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Zamboulis DE, Marr N, Lenzi L, Birch HL, Screen HRC, Clegg PD, Thorpe CT. The Interfascicular Matrix of Energy Storing Tendons Houses Heterogenous Cell Populations Disproportionately Affected by Aging. Aging Dis 2024; 15:295-310. [PMID: 37307816 PMCID: PMC10796100 DOI: 10.14336/ad.2023.0425-1] [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: 02/17/2023] [Accepted: 04/25/2023] [Indexed: 06/14/2023] Open
Abstract
Energy storing tendons such as the human Achilles and equine superficial digital flexor tendon (SDFT) are prone to injury, with incidence increasing with aging, peaking in the 5th decade of life in the human Achilles tendon. The interfascicular matrix (IFM), which binds tendon fascicles, plays a key role in energy storing tendon mechanics, and aging alterations to the IFM negatively impact tendon function. While the mechanical role of the IFM in tendon function is well-established, the biological role of IFM-resident cell populations remains to be elucidated. Therefore, the aim of this study was to identify IFM-resident cell populations and establish how these populations are affected by aging. Cells from young and old SDFTs were subjected to single cell RNA-sequencing, and immunolabelling for markers of each resulting population used to localise cell clusters. Eleven cell clusters were identified, including tenocytes, endothelial cells, mural cells, and immune cells. One tenocyte cluster localised to the fascicular matrix, whereas nine clusters localised to the IFM. Interfascicular tenocytes and mural cells were preferentially affected by aging, with differential expression of genes related to senescence, dysregulated proteostasis and inflammation. This is the first study to establish heterogeneity in IFM cell populations, and to identify age-related alterations specific to IFM-localised cells.
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Affiliation(s)
- Danae E. Zamboulis
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, NW1 0TU, UK.
| | - Neil Marr
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, NW1 0TU, UK.
| | - Luca Lenzi
- Centre for Genomic Research, University of Liverpool, Liverpool, L69 7ZB, UK.
| | - Helen L. Birch
- Department of Orthopaedics and Musculoskeletal Science, University College London, Royal National Orthopaedic Hospital, Stanmore, HA7 4LP, UK.
| | - Hazel R. C. Screen
- Institute of Bioengineering, School of Engineering and Materials Science, Queen Mary University of London, London, E1 4NS, UK.
| | - Peter D. Clegg
- Department of Musculoskeletal and AgingScience, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, L7 8TX, UK.
| | - Chavaunne T. Thorpe
- Department of Comparative Biomedical Sciences, Royal Veterinary College, London, NW1 0TU, UK.
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2
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Watson BNJ, Capria L, Alseth EO, Pons BJ, Biswas A, Lenzi L, Buckling A, van Houte S, Westra ER, Meaden S. CRISPR-Cas in Pseudomonas aeruginosa provides transient population-level immunity against high phage exposures. ISME J 2024; 18:wrad039. [PMID: 38366022 PMCID: PMC10873826 DOI: 10.1093/ismejo/wrad039] [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] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/12/2023] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
Abstract
The prokaryotic adaptive immune system, CRISPR-Cas (clustered regularly interspaced short palindromic repeats; CRISPR-associated), requires the acquisition of spacer sequences that target invading mobile genetic elements such as phages. Previous work has identified ecological variables that drive the evolution of CRISPR-based immunity of the model organism Pseudomonas aeruginosa PA14 against its phage DMS3vir, resulting in rapid phage extinction. However, it is unclear if and how stable such acquired immunity is within bacterial populations, and how this depends on the environment. Here, we examine the dynamics of CRISPR spacer acquisition and loss over a 30-day evolution experiment and identify conditions that tip the balance between long-term maintenance of immunity versus invasion of alternative resistance strategies that support phage persistence. Specifically, we find that both the initial phage dose and reinfection frequencies determine whether or not acquired CRISPR immunity is maintained in the long term, and whether or not phage can coexist with the bacteria. At the population genetics level, emergence and loss of CRISPR immunity are associated with high levels of spacer diversity that subsequently decline due to invasion of bacteria carrying pilus-associated mutations. Together, these results provide high resolution of the dynamics of CRISPR immunity acquisition and loss and demonstrate that the cumulative phage burden determines the effectiveness of CRISPR over ecologically relevant timeframes.
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Affiliation(s)
- Bridget N J Watson
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Loris Capria
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Ellinor O Alseth
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Benoit J Pons
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Ambarish Biswas
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9059, Otago, New Zealand
| | - Luca Lenzi
- Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, L69 7BE, United Kingdom
| | - Angus Buckling
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Stineke van Houte
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Edze R Westra
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Sean Meaden
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
- Department of Biology, University of York, Wentworth Way, York, North Yorkshire YO10 3DB, United Kingdom
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Lenzi L, Degli Esposti M, Braccini S, Siracusa C, Quartinello F, Guebitz GM, Puppi D, Morselli D, Fabbri P. Further Step in the Transition from Conventional Plasticizers to Versatile Bioplasticizers Obtained by the Valorization of Levulinic Acid and Glycerol. ACS Sustain Chem Eng 2023; 11:9455-9469. [PMID: 37389191 PMCID: PMC10302884 DOI: 10.1021/acssuschemeng.3c01536] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/24/2023] [Indexed: 07/01/2023]
Abstract
In the last two decades, the use of phthalates has been restricted worldwide due to their well-known toxicity. Nonetheless, phthalates are still widely used for their versatility, high plasticization effect, low cost, and lack of valuable alternatives. This study presents the fully bio-based and versatile glycerol trilevulinate plasticizer (GT) that was obtained by the valorization of glycerol and levulinic acid. The mild-conditions and solvent-free esterification used to synthesize GT was optimized by investigating the product by Fourier transform infrared and NMR spectroscopy. An increasing content of GT, from 10 to 40 parts by weight per hundred parts of resin (phr), was tested with poly(vinyl chloride), poly(3-hydroxybutyrate), poly(3-hydroxybutyrate-co-3-hydroxyvalerate), poly(lactic acid), and poly(caprolactone), which typically present complicated processability and/or mechanical properties. GT produced a significant plasticization effect on both amorphous and semicrystalline polymers, reducing their glass-transition temperature and stiffness, as observed by differential scanning calorimetry measurements and tensile tests. Remarkably, GT also decreased both the melting temperature and crystallinity degree of semicrystalline polymers. Furthermore, GT underwent enzyme-mediated hydrolysis to its initial constituents, envisioning a promising prospective for environmental safety and upcycling. Furthermore, 50% inhibitory concentration (IC50) tests, using mouse embryo fibroblasts, proved that GT is an unharmful alternative plasticizer, which makes it potentially applicable in the biomedical field.
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Affiliation(s)
- Luca Lenzi
- Department
of Civil, Chemical, Environmental, and Materials Engineering (DICAM), Università di Bologna, Via U. Terracini 28, 40131 Bologna, Italy
- National
Interuniversity Consortium of Materials Science and Technology (INSTM), Via G. Giusti 9, 50121 Firenze, Italy
| | - Micaela Degli Esposti
- Department
of Civil, Chemical, Environmental, and Materials Engineering (DICAM), Università di Bologna, Via U. Terracini 28, 40131 Bologna, Italy
- National
Interuniversity Consortium of Materials Science and Technology (INSTM), Via G. Giusti 9, 50121 Firenze, Italy
| | - Simona Braccini
- National
Interuniversity Consortium of Materials Science and Technology (INSTM), Via G. Giusti 9, 50121 Firenze, Italy
- BIOLab
Research Group, Department of Chemistry and Industrial Chemistry, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Chiara Siracusa
- Institute
of Environmental Biotechnology University of Natural Resources and
Life Sciences Vienna, Department of Agrobiotechnology, IFA-Tulln, Konrad-Lorenz-Strasse 20, 3430 Tulln an der Donau, Austria
| | - Felice Quartinello
- Institute
of Environmental Biotechnology University of Natural Resources and
Life Sciences Vienna, Department of Agrobiotechnology, IFA-Tulln, Konrad-Lorenz-Strasse 20, 3430 Tulln an der Donau, Austria
| | - Georg M. Guebitz
- Institute
of Environmental Biotechnology University of Natural Resources and
Life Sciences Vienna, Department of Agrobiotechnology, IFA-Tulln, Konrad-Lorenz-Strasse 20, 3430 Tulln an der Donau, Austria
| | - Dario Puppi
- National
Interuniversity Consortium of Materials Science and Technology (INSTM), Via G. Giusti 9, 50121 Firenze, Italy
- BIOLab
Research Group, Department of Chemistry and Industrial Chemistry, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Davide Morselli
- Department
of Civil, Chemical, Environmental, and Materials Engineering (DICAM), Università di Bologna, Via U. Terracini 28, 40131 Bologna, Italy
- National
Interuniversity Consortium of Materials Science and Technology (INSTM), Via G. Giusti 9, 50121 Firenze, Italy
| | - Paola Fabbri
- Department
of Civil, Chemical, Environmental, and Materials Engineering (DICAM), Università di Bologna, Via U. Terracini 28, 40131 Bologna, Italy
- National
Interuniversity Consortium of Materials Science and Technology (INSTM), Via G. Giusti 9, 50121 Firenze, Italy
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Bay V, Gillespie A, Ganda E, Evans NJ, Carter SD, Lenzi L, Lucaci A, Haldenby S, Barden M, Griffiths BE, Sánchez-Molano E, Bicalho R, Banos G, Darby A, Oikonomou G. The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions. Microbiome 2023; 11:4. [PMID: 36624507 PMCID: PMC9830885 DOI: 10.1186/s40168-022-01440-7] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. We describe herein the bovine foot skin microbiota and its associations with BDD using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms. RESULTS We show evidence of dysbiosis, and differences in taxonomy and functional profiles in the bovine foot skin microbiome of clinically healthy animals that subsequently develop BDD lesions, compared to those that do not. Our results suggest that taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and certain members of the foot skin microbiota. We show the existence of significant genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation. CONCLUSIONS Collectively this work shows early changes in taxonomic and functional profiles of the bovine foot-skin microbiota in clinically healthy animals which are associated with subsequent development of BDD and could be relevant to prevention of disease. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD development offer new insights into a complex relationship that can be exploited in selective breeding programmes. Video Abstract.
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Affiliation(s)
- V Bay
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Faculty of Agriculture, Ege University, İzmir, Turkey
| | - A Gillespie
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - E Ganda
- Department of Animal Science, Penn State University, State College, PA, USA
| | - N J Evans
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - S D Carter
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - L Lenzi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - A Lucaci
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - S Haldenby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - M Barden
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - B E Griffiths
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | - R Bicalho
- FERA Diagnostics and Biologicals, College Station, TX, USA
| | - G Banos
- Scotland's Rural College (SRUC), Easter Bush, Midlothian, UK
| | - A Darby
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - G Oikonomou
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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5
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Frau A, Ijaz UZ, Slater R, Jonkers D, Penders J, Campbell BJ, Kenny JG, Hall N, Lenzi L, Burkitt MD, Pierik M, Darby AC, Probert CSJ. Inter-kingdom relationships in Crohn's disease explored using a multi-omics approach. Gut Microbes 2022; 13:1930871. [PMID: 34241567 PMCID: PMC8274447 DOI: 10.1080/19490976.2021.1930871] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The etiology of Crohn's disease (CD) is multifactorial. Bacterial and fungal microbiota are involved in the onset and/or progression of the disease. A bacterial dysbiosis in CD patients is accepted; however, less is known about the mycobiome and the relationships between the two communities. We investigated the interkingdom relationships, their metabolic consequences, and the changes in the fungal community during relapse and remission in CD.Two cohorts were evaluated: a British cohort (n = 63) comprising CD and ulcerative colitis patients, and controls. The fungal and bacterial communities of biopsy and fecal samples were analyzed, with the fecal volatiles; datasets were also integrated; and a Dutch cohort (n = 41) comprising CD patients and healthy controls was analyzed for stability of the gut mycobiome.A dysbiosis of the bacterial community was observed in biopsies and stool. Results suggest Bacteroides is likely key in CD and may modulate Candida colonization. A dysbiosis of the fungal community was observed only in the Dutch cohort; Malassezia and Candida were increased in patients taking immunosuppressants. Longitudinal analysis showed an increase in Cyberlindnera in relapse. Saccharomyces was dominant in all fecal samples, but not in biopsies, some of which did not yield fungal reads; amino acid degradation was the main metabolic change associated with CD and both bacteria and fungi might be implicated.We have shown that Bacteroides and yeasts may play a role in CD; understanding their role and relationship in the disease would shed new light on the development and treatment of CD.
