DOI: 10.1016/j.protis.2015.05.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 05/10/2015] [Accepted: 05/14/2015] [Indexed: 11/29/2022]
Abstract
Protein import into mitochondria requires a wide variety of proteins, forming complexes in both mitochondrial membranes. The TOM complex (translocase of the outer membrane) is responsible for decoding of targeting signals, translocation of imported proteins across or into the outer membrane, and their subsequent sorting. Thus the TOM complex is regarded as the main gate into mitochondria for imported proteins. Available data indicate that mitochondria of representative organisms from across the major phylogenetic lineages of eukaryotes differ in subunit organization of the TOM complex. The subunit organization of the TOM complex in the Amoebozoa is still elusive, so we decided to investigate its organization in the soil amoeba Acanthamoeba castellanii and the slime mold Dictyostelium discoideum. They represent two major subclades of the Amoebozoa: the Lobosa and Conosa, respectively. Our results confirm the presence of Tom70, Tom40 and Tom7 in the A. castellanii and D. discoideum TOM complex, while the presence of Tom22 and Tom20 is less supported. Interestingly, the Tom proteins display the highest similarity to Opisthokonta cognate proteins, with the exception of Tom40. Thus representatives of two major subclades of the Amoebozoa appear to be similar in organization of the TOM complex, despite differences in their lifestyle.
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Affiliation(s)
- Małgorzata Wojtkowska
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland.
| | - Dorota Buczek
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland; University of Muenster, Faculty of Medicine Institute of Bioinformatics, Muenster, Germany
| | - Olgierd Stobienia
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland
| | - Andonis Karachitos
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland
| | - Monika Antoniewicz
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland
| | - Małgorzata Slocinska
- Adam Mickiewicz University, Faculty of Biology, Institute of Experimental Biology, Department of Animal Physiology and Development, Poznań, Poland
| | - Wojciech Makałowski
- University of Muenster, Faculty of Medicine Institute of Bioinformatics, Muenster, Germany
| | - Hanna Kmita
- Adam Mickiewicz University, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Department of Bioenergetics, Poznań, Poland
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Rapoport EM, Matveeva VK, Kaltner H, André S, Vokhmyanina OA, Pazynina GV, Severov VV, Ryzhov IM, Korchagina EY, Belyanchikov IM, Gabius HJ, Bovin NV. Comparative lectinology: Delineating glycan-specificity profiles of the chicken galectins using neoglycoconjugates in a cell assay. Glycobiology 2015; 25:726-34. [PMID: 25681326 DOI: 10.1093/glycob/cwv012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 02/05/2015] [Indexed: 12/22/2022] Open
Abstract
A major aspect of carbohydrate-dependent galectin functionality is their cross-linking capacity. Using a cell surface as biorelevant platform for galectin binding and a panel of 40 glycans as sensor part of a fluorescent polyacrylamide neoglycopolymer for profiling galectin reactivity, properties of related proteins can be comparatively analyzed. The group of the chicken galectins (CGs) is an especially suited system toward this end due to its relatively small size, compared with mammalian galectins. The experiments reveal particularly strong reactivity toward N-acetyllactosamine repeats for all tested CGs and shared reactivity of CG-1A and CG-2 to histo-blood group ABH determinants. In cross-species comparison, CG-1B's properties closely resembled those of human galectin-1, as was the case for the galectin-2 (but not galectin-3) ortholog pair. Although binding-site architectures are rather similar, reactivity patterns can well differ.
