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Liuu S, Nepelska M, Pfister H, Gamelas Magalhaes J, Chevalier G, Strozzi F, Billerey C, Maresca M, Nicoletti C, Di Pasquale E, Pechard C, Bardouillet L, Girardin SE, Boneca IG, Doré J, Blottière HM, Bonny C, Chene L, Cultrone A. Identification of a muropeptide precursor transporter from gut microbiota and its role in preventing intestinal inflammation. Proc Natl Acad Sci U S A 2023; 120:e2306863120. [PMID: 38127978 PMCID: PMC10756304 DOI: 10.1073/pnas.2306863120] [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: 05/10/2023] [Accepted: 10/31/2023] [Indexed: 12/23/2023] Open
Abstract
The gut microbiota is a considerable source of biologically active compounds that can promote intestinal homeostasis and improve immune responses. Here, we used large expression libraries of cloned metagenomic DNA to identify compounds able to sustain an anti-inflammatory reaction on host cells. Starting with a screen for NF-κB activation, we have identified overlapping clones harbouring a heterodimeric ATP-binding cassette (ABC)-transporter from a Firmicutes. Extensive purification of the clone's supernatant demonstrates that the ABC-transporter allows for the efficient extracellular accumulation of three muropeptide precursor, with anti-inflammatory properties. They induce IL-10 secretion from human monocyte-derived dendritic cells and proved effective in reducing AIEC LF82 epithelial damage and IL-8 secretion in human intestinal resections. In addition, treatment with supernatants containing the muropeptide precursor reduces body weight loss and improves histological parameters in Dextran Sulfate Sodium (DSS)-treated mice. Until now, the source of peptidoglycan fragments was shown to come from the natural turnover of the peptidoglycan layer by endogenous peptidoglycan hydrolases. This is a report showing an ABC-transporter as a natural source of secreted muropeptide precursor and as an indirect player in epithelial barrier strengthening. The mechanism described here might represent an important component of the host immune homeostasis.
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Affiliation(s)
| | - Malgorzata Nepelska
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Food Microbial Ecology lab (Micalis), Université Paris-Saclay, Jouy-en-Josas78350, France
| | | | | | | | | | | | - Marc Maresca
- CNRS, Centrale Marseille, Institut des Sciences Moléculaires (iSm2) UMR7313, Aix Marseille Université, Marseille13013, France
| | - Cendrine Nicoletti
- CNRS, Centrale Marseille, Institut des Sciences Moléculaires (iSm2) UMR7313, Aix Marseille Université, Marseille13013, France
| | - Eric Di Pasquale
- Institut de NeuroPhysioPathologie (INP), Aix Marseille Université, UMR 7051, Marseille13005, France
| | | | | | - Stephen E. Girardin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ivo Gomperts Boneca
- Institut Pasteur, Université Paris Cité, CNRS Unité Mixe de Recherche 6047, INSERM U1306, Unité de Biologie et génétique de la paroi bactérienne, Paris75015, France
| | - Joel Doré
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Food Microbial Ecology lab (Micalis), Université Paris-Saclay, Jouy-en-Josas78350, France
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaGenoPolis, Université Paris-Saclay, Jouy-en-Josas78350, France
| | - Hervé M. Blottière
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech, Food Microbial Ecology lab (Micalis), Université Paris-Saclay, Jouy-en-Josas78350, France
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaGenoPolis, Université Paris-Saclay, Jouy-en-Josas78350, France
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Bianchini Massoni C, Strozzi F, Epifani E, Zenunaj G, Ucci A, Paladini I, Gasbarro V, Tusini N, Freyrie A. Real-world outcomes of Cook Zilver PTX in femoro-popliteal district from multicenter experience. INT ANGIOL 2023; 42:9-18. [PMID: 36534022 DOI: 10.23736/s0392-9590.22.04959-8] [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: 12/23/2022]
Abstract
BACKGROUND The purpose is to evaluate the follow-up outcomes after femoro-popliteal stenting with Cook Zilver PTX in a multicenter experience. METHODS Collected data from four Units were retrospectively joined and analyzed considering Zilver PTX deployed from August 2009 according to the instruction for use. Patient demographics, preoperative comorbidities, Rutherford classification, arterial characteristics and stent data were considered. Target lesion revascularization (TLR) was defined as reintervention performed for ≥50% diameter stenosis after recurrent clinical symptoms. Primary outcome was the freedom from TLR (ffTLR) and its risk factors. Secondary outcomes were primary patency (PP) of the stent, amputation-free survival (AFS) and their risk factors. RESULTS Considering 203 patients (mean age: 73.5 years ±10.6; male: 66.5%) and 263 stents (median 2 stents/patient, range 1-5stent/patient), chronic limb-threatening ischemia (CLTI) affected 154 patients (75.9%). The length of the treated lesion was <120 mm in 99 (48.8%), ≥120 mm and <200 mm in 65 (32%) and ≥200 mm in 39 (19.2%) cases, respectively; the reference vessel mean diameter was 5.5±0.7 mm; chronic total occlusion was treated in 153 (75.4%) patients, the popliteal artery was involved in 56 (27.6%) cases and prior endovascular intervention was performed in 27 (13.3%) cases. Two or more crural run-off vessels were patent in 124 (61.1%). Mean follow-up was 23.2 months ±21.3. At 1, 2 and 3 years, the ffTLR was 90.6±4.2%, 86.4±6.1% and 80.4±8.3%, respectively, and the PP was 85.6±5.0%, 74.2±7.6% and 72.7±8.2%, respectively. Negative prognostic factor for ffTLR and PP was the reference vessel diameter (P=0.001 and P<0.001, respectively). At 1, 2 and 3 years, the AFS was 81.8±6.0%, 75.5±7.1% and 74.2±7.5% respectively; coronary artery disease (P=0.041) and CLTI (P=0.011) resulted negative prognostic factors. CONCLUSIONS In the real-world practice, around 3/4 of patients were treated for CLTI. The rate of ffTLR is high, and PP is substantially lower. A small vessel diameter (<5 mm) is a negative factor for both ffTLR and PP. The rate of AFS is about 75% at 2 years and CLTI and coronary artery disease are negative prognostic factors.