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Affiliation(s)
- Alessandra Frau
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK,CONTACT Alessandra Frau Department of Molecular and Clinical Cancer Medicine, Nuffield Building, Ashton Street, LiverpoolL69 3GE, UK
| | - Umer Z. Ijaz
- School of Engineering, University of Glasgow, Glasgow, UK,Umer Z. Ijaz School of Engineering, University of Glasgow, Glasgow, UK
| | - Rachael Slater
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Daisy Jonkers
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - John Penders
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Barry J. Campbell
- Department of Infection & Microbiomes, University of Liverpool, Liverpool, UK
| | | | - Neil Hall
- Earlham Institute, Norwich, UK,School of Biological Sciences, University of East Anglia, Norwich, Norfolk, UK
| | - Luca Lenzi
- Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Michael D. Burkitt
- Division of Diabetes, Endocrinology and Gastroenterology, University of Manchester, Manchester, UK
| | - Marieke Pierik
- School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, Netherlands
| | - Alistair C. Darby
- Department of Infection & Microbiomes, University of Liverpool, Liverpool, UK
| | - Christopher S. J. Probert
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
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Rodrigues ALM, Ribeiro RC, Godinho PR, Costa JT, Wanderley AV, Silva AMM, Carvalho CR, Junior CGC, Lee MLM, Lins MM, Oliveira AF, Lenzi L. DOSE INTENSITY OF INDUCTION CHEMOTHERAPY IN PEDIATRIC ACUTE MYELOID LEUKEMIA: A SYSTEMATIC REVIEW AND META-ANALYSIS. Hematol Transfus Cell Ther 2021. [DOI: 10.1016/j.htct.2021.10.480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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7
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Meaden S, Capria L, Alseth E, Gandon S, Biswas A, Lenzi L, van Houte S, Westra ER. Correction: Phage gene expression and host responses lead to infection-dependent costs of CRISPR immunity. ISME J 2021; 15:2491. [PMID: 34112970 PMCID: PMC8319296 DOI: 10.1038/s41396-020-00846-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Sean Meaden
- Biosciences, University of Exeter, Exeter, TR10 9EZ, UK.
| | - Loris Capria
- Biosciences, University of Exeter, Exeter, TR10 9EZ, UK
| | | | - Sylvain Gandon
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Univ Paul Valéry Montpellier 3, Montpellier, France
| | - Ambarish Biswas
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Luca Lenzi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | | | - Edze R Westra
- Biosciences, University of Exeter, Exeter, TR10 9EZ, UK.
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Papoutsopoulou S, Pollock L, Walker C, Tench W, Samad SS, Bergey F, Lenzi L, Sheibani-Tezerji R, Rosenstiel P, Alam MT, Martins Dos Santos VAP, Müller W, Campbell BJ. Impact of Interleukin 10 Deficiency on Intestinal Epithelium Responses to Inflammatory Signals. Front Immunol 2021; 12:690817. [PMID: 34220850 PMCID: PMC8244292 DOI: 10.3389/fimmu.2021.690817] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 05/25/2021] [Indexed: 12/30/2022] Open
Abstract
Interleukin 10 (IL-10) is a pleiotropic, anti-inflammatory cytokine that has a major protective role in the intestine. Although its production by cells of the innate and adaptive immune system has been extensively studied, its intrinsic role in intestinal epithelial cells is poorly understood. In this study, we utilised both ATAC sequencing and RNA sequencing to define the transcriptional response of murine enteroids to tumour necrosis factor (TNF). We identified that the key early phase drivers of the transcriptional response to TNF within intestinal epithelium were NFκB transcription factor dependent. Using wild-type and Il10-/- enteroid cultures, we showed an intrinsic, intestinal epithelium specific effect of IL-10 deficiency on TNF-induced gene transcription, with significant downregulation of identified NFκB target genes Tnf, Ccl20, and Cxcl10, and delayed overexpression of NFκB inhibitor encoding genes, Nfkbia and Tnfaip3. IL-10 deficiency, or immunoblockade of IL-10 receptor, impacted on TNF-induced endogenous NFκB activity and downstream NFκB target gene transcription. Intestinal epithelium-derived IL-10 appears to play a crucial role as a positive regulator of the canonical NFκB pathway, contributing to maintenance of intestinal homeostasis. This is particularly important in the context of an inflammatory environment and highlights the potential for future tissue-targeted IL-10 therapeutic intervention.
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Affiliation(s)
- Stamatia Papoutsopoulou
- The Henry Wellcome Laboratories of Molecular & Cellular Gastroenterology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, United Kingdom
- Department of Biochemistry and Biotechnology, School of Health Sciences, University of Thessaly, Larissa, Greece
| | - Liam Pollock
- The Henry Wellcome Laboratories of Molecular & Cellular Gastroenterology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Catherine Walker
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - William Tench
- The Henry Wellcome Laboratories of Molecular & Cellular Gastroenterology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Sakim Shakh Samad
- The Henry Wellcome Laboratories of Molecular & Cellular Gastroenterology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | - Luca Lenzi
- Centre for Genomic Research (CGR), Department of Evolution, Ecology & Behaviour, University of Liverpool, Liverpool, United Kingdom
| | | | - Phillip Rosenstiel
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Mohammad Tauqeer Alam
- Warwick Medical School, Bioinformatics Research Technology Platform (RTP), University of Warwick, Coventry, United Kingdom
- Department of Biology, College of Science, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Vitor A. P. Martins Dos Santos
- LifeGlimmer GmbH, Berlin, Germany
- Laboratory of Systems & Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Werner Müller
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Barry J. Campbell
- The Henry Wellcome Laboratories of Molecular & Cellular Gastroenterology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, United Kingdom
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9
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Duncan JS, Angell JW, Richards P, Lenzi L, Staton GJ, Grove-White D, Clegg S, Oikonomou G, Carter SD, Evans NJ. The dysbiosis of ovine foot microbiome during the development and treatment of contagious ovine digital dermatitis. Anim Microbiome 2021; 3:19. [PMID: 33597028 PMCID: PMC7888161 DOI: 10.1186/s42523-021-00078-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/15/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Contagious Ovine Digital Dermatitis (CODD) is an emerging and common infectious foot disease of sheep which causes severe welfare and economic problems for the sheep industry. The aetiology of the disease is not fully understood and control of the disease is problematic. The aim of this study was to investigate the polybacterial aetiopathogenesis of CODD and the effects of antibiotic treatment, in a longitudinal study of an experimentally induced disease outbreak using a 16S rRNA gene amplicon sequencing approach. RESULTS CODD was induced in 15/30 experimental sheep. During the development of CODD three distinct phenotypic lesion stages were observed. These were an initial interdigital dermatitis (ID) lesion, followed by a footrot (FR) lesion, then finally a CODD lesion. Distinct microbiota were observed for each lesion in terms of microbial diversity, clustering and composition. Porphyromonadaceae, Family XI, Veillonellaceae and Fusobacteriaceae were significantly associated with the diseased feet. Veillonellaceae and Fusobacteriaceae were most associated with the earlier stages of ID and footrot rather than CODD. Following antibiotic treatment of the sheep, the foot microbiota showed a strong tendency to return to the composition of the healthy state. The microbiota composition of CODD lesions collected by swab and biopsy methods were different. In particular, the Spirochaetaceae family were more abundant in samples collected by the biopsy method, suggesting that these bacteria are present in deeper tissues of the diseased foot. CONCLUSION In this study, CODD presented as part of a spectrum of poly-bacterial foot disease strongly associated with bacterial families Porphyromonadaceae, Family XI (a family in Clostridiales also known as Clostridium cluster XI), Veillonellaceae and Fusobacteriaceae which are predominately Gram-negative anaerobes. Following antibiotic treatment, the microbiome showed a strong tendency to return to the composition of the healthy state. The composition of the healthy foot microbiome does not influence susceptibility to CODD. Based on the data presented here and that CODD appears to be the severest end stage of sheep infectious foot disease lesions, better control of the initial ID and FR lesions would enable better control of CODD and enable better animal welfare.
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Affiliation(s)
- J. S. Duncan
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - J. W. Angell
- Wern Veterinary Surgeons, Department of Research and Innovation, Unit 11, Lon Parcwr Industrial Estate, Ruthin, LL15 1NJ UK
| | - P. Richards
- Department of Veterinary Pathology, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - L. Lenzi
- Centre for Genomic Research, Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Liverpool, L69 7ZB UK
| | - G. J. Staton
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Science, The University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - D. Grove-White
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - S. Clegg
- School of Life Sciences, College of Science, University of Lincoln, Brayford Pool Campus, Lincoln, LN6 7TS UK
| | - G. Oikonomou
- Department of Livestock and One Health, Institute of Infection, Veterinary and Ecological Science, University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - S. D. Carter
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Science, The University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
| | - N. J. Evans
- Department of Infection Biology & Microbiomes, Institute of Infection, Veterinary and Ecological Science, The University of Liverpool, Leahurst Campus, Neston, Wirral CH64 7TE UK
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10
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Barden M, Richards-Rios P, Ganda E, Lenzi L, Eccles R, Neary J, Oultram J, Oikonomou G. Maternal influences on oral and faecal microbiota maturation in neonatal calves in beef and dairy production systems. Anim Microbiome 2020; 2:31. [PMID: 33499967 PMCID: PMC7807724 DOI: 10.1186/s42523-020-00049-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 04/21/2020] [Accepted: 08/13/2020] [Indexed: 02/07/2023] Open
Abstract
Background The dam is considered an important source of microbes for the calf; consequently, the development of calf microbiota may vary with farming system due to differences between the contact the calf has with the dam. The objective of this study was to characterise the early changes in the composition of oral and faecal microbiota in beef and dairy calves (N = 10) using high-throughput sequencing of the 16S rRNA gene. The microbiota of calves was compared to selected anatomical niches on their dams which were likely to contribute to the vertical transfer of microbes. Results A total of 14,125 amplicon sequence variants (ASVs) were identified and taxonomically assigned. The oral microbiota of calves and their dams were composed of more similar microbes after the first 4 weeks of life than immediately after calving. The faecal microbiota of four-week old calves was composed of microbes which were more similar to those found in the oral microbiota of calves and adult cows than the faecal microbiota of adult cows. Specific ASVs were identified in the oral microbiota of four-week old calves that were also present in cow niches at calving, whereas very few ASVs were present in the calf faecal microbiota at four-weeks of age were present in any adult cow niche at calving. These results were observed in both beef and dairy calves. Conclusions We did not observe any marked differences in the maturation of the oral and faecal microbiota between beef or dairy calves, despite dairy calves having very limited contact with their dam. This suggests the development of gastrointestinal microbiota in calves may not be affected by continued vertical transmission of microbes from the dam. Although the calf faecal microbiota changed over the first four-weeks of life, it was composed of microbes which were phylogenetically closer to those in the oral microbiota of calves and adult cows than the faeces of adult cows. There was little evidence of persistent microbial seeding of the calf faeces from anatomical niches on the cow at calving in either beef or dairy animals.
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Affiliation(s)
- Matthew Barden
- Department of Livestock and One Health, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Peter Richards-Rios
- Department of Veterinary Anatomy, Physiology and Pathology, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Erika Ganda
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
| | - Luca Lenzi
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Richard Eccles
- Department of Functional and Comparative Genomics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, Liverpool, UK
| | - Joseph Neary
- Department of Livestock and One Health, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Joanne Oultram
- Department of Livestock and One Health, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Georgios Oikonomou
- Department of Livestock and One Health, Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK.