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Affiliation(s)
- Eugenia M Rapoport
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, ul. Miklukho-Maklaya16/10, Moscow, Russia
| | - Varvara K Matveeva
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, ul. Miklukho-Maklaya16/10, Moscow, Russia
| | - Herbert Kaltner
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University, Veterinärstr. 13, Munich 80539, Germany
| | - Sabine André
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University, Veterinärstr. 13, Munich 80539, Germany
| | - Olga A Vokhmyanina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, ul. Miklukho-Maklaya16/10, Moscow, Russia
| | - Galina V Pazynina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, ul. Miklukho-Maklaya16/10, Moscow, Russia
| | - Vyacheslav V Severov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, ul. Miklukho-Maklaya16/10, Moscow, Russia
| | - Ivan M Ryzhov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, ul. Miklukho-Maklaya16/10, Moscow, Russia
| | - Elena Yu Korchagina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, ul. Miklukho-Maklaya16/10, Moscow, Russia
| | - Ivan M Belyanchikov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, ul. Miklukho-Maklaya16/10, Moscow, Russia
| | - Hans-J Gabius
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University, Veterinärstr. 13, Munich 80539, Germany
| | - Nicolai V Bovin
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, ul. Miklukho-Maklaya16/10, Moscow, Russia
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D'Angelo L, De Girolamo P, Lucini C, Terzibasi ET, Baumgart M, Castaldo L, Cellerino A. Brain-derived neurotrophic factor: mRNA expression and protein distribution in the brain of the teleost Nothobranchius furzeri. J Comp Neurol 2014; 522:1004-30. [PMID: 23983038 DOI: 10.1002/cne.23457] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/28/2013] [Accepted: 08/06/2013] [Indexed: 12/25/2022]
Abstract
BDNF (brain-derived neurotrophic factor) is a member of the neurotrophin family and it is implicated in regulating brain development and function. The BDNF gene organization and coding sequence are conserved in all vertebrates. The present survey was conducted in a teleost fish, Nothobranchius furzeri, because it is an emerging model of aging studies due to its short lifespan and shows the high rate of adult neurogenesis typical of anamniotes. The present survey reports: 1) the identification and characterization of the cDNA fragment encoding BDNF protein, and 2) the localization of BDNF in the whole brain. BDNF mRNA expression was assessed by in situ hybridization, by employing an antisense RNA probe; BDNF protein was detected by employing a sensitive immunohistochemical technique, along with highly specific affinity-purified antibodies to BDNF. Both BDNF mRNA and protein were detected in neurons and glial cells of all regions of the brain of N. furzeri. Interestingly, BDNF was localized also in brain areas involved in adult neurogenic activities, suggesting a specific role for this neurotrophic factor in controlling cell proliferation. These results provide baseline information for future studies concerning BDNF involvement in the aging processes of the teleost brain.
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Affiliation(s)
- Livia D'Angelo
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Napoli, Italy; Biology of Ageing, Leibniz Institute for Age Research, Fritz-Lipmann Institute, Jena, Germany
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Santoro MM, Fabeni L, Armenia D, Alteri C, Di Pinto D, Forbici F, Bertoli A, Di Carlo D, Gori C, Carta S, Fedele V, D'Arrigo R, Berno G, Ammassari A, Pinnetti C, Nicastri E, Latini A, Tommasi C, Boumis E, Petrosillo N, D'Offizi G, Andreoni M, Ceccherini-Silberstein F, Antinori A, Perno CF. Reliability and clinical relevance of the HIV-1 drug resistance test in patients with low viremia levels. Clin Infect Dis 2014; 58:1156-64. [PMID: 24429430 DOI: 10.1093/cid/ciu020] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND We evaluated reliability and clinical usefulness of genotypic resistance testing (GRT) in patients for whom combination antiretroviral therapy (cART) was unsuccessful with viremia levels 50-1000 copies/mL, for whom GRT is generally not recommended by current guidelines. METHODS The genotyping success rate was evaluated in 12 828 human immunodeficiency virus type 1 (HIV-1) plasma samples with viremia >50 copies/mL, tested using the commercial ViroSeq HIV-1 Genotyping System or a homemade system. Phylogenetic analysis was performed to test the reliability and reproducibility of the GRT at low-level viremia (LLV). Drug resistance was evaluated in 3895 samples from 2200 patients for whom treatment was unsuccessful (viremia >50 copies/mL) by considering the resistance mutations paneled in the 2013 International Antiviral Society list. RESULTS Overall, the success rate of amplification/sequencing was 96.4%. Viremia levels of 50-200 and 201-500 copies/mL afforded success rates of 67.2% and 88.1%, respectively, reaching 93.2% at 501-1000 copies/mL and ≥97.3% above 1000 copies/mL. A high homology among sequences belonging to the same subject for 96.4% of patients analyzed was found. The overall resistance prevalence was 74%. Drug resistance was commonly found also at LLV. In particular, by stratifying for different viremia ranges, detection of resistance was as follows: 50-200 copies/mL = 52.8%; 201-500 = 70%; 501-1000 = 74%; 1001-10 000 = 86.1%; 10 001-100 000 = 76.7%; and >100 000 = 63% (P < .001). Similar bell-shaped results were found when the GRT analysis was restricted to 2008-2012, although at a slightly lower prevalence. CONCLUSIONS In patients failing cART with LLV, HIV-1 genotyping provides reliable and reproducible results that are informative about emerging drug resistance.