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Affiliation(s)
- Claudio Bianchini Massoni
- Unit of Vascular Surgery, Department of Medicine and Surgery, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy -
| | - Francesco Strozzi
- Unit of Vascular Surgery, Department of General and Specialist Surgery, Arcispedale S. Maria Nuova, Reggio Emilia, Italy
| | - Enrico Epifani
- Unit of Radiology, Diagnostic Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Gladiol Zenunaj
- Unit of Vascular Surgery, Department of Surgery, Azienda Ospedaliero-Universitaria di Ferrara, Ferrara, Italy
| | - Alessandro Ucci
- Unit of Vascular Surgery, Department of Medicine and Surgery, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Ilaria Paladini
- Unit of Radiology, Diagnostic Department, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Vincenzo Gasbarro
- Unit of Vascular Surgery, Department of Surgery, Azienda Ospedaliero-Universitaria di Ferrara, Ferrara, Italy
| | - Nicola Tusini
- Unit of Vascular Surgery, Department of General and Specialist Surgery, Arcispedale S. Maria Nuova, Reggio Emilia, Italy
| | - Antonio Freyrie
- Unit of Vascular Surgery, Department of Medicine and Surgery, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
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Carpier JM, Talpin A, Kulakowski G, Dos Santos Leite A, Laviolette K, Noguerol J, Mersceman T, Garnier A, Gaal C, Pereira Oliveira C, Calderon C, Boullerot L, Malfroy M, Strozzi F, Gouttefangeas C, Adotevi O, Joffre O, Gamelas Magalhaes J, Chêne L, Bonny C. 180P Recalling pre-existing microbiota-specific T cells to target tumors. Immuno-Oncology and Technology 2022. [DOI: 10.1016/j.iotech.2022.100292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Tchitchek N, Nguekap Tchoumba O, Pires G, Dandou S, Campagne J, Churlaud G, Fourcade G, Hoffmann TW, Strozzi F, Gaal C, Bonny C, Le Chatelier E, Erlich SD, Sokol H, Klatzmann D. Low-dose interleukin-2 shapes a tolerogenic gut microbiota that improves autoimmunity and gut inflammation. JCI Insight 2022; 7:159406. [PMID: 35917175 PMCID: PMC9536277 DOI: 10.1172/jci.insight.159406] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/27/2022] [Indexed: 11/17/2022] Open
Abstract
Gut microbiota dysbiosis is associated with inflammatory bowel diseases and with cardiometabolic, neurological, and autoimmune diseases. Gut microbiota composition has a direct effect on the immune system, and vice versa, and it has a particular effect on Treg homeostasis. Low-dose IL-2 (IL-2LD) stimulates Tregs and is a promising treatment for autoimmune and inflammatory diseases. We aimed to evaluate the impact of IL-2LD on gut microbiota and correlatively on the immune system. We used 16S ribosomal RNA profiling and metagenomics to characterize gut microbiota of mice and humans treated or not with IL-2LD. We performed fecal microbiota transplantation (FMT) from IL-2LD–treated to naive recipient mice and evaluated its effects in models of gut inflammation and diabetes. IL-2LD markedly affected gut microbiota composition in mice and humans. Transfer of an IL-2–tuned microbiota by FMT protected C57BL/6J mice from dextran sulfate sodium–induced colitis and prevented diabetes in NOD mice. Metagenomic analyses highlighted a role for several species affected by IL-2LD and for microbial pathways involved in the biosynthesis of amino acids, short-chain fatty acids, and L-arginine. Our results demonstrate that IL-2LD induced changes in gut microbiota that are involved in the immunoregulatory effects of IL-2LD and suggest a crosstalk between Tregs and gut microbiota. These results provide potentially novel insight for understanding the mode of action of Treg-directed therapies.
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Affiliation(s)
- Nicolas Tchitchek
- Immunology-Immunopathology-Immunotherapy (i3), Sorbonne Université, Paris, France
| | | | - Gabriel Pires
- Immunology-Immunopathology-Immunotherapy (i3), Sorbonne Université, Paris, France
| | - Sarah Dandou
- Immunology-Immunopathology-Immunotherapy (i3), Sorbonne Université, Paris, France
| | - Julien Campagne
- Immunology-Immunopathology-Immunotherapy (i3), Sorbonne Université, Paris, France
| | - Guillaume Churlaud
- Immunology-Immunopathology-Immunotherapy (i3), Sorbonne Université, Paris, France
| | - Gwladys Fourcade
- Immunology-Immunopathology-Immunotherapy (i3), Sorbonne Université, Paris, France
| | - Thomas W Hoffmann
- Micalis Institute, Institut National de la Recherche Agronomique, University Paris-Saclay, Paris, France
| | | | | | | | | | | | - Harry Sokol
- Department of Gastroenterology and Inflammation, Saint-Antoine Hospital, Paris, France
| | - David Klatzmann
- Immunology-Immunopathology-Immunotherapy (I3), Sorbonne Université, Paris, France
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Chevalier G, Laveissière A, Desachy G, Barnich N, Sivignon A, Maresca M, Nicoletti C, Di Pasquale E, Martinez-Medina M, Simpson KW, Yajnik V, Sokol H, Plassais J, Strozzi F, Cervino A, Morra R, Bonny C. Blockage of bacterial FimH prevents mucosal inflammation associated with Crohn's disease. Microbiome 2021; 9:176. [PMID: 34425887 PMCID: PMC8383459 DOI: 10.1186/s40168-021-01135-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 04/27/2021] [Accepted: 07/01/2021] [Indexed: 05/14/2023]
Abstract
BACKGROUND An Escherichia coli (E. coli) pathotype with invasive properties, first reported by Darfeuille-Michaud and termed adherent-invasive E. coli (AIEC), was shown to be prevalent in up to half the individuals with Crohn's Disease (CD), suggesting that these bacteria could be involved in the pathophysiology of CD. Among the genes related to AIEC pathogenicity, fim has the potential to generate an inflammatory reaction from the intestinal epithelial cells and macrophages, as it interacts with TLR4, inducing the production of inflammatory cytokines independently of LPS. Therefore, targeting the bacterial adhesion of FimH-expressing bacteria seems a promising therapeutic approach, consisting of disarming bacteria without killing them, representing a selective strategy to suppress a potentially critical trigger of intestinal inflammation, without disturbing the intestinal microbiota. RESULTS We analyzed the metagenomic composition of the gut microbiome of 358 patients with CD from two different cohorts and characterized the presence of FimH-expressing bacteria. To assess the pathogenic role of FimH, we used human intestinal explants and tested a specific FimH blocker to prevent bacterial adhesion and associated inflammation. We observed a significant and disease activity-dependent enrichment of Enterobacteriaceae in the gut microbiome of patients with CD. Bacterial FimH expression was functionally confirmed in ileal biopsies from 65% of the patients with CD. Using human intestinal explants, we further show that FimH is essential for adhesion and to trigger inflammation. Finally, a specific FimH-blocker, TAK-018, inhibits bacterial adhesion to the intestinal epithelium and prevents inflammation, thus preserving mucosal integrity. CONCLUSIONS We propose that TAK-018, which is safe and well tolerated in humans, is a promising candidate for the treatment of CD and in particular in preventing its recurrence. Video abstract.