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11
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Pasqualini P, Rizzo L, Facchi E, Culicchi V, Lenzi L, Mucci D, Erba F, Moscatelli C, Pagliara C, Doretti V. Health and Gender Medicine Clinic: 2 years of multidisclipinary team experience. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa166.1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Cardiovascular disease (CVD) is the leading cause of mortality in western countries and the first cause of mortality in women.
Purpose
Women generally do not concern about CVD and that represents the main risk for them.
Methods
Misericordia Hospital, Grosseto, started a Clinic of Health and Gender Medicine on 2017. On the first and third Monday of every month, we evaluate < 60 years patients who are at risk for traditional CVD, depression, early menopause, polycystic ovary, autoimmune and rheumatic disease. On the first visit, medical history, arterial pressure, electrocardiogram, body mass index, waist circumference and lipid profile, were collected. We also supply questionnaires to evaluate diabetes and depression risk by Generalized Anxiety Disorder (GAD-7), Patient Health Questionnaire (PHQ-9) and food diary. Two weeks later, a multidisciplinary team (cardiologist-diabetologist-nutritionist-gynecologist-psychiatrist and a nurse) evaluates the patients defining the personal risk profile.
Results
From 2017 to December 2019, 74 females and 7 males belonging to the target population were examined. Age group: <45(61%), 46-50(26%), 51-60(48%), >60(19%). Clinical characteristics: Hypertension: 64%; Obesity 5%; Unknown dyslipidemia 44%; Risk of diabetes: 39%; Gestational diabetes: 5%; Gestational hypertension: 5% CVD risk: 42%; Depression: 33% Autoimmune disease: 30%. From them 60.5% have needed further investigation. Follow-up is going on.
Conclusions
according with the literature, more than 50% of the cohort was unconsciously at high risk of CVD. So a multidisciplinary approach is needed in order to frame a complex health status. Thus we established collaboration with patients to improve lifestyles as CVD-prevention's tool.
Key messages
Cardiovascular disease represent often an hidden health problem, especially in women. Multidisciplinary approach is needed to face CVD.
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Affiliation(s)
- P Pasqualini
- Health and Gender Medicine Clinic, Grosseto Hospital, Grosseto, Italy
| | - L Rizzo
- Health and Gender Medicine Clinic, Grosseto Hospital, Grosseto, Italy
| | - E Facchi
- Health and Gender Medicine Clinic, Grosseto Hospital, Grosseto, Italy
| | - V Culicchi
- Health and Gender Medicine Clinic, Grosseto Hospital, Grosseto, Italy
| | - L Lenzi
- UOC Health Promotion, AUSL SudEst Tuscany, Grosseto, Italy
| | - D Mucci
- Health and Gender Medicine Clinic, Grosseto Hospital, Grosseto, Italy
| | - F Erba
- Department of Clinical Science and Translational Medicine, University Tor Vergata, Rome, Italy
| | - C Moscatelli
- UOC Health Promotion, AUSL SudEst Tuscany, Grosseto, Italy
| | - C Pagliara
- UOC Health Promotion, AUSL SudEst Tuscany, Grosseto, Italy
| | - V Doretti
- UOC Health Promotion, AUSL SudEst Tuscany, Grosseto, Italy
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12
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Griffiths SM, Antwis RE, Lenzi L, Lucaci A, Behringer DC, Butler MJ, Preziosi RF. Host genetics and geography influence microbiome composition in the sponge Ircinia campana. J Anim Ecol 2019; 88:1684-1695. [PMID: 31325164 PMCID: PMC6899969 DOI: 10.1111/1365-2656.13065] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/09/2019] [Indexed: 12/22/2022]
Abstract
Marine sponges are hosts to large, diverse communities of microorganisms. These microbiomes are distinct among sponge species and from seawater bacterial communities, indicating a key role of host identity in shaping its resident microbial community. However, the factors governing intraspecific microbiome variability are underexplored and may shed light on the evolutionary and ecological relationships between host and microbiome. Here, we examined the influence of genetic variation and geographic location on the composition of the Ircinia campana microbiome. We developed new microsatellite markers to genotype I. campana from two locations in the Florida Keys, USA, and characterized their microbiomes using V4 16S rRNA amplicon sequencing. We show that microbial community composition and diversity is influenced by host genotype, with more genetically similar sponges hosting more similar microbial communities. We also found that although I. campana was not genetically differentiated between sites, microbiome composition differed by location. Our results demonstrate that both host genetics and geography influence the composition of the sponge microbiome. Host genotypic influence on microbiome composition may be due to stable vertical transmission of the microbial community from parent to offspring, making microbiomes more similar by descent. Alternatively, sponge genotypic variation may reflect variation in functional traits that influence the acquisition of environmental microbes. This study reveals drivers of microbiome variation within and among locations, and shows the importance of intraspecific variability in mediating eco-evolutionary dynamics of host-associated microbiomes.
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Affiliation(s)
- Sarah M. Griffiths
- Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
| | - Rachael E. Antwis
- School of Environment and Life SciencesUniversity of SalfordSalfordUK
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Anita Lucaci
- Centre for Genomic Research, Institute of Integrative BiologyUniversity of LiverpoolLiverpoolUK
| | - Donald C. Behringer
- Fisheries and Aquatic SciencesUniversity of FloridaGainesvilleFLUSA
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFLUSA
| | - Mark J. Butler
- Department of Biological SciencesOld Dominion UniversityNorfolkVAUSA
| | - Richard F. Preziosi
- Ecology and Environment Research CentreManchester Metropolitan UniversityManchesterUK
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13
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Frau A, Kenny JG, Lenzi L, Campbell BJ, Ijaz UZ, Duckworth CA, Burkitt MD, Hall N, Anson J, Darby AC, Probert CSJ. DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies. Sci Rep 2019; 9:9328. [PMID: 31249384 PMCID: PMC6597572 DOI: 10.1038/s41598-019-44974-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/28/2019] [Indexed: 12/28/2022] Open
Abstract
Microbial ecology studies are often performed through extraction of metagenomic DNA followed by amplification and sequencing of a marker. It is known that each step may bias the results. These biases have been explored for the study of bacterial communities, but rarely for fungi. Our aim was therefore to evaluate methods for the study of the gut mycobiome. We first evaluated DNA extraction methods in fungal cultures relevant to the gut. Afterwards, to assess how these methods would behave with an actual sample, stool from a donor was spiked with cells from the same cultures. We found that different extraction kits favour some species and bias against others. In terms of amplicon sequencing, we evaluated five primer sets, two for ITS2 and one for ITS1, 18S and 28S rRNA. Results showed that 18S rRNA outperformed the other markers: it was able to amplify all the species in the mock community and to discriminate among them. ITS primers showed both amplification and sequencing biases, the latter related to the variable length of the product. We identified several biases in the characterisation of the gut mycobiome and showed how crucial it is to be aware of these before drawing conclusions from the results of these studies.
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Affiliation(s)
- Alessandra Frau
- Gastroenterology Research Unit, Department of Cellular & Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK
| | - John G Kenny
- Centre for Genomic Research (CGR), University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.,Teagasc Food Research Centre, Moorepark, Cork, Ireland
| | - Luca Lenzi
- Centre for Genomic Research (CGR), University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Barry J Campbell
- Gastroenterology Research Unit, Department of Cellular & Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK
| | - Umer Z Ijaz
- School of Engineering, University of Glasgow, Oakfield Avenue, Glasgow, G12 8LT, UK
| | - Carrie A Duckworth
- Gastroenterology Research Unit, Department of Cellular & Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK
| | - Michael D Burkitt
- Gastroenterology Research Unit, Department of Cellular & Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK.,Division of Diabetes, Endocrinology and Gastroenterology, University of Manchester, Dover Street, Manchester, M13 9PT, UK
| | - Neil Hall
- Earlham Institute, Colney Ln, Norwich, NR4 7UZ, UK
| | - Jim Anson
- Liverpool Clinical Laboratories Directorate of Infection and Immunity, Royal Liverpool and Broadgreen University Hospitals NHS Trust, Prescot Street, Liverpool, L7 8XP, UK
| | - Alistair C Darby
- Centre for Genomic Research (CGR), University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Christopher S J Probert
- Gastroenterology Research Unit, Department of Cellular & Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Ashton Street, Liverpool, L69 3GE, UK.
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14
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Jayaraman S, Harris C, Paxton E, Donachie AM, Vaikkinen H, McCulloch R, Hall JPJ, Kenny J, Lenzi L, Hertz-Fowler C, Cobbold C, Reeve R, Michoel T, Morrison LJ. Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections. PLoS Negl Trop Dis 2019; 13:e0007262. [PMID: 30943202 PMCID: PMC6464242 DOI: 10.1371/journal.pntd.0007262] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/15/2019] [Accepted: 02/25/2019] [Indexed: 12/31/2022] Open
Abstract
Antigenic variation is employed by many pathogens to evade the host immune response, and Trypanosoma brucei has evolved a complex system to achieve this phenotype, involving sequential use of variant surface glycoprotein (VSG) genes encoded from a large repertoire of ~2,000 genes. T. brucei express multiple, sometimes closely related, VSGs in a population at any one time, and the ability to resolve and analyse this diversity has been limited. We applied long read sequencing (PacBio) to VSG amplicons generated from blood extracted from batches of mice sacrificed at time points (days 3, 6, 10 and 12) post-infection with T. brucei TREU927. The data showed that long read sequencing is reliable for resolving variant differences between VSGs, and demonstrated that there is significant expressed diversity (449 VSGs detected across 20 mice) and across the timeframe of study there was a clear semi-reproducible pattern of expressed diversity (median of 27 VSGs per sample at day 3 post infection (p.i.), 82 VSGs at day 6 p.i., 187 VSGs at day 10 p.i. and 132 VSGs by day 12 p.i.). There was also consistent detection of one VSG dominating expression across replicates at days 3 and 6, and emergence of a second dominant VSG across replicates by day 12. The innovative application of ecological diversity analysis to VSG reads enabled characterisation of hierarchical VSG expression in the dataset, and resulted in a novel method for analysing such patterns of variation. Additionally, the long read approach allowed detection of mosaic VSG expression from very few reads–the earliest in infection that such events have been detected. Therefore, our results indicate that long read analysis is a reliable tool for resolving diverse gene expression profiles, and provides novel insights into the complexity and nature of VSG expression in trypanosomes, revealing significantly higher diversity than previously shown and the ability to identify mosaic gene formation early during the infection process. Antigenic variation is a system whereby pathogens switch identity of a protein that is exposed to the host adaptive immune response as a way of remaining one step ahead and avoiding being detected. African trypanosomes have evolved a spectacularly elaborate system of antigenic variation, with variants being used from a library of ~2,000 genes. Our ability to understand how this rich repository is used has been hampered by the resolution of available technologies to discriminate between what can be closely related gene variants. We have applied a long read sequencing technology, which generates sequence information for the whole length of the antigen gene variants, thereby avoiding having to try and piece together antigen sequences from lots of small fragments, the pitfall of standard sequencing. Applying this technology to material taken at specific time points from batches of mice infected with trypanosomes reveals that the diversity of variants is much higher than previously suspected, and that there is a clear semi-predictable pattern in the gene expression. Additionally, using this technology we have been able to detect the presence of ‘mosaic’ genes, which are created by stitching together fragments from several donor genes in the library, much earlier in infection than has been shown previously. Therefore, we shed new light on the complexity of antigenic variation and show that long read sequencing will be a very useful tool in analysing and understanding the expression patterns of closely related genes, and how pathogens use them to cause persistent infections and disease.