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Abstract
Deadenylases catalyze the shortening of the poly(A) tail at the messenger ribonucleic acid (mRNA) 3′-end in eukaryotes. Therefore, these enzymes influence mRNA decay, and constitute a major emerging group of promising anti-cancer pharmacological targets. Herein, we conducted full phylogenetic analyses of the deadenylase homologs in all available genomes in an effort to investigate evolutionary relationships between the deadenylase families and to identify invariant residues, which probably play key roles in the function of deadenylation across species. Our study includes both major Asp-Glu-Asp-Asp (DEDD) and exonuclease-endonuclease-phospatase (EEP) deadenylase superfamilies. The phylogenetic analysis has provided us with important information regarding conserved and invariant deadenylase amino acids across species. Knowledge of the phylogenetic properties and evolution of the domain of deadenylases provides the foundation for the targeted drug design in the pharmaceutical industry and modern exonuclease anti-cancer scientific research.
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Affiliation(s)
- Athanasia Pavlopoulou
- Bioinformatics and Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece
| | - Dimitrios Vlachakis
- Bioinformatics and Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece
| | - Nikolaos A A Balatsos
- Department of Biochemistry and Biotechnology, University of Thessaly, 26 Ploutonos st., 41 221 Larissa, Greece
| | - Sophia Kossida
- Bioinformatics and Medical Informatics Team, Biomedical Research Foundation, Academy of Athens, Soranou Efessiou 4, Athens 11527, Greece
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Matsuyama-Murata M, Inaba K, Horiuchi R, Fukazawa Y, Ibuki K, Hayami M, Miura T. Genetic similarity of circulating and small intestinal virus at the end stage of acute pathogenic simian-human immunodeficiency virus infection. Front Microbiol 2013; 4:204. [PMID: 23885255 PMCID: PMC3717482 DOI: 10.3389/fmicb.2013.00204] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Accepted: 07/01/2013] [Indexed: 11/13/2022] Open
Abstract
To understand the pathogenicity of acquired immune deficiency syndrome (AIDS), it is important to clarify where, when and how the virus replicates in the body of infected individuals. To identify the major virus replication site at the end stage of SHIV infection, we investigated the systemic tissues of SHIV-infected monkeys that developed AIDS-like disease. We quantified proviral DNA, and compared the mutation patterns of the viruses in various systemic tissues and in peripheral blood through phylogenetic analysis of the full genome sequence. We found that the amounts of proviral DNA detected in internal tissues were higher than those in peripheral blood mononuclear cells. In the sequence and phylogenetic tree analyses, the mutation patterns of the viruses in each tissue were generally different. However, the mutation pattern of the viruses in the jejunum and mesenteric lymph node were most similar to that of plasma viral RNA among the tissues examined in all three monkeys. In two of the three monkeys, which were euthanized earlier, viruses in the jejunum and mesenteric lymph node occupied the root position of the phylogenetic tree. Furthermore, in these tissues, more than 50% of SHIV-expressing cells were identified as macrophages based on co-expression of CD68. These results suggest that macrophages of the small intestine and/or mesenteric lymph node are the major virus production site at the end stage of SHIV infection of macaques.