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Affiliation(s)
| | | | | | - Nicolas Barnich
- Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRA 2018, F-63000, Clermont-Ferrand, France
| | - Adeline Sivignon
- Université Clermont Auvergne, Inserm U1071, M2iSH, USC-INRA 2018, F-63000, Clermont-Ferrand, France
| | - Marc Maresca
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Cendrine Nicoletti
- Aix Marseille Université, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Eric Di Pasquale
- Aix-Marseille Université, CNRS, INP, Institut de Neurophysiopathologie, Marseille, France
| | | | | | - Vijay Yajnik
- GI Therapeutic Area Unit, Takeda Pharmaceuticals, Cambridge, MA, 02139, USA
| | - Harry Sokol
- Gastroenterology Department, Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Saint Antoine Hospital, 75012, Paris, France
- INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France
- Paris Center for Microbiome Medicine (PaCeMM) FHU, AP-HP, Paris, France
| | | | | | | | - Rachel Morra
- Enterome, 94-96 Avenue Ledru-Rollin, 75011, Paris, France
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Lomsadze A, Bonny C, Strozzi F, Borodovsky M. GeneMark-HM: improving gene prediction in DNA sequences of human microbiome. NAR Genom Bioinform 2021; 3:lqab047. [PMID: 34056597 PMCID: PMC8153819 DOI: 10.1093/nargab/lqab047] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 04/27/2021] [Accepted: 05/24/2021] [Indexed: 11/14/2022] Open
Abstract
Computational reconstruction of nearly complete genomes from metagenomic reads may identify thousands of new uncultured candidate bacterial species. We have shown that reconstructed prokaryotic genomes along with genomes of sequenced microbial isolates can be used to support more accurate gene prediction in novel metagenomic sequences. We have proposed an approach that used three types of gene prediction algorithms and found for all contigs in a metagenome nearly optimal models of protein-coding regions either in libraries of pre-computed models or constructed de novo. The model selection process and gene annotation were done by the new GeneMark-HM pipeline. We have created a database of the species level pan-genomes for the human microbiome. To create a library of models representing each pan-genome we used a self-training algorithm GeneMarkS-2. Genes initially predicted in each contig served as queries for a fast similarity search through the pan-genome database. The best matches led to selection of the model for gene prediction. Contigs not assigned to pan-genomes were analyzed by crude, but still accurate models designed for sequences with particular GC compositions. Tests of GeneMark-HM on simulated metagenomes demonstrated improvement in gene annotation of human metagenomic sequences in comparison with the current state-of-the-art gene prediction tools.
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Affiliation(s)
| | | | | | - Mark Borodovsky
- Gene Probe, Inc., 1106 Wrights Mill Ct, Atlanta, GA 30324, USA
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Burz SD, Monnoye M, Philippe C, Farin W, Ratziu V, Strozzi F, Paillarse JM, Chêne L, Blottière HM, Gérard P. Fecal Microbiota Transplant from Human to Mice Gives Insights into the Role of the Gut Microbiota in Non-Alcoholic Fatty Liver Disease (NAFLD). Microorganisms 2021; 9:microorganisms9010199. [PMID: 33477939 PMCID: PMC7833443 DOI: 10.3390/microorganisms9010199] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
Non-alcoholic fatty liver diseases (NAFLD) are associated with changes in the composition and metabolic activities of the gut microbiota. However, the causal role played by the gut microbiota in individual susceptibility to NAFLD and particularly at its early stage is still unclear. In this context, we transplanted the microbiota from a patient with fatty liver (NAFL) and from a healthy individual to two groups of mice. We first showed that the microbiota composition in recipient mice resembled the microbiota composition of their respective human donor. Following administration of a high-fructose, high-fat diet, mice that received the human NAFL microbiota (NAFLR) gained more weight and had a higher liver triglycerides level and higher plasma LDL cholesterol than mice that received the human healthy microbiota (HR). Metabolomic analyses revealed that it was associated with lower and higher plasma levels of glycine and 3-Indolepropionic acid in NAFLR mice, respectively. Moreover, several bacterial genera and OTUs were identified as differently represented in the NAFLR and HR microbiota and therefore potentially responsible for the different phenotypes observed. Altogether, our results confirm that the gut bacteria play a role in obesity and steatosis development and that targeting the gut microbiota may be a preventive or therapeutic strategy in NAFLD management.
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Affiliation(s)
- Sebastian D. Burz
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (S.D.B.); (M.M.); (C.P.); (H.M.B.)
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350 Jouy-en-Josas, France
| | - Magali Monnoye
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (S.D.B.); (M.M.); (C.P.); (H.M.B.)
| | - Catherine Philippe
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (S.D.B.); (M.M.); (C.P.); (H.M.B.)
| | - William Farin
- Enterome, 75011 Paris, France; (W.F.); (F.S.); (J.-M.P.); (L.C.)
| | - Vlad Ratziu
- INSERM UMRS 1138, Centre de Recherche des Cordeliers, Hôpital Pitié-Salpêtrière, Sorbonne-Université, 75006 Paris, France;
| | | | | | - Laurent Chêne
- Enterome, 75011 Paris, France; (W.F.); (F.S.); (J.-M.P.); (L.C.)
| | - Hervé M. Blottière
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (S.D.B.); (M.M.); (C.P.); (H.M.B.)
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350 Jouy-en-Josas, France
| | - Philippe Gérard
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (S.D.B.); (M.M.); (C.P.); (H.M.B.)