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Affiliation(s)
- Siddharth Jayaraman
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Claire Harris
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Edith Paxton
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Anne-Marie Donachie
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Heli Vaikkinen
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard McCulloch
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - James P. J. Hall
- Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - John Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Christiane Hertz-Fowler
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Christina Cobbold
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- School of Mathematics and Statistics, University of Glasgow, Glasgow, United Kingdom
| | - Richard Reeve
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Tom Michoel
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Liam J. Morrison
- Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
- * E-mail:
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15
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Bay V, Griffiths B, Carter S, Evans NJ, Lenzi L, Bicalho RC, Oikonomou G. 16S rRNA amplicon sequencing reveals a polymicrobial nature of complicated claw horn disruption lesions and interdigital phlegmon in dairy cattle. Sci Rep 2018; 8:15529. [PMID: 30341326 PMCID: PMC6195575 DOI: 10.1038/s41598-018-33993-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/08/2018] [Indexed: 11/08/2022] Open
Abstract
Lameness represents an intractable problem for the dairy industry. Complicated claw horn disruption lesions, interdigital hyperplasia, and interdigital phlegmon are important lameness causing foot lesions. Their aetiology is multifactorial, but infectious processes are likely implicated in disease pathogenesis. Our aim was to investigate the bacterial profiles of these lesions using 16S rRNA gene sequencing of samples obtained from 51 cattle across ten farms in the UK. In this study, interdigital hyperplasia, interdigital hyperplasia with signs of interdigital dermatitis, interdigital phlegmon, complicated sole ulcers, complicated toe ulcers lesions, and complicated white line lesions were investigated; corresponding healthy skin control samples were also analysed. All diseased tissues displayed reduced microbial richness and diversity (as described by Chao1, Shannon, and Simpson alpha-diversity indices) compared to their healthy skin control samples. Our results confirm the association of Treponema spp with some of these disorders. Other anaerobic bacteria including Fusobacterium spp., Fastidiosipila spp. and Porphyromonas spp. were implicated in the aetiology of all these lesions with the exception of interdigital hyperplasia. Complicated claw horn disruption lesions, and interdigital phlegmon were found to have similar bacterial profiles. Such sharing of bacterial genera suggests many of the infectious agents detected in these foot lesions are acting opportunistically; this finding could contribute towards future treatment and control strategies.
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Affiliation(s)
- V Bay
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - B Griffiths
- Department of Livestock Health and Welfare, Institute of Veterinary Sciences, University of Liverpool, Liverpool, UK
| | - S Carter
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - N J Evans
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - L Lenzi
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - R C Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, USA
| | - G Oikonomou
- Department of Epidemiology and Population Health, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
- Department of Livestock Health and Welfare, Institute of Veterinary Sciences, University of Liverpool, Liverpool, UK.
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16
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Hicks N, Liu X, Gregory R, Kenny J, Lucaci A, Lenzi L, Paterson DM, Duncan KR. Temperature Driven Changes in Benthic Bacterial Diversity Influences Biogeochemical Cycling in Coastal Sediments. Front Microbiol 2018; 9:1730. [PMID: 30190707 PMCID: PMC6115492 DOI: 10.3389/fmicb.2018.01730] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [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: 03/22/2017] [Accepted: 07/11/2018] [Indexed: 11/13/2022] Open
Abstract
Marine sediments are important sites for global biogeochemical cycling, mediated by macrofauna and microalgae. However, it is the microorganisms that drive these key processes. There is strong evidence that coastal benthic habitats will be affected by changing environmental variables (rising temperature, elevated CO2), and research has generally focused on the impact on macrofaunal biodiversity and ecosystem services. Despite their importance, there is less understanding of how microbial community assemblages will respond to environmental changes. In this study, a manipulative mesocosm experiment was employed, using next-generation sequencing to assess changes in microbial communities under future environmental change scenarios. Illumina sequencing generated over 11 million 16S rRNA gene sequences (using a primer set biased toward bacteria) and revealed Bacteroidetes and Proteobacteria dominated the total bacterial community of sediment samples. In this study, the sequencing coverage and depth revealed clear changes in species abundance within some phyla. Bacterial community composition was correlated with simulated environmental conditions, and species level community composition was significantly influenced by the mean temperature of the environmental regime (p = 0.002), but not by variation in CO2 or diurnal temperature variation. Species level changes with increasing mean temperature corresponded with changes in NH4 concentration, suggesting there is no functional redundancy in microbial communities for nitrogen cycling. Marine coastal biogeochemical cycling under future environmental conditions is likely to be driven by changes in nutrient availability as a direct result of microbial activity.
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Affiliation(s)
- Natalie Hicks
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Xuan Liu
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Richard Gregory
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - John Kenny
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Anita Lucaci
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - David M. Paterson
- Sediment Ecology Research Group, School of Biology, Scottish Oceans Institute, University of St Andrews, Fife, United Kingdom
| | - Katherine R. Duncan
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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17
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Parsons BN, Ijaz UZ, D'Amore R, Burkitt MD, Eccles R, Lenzi L, Duckworth CA, Moore AR, Tiszlavicz L, Varro A, Hall N, Pritchard DM. Comparison of the human gastric microbiota in hypochlorhydric states arising as a result of Helicobacter pylori-induced atrophic gastritis, autoimmune atrophic gastritis and proton pump inhibitor use. PLoS Pathog 2017; 13:e1006653. [PMID: 29095917 PMCID: PMC5667734 DOI: 10.1371/journal.ppat.1006653] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/18/2017] [Indexed: 12/13/2022] Open
Abstract
Several conditions associated with reduced gastric acid secretion confer an altered risk of developing a gastric malignancy. Helicobacter pylori-induced atrophic gastritis predisposes to gastric adenocarcinoma, autoimmune atrophic gastritis is a precursor of type I gastric neuroendocrine tumours, whereas proton pump inhibitor (PPI) use does not affect stomach cancer risk. We hypothesised that each of these conditions was associated with specific alterations in the gastric microbiota and that this influenced subsequent tumour risk. 95 patients (in groups representing normal stomach, PPI treated, H. pylori gastritis, H. pylori-induced atrophic gastritis and autoimmune atrophic gastritis) were selected from a cohort of 1400. RNA extracted from gastric corpus biopsies was analysed using 16S rRNA sequencing (MiSeq). Samples from normal stomachs and patients treated with PPIs demonstrated similarly high microbial diversity. Patients with autoimmune atrophic gastritis also exhibited relatively high microbial diversity, but with samples dominated by Streptococcus. H. pylori colonisation was associated with decreased microbial diversity and reduced complexity of co-occurrence networks. H. pylori-induced atrophic gastritis resulted in lower bacterial abundances and diversity, whereas autoimmune atrophic gastritis resulted in greater bacterial abundance and equally high diversity compared to normal stomachs. Pathway analysis suggested that glucose-6-phospahte1-dehydrogenase and D-lactate dehydrogenase were over represented in H. pylori-induced atrophic gastritis versus autoimmune atrophic gastritis, and that both these groups showed increases in fumarate reductase. Autoimmune and H. pylori-induced atrophic gastritis were associated with different gastric microbial profiles. PPI treated patients showed relatively few alterations in the gastric microbiota compared to healthy subjects. Different conditions such as autoimmune atrophic gastritis and Helicobacter pylori associated atrophic gastritis are associated with different types of gastric cancer, specifically neuroendocrine tumours and adenocarcinoma. Both conditions result in reduced gastric acid secretion, potentially allowing non-H. pylori bacteria to colonise the stomach. However patients receiving proton pump inhibitors (PPI) experience similar levels of acid secretion, but do not develop gastric cancer. The aims of this study were to investigate the contribution of non-H. pylori microbiota to gastric tumour development in the presence of reduced gastric acid secretion. 16S rRNA sequencing identified relatively few alterations in the gastric microbiota in patients receiving PPI therapy, despite reduced acid secretion, but more substantial alterations in those patents who had atrophic gastritis. Significant differences were also found between the patients who had atrophic gastritis of autoimmune and H. pylori associated types. Differences in biochemical pathways that potentially contribute to gastric tumorigenesis were also predicted. This work increases understanding of the mechanisms involved in gastric tumour development, and demonstrates how non-H. pylori bacteria may be important. This work may eventually lead to the development of novel chemopreventive therapies for stomach cancer that are based on altering the composition of the gastric microbiota.
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Affiliation(s)
- Bryony N Parsons
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UNITED KINGDOM
| | - Umer Z Ijaz
- Department of Infrastructure and Environment University of Glasgow, School of Engineering, Glasgow, UNITED KINGDOM
| | - Rosalinda D'Amore
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UNITED KINGDOM
| | - Michael D Burkitt
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UNITED KINGDOM.,Department of Gastroenterology, Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UNITED KINGDOM
| | - Richard Eccles
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UNITED KINGDOM
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UNITED KINGDOM
| | - Carrie A Duckworth
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UNITED KINGDOM
| | - Andrew R Moore
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UNITED KINGDOM.,Department of Gastroenterology, Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UNITED KINGDOM
| | | | - Andrea Varro
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UNITED KINGDOM
| | - Neil Hall
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, UNITED KINGDOM.,The Earlham Institute, Norwich Research Park, Norwich, UNITED KINGDOM.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk, UNITED KINGDOM
| | - D Mark Pritchard
- Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UNITED KINGDOM.,Department of Gastroenterology, Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool, UNITED KINGDOM
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Terlizzi V, Lenzi L, Fusco I, Biagi L, Ingicco A, Braggion C. 283 Cystic fibrosis-related diabetes screening: are there easy measures to implement the guidelines? J Cyst Fibros 2017. [DOI: 10.1016/s1569-1993(17)30622-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Gómez P, Paterson S, De Meester L, Liu X, Lenzi L, Sharma MD, McElroy K, Buckling A. Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community. Nat Commun 2016; 7:12453. [PMID: 27501868 PMCID: PMC4980492 DOI: 10.1038/ncomms12453] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 07/04/2016] [Indexed: 01/26/2023] Open
Abstract
Local adaptation of a species can affect community composition, yet the importance of local adaptation compared with species presence per se is unknown. Here we determine how a compost bacterial community exposed to elevated temperature changes over 2 months as a result of the presence of a focal bacterium, Pseudomonas fluorescens SBW25, that had been pre-adapted or not to the compost for 48 days. The effect of local adaptation on community composition is as great as the effect of species presence per se, with these results robust to the presence of an additional strong selection pressure: an SBW25-specific virus. These findings suggest that evolution occurring over ecological time scales can be a key driver of the structure of natural microbial communities, particularly in situations where some species have an evolutionary head start following large perturbations, such as exposure to antibiotics or crop planting and harvesting. Though both the presence and traits of a species can influence the dynamics of its ecological community, the effects of these factors are difficult to disentangle. Here, Gómez et al. demonstrate in a microbial mesocosm that local adaptation of a focal species can influence the community as much as the presence of the focal species per se.
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Affiliation(s)
- Pedro Gómez
- ESI and CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK.,CEBAS-CSIC, Campus Espinardo, 30100 Murcia, Spain
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation, KU Leuven, 3000 Leuven, Belgium
| | - Xuan Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Luca Lenzi
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - M D Sharma
- CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
| | - Kerensa McElroy
- Common wealth Scientific and Industrial Research Organisation (CSIRO), Canberra GPO Box 1700, Australia
| | - Angus Buckling
- ESI and CEC, Biosciences, University of Exeter, Penryn Campus, Cornwall TR10 9FE, UK
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Abstract
The gut microbiota profoundly affects the biology of its host. The composition of the microbiota is dynamic and is affected by both host genetic and many environmental effects. The gut microbiota of laboratory mice has been studied extensively, which has uncovered many of the effects that the microbiota can have. This work has also shown that the environments of different research institutions can affect the mouse microbiota. There has been relatively limited study of the microbiota of wild mice, but this has shown that it typically differs from that of laboratory mice (and that maintaining wild caught mice in the laboratory can quite quickly alter the microbiota). There is also inter-individual variation in the microbiota of wild mice, with this principally explained by geographical location. In this study we have characterised the gut (both the caecum and rectum) microbiota of wild caught Mus musculus domesticus at three UK sites and have investigated how the microbiota varies depending on host location and host characteristics. We find that the microbiota of these mice are generally consistent with those described from other wild mice. The rectal and caecal microbiotas of individual mice are generally more similar to each other, than they are to the microbiota of other individuals. We found significant differences in the diversity of the microbiotas among mice from different sample sites. There were significant correlations of microbiota diversity and body weight, a measure of age, body-mass index, serum concentration of leptin, and virus, nematode and mite infection.