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Affiliation(s)
- Megumi Matsuyama-Murata
- Laboratory of Primate Model, Experimental Research Center for Infectious Diseases, Institute for Virus Research, Kyoto University Kyoto, Japan
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Kaltner H, Raschta AS, Manning JC, Gabius HJ. Copy-number variation of functional galectin genes: studying animal galectin-7 (p53-induced gene 1 in man) and tandem-repeat-type galectins-4 and -9. Glycobiology 2013; 23:1152-63. [PMID: 23840039 DOI: 10.1093/glycob/cwt052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Galectins are potent adhesion/growth-regulatory effectors with characteristic expression profiles. Understanding the molecular basis of gene regulation in each case requires detailed information on copy number of genes and sequence(s) of their promoter(s). Our report reveals plasticity in this respect between galectins and species. We here describe occurrence of a two-gene constellation for human galectin (Gal)-7 and define current extent of promoter-sequence divergence. Interestingly, cross-species genome analyses also detected single-copy display. Because the regulatory potential will then be different, extrapolations of expression profiles are precluded between respective species pairs. Gal-4 coding in chromosomal vicinity was found to be confined to one gene, whereas copy-number variation also applied to Gal-9. The example of rat Gal-9 teaches the lesson that the presence of multiple bands in Southern blotting despite a single-copy gene constellation is attributable to two pseudogenes. The documented copy-number variability should thus be taken into consideration when studying regulation of galectin genes, in a species and in comparison between species.
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Affiliation(s)
- Herbert Kaltner
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University Munich, Veterinärstr. 13, 80539 München, Germany
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Cordero MA, Robbins RT, Szalanski AL. Taxonomic and molecular identification of bakernema, criconema, hemicriconemoides, ogma and xenocriconemella species (nematoda: criconematidae). J Nematol 2012; 44:427-446. [PMID: 23482683 PMCID: PMC3592369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Indexed: 06/01/2023] Open
Abstract
Populations of Bakernema inaequale, C. petasum, C. sphagni, C. mutabile, Ogma octangulare, Xenocriconemella macrodora and Hemicriconemoides chitwoodi were identified and re-described from different geographical areas in the continental United States and molecularly characterized. Two new species of spine nematodes Criconema arkaense n. sp. from Washington County and Lee County, Arkansas and Criconema warrenense n. sp from Warren, Bradley County, Arkansas are also described and named. Criconema arkaense is characterize by having a conspicuous lip region offset from the body with two annuli, short rounded tail with a thin cuticular sheath and subterminal anus. Criconema warrenense n. sp. has two lip region annuli about the same width, first annulus directed posteriorly, separated by a narrow neck annulus and a short conoid tail, unilobed non-folded annulus. The molecular characterization of Criconema arkaense and Criconema warrenense using ITS1 rDNA gene sequence and the molecular phylogenetic relationships of these new species along with the known spines nematodes are provided.
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Affiliation(s)
- Marco A Cordero
- Graduate assistant and University Professor, Department of Plant Pathology, Cralley/Warren Research Lab., 2601 N Young Ave., University of Arkansas, Fayetteville, AR 72704
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Cordero MA, Robbins RT, Szalanski AL. Taxonomic and molecular identification of mesocriconema and criconemoides species (nematoda: criconematidae). J Nematol 2012; 44:399-426. [PMID: 23482878 PMCID: PMC3592372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Indexed: 06/01/2023] Open
Abstract
Populations of Mesocriconema curvatum, M. kirjanovae, M. onoense, M. ornatum, M. sphaerocephala, M. surinamense, M. vadense, M. xenoplax, and Criconemoides informis from different geographical areas in the continental United States were characterized morphologically and molecularly. A new ring nematode from Washington County, Arkansas, is also described and named Mesocriconema ozarkiense n. sp., This new species is characterized by females with small flattened submedian lobes, lower than or at the same level as the labial disc, vagina straight, very well developed spermatheca without sperm, no more than one anastomoses, L=379-512 μm, V=89-93, stylet length = 49-61 μm, R=107-119, annuli with slightly crenate margins on tail portion and a simple anterior vulval lip. The molecular characterization of M. ozarkiense n. sp. using the ITS rRNA gene sequence and the phylogenesis relationship of this new species with the ring nematodes included in this study are provided.
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Affiliation(s)
- Marco A Cordero
- Graduate assistant and University Professor, Department of Plant Pathology, Cralley/Warren Research Lab., 2601 N. Young Ave., University of Arkansas, Fayetteville, AR 72704
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