- Correspondence: ; Tel.: +33-134652428
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8
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Martinez-Medina M, Strozzi F, Ruiz Del Castillo B, Serrano-Morillas N, Ferrer Bustins N, Martínez-Martínez L. Antimicrobial Resistance Profiles of Adherent Invasive Escherichia coli Show Increased Resistance to β-Lactams. Antibiotics (Basel) 2020; 9:antibiotics9050251. [PMID: 32414140 PMCID: PMC7277491 DOI: 10.3390/antibiotics9050251] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
The adherent invasive Escherichia coli (AIEC) pathotype has been associated with the aetiology of Crohn’s disease (CD). Scarce reports have shown the antimicrobial resistance (AMR) profiles of AIEC. Despite antibiotics not being recommended to treat CD, antimicrobial therapy could be useful in stratified patients, such as AIEC carriers. We examined the antimicrobial resistance profiles of AIEC strains to identify which therapies could be effective or confer a risk for such patients. Phenotypic resistance to 30 antimicrobials was tested according to CLSI standards. AIEC (n = 22) and non-pathogenic E. coli (non-AIEC) strains (n = 37) isolated from the gut mucosa of 31 CD patients and 18 controls were studied. De novo genome sequencing was carried out for 39 of the 59 strains, and AMR genes were searched using the DeepARG database in these genomes and 33 additional AIEC publicly available genomes. The strains isolated from CD and controls showed similar phenotypic AMR profiles. The genomic analysis did not reveal an increased prevalence of AMR genes. However, AIEC strains were more frequently resistant to β-lactams than non-AIEC strains (11 AIEC (50%) and 5 non-AIEC (22%) strains were resistant to at least one β-lactam; p < 0.042). Two AIEC strains were resistant to expanded-spectrum cephalosporins. One strain carried a plasmid-mediated AmpC β-lactamase (CMY-69), and the other presented mutations in the promotor of the intrinsic chromosomal AmpC related to the hyperproduction of this enzyme. The rest of the strains were resistant to β-lactams not including expanded-spectrum cephalosporins. The majority carried TEM-related β-lactamases. Genomic analysis including external AIEC revealed that the gene sul1 encoding for sulphonamide resistance was more frequent in AIEC strains than non-AIEC strains (34.6% vs. 9.5%, p = 0.030). AMR in AIEC is a matter of concern regarding the putative implication of the pathotype in CD. The high proportion of AIEC resistant to β-lactams warrants caution about the risk there may be in the use of these antimicrobials in AIEC-colonized CD patients.
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Affiliation(s)
- Margarita Martinez-Medina
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
- Correspondence: ; Tel.: +34-972-418261
| | - Francesco Strozzi
- Data Science Departement, Enterome Biosciences S.A., 75011 Paris, France;
| | - Belén Ruiz Del Castillo
- Service of Microbiology, Hospital Universitario Marqués de Valdecilla, Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39008 Santander, Spain;
| | - Natalia Serrano-Morillas
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
| | - Nuria Ferrer Bustins
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
| | - Luis Martínez-Martínez
- Unit of Microbiology, University Hospital Reina Sofia, 14004 Córdoba, Spain;
- Maimonides Biomedical Research Institute, 14004 Córdoba, Spain
- Department of Agricultural Chemistry and Microbiology, University of Córdoba, 14004 Córdoba, Spain
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9
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Bustos‐Korts D, Dawson IK, Russell J, Tondelli A, Guerra D, Ferrandi C, Strozzi F, Nicolazzi EL, Molnar‐Lang M, Ozkan H, Megyeri M, Miko P, Çakır E, Yakışır E, Trabanco N, Delbono S, Kyriakidis S, Booth A, Cammarano D, Mascher M, Werner P, Cattivelli L, Rossini L, Stein N, Kilian B, Waugh R, van Eeuwijk FA. Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley. Plant J 2019; 99:1172-1191. [PMID: 31108005 PMCID: PMC6851764 DOI: 10.1111/tpj.14414] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/30/2019] [Accepted: 05/13/2019] [Indexed: 05/25/2023]
Abstract
Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.
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Affiliation(s)
- Daniela Bustos‐Korts
- BiometrisWageningen University and Research CentrePO Box 166700 ACWageningenThe Netherlands
| | - Ian K. Dawson
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Joanne Russell
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Alessandro Tondelli
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | - Davide Guerra
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | - Chiara Ferrandi
- PTP Science ParkVia Einstein, Loc. Cascina Codazza26900LodiItaly
| | | | | | - Marta Molnar‐Lang
- Agricultural InstituteCentre for Agricultural ResearchHungarian Academy of Sciences2462MartonvásárHungary
| | - Hakan Ozkan
- University of ÇukurovaFaculty of AgricultureDepartment of Field Crops01330AdanaTurkey
| | - Maria Megyeri
- Agricultural InstituteCentre for Agricultural ResearchHungarian Academy of Sciences2462MartonvásárHungary
| | - Peter Miko
- Agricultural InstituteCentre for Agricultural ResearchHungarian Academy of Sciences2462MartonvásárHungary
| | - Esra Çakır
- University of ÇukurovaFaculty of AgricultureDepartment of Field Crops01330AdanaTurkey
| | - Enes Yakışır
- Bahri Dagdas International Agricultural Research InstituteKonyaTurkey
| | - Noemi Trabanco
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Stefano Delbono
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | | | - Allan Booth
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Davide Cammarano
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466SeelandGermany
| | - Peter Werner
- KWS UK Ltd56 Church StreetThriplow, RoystonSG8 7REUK
| | - Luigi Cattivelli
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | - Laura Rossini
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466SeelandGermany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466SeelandGermany
- Present address:
Global Crop Diversity TrustPlatz der Vereinten Nationen 753113BonnGermany
| | - Robbie Waugh
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | - Fred A. van Eeuwijk
- BiometrisWageningen University and Research CentrePO Box 166700 ACWageningenThe Netherlands
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10
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Chene L, Sader CD, Magalhaes J, Strozzi F, Tibaldi L, Mendez C, Baeriswyl S, Laveissiere A, Bonny C. Abstract 1475: Microbiome derived peptides stimulate strong immune response against tumor associated antigens and trigger in vivo tumor regression after vaccination. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-1475] [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: 11/16/2022]
Abstract
Abstract
Peptide-based vaccination is an immunotherapeutic approach for the treatment of cancer that aims to deliver immunogenic peptides corresponding to specific tumor associated antigens to patients. Despite promising pre-clinical results in animal models, most cancer vaccination approach has not demonstrated unequivocal efficacy in patients. The ability of a peptide cancer vaccine to generate a strong immune response depends on several factors including the avidity of the peptide for the MHC complexes, the capacity of the antigen to be recognized by the immune system as self or non-self and the existence of T cell clones (naïve or memory) that are able to recognize those peptides. Gut colonization is one of the factor that drive the development of T cells and the presence of commensal specific memory T-cell is well reported in the literature and is now currently admitted. Several evidences support that these T cells can be re-activated and can migrate to inflammatory sites where the antigen is expressed. We have developed an innovative, microbiome-based approach for the development of therapeutic peptide cancer vaccines base. Our approach is based on the notion of molecular mimicry, by which a microbial derived peptide vaccine holding molecular similarity with a tumor-associated epitope would trigger a tumor-specific cytotoxic T cell immune response. By developing a dedicated in silico pipeline, we were able to identify bacterial antigens that could elicit strong immune response in WT mice. Furthermore, these bacterial antigens could be selected to generate T cell reactivity against self-peptides that are by themselves not immunogenic. The same pipeline was used to identify bacterial antigens able to bind human HLA-A2 and displaying molecular mimicry with selected tumor associated antigens. While HLA-A2 transgenic mice vaccination with tumor associated antigens doesn’t lead to immunization, vaccination with bacterial antigens results in a strong immune response against both bacterial peptides and selected tumor associated antigens. Furthermore, adoptive transfer of T cell from mice immunized with bacterial peptides into tumor engrafted nude mice leads to tumor control in the presence of Check Point Inhibitors. A first vaccine candidate targeting three different tumor drivers overexpressed in Glioblastoma and other solid tumors will enter the clinic this year.