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Affiliation(s)
- Laura Weldon
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Stephen Abolins
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Christian Bourne
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Eleanor M. Riley
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Mark Viney
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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Ilott NE, Heward JA, Roux B, Tsitsiou E, Fenwick PS, Lenzi L, Goodhead I, Hertz-Fowler C, Heger A, Hall N, Donnelly LE, Sims D, Lindsay MA. Corrigendum: Long non-coding RNAs and enhancer RNAs regulate the lipopolysaccharide-induced inflammatory response in human monocytes. Nat Commun 2015; 6:6814. [PMID: 25855049 PMCID: PMC5784311 DOI: 10.1038/ncomms7814] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Abstract
A work undertaken by pot and field experiments to assess the suitability of poplars and ferns for the in-situ, phytoextraction, of a dumping site with residues from the roasting process of arseno-pyrite is reported. The main characteristic of this site is the high content of both the As metalloid and heavy metals (e.g., Al, Fe, Cu, Co, Cr, Pb). Two poplar clones (Populus deltoides 'Dvina' and Populus x canadensis 'Orion') and Pteris vittata (Chinese brake fern) were planted in the contaminated soil both ex situ in pots and in situ. Plant survival, As accumulation in plant tissues, leaf content of pigments, soluble proteins, activity of catalase and SH-groups in both roots and leaves were evaluated during a 24-month study period. Both poplar and fern plants exhibited an increase in the activity of catalase and SH group contents when grown in the presence of pyrite ashes. The results showed that the co-planting system (arsenic-hyperaccumulator fern Pteris vittata and Populus clones) was suitable for phytoextraction of multi-contaminated dumping sites. Agronomic measures such as irrigation, soil tillage and amendments also seem to be necessary for the successful establishment of poplar trees and ferns in contaminated soils in order to enhance plant growth through the improvement of soil conditions.
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Abstract
Type 1 diabetes (T1D) is a heterogeneous disorder characterized by destruction of pancreatic beta cells, culminating in loss of insulin secretion. Data from large epidemiologic studies worldwide indicate that during the last decades the incidence of T1D has increased significantly, reaching percentages of 2-5% annually. This increase suggests that there is a significant environmental contribution impacting the development of the disease, since genetic factors alone can hardly explain the rapid increase. Studies regarding T1D epidemiology in diverse populations aim to identify the disease causal factors and new targets for intervention. Viruses are one of the environmental factors implicated in the development of T1D in susceptible individuals. Recent studies suggest an association of T1D with H1N1 influenza. We would like to comment on this association and report our experience. Prospective studies are necessary to assess whether H1N1 infection is involved in T1D pathogenesis and provide directions on how to deal with viral infections in diabetes-susceptible individuals.
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Bonadonna P, Zanotti R, Melioli G, Antonini F, Romano I, Lenzi L, Caruso B, Passalacqua G. The role of basophil activation test in special populations with mastocytosis and reactions to hymenoptera sting. Allergy 2012; 67:962-5. [PMID: 22676063 DOI: 10.1111/j.1398-9995.2012.02849.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND Systemic mastocytosis (SM) may be associated with hymenoptera allergy. In such cases, immunotherapy is a life-saving treatment, but a circumstantiated diagnosis is needed for its prescription. Patients with SM and previous reactions to stings, but with negative tests represent a diagnostic dilemma. The basophil activation test (BAT) may be helpful in refining the diagnosis. OBJECTIVE We assessed the usefulness of BAT in subpopulations of mastocytosis patients, including those with negative tests for insect allergy. METHODS Within a population of patients with mastocytosis and previous stings, we studied by BAT and augmented intradermal test (IDT) (10 µg/ml) two groups: (1) with reactions to stings and negative tests; (2) without reactions and negative tests. Basophil activation test was performed with different venoms, assessing at flow cytometry basophils' activation. RESULTS Sixty-three patients had mastocytosis and 52 had reactions to previous hymenoptera stings. Of them, seven proved negative to diagnostic tests. In six of seven of those patients, BAT was negative with all venoms, and in one, basophils resulted activated also with the negative control. In six patients without previous reactions and negative tests, BAT was totally negative in five of six patients and weakly positive to Hornet in one. Finally, the IDT at 10 µg/ml venom produced nonspecific positive results in most cases. CONCLUSION In patients with mastocytosis, the negative results of standard tests are reliable, because BAT and IDT at higher concentration do not add useful information.
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Affiliation(s)
- P. Bonadonna
- Allergy Unit; Azienda Ospedaliera Universitaria Integrata; Verona; Italy
| | - R. Zanotti
- Section of Haematology; Deparment of Clinical and Experimental Medicine; University of Verona; Verona; Italy
| | - G. Melioli
- Deparment of Research and Medical Diagnostics; Istituto Giannina Gaslini; Genoa; Italy
| | - F. Antonini
- Deparment of Research and Medical Diagnostics; Istituto Giannina Gaslini; Genoa; Italy
| | - I. Romano
- Deparment of Research and Medical Diagnostics; Istituto Giannina Gaslini; Genoa; Italy
| | - L. Lenzi
- Deparment of Research and Medical Diagnostics; Istituto Giannina Gaslini; Genoa; Italy
| | - B. Caruso
- Laboratory of Clinical Chemistry and Haematology; Azienda Ospedaliera Universitaria Integrata; Verona; Italy
| | - G. Passalacqua
- Allergy and Respiratory Diseases; DIMI; University of Genoa; Genoa; Italy
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AlSaadi MM, Gaunt TR, Boustred CR, Guthrie PAI, Liu X, Lenzi L, Rainbow L, Hall N, Alharbi KK, Day INM. From a single whole exome read to notions of clinical screening: primary ciliary dyskinesia and RSPH9 p.Lys268del in the Arabian Peninsula. Ann Hum Genet 2012; 76:211-20. [PMID: 22384920 PMCID: PMC3575730 DOI: 10.1111/j.1469-1809.2012.00704.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [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] [Indexed: 01/23/2023]
Abstract
Primary ciliary dyskinesia (PCD) is a genetic disorder, usually autosomal recessive, causing early respiratory disease and later subfertility. Whole exome sequencing may enable efficient analysis for locus heterogeneous disorders such as PCD. We whole-exome-sequenced one consanguineous Saudi Arabian with clinically diagnosed PCD and normal laterality, to attempt ab initio molecular diagnosis. We reviewed 13 known PCD genes and potentially autozygous regions (extended homozygosity) for homozygous exon deletions, non-dbSNP codon, splice-site base variants or small indels. Homozygous non-dbSNP changes were also reviewed exome-wide. One single molecular read representing RSPH9 p.Lys268del was observed, with no wild-type reads, and a notable deficiency of mapped reads at this location. Among all observations, RSPH9 was the strongest candidate for causality. Searching unmapped reads revealed seven more mutant reads. Direct assay for p.Lys268del (MboII digest) confirmed homozygosity in the affected individual, then confirmed homozygosity in three siblings with bronchiectasis. Our finding in southwest Saudi Arabia indicates that p.Lys268del, previously observed in two Bedouin families (Israel, UAE), is geographically widespread in the Arabian Peninsula. Analogous with cystic fibrosis CFTR p.Phe508del, screening for RSPH9 p.Lys268del (which lacks sentinel dextrocardia) in those at risk would help in early diagnosis, tailored clinical management, genetic counselling and primary prevention.
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Affiliation(s)
- Muslim M AlSaadi
- College of Medicine, King Saud University, P O Box 2925 Riyadh 11472, Kingdom of Saudi Arabia
| | - Tom R Gaunt
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Christopher R Boustred
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Philip AI Guthrie
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
| | - Xuan Liu
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Luca Lenzi
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Lucille Rainbow
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Neil Hall
- Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Khalid K Alharbi
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, P.O.Box 10219, Riyadh 11433, Kingdom of Saudi Arabia
| | - Ian NM Day
- Bristol Genetic Epidemiology Laboratories and MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, United Kingdom
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Casadei R, Pelleri MC, Vitale L, Facchin F, Lenzi L, Canaider S, Strippoli P, Frabetti F. Identification of housekeeping genes suitable for gene expression analysis in the zebrafish. Gene Expr Patterns 2011; 11:271-6. [DOI: 10.1016/j.gep.2011.01.003] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 01/19/2011] [Accepted: 01/24/2011] [Indexed: 11/28/2022]
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Falsetti P, Acciai C, Carpinteri F, Palilla R, Lenzi L. Bedside ultrasonography of musculoskeletal complications in brain injured patients. J Ultrasound 2010; 13:134-41. [PMID: 23396883 DOI: 10.1016/j.jus.2010.09.001] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
INTRODUCTION The aim of this study was to evaluate the role of bedside ultrasonography (US) in early diagnosis of musculoskeletal complications (MSC) of acquired brain injuries, to describe its incidence and US features in a neurorehabilitation setting. MATERIALS AND METHODS All 163 patients admitted in tertiary-level neurorehabilitation unit with diagnosis of stroke or severe brain injury (SBI), with symptoms or signs of musculoskeletal pathology, underwent bedside US. RESULTS MSC were diagnosed in 51.5%. In 86.9% US clarified diagnosis and/or modified therapeutic approach. Shoulder pain was observed in 27.6%. US showed a shoulder subluxation in 73.3% and a frozen shoulder in 8.8% of painful shoulders. In all the cases rotator cuff abnormalities were noted. Wrist-hand syndrome was observed in 29.4%. US showed mild effusion in wrist joints and tendon sheaths and subcutaneous edema without significant vascularity. Neurogenic heterotopic ossification was observed in 1.8%. US demonstrated the "zone phenomenon" or heterogeneously hypoechoic mass with low resistance vessels within the lesions. Contractures and spasticity were observed in 18.4%. US allowed reliable guidance for Botulinum toxin A injection. Relapsing osteoarthritis and acute arthritis were diagnosed in 15.3% and 7.3% respectively. Patients with MSC had lower Functional Independence Measurement (FIM) and Katz index scores in discharge (p < 0.04 and p < 0.0294 respectively) and more length of hospital stay (p = 0.0024). DISCUSSION Musculoskeletal pathology frequently complicates the course of acquired brain injuries and it delays functional recovery. Bedside US is a cheap and sensitive diagnostic tool and it can aid clinicians to define diagnosis and to choose therapeutic approach.
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Affiliation(s)
- P Falsetti
- Neurorehabilitation Unit, Department of Rehabilitation, Local Health Unit (AUSL) 8, S. Donato Hospital, Arezzo, Italy
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Falsetti P, Acciai C, Volpe A, Lenzi L. Ultrasonography in early assessment of elderly patients with polymyalgic symptoms: a role in predicting diagnostic outcome? Scand J Rheumatol 2010; 40:57-63. [DOI: 10.3109/03009742.2010.486766] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Antonelli A, Lenzi L, Nakagawara A, Osaki T, Chiaretti A, Aloe L. Tumor Suppressor Proteins are Differentially Affected in Human Ependymoblastoma and Medulloblastoma Cells Exposed to Nerve Growth Factor. Cancer Invest 2009; 25:94-101. [PMID: 17453820 DOI: 10.1080/07357900701205689] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The aim of our study was to investigate the role of nerve growth factor (NGF) on the expression of the p73 protein in human ependymoblastoma (EP) and medulloblastoma (MB) cells. It was found that NGF exposure on MB cells blocks proliferation, as well as on EP cells and induces overexpression of p73. NGF reduces the number of cells and promotes the expression of TrkA of these neoplastic cells. Moreover, NGF plus cisplatin treatment reduces the cytotoxic effect of cisplatin. These observations indicate that NGF by interfering with mechanisms associated with cells proliferation and survival might induce the differentiation event through TrkA pathways.
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Affiliation(s)
- A Antonelli
- Institute of Neurobiology and Molecular Medicine, CNR-EBRI, Rome, Italy
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Frabetti F, Casadei R, Lenzi L, Canaider S, Vitale L, Facchin F, Carinci P, Zannotti M, Strippoli P. Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach. Biol Direct 2007; 2:34. [PMID: 18042283 PMCID: PMC2222617 DOI: 10.1186/1745-6150-2-34] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 11/27/2007] [Indexed: 11/15/2022] Open
Abstract
Background All standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. The aim of this work was to estimate mRNA open reading frame (ORF) 5' region sequence completeness in the model organism Danio rerio (zebrafish). Results We implemented a novel automated approach (5'_ORF_Extender) that systematically compares available expressed sequence tags (ESTs) with all the zebrafish experimentally determined mRNA sequences, identifies additional sequence stretches at 5' region and scans for the presence of all conditions needed to define a new, extended putative ORF. Our software was able to identify 285 (3.3%) mRNAs with putatively incomplete ORFs at 5' region and, in three example cases selected (selt1a, unc119.2, nppa), the extended coding region at 5' end was cloned by reverse transcription-polymerase chain reaction (RT-PCR). Conclusion The implemented method, which could also be useful for the analysis of other genomes, allowed us to describe the relevance of the "5' end mRNA artifact" problem for genomic annotation and functional genomic experiment design in zebrafish. Open peer review This article was reviewed by Alexey V. Kochetov (nominated by Mikhail Gelfand), Shamil Sunyaev, and Gáspár Jékely. For the full reviews, please go to the Reviewers' Comments section.
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Affiliation(s)
- Flavia Frabetti
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embryology and Applied Biology, University of Bologna, via Belmeloro 8, 40126 Bologna (BO), Italy.
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Lenzi L, Frabetti F, Facchin F, Casadei R, Vitale L, Canaider S, Carinci P, Zannotti M, Strippoli P. UniGene Tabulator: a full parser for the UniGene format. Bioinformatics 2006; 22:2570-1. [PMID: 16895929 DOI: 10.1093/bioinformatics/btl425] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes related tables for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2 or later) operating systems-based computers. AVAILABILITY The current release, including both the FileMaker runtime applications, is freely available at http://apollo11.isto.unibo.it/software/
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Affiliation(s)
- Luca Lenzi
- Department of Histology, Embryology and Applied Biology University of Bologna, 40126 Bologna, Italy
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Canaider S, Facchin F, Griffoni C, Casadei R, Vitale L, Lenzi L, Frabetti F, D'Addabbo P, Carinci P, Zannotti M, Strippoli P. Proteins encoded by human Down syndrome critical region gene 1-like 2 (DSCR1L2) mRNA and by a novel DSCR1L2 mRNA isoform interact with cardiac troponin I (TNNI3). Gene 2006; 372:128-36. [PMID: 16516408 DOI: 10.1016/j.gene.2005.12.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Accepted: 12/19/2005] [Indexed: 11/25/2022]
Abstract
Down syndrome critical region gene 1-like 2 (DSCR1L2) belongs to the human DSCR1-like gene family, which also includes DSCR1 and DSCR1L1. Both DSCR1 and DSCR1L1 proteins interact with calcineurin, a calcium/calmodulin-dependent phosphatase. To date, no interactor has been described for DSCR1L2. The aim of this work was to perform a first functional study of DSCR1L2 using yeast two-hybrid analysis conducted on a human heart cDNA library. Here, we report the interaction between DSCR1L2 and the human cardiac troponin I (TNNI3), the heart-specific inhibitory subunit of the troponin complex, a central component of the contractile apparatus. This interaction was confirmed by both yeast cotransformation and GST (glutathione-sepharose transferase) fusion protein assay. Moreover, a new DSCR1L2 mRNA isoform, generated by alternative splicing, was identified and cloned in different tissues: it lacks two central exons, encoding the most conserved domains among the DSCR1-like protein family. A quantitative relative reverse transcription-polymerase chain reaction (RT-PCR) assay showed that in heart tissue the normalized expression level ratio for DSCR1L2 and DSCR1L2-E2E5 mRNA isoforms is 3.5:1, respectively. The yeast cotransformation and GST fusion protein assay demonstrated the interaction between this new DSCR1L2 variant and the human cardiac troponin I and the prominent role of DSCR1L2 exon 2 in determining binding between both DSCR1L2 isoforms and TNNI3. These data indicate an entirely new role for a DSCR1-like family gene, suggesting a possible involvement of DSCR1L2 in cardiac contraction.
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Affiliation(s)
- Silvia Canaider
- Department of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna, Italy
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Vitale L, Lenzi L, Huntsman SA, Canaider S, Frabetti F, Casadei R, Facchin F, Carinci P, Zannotti M, Coppola D, Strippoli P. Differential expression of alternatively spliced mRNA forms of the insulin-like growth factor 1 receptor in human neuroendocrine tumors. Oncol Rep 2006; 15:1249-56. [PMID: 16596194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023] Open
Abstract
The activation of the insulin-like growth factor 1/IGF1 receptor system (IGF1/IGF1R) is a critical event in the transformation and tumorigenicity processes in a wide variety of human tumors. The IGF1/IGF1R system has been recently studied in carcinoid tumors that often arise in the gastrointestinal tract; these tumors are characterized by hypersecretion of bioamines and neuropeptides, leading to functional tumor disease. Two alternatively spliced IGF1R mRNA transcripts have been described to differ by only three nucleotides (CAG) in the coding sequence, resulting in an amino-acid change from the originally described Thr-Gly to an Arg in the extracellular portion of the receptor beta subunit. In transfected Chinese hamster ovary cells, the form without CAG (CAG-) exhibited an approximate 2-fold increase in IGF1 stimulation of activities required for its mitogenic properties. In this study, we examine the relative expression of the two IGF1R mRNA isoforms by a semiquantitative RT-PCR approach using highly standardized conditions, beta-2 microglobulin (B2M) as a reference gene and gel imaging analysis. We analyzed a large series of human neuroendocrine tumors (32 samples) and 9 normal tissues. A significant higher expression of both isoforms in the tumor samples (approximately 2-fold increase) was found, while a constant CAG+/CAG- IGF1R mRNA isoforms of an approximate 3:1 ratio was observed in all tumoral and normal cell types studied. The phylogenetic study of the IGF1R locus in several species suggests that human IGF1R CAG- mRNA isoform is evolutionarily more recent compared to the IGF1R CAG+ mRNA isoform and it could be used by the splicing apparatus at this intron/exon junction with a lower efficiency. This study highlights the relevance of IGF1R mRNA expression in neuroendocrine tumor cells, and the constant presence of 'subtle' alternative splicing for the IGF1R locus.
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Affiliation(s)
- Lorenza Vitale
- Dipartimento di Istologia, Embriologia e Biologia Applicata, Università di Bologna, I-40126 Bologna, Italy
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Vitale L, Lenzi L, Huntsman S, Canaider S, Frabetti F, Casadei R, Facchin F, Carinci P, Zannotti M, Coppola D, Strippoli P. Differential expression of alternatively spliced mRNA forms of the insulin-like growth factor 1 receptor in human neuroendocrine tumors. Oncol Rep 2006. [DOI: 10.3892/or.15.5.1249] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Seminara S, Stagi S, Candura L, Scrivano M, Lenzi L, Nanni L, Pagliai F, Chiarelli F. Changes of thyroid function during long-term hGH therapy in GHD children. A possible relationship with catch-up growth? Horm Metab Res 2005; 37:751-6. [PMID: 16372229 DOI: 10.1055/s-2005-921104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND Growth hormone (GH) treatment in patients with GH deficiency (GHD) can determine changes in the thyroid function. The clinical significance of these changes remains controversial, and all studies have so far covered rather a short period--usually no longer than one year. OBJECTIVE To determine the effect of long-term recombinant hGH treatment in children with idiopathic GHD on the thyroid function. PATIENTS AND METHODS Nineteen prepubertal children (12 boys and 7 girls, mean age 9.2 +/- 3.1 years) with idiopathic GHD were studied and followed for twenty-four months. None of the patients showed multiple pituitary hormone deficiencies. Nineteen healthy children matched for age and sex acted as controls. RESULTS Patients with GHD showed a significant increase in TT (3) at twelve months and in FT (3) at six and twelve months after starting GH treatment, with a significant decrease at eighteen and twenty-four months. TT (4) level decreased significantly at twelve months and increased significantly at eighteen and twenty-four months. FT (4) also decreased, but only slightly, after twelve months of hGH treatment, and then increased significantly at twenty-four months. TSH levels did not vary significantly during the course of therapy. TT (3)/TT (4) and FT (3)/FT (4) ratios increased significantly after six and twelve months of therapy and significantly decreased later, approaching pre-therapy values. The SDS of Growth Velocity (SDS-GV) increased remarkably during the first year of therapy and then decreased significantly during the second year, although it remained significantly higher than the pre-therapy values. TT (3) and TT (3)/TT (4) ratio displayed a significant correlation with SDS-GV at twelve months of therapy. In a multiple regression analysis with age, bone age, parental height, GH dose, TT (3,) TT (3)/TT (4), and the SDS of IGF-I, only the TT (3)/TT (4) ratio at twelve months of therapy (p < 0.001) was identified as a significant predictor of SDS-GV. CONCLUSION Our data confirm that changes in thyroid function are present in GHD children during long-term hGH therapy. These changes probably resulted from the effect of hGH on the peripheral metabolism of thyroid hormones and appear to be transitory, disappearing during the second year of hGH treatment. We speculate on the functional significance of these changes, and in particular, on their role in catch-up growth after hGH therapy.
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Affiliation(s)
- S Seminara
- Department of Paediatrics, University of Florence, Anna Meyer Children's Hospital, Via Luca Giordano 13, Florence, Italy.
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Strippoli P, Canaider S, Noferini F, D'Addabbo P, Vitale L, Facchin F, Lenzi L, Casadei R, Carinci P, Zannotti M, Frabetti F. Uncertainty principle of genetic information in a living cell. Theor Biol Med Model 2005; 2:40. [PMID: 16197549 PMCID: PMC1262781 DOI: 10.1186/1742-4682-2-40] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Accepted: 09/30/2005] [Indexed: 11/30/2022] Open
Abstract
Background Formal description of a cell's genetic information should provide the number of DNA molecules in that cell and their complete nucleotide sequences. We pose the formal problem: can the genome sequence forming the genotype of a given living cell be known with absolute certainty so that the cell's behaviour (phenotype) can be correlated to that genetic information? To answer this question, we propose a series of thought experiments. Results We show that the genome sequence of any actual living cell cannot physically be known with absolute certainty, independently of the method used. There is an associated uncertainty, in terms of base pairs, equal to or greater than μs (where μ is the mutation rate of the cell type and s is the cell's genome size). Conclusion This finding establishes an "uncertainty principle" in genetics for the first time, and its analogy with the Heisenberg uncertainty principle in physics is discussed. The genetic information that makes living cells work is thus better represented by a probabilistic model rather than as a completely defined object.