Citation Format: Laurent Chene, Caroline Diveu Sader, Joao Magalhaes, Francesco Strozzi, Lorenzo Tibaldi, Celia Mendez, Simon Baeriswyl, Arnaud Laveissiere, Christophe Bonny. Microbiome derived peptides stimulate strong immune response against tumor associated antigens and trigger in vivo tumor regression after vaccination [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1475.
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11
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Wallace RJ, Sasson G, Garnsworthy PC, Tapio I, Gregson E, Bani P, Huhtanen P, Bayat AR, Strozzi F, Biscarini F, Snelling TJ, Saunders N, Potterton SL, Craigon J, Minuti A, Trevisi E, Callegari ML, Cappelli FP, Cabezas-Garcia EH, Vilkki J, Pinares-Patino C, Fliegerová KO, Mrázek J, Sechovcová H, Kopečný J, Bonin A, Boyer F, Taberlet P, Kokou F, Halperin E, Williams JL, Shingfield KJ, Mizrahi I. A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions. Sci Adv 2019; 5:eaav8391. [PMID: 31281883 PMCID: PMC6609165 DOI: 10.1126/sciadv.aav8391] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 05/30/2019] [Indexed: 05/19/2023]
Abstract
A 1000-cow study across four European countries was undertaken to understand to what extent ruminant microbiomes can be controlled by the host animal and to identify characteristics of the host rumen microbiome axis that determine productivity and methane emissions. A core rumen microbiome, phylogenetically linked and with a preserved hierarchical structure, was identified. A 39-member subset of the core formed hubs in co-occurrence networks linking microbiome structure to host genetics and phenotype (methane emissions, rumen and blood metabolites, and milk production efficiency). These phenotypes can be predicted from the core microbiome using machine learning algorithms. The heritable core microbes, therefore, present primary targets for rumen manipulation toward sustainable and environmentally friendly agriculture.
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Affiliation(s)
- R. John Wallace
- The Rowett Institute, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, UK
- Corresponding author. (R.J.W.); (I.M.)
| | - Goor Sasson
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Philip C. Garnsworthy
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Ilma Tapio
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Emma Gregson
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Paolo Bani
- Department of Animal Science, Food and Nutrition-DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Pekka Huhtanen
- Swedish University of Agricultural Sciences, Department of Agriculture for Northern Sweden, S-90 183 Umeå, Sweden
| | - Ali R. Bayat
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | | | | | - Timothy J. Snelling
- The Rowett Institute, University of Aberdeen, Ashgrove Road West, Aberdeen AB25 2ZD, UK
| | - Neil Saunders
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Sarah L. Potterton
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - James Craigon
- University of Nottingham, School of Biosciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Andrea Minuti
- Department of Animal Science, Food and Nutrition-DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Erminio Trevisi
- Department of Animal Science, Food and Nutrition-DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Maria L. Callegari
- Institute of Microbiology, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Fiorenzo Piccioli Cappelli
- Department of Animal Science, Food and Nutrition-DIANA, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
| | - Edward H. Cabezas-Garcia
- Swedish University of Agricultural Sciences, Department of Agriculture for Northern Sweden, S-90 183 Umeå, Sweden
| | - Johanna Vilkki
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Cesar Pinares-Patino
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Kateřina O. Fliegerová
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic
| | - Jakub Mrázek
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic
| | - Hana Sechovcová
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic
| | - Jan Kopečný
- Institute of Animal Physiology and Genetics, CAS, v.v.i., Vídeňská 1083, Prague 14220, Czech Republic
| | - Aurélie Bonin
- Laboratoire d'Ecologie Alpine, Domaine Universitaire de St Martin d'Hères CNRS, 38041 Grenoble, France
| | - Frédéric Boyer
- Laboratoire d'Ecologie Alpine, Domaine Universitaire de St Martin d'Hères CNRS, 38041 Grenoble, France
| | - Pierre Taberlet
- Laboratoire d'Ecologie Alpine, Domaine Universitaire de St Martin d'Hères CNRS, 38041 Grenoble, France
| | - Fotini Kokou
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel
| | - Eran Halperin
- Departments of Computer Science, Computational Medicine, Human Genetics, and Anesthesiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | | | - Kevin J. Shingfield
- Production Systems, Natural Resources Institute Finland (Luke), 31600 Jokioinen, Finland
| | - Itzhak Mizrahi
- Department of Life Sciences and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva, Israel
- Corresponding author. (R.J.W.); (I.M.)