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Affiliation(s)
- Pierluigi Strippoli
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Silvia Canaider
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Francesco Noferini
- Department of Physics, University of Bologna, Via Irnerio 46, 40126 Bologna (BO), Italy; Sezione INFN, Bologna, Italy
| | - Pietro D'Addabbo
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
- Dipartimento di Genetica e Microbiologia, University of Bari, 70126 Bari, Italy
| | - Lorenza Vitale
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Federica Facchin
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Luca Lenzi
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Raffaella Casadei
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Paolo Carinci
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Maria Zannotti
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
| | - Flavia Frabetti
- Center for Research in Molecular Genetics "Fondazione CARISBO", Department of Histology, Embriology and Applied Biology, University of Bologna, Via Belmeloro 8, 40126 Bologna (BO), Italy
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Giannone S, Strippoli P, Vitale L, Casadei R, Canaider S, Lenzi L, D'Addabbo P, Frabetti F, Facchin F, Farina A, Carinci P, Zannotti M. Gene expression profile analysis in human T lymphocytes from patients with Down Syndrome. Ann Hum Genet 2005; 68:546-54. [PMID: 15598213 DOI: 10.1046/j.1529-8817.2003.00123.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Down Syndrome (DS) is caused by the presence of three copies of the whole human chromosome 21 (HC21) or of a HC21 restricted region; the phenotype is likely to have originated from the altered expression of genes in the HC21. We apply the cDNA microarray method to the study of gene expression in human T lymphocytes with trisomy 21 in comparison to normal cells. Two patients with DS were investigated, along with two normal subjects as a control, all being tested in independent, duplicated cell culture experiments. The most consistent finding was the overexpression of the superoxide dismutase gene (SOD1), located on 21q, and of MHC DR beta 3 (HLA-DRB3), GABA receptor A gamma 2 (GABRG2), acetyltransferase Coenzyme, A 2 (ACAT2) and ras suppressor protein 1 (RSU1) genes. When the data were clustered according to chromosome localization, the HC21 gene set showed, on average, the highest expression in DS cells in all the experiments. Moreover, separate clustering of patients and controls was obtained when analysis was restricted to HC21 gene expression values. These findings reinforce the specific gene dosage theory for the pathogenesis of the DS phenotype, and show a consistent overexpression of the SOD1 gene on 21q.
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Affiliation(s)
- S Giannone
- Center for Research in Molecular Genetics Fondazione CARISBO, at the Institute of Histology and General Embriology, University of Bologna, V. Belmeloro 8, 40126 Bologna, Italy
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Solmi R, De Sanctis P, Zucchini C, Ugolini G, Rosati G, Del Governatore M, Coppola D, Yeatman TJ, Lenzi L, Caira A, Zanotti S, Taffurelli M, Carinci P, Valvassori L, Strippoli P. Search for epithelial-specific mRNAs in peripheral blood of patients with colon cancer by RT-PCR. Int J Oncol 2004; 25:1049-56. [PMID: 15375555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Research has widely supported the efficacy of screening for colorectal cancer in reducing mortality. A blood-based assay potentially represents a more accessible early detection tool for the identification of solid tumor cells originating from a primary tumor site in the body. We demonstrate a relatively easy and highly reproducible technique for the detection of mRNA expression of genes as markers of malignancy in blood samples of patients with colon cancer. The present study aims to identify a set of specific mRNAs expressed in epithelial cells but not in blood cells, which may be useful as markers for early detection of circulating colon cancer cells by a simple, qualitative RT-PCR assay following semi-automated RNA extraction from peripheral blood samples. Our approach includes a systematic search for candidate markers using digital differential display, search on UniGene colon EST libraries and analysis of published data on colon cancer gene expression. A final list included the following genes: bone morphogenetic protein 4 (BMP4), cyclin D (CycD), family with sequence similarity 3, member D (FAM3D), gastrin (GAS), glycoprotein A33 transmembrane (GPA33), glutathione peroxidase 2 gastrointestinal (GPX2), galactoside-binding, soluble, 4 (galectin 4) (LGALS4), non-SMC, structural maintenance of chromosomes, element 1 protein (NSE1), tumor-associated calcium signal transducer 1 (TACSTD1), telomerase reverse transcriptase (hTERT), trefoil factor 3 intestinal (TFF3), transmembrane 4 superfamily member 3 (TM4SF3), UDP glycosyltransferase 1 family, polypeptide A9 (UGT1A9), villin 1 (VIL1), and the novel gene FLJ20127. The mRNA expression of these genes was evaluated in a pool of 16 samples from subjects diagnosed with colon cancer and from 16 normal-controls. We observed expression in 13 of the 15 investigated genes from the blood samples of the vast majority of patients considered, but also in a certain percentage of the controls (from 14.3 to 100%). This finding confirms that the extreme sensitivity of RT-PCR is able to detect minimal amounts of mRNA expressed in a non tissue-specific manner ('illegitimate transcription'). On the contrary, NSE1 and GAS mRNAs were not detected either in patient or in control blood samples; however, they were abundantly expressed in normal and cancerous colon mucosa, encouraging further search for useful markers able to detect epithelial cells in peripheral blood.
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Affiliation(s)
- Rossella Solmi
- Institute of Histology and General Embriology, University of Bologna, Fondazione CARISBO Centre for Research into Molecular Genetics, I-40126 Bologna, Italy
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Amore M, Strippoli P, Laterza C, Tagariello P, Vitale L, Casadei R, Frabetti F, Canaider S, Lenzi L, D'Addabbo P, Carinci P, Torroni A, Ferrari G, Zannotti M. Sequence analysis of ADARB1 gene in patients with familial bipolar disorder. J Affect Disord 2004; 81:79-85. [PMID: 15183604 DOI: 10.1016/j.jad.2003.08.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2003] [Revised: 08/06/2003] [Accepted: 08/08/2003] [Indexed: 11/20/2022]
Abstract
BACKGROUND The ADARB1 gene is located in 21q22.3 region, previously linked to familial bipolar disorder, and its product has a documented action in the editing of the pre-mRNA of glutamate receptor B subunit. Dysfunction of glutamatergic neurotransmission could play an important role in the pathophysiology of bipolar disorder (BD). Glutamate excitatory neurotransmission regulation is a possible mechanism of the initial effect of anticonvulsants in regulating mood. METHODS To investigate the hypothesis of an involvement of ADARB1 gene in the BD, the ADARB1 cDNA has been cloned and sequenced in seven selected bipolar I disorder patients with evidence of familiarity of mood disorders. A detailed investigation of the gene nucleotide sequence in the open reading frame has been performed. RESULTS No alteration in the sequence of the ADARB1 gene cDNA was found in any patient, except a common neutral polymorphism in three out of seven patients. CONCLUSIONS Mutations in ADARB1 gene are not commonly associated with bipolar I disorder, therefore other genes in the 21q22 region could be associated with bipolar illness in some families, likely in the context of a multifactorial transmission model.
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Affiliation(s)
- Mario Amore
- Institute of Psychiatry, University of Parma, p.zza Matteotti, 9, 43100, Italy.
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McCloskey SM, McMullin MF, Morris TCM, Markey GM, Izraeli S, O‘Shaughnessy DF, Atterbury C, Bolton Maggs P, Murphy M, Thomas D, Yates S, Williamson LM, Ambrosetti A, Zanotti R, Pattaro C, Lenzi L, Chilosi M, Caramaschi P, Arcaini L, Pasini F, Biasi D, Orlandi E, D'Adda M, Lucioni M, Pizzolo G, Mitsui T, Maekawa I, Yamane A, Ishikawa T, Koiso H, Yokohama A, Handa H, Matsushima T, Tsukamoto N, Murakami H, Nojima Y, Karasawa M, Stewart JP, Thompson A, Santra M, Barlogie B, Lappin TRJ, Shaughnessy J, Henschler R, Fehervizyova Z, Bistrian R, Seifried E, Stanworth SJ, Brunskill SJ, Hyde CJ, McClelland DBL, Murphy MF, Strawn WB, Richmond RS, Tallant EA, Gallagher PE, Ferrario CM. Papers to be published in forthcoming issues. Bone marrow architecture in acute myeloid/erythroid leukaemia. Leukemia - a developmental perspective. Guidelines for the use of fresh frozen plasma, cryoprecipitate and cryosupernatant. Most cases of primary. Br J Haematol 2004. [DOI: 10.1111/j.1365-2141.2004.v125_i6_forth.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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D'Addabbo P, Lenzi L, Facchin F, Casadei R, Canaider S, Vitale L, Frabetti F, Carinci P, Zannotti M, Strippoli P. GeneRecords: a relational database for GenBank flat file parsing and data manipulation in personal computers. Bioinformatics 2004; 20:2883-5. [PMID: 15145799 DOI: 10.1093/bioinformatics/bth321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
UNLABELLED Extracting the desired data from a database entry for later analysis is a constant need in the biological sequence analysis community; GeneRecords 1.0 is a solution for GenBank biological flat file parsing, as it implements a structured representation of each feature and feature qualifier in GenBank following import in a common database managing system usable in a personal computer (Macintosh and Windows environments). This collection of related databases enables the local management of GenBank records, allowing indexing, retrieval and analysis of both information and sequences on a personal computer. AVAILABILITY The current release, including the FileMaker Pro runtime application (built for Windows and Macintosh environments), is freely available at http://apollo11.isto.unibo.it/software/
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Affiliation(s)
- P D'Addabbo
- Center for Research into Molecular Genetics Fondazione CARISBO, Institute of Histology and General Embriology, University of Bologna, Via Belmeloro, 8-40126 Bologna, Italy
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Casadei R, Strippoli P, D'Addabbo P, Canaider S, Lenzi L, Vitale L, Giannone S, Frabetti F, Facchin F, Carinci P, Zannotti M. mRNA 5′ region sequence incompleteness: a potential source of systematic errors in translation initiation codon assignment in human mRNAs. Gene 2003; 321:185-93. [PMID: 14637006 DOI: 10.1016/s0378-1119(03)00835-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The amino acid sequence of gene products is routinely deduced from the nucleotide sequence of the relative cloned cDNA, according to the rules for recognition of start codon (first-AUG rule, optimal sequence context) and the genetic code. From this prediction stem most subsequent types of product analysis, although all standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. Revision by bioinformatics and cloning methods of 109 known genes located on human chromosome 21 (HC 21) shows that 60 mRNAs lack any in-frame stop upstream of the first-AUG, and that in five cases (DSCR1, KIAA0184, KIAA0539, SON, and TFF3) the coding region at the 5' end was incompletely characterized in the original descriptions. We describe the respective consequences for genomic annotation, domain and ortholog identification, and functional experiments design. We have also analyzed the sequences of 13,124 human mRNAs (RefSeq databank), discovering that in 6448 cases (49%), an in-frame stop codon is present upstream of the initiation codon, while in the other 6676 mRNAs (51%), identification of additional bases at the mRNA 5' region could well reveal some new upstream in-frame AUG codons in the optimal context. Proportionally to the HC 21 data, about 550 known human genes might thus be affected by this 5' end mRNA artifact.
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Affiliation(s)
- Raffaella Casadei
- Center for Research into Molecular Genetics Fondazione CARISBO, Institute of Histology and General Embryology, University of Bologna, Via Belmeloro, 8-40126 Bologna, Italy
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Zucchini C, Strippoli P, Biolchi A, Solmi R, Lenzi L, D'Addabbo P, Carinci P, Valvassori L. The human TruB family of pseudouridine synthase genes, including the Dyskeratosis Congenita 1 gene and the novel member TRUB1. Int J Mol Med 2003; 11:697-704. [PMID: 12736709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
A novel human gene denominated TruB pseudouridine (psi) synthase homolog 1 (E. coli) (approved symbol, TRUB1) has been identified and characterized. Spanning approximately 40 kb on chromosome 10 and including 8 exons, TRUB1 is the first described human ortholog of bacterial TruB/psi55, a gene involved in tRNA pseudouridinilation. TRUB1 gene encodes a 349-amino acid product, with a VFAVHKPKGPTSA box in positions 71-83 corresponding to motif I of the TruB family (probably involved in conserving protein structure). The TruB domain of TRUB1 lies between W104 and I255, and contains another short motif, GGTLDS AARGVLVV, including the highly conserved D residue that characterizes motif II (involved in uridine recognition and in catalytic function of psi synthases). Northern blot analysis revealed that TRUB1 mRNA is widely expressed in various human tissues (especially heart, skeletal muscle and liver). Phylogenetic analysis of the TruB domain revealed another human gene (approved symbol TRUB2) encoding a conserved TruB domain, located on human chromosome 9. Thus, the human TruB family includes at least three members: i.e. DKC1 (previously identified), TRUB1 and TRUB2. The TRUB1 and TRUB2 products could be the hitherto unidentified human tRNA psi synthases. Although TRUB1 is not highly similar to DKC1/dyskerin (whose mutations cause X-linked dyskeratosis congenita) and putatively affects tRNA rather than rRNA modification, it is the most similar human protein to dyskerin. Study of TRUB1 (and TRUB2) should facilitate understanding of the molecular mechanisms of RNA modification and the involvement of psi synthases in human pathology, including dyskeratosis-like diseases.