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12
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Mencaglia L, Cerboneschi M, Ciociola F, Ricci S, Mancioppi I, Ambrosino V, Ferrandi C, Strozzi F, Piffanelli P, Grasselli A. Characterization of microRNA in the follicular fluid of patients undergoing assisted reproductive technology. J BIOL REG HOMEOS AG 2019; 33:946-956. [PMID: 31190512] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Female fertility plays a decisive role in the reproduction of mammals, with related issues that include oocyte or embryo quality, establishment of pregnancy, and the physiology of the tissues that contribute to reproduction and metabolic disorders associated with reproductive failure. Although reproductive failure may be attributed to various factors in different species, female infertility is largely controlled by a number of molecular signals that can be regulated in a cycle- and tissue-dependent manner.
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Affiliation(s)
- L Mencaglia
- Azienda USL Sud Est, Regione Toscana Centro di PMA Ospedale Santa Margherita La Fratta Cortona, Arezzo, Italy
| | - M Cerboneschi
- NEXT Genomics Srl, Prato, Italy
- Department of AgriFood Production and Envi¬ronmental Sciences (DISPAA), University of Florence, Sesto Fiorentino (Florence), Italy
| | - F Ciociola
- Azienda USL Sud Est, Regione Toscana Centro di PMA Ospedale Santa Margherita La Fratta Cortona, Arezzo, Italy
| | - S Ricci
- Azienda USL Sud Est, Regione Toscana Centro di PMA Ospedale Santa Margherita La Fratta Cortona, Arezzo, Italy
| | - I Mancioppi
- Azienda USL Sud Est, Regione Toscana Centro di PMA Ospedale Santa Margherita La Fratta Cortona, Arezzo, Italy
| | - V Ambrosino
- Azienda USL Sud Est, Regione Toscana Centro di PMA Ospedale Santa Margherita La Fratta Cortona, Arezzo, Italy
| | | | | | | | - A Grasselli
- IBSA Farmaceutici Italia Srl, Medical Scientific Division, Lodi, Italy
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13
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Strozzi F, Janssen R, Wurmus R, Crusoe MR, Githinji G, Di Tommaso P, Belhachemi D, Möller S, Smant G, de Ligt J, Prins P. Scalable Workflows and Reproducible Data Analysis for Genomics. Methods Mol Biol 2019; 1910:723-745. [PMID: 31278683 PMCID: PMC7613310 DOI: 10.1007/978-1-4939-9074-0_24] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Biological, clinical, and pharmacological research now often involves analyses of genomes, transcriptomes, proteomes, and interactomes, within and between individuals and across species. Due to large volumes, the analysis and integration of data generated by such high-throughput technologies have become computationally intensive, and analysis can no longer happen on a typical desktop computer.In this chapter we show how to describe and execute the same analysis using a number of workflow systems and how these follow different approaches to tackle execution and reproducibility issues. We show how any researcher can create a reusable and reproducible bioinformatics pipeline that can be deployed and run anywhere. We show how to create a scalable, reusable, and shareable workflow using four different workflow engines: the Common Workflow Language (CWL), Guix Workflow Language (GWL), Snakemake, and Nextflow. Each of which can be run in parallel.We show how to bundle a number of tools used in evolutionary biology by using Debian, GNU Guix, and Bioconda software distributions, along with the use of container systems, such as Docker, GNU Guix, and Singularity. Together these distributions represent the overall majority of software packages relevant for biology, including PAML, Muscle, MAFFT, MrBayes, and BLAST. By bundling software in lightweight containers, they can be deployed on a desktop, in the cloud, and, increasingly, on compute clusters.By bundling software through these public software distributions, and by creating reproducible and shareable pipelines using these workflow engines, not only do bioinformaticians have to spend less time reinventing the wheel but also do we get closer to the ideal of making science reproducible. The examples in this chapter allow a quick comparison of different solutions.
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14
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Pasquariello R, Fernandez-Fuertes B, Strozzi F, Pizzi F, Mazza R, Lonergan P, Gandolfi F, Williams JL. Profiling bovine blastocyst microRNAs using deep sequencing. Reprod Fertil Dev 2018; 29:1545-1555. [PMID: 27623773 DOI: 10.1071/rd16110] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/24/2016] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are known to control several reproductive functions, including oocyte maturation, implantation and early embryonic development. Recent advances in deep sequencing have allowed the analysis of all miRNAs of a sample. However, when working with embryos, due to the low RNA content, miRNA profiling is challenging because of the relatively large amount of total RNA required for library preparation protocols. In the present study we compared three different procedures for RNA extraction and prepared libraries using pools of 30 bovine blastocysts. In total, 14 of the 15 most abundantly expressed miRNAs were common to all three procedures. Furthermore, using miRDeep discovery and annotation software (Max Delbrück Center), we identified 1363 miRNA sequences, of which bta-miR-10b and bta-miR-378 were the most abundant. Most of the 179 genes identified as experimentally validated (86.6%) or predicted targets (13.4%) were associated with cancer canonical pathways. We conclude that reliable analysis of bovine blastocyst miRNAs can be achieved using the procedures described herein. The repeatability of the results across different procedures and independent replicates, as well as their consistency with results obtained in other species, support the biological relevance of these miRNAs and of the gene pathways they modulate in early embryogenesis.