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Affiliation(s)
- Cinzia Zucchini
- Centro di Ricerca in Genetica Molecolare Fondazione CARISBO at the Istituto di Istologia ed Embriologia Generale, University of Bologna, 40126 Bologna, Italy
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Zucchini C, Strippoli P, Biolchi A, Solmi R, Lenzi L, D'Addabbo P, Carinci P, Valvassori L. The human TruB family of pseudouridine synthase genes, including the Dyskeratosis Congenita 1 gene and the novel member TRUB1. Int J Mol Med 2003. [DOI: 10.3892/ijmm.11.6.697] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Strippoli P, D'Addabbo P, Lenzi L, Giannone S, Canaider S, Casadei R, Vitale L, Carinci P, Zannotti M. Segmental paralogy in the human genome: a large-scale triplication on 1p, 6p, and 21q. Mamm Genome 2002; 13:456-62. [PMID: 12226712 DOI: 10.1007/s00335-001-2157-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2001] [Accepted: 04/17/2002] [Indexed: 11/25/2022]
Abstract
Few cases of large-scale segmental paralogy have been reported in the human genome. We have identified a large (approximately 500 kb) segment on human chromosome (HC) 21 (21q22) that is triplicated on HC 1 (1p35) and HC 6 (6p12-21). We also identified a new member of CLIC (Chloride Intracellular Channel) family on 21q, namely CLIC6. All three segments appear to include three functional members of three different gene families: DSCR1-like (Down Syndrome Candidate Region 1-like), CLIC, and AML/Runt (Acute Myeloid Leukemia/Runt). Molecular evolution analysis shows a common evolutionary origin for the triplicated regions. This finding of a further large-scale genomic triplication that went undetected at previously systematic automated searches provides a new model for gene divergence study and underlines the need for new tools to effectively detect inter-chromosomal similarity. An algorithm to overcome current limitations is proposed.
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Affiliation(s)
- Pierluigi Strippoli
- Research Center for Molecular Genetics Fondazione CARISBO at the Institute of Histology and General Embryology, University of Bologna, 40126, Bologna, Italy
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Vitale L, Casadei R, Canaider S, Lenzi L, Strippoli P, D'Addabbo P, Giannone S, Carinci P, Zannotti M. Cysteine and tyrosine-rich 1 (CYYR1), a novel unpredicted gene on human chromosome 21 (21q21.2), encodes a cysteine and tyrosine-rich protein and defines a new family of highly conserved vertebrate-specific genes. Gene 2002; 290:141-51. [PMID: 12062809 DOI: 10.1016/s0378-1119(02)00550-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A novel human gene has been identified by in-depth bioinformatics analysis of chromosome 21 segment 40/105 (21q21.1), with no coding region predicted in any previous analysis. Brain-derived DNA complementary to RNA (cDNA) sequencing predicts a 154-amino acid product with no similarity to any known protein. The gene has been named cysteine and tyrosine-rich protein 1 gene (symbol cysteine and tyrosine-rich 1, CYYR1). The CYYR1 messenger RNA was found by Northern blot analysis in a broad range of tissues (two transcripts of 3.4 and 2.2 kb). The gene consists of four exons and spans about 107 kb, including a very large intron of 85.8 kb. Analysis of expressed sequence tags shows high CYYR1 expression in cells belonging to the amine precursor uptake and decarboxylation system. We also cloned the cDNA of the murine ortholog Cyyr1, which was mapped by a radiation hybrid panel on chromosome 16 within the region corresponding to that containing the respective human homolog on chromosome 21. Sequence and phylogenetic analysis led to identification of several genes encoding CYYR1 homologous proteins. The most prominent feature identified in the protein family is a central, unique cysteine and tyrosine-rich domain, which is strongly conserved from lower vertebrates (fishes) to humans but is absent in bacteria and invertebrates.
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MESH Headings
- Amino Acid Sequence
- Animals
- Blotting, Northern
- Chromosomes, Human, Pair 21/genetics
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- Databases, Nucleic Acid
- Evolution, Molecular
- Expressed Sequence Tags
- Female
- Gene Expression
- Humans
- Membrane Proteins
- Mice
- Molecular Sequence Data
- Phylogeny
- Proteins/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Radiation Hybrid Mapping
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Vertebrates/genetics
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Affiliation(s)
- Lorenza Vitale
- Istituto di Istologia ed Embriologia Generale, Università di Bologna, Bologna-Centro di Ricerca in Genetica Molecolare Fondazione CARISBO, Bologna, Via Belmeloro, Bologna, Italy
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Gobbi G, Sangiorgi L, Lenzi L, Casadei R, Canaider S, Strippoli P, Lucarelli E, Ghedini I, Donati D, Fabbri N, Warzecha J, Yeoung C, Helman LJ, Picci P, Carinci P. Seven BMPs and all their receptors are simultaneously expressed in osteosarcoma cells. Int J Oncol 2002; 20:143-7. [PMID: 11743655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
Members of the bone morphogenetic protein (BMP) family and their receptors (BMPRs and activin receptors-ActRs) promote the development of bones with a fine regulation of their expression. Mutations in BMPs or BMPRs cause several diseases, as shown in knockout mice, such as skeletal defects, familial primary pulmonary hypertension and neoplasias. Osteosarcoma is the most frequent primary malignant tumor of bone. Due to their importance in bone development, BMPs, BMPRs and ActRs could also play a role in osteosarcoma growth and development. Previous data have shown that the overexpression of the BMPR-II was related to poor prognosis in malignant and metastatic bone tumors. We evaluate by reverse transcription-linked polymerase chain reaction analysis (RT-PCR) the expression pattern of BMPs, BMPRs and ActRs in five different human osteosarcoma cell lines (MG63, G292, HOS, SaOS and U2). Moreover, we performed the mutational screening of the complete BMPR-II mRNA by automated sequencing of the correspondent cDNA to evaluate the presence of point mutations in osteosarcoma cell lines. All the osteosarcoma cell lines studied simultaneously expressed the BMPs, BMPRs and ActRs investigated. No mutations were detected in the BMPR-II cDNA. Our results suggest the presence of a mechanism involving the simultaneous activation of the BMPs and their receptors in osteosarcoma cell lines.
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Affiliation(s)
- Giuliana Gobbi
- Laboratory of Oncology Research, Rizzoli Orthopaedic Institute, Bologna, Italy
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Gobbi G, Sangiorgi L, Lenzi L, Casadei R, Canaider S, Strippoli P, Lucarelli E, Ghedini I, Donati D, Fabbri N, Warzecha J, Yeoung C, Helman L, Picci P, Carinci P. Seven BMPs and all their receptors are simultaneously expressed in osteosarcoma cells. Int J Oncol 2002. [DOI: 10.3892/ijo.20.1.143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Strippoli P, Petrini M, Lenzi L, Carinci P, Zannotti M. The murine DSCR1-like (Down syndrome candidate region 1) gene family: conserved synteny with the human orthologous genes. Gene 2000; 257:223-32. [PMID: 11080588 DOI: 10.1016/s0378-1119(00)00407-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A recently recognized gene family, conserved from yeast to humans, includes Down syndrome candidate region 1 gene (DSCR1), Adapt78 (recognized as the hamster ortholog of the DSCR1 isoform 4), ZAKI-4 (renamed DSCR1-like 1, DSCR1L1) and DSCR1L2 (a novel gene on human chromosome 1), along with yeast and C. elegans single members (Strippoli P., Lenzi L., Petrini M., Carinci P., Zannotti M., 2000. A new gene family including DSCR1 (Down Syndrome Candidate Region 1) and ZAKI-4: characterization from yeast to human and identification of DSCR1-like 2, a novel human member. Genomics 64, 252-263). The proposed family labels were a putative single-strand nucleic acid binding domain similar to the RNA recognition motif, and a unique, highly-conserved serine-proline motif. We have used a bioinformatics-driven molecular biology approach to characterize the murine members of DSCR1-like gene family. Systematic expressed-sequence-tags (EST) database search and reverse-transcription polymerase chain rection (RT-PCR) product sequencing allowed identification of the murine DSCR1, DSCR1L1 and DSCR1L2. The sequences of the respective protein products are of 198, 197 and 241 amino acids, respectively, and are very similar to the corresponding human proteins. The very broad expression pattern of the murine DSCR1 genes is similar to that of the human genes. Using a radiation hybrid panel, we mapped the murine DSCR1-like family members. The murine DSCR1 ortholog is located on the chromosome 16, in a region corresponding to that on human chromosome 21 just upstream of the Down syndrome candidate region. DSCR1L1 and DSCR1L2 murine genes are also located in chromosomal segments of chromosome 17 and 4, respectively, exactly corresponding to those containing the respective human homologs on chromosomes 6 and 1. Description of the mouse orthologs for DSCR1-like genes will allow knockout mice to be obtained for specific family members.
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MESH Headings
- Adaptor Proteins, Signal Transducing
- Amino Acid Sequence
- Animals
- Blotting, Northern
- Chromosome Mapping
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA-Binding Proteins
- Databases, Factual
- Embryo, Mammalian/metabolism
- Evolution, Molecular
- Expressed Sequence Tags
- Gene Expression
- Gene Expression Regulation, Developmental
- Intracellular Signaling Peptides and Proteins
- Male
- Mice
- Molecular Sequence Data
- Multigene Family/genetics
- Muscle Proteins/genetics
- Phylogeny
- Proteins/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Radiation Hybrid Mapping
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Tissue Distribution
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Affiliation(s)
- P Strippoli
- Istituto di Istologia ed Embriologia GeneraleVia Belmeloro, 8-40126 (BO), Bologna, Italy
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Strippoli P, Lenzi L, Petrini M, Carinci P, Zannotti M. A new gene family including DSCR1 (Down Syndrome Candidate Region 1) and ZAKI-4: characterization from yeast to human and identification of DSCR1-like 2, a novel human member (DSCR1L2). Genomics 2000; 64:252-63. [PMID: 10756093 DOI: 10.1006/geno.2000.6127] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A new gene family has been identified on the basis of in-depth bioinformatics analysis of the Down syndrome candidate region 1 (DSCR1) gene, located on 21q22.1. We have determined the complete coding sequences of similar genes in Saccharomyces cerevisiae and Caenorhabditis elegans, as well as that of a novel human gene, named DSCR1L2 (DSCR1-like 2). Peripheral blood leukocyte cDNA sequencing predicts as its product a 241-amino-acid protein highly similar to products of the human genes DSCR1 and ZAKI-4 (HGMW-approved symbol DSCR1L1). The highest level of expression of DSCR1L2 mRNA was found by Northern blot analysis in heart and skeletal muscles, liver, kidney, and peripheral blood leukocytes (three transcripts of 3.2, 5. 2, and 7.5 kb). The gene consists of four exons and spans about 22 kb on chromosome 1 (1p33-p35.3) (Human Chromosome 1, Sanger Centre). Exon/intron organization is highly conserved between DSCR1 and DSCR1L2. Two alternative DSCR1L2 mRNA splicing forms have been recognized, with one lacking 10 amino acids in the middle of the protein. Analysis of expressed sequence tags (ESTs) shows DSCR1L2 expression in fetal tissues (heart, liver, and spleen) and in adenocarcinomas. ESTs related to the murine DSCR1L2 orthologue are found in the 2-cell stage mouse embryo, in developing brain stem and spinal cord, and in thymus and T cells. The most prominent feature identified in the protein family is a central short, unique serine-proline motif (including an ISPPXSPP box), which is strongly conserved from yeast to human but is absent in bacteria. Moreover, homology with the RNA-binding domain was weakly but consistently detected in a stretch of 80 amino acids at the amino-terminus by fine sequence analysis based on tools utilizing both hidden Markov models and BLAST. The identification of this new gene family should allow a better understanding of the functions of the genes belonging to it.
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Affiliation(s)
- P Strippoli
- Istituto di Istologia ed Embriologia Generale, Università di Bologna, Bologna, Italy
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