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Affiliation(s)
- R Pasquariello
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territori, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - B Fernandez-Fuertes
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
| | - F Strozzi
- Parco Tecnologico Padano, Via Einstein Albert, 26900, Lodi, Italy
| | - F Pizzi
- Istituto di Biologia e Biotecnologia Agraria - Consiglio Nazionale delle Ricerche, Via Einstein Albert, 26900, Lodi, Italy
| | - R Mazza
- Associazione Italiana Allevatori, Via Bergamo 292, 26100, Cremona, Italy
| | - P Lonergan
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Dublin, Ireland
| | - F Gandolfi
- Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territori, Università degli Studi di Milano, Via Celoria 2, 20133, Milan, Italy
| | - J L Williams
- School of Animal and Veterinary Sciences, Faculty of Science, University of Adelaide, Roseworthy, SA 5371, Australia
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15
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Williams JL, Iamartino D, Pruitt KD, Sonstegard T, Smith TPL, Low WY, Biagini T, Bomba L, Capomaccio S, Castiglioni B, Coletta A, Corrado F, Ferré F, Iannuzzi L, Lawley C, Macciotta N, McClure M, Mancini G, Matassino D, Mazza R, Milanesi M, Moioli B, Morandi N, Ramunno L, Peretti V, Pilla F, Ramelli P, Schroeder S, Strozzi F, Thibaud-Nissen F, Zicarelli L, Ajmone-Marsan P, Valentini A, Chillemi G, Zimin A. Genome assembly and transcriptome resource for river buffalo, Bubalus bubalis (2n = 50). Gigascience 2018; 6:1-6. [PMID: 29048578 PMCID: PMC5737279 DOI: 10.1093/gigascience/gix088] [Citation(s) in RCA: 33] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/28/2017] [Indexed: 11/12/2022] Open
Abstract
Water buffalo is a globally important species for agriculture and local economies. A de novo assembled, well-annotated reference sequence for the water buffalo is an important prerequisite for studying the biology of this species, and is necessary to manage genetic diversity and to use modern breeding and genomic selection techniques. However, no such genome assembly has been previously reported. There are 2 species of domestic water buffalo, the river (2 n = 50) and the swamp (2 n = 48) buffalo. Here we describe a draft quality reference sequence for the river buffalo created from Illumina GA and Roche 454 short read sequences using the MaSuRCA assembler. The assembled sequence is 2.83 Gb, consisting of 366 983 scaffolds with a scaffold N50 of 1.41 Mb and contig N50 of 21 398 bp. Annotation of the genome was supported by transcriptome data from 30 tissues and identified 21 711 predicted protein coding genes. Searches for complete mammalian BUSCO gene groups found 98.6% of curated single copy orthologs present among predicted genes, which suggests a high level of completeness of the genome. The annotated sequence is available from NCBI at accession GCA_000471725.1.
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Affiliation(s)
- John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.,Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy
| | - Daniela Iamartino
- AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy.,Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy
| | - Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Tad Sonstegard
- Recombinetics, 1246 University Ave W, St Paul, MN 55104, USA
| | - Timothy P L Smith
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Wai Yee Low
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia
| | - Tommaso Biagini
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, S. Giovanni Rotondo, Italy
| | - Lorenzo Bomba
- Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy.,Human Genetics, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, CB10 1HH, UK
| | - Stefano Capomaccio
- Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy
| | - Bianca Castiglioni
- CNR, Istituto di Biologia e Biotecnologia Agraria Via Einstein, 26900 Lodi, Italy
| | - Angelo Coletta
- ANASB Associazione Nazionale Allevatori Specie Bufalina, Centuran, Caserta, Italy
| | - Federica Corrado
- IZSM, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2-80055, Portici (NA), Italy
| | - Fabrizio Ferré
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Belmeloro 8/2, 40126 Bologna, Italy
| | - Leopoldo Iannuzzi
- CNR, Istituto Per Il Sistema Produzione Animale In Ambiente Mediterraneo, Via Argine, 1085, 80147 Napoli, Italy
| | - Cynthia Lawley
- Illumina, Inc. 499 Illinois St. Suite 210, San Francisco, CA 94158, USA
| | - Nicolò Macciotta
- Università degli Studi di Sassari, Piazza Università 21, 07100 Sassari, Italy
| | - Matthew McClure
- USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350, USA.,Irish Cattle Breeding Federation, Highfield House, Shinagh, Bandon, Co., Cork, P72 × 050, Ireland
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7, 56125 Pisa, Italy
| | - Donato Matassino
- ConSDABI, Consorzio per la Sperimentazione, Divulgazione e Applicazione di Biotecniche Innovative, Contrada Piano Cappelle, Benevento (BN), Italy
| | - Raffaele Mazza
- AIA-LGS, Associazione Italiana Allevatori, Laboratorio Genetica e Servizi, Via Bergamo 292, 26100 Cremona (CR), Italy
| | - Marco Milanesi
- Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy
| | - Bianca Moioli
- CRA Centro di Ricerca per la Produzione delle Carni ed il Miglioramento Genetico, Via Salaria 31, 00015, Montorotondo, Italy
| | | | - Luigi Ramunno
- Dipartimento di Agraria, Università degli Studi di Napoli "Federico II", via Università 100, 80055 Portici (NA), Italy
| | - Vincenzo Peretti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, 80137 Napoli, Italy
| | - Fabio Pilla
- Department of Agriculture, Environment and Food, University of Molise
| | - Paola Ramelli
- Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy
| | - Steven Schroeder
- USDA, ARS, Animal Genomics and Improvement Laboratory, Building 306 BARC-East, Beltsville, MD 20705-2350, USA
| | - Francesco Strozzi
- Parco Tecnologico Padano, Via Einstein, 26500, Lodi, Italy.,Enterome, 94-96 Avenue Ledru-Rollin, 75011 Paris, France
| | - Francoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Luigi Zicarelli
- Department of Agriculture, Environment and Food, University of Molise
| | - Paolo Ajmone-Marsan
- Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza PC, Italy
| | - Alessio Valentini
- Universit à della Tuscia, Via S. Camillo de Lellis, 01100 Viterbo, Italy
| | - Giovanni Chillemi
- SCAI Super Computing Applications and Innovation Department, Cineca, Via dei Tizii 6, 00185, Rome
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16
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Ronchetti D, Agnelli L, Taiana E, Galletti S, Manzoni M, Todoerti K, Musto P, Strozzi F, Neri A. Distinct lncRNA transcriptional fingerprints characterize progressive stages of multiple myeloma. Oncotarget 2018; 7:14814-30. [PMID: 26895470 PMCID: PMC4924754 DOI: 10.18632/oncotarget.7442] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/29/2016] [Indexed: 12/25/2022] Open
Abstract
Although many efforts have recently contributed to improve our knowledge of molecular pathogenesis of multiple myeloma (MM), the role and significance of long non-coding RNAs (lncRNAs) in plasma cells (PC) malignancies remains virtually absent. To this aim, we developed a custom annotation pipeline of microarray data investigating lncRNA expression in PCs from 20 monoclonal gammopathies of undetermined significance, 33 smoldering MM, 170 MM, and 36 extra-medullary MMs/plasma cell leukemia patients, and 9 healthy donors. Our study identified 31 lncRNAs deregulated in tumor samples compared to normal controls; among these, the upregulation of MALAT1 appeared associated in MM patients with molecular pathways involving cell cycle regulation, p53-mediated DNA damage response, and mRNA maturation processes. Furthermore, we found 21 lncRNAs whose expression were progressively deregulated trough the more aggressive stages of PC dyscrasia, suggesting a possible role in the progression of the disease. Finally, in the context of molecular heterogeneity of MM, we identified a transcriptional fingerprint in hyperdiploid patients, characterized by the upregulation of lncRNAs/pseudogenes related to ribosomal protein genes, known to be upregulated in this molecular group. Overall, the data provides an important resource for future studies on the functions of lncRNAs in the pathology.
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Affiliation(s)
- Domenica Ronchetti
- Department of Oncology and Hemato-Oncology, University of Milano, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Agnelli
- Department of Oncology and Hemato-Oncology, University of Milano, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Elisa Taiana
- Department of Oncology and Hemato-Oncology, University of Milano, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Serena Galletti
- Department of Oncology and Hemato-Oncology, University of Milano, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Martina Manzoni
- Department of Oncology and Hemato-Oncology, University of Milano, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Katia Todoerti
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, Potenza, Italy
| | - Pellegrino Musto
- Laboratory of Pre-Clinical and Translational Research, IRCCS-CROB, Referral Cancer Center of Basilicata, Rionero in Vulture, Potenza, Italy
| | | | - Antonino Neri
- Department of Oncology and Hemato-Oncology, University of Milano, Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
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Marino R, Capoferri R, Panelli S, Minozzi G, Strozzi F, Trevisi E, Snel GGM, Ajmone-Marsan P, Williams JL. Johne's disease in cattle: an in vitro model to study early response to infection of Mycobacterium avium subsp. paratuberculosis using RNA-seq. Mol Immunol 2017; 91:259-271. [PMID: 28988040 DOI: 10.1016/j.molimm.2017.08.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/07/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]
Abstract
Johne's disease is a chronic granulomatous enteritis caused by Mycobacterium avium subsp. paratubercolosis (MAP) which affects ruminants worldwide and has a significant economic impact. MAP has also been associated with human Crohn's disease, although this connection is not well established. MAP is highly adapted for survival within host macrophages and prevents macrophage activation, blocks phagosome acidification and maturation, and attenuates presentation of antigens to the immune system. The consequence is a very long silent infection before clinical signs are observed. The present work examined the transcriptome of bovine monocyte-derived macrophages (MDM) infected with the L1 strain of MAP at 2h, 6h and 24h post infection using RNA-seq. Pathway over-representation analysis of genes differentially expressed between infected vs. control MDM identified that immune related pathways were affected. Genes belonging to the cytokine-cytokine receptor interaction pathway and members of the JAK-STAT pathway, which is involved in the regulation of immune response, were up-regulated. However, in parallel inhibitors of immune functions were activated, including suppressor of cytokine signaling (SOCS) and cytokine-inducible SH2-containing protein (CISH), which most likely suppresses IFNγ and the JAK/STAT signaling cascade in infected MDM, which may favour MAP survival. After exposure, macrophages phagocytise pathogens, activate the complement cascade and the adaptive immune system through the antigen presentation process. However, data presented here suggest that genes related to phagocytosis and lysosome function are down regulated in MAP infected MDM. Genes of MHC class II and complement pathway were also down-regulated. This study therefore shows that MAP infection is associated with changes in expression of genes related to the host immune response that may affect its ability to survive and multiply inside the host cell.
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Affiliation(s)
- Rosanna Marino
- CREA Research Centre for Animal Production and Aquaculture, Via Antonio Lombardo 11, 26900 Lodi, Italy; Istituto Sperimentale Italiano "Lazzaro Spallanzani", 26027, Rivolta d'Adda, Cremona, Italy; Institute of Zootechnics, Università Cattolica del S. Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy.
| | - Rossana Capoferri
- Istituto Sperimentale Italiano "Lazzaro Spallanzani", 26027, Rivolta d'Adda, Cremona, Italy.
| | - Simona Panelli
- Parco Tecnologico Padano, via Einstein, 26900 Lodi, Italy.
| | | | | | - Erminio Trevisi
- Institute of Zootechnics, Università Cattolica del S. Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; Nutrigenomics and Proteomic Research Center - PRONUTRIGEN, Università Cattolica del S. Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy.
| | | | - Paolo Ajmone-Marsan
- Institute of Zootechnics, Università Cattolica del S. Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy; Nutrigenomics and Proteomic Research Center - PRONUTRIGEN, Università Cattolica del S. Cuore, via Emilia Parmense 84, 29122 Piacenza, Italy.
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA 5371, Australia.
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Wallace RJ, Snelling TJ, McCartney CA, Tapio I, Strozzi F. Erratum to: Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism. Genet Sel Evol 2017; 49:27. [PMID: 28245807 PMCID: PMC5330120 DOI: 10.1186/s12711-017-0304-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 02/22/2017] [Indexed: 12/02/2022] Open
Affiliation(s)
- Robert J Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD, UK.
| | - Timothy J Snelling
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD, UK
| | - Christine A McCartney
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD, UK
| | - Ilma Tapio
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
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Maschietto V, Colombi C, Pirona R, Pea G, Strozzi F, Marocco A, Rossini L, Lanubile A. QTL mapping and candidate genes for resistance to Fusarium ear rot and fumonisin contamination in maize. BMC Plant Biol 2017; 17:20. [PMID: 28109190 PMCID: PMC5251214 DOI: 10.1186/s12870-017-0970-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 01/02/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Fusarium verticillioides is a common maize pathogen causing ear rot (FER) and contamination of the grains with the fumonisin B1 (FB1) mycotoxin. Resistance to FER and FB1 contamination are quantitative traits, affected by environmental conditions, and completely resistant maize genotypes to the pathogen are so far unknown. In order to uncover genomic regions associated to reduced FER and FB1 contamination and identify molecular markers for assisted selection, an F2:3 population of 188 progenies was developed crossing CO441 (resistant) and CO354 (susceptible) genotypes. FER severity and FB1 contamination content were evaluated over 2 years and sowing dates (early and late) in ears artificially inoculated with F. verticillioides by the use of either side-needle or toothpick inoculation techniques. RESULTS Weather conditions significantly changed in the two phenotyping seasons and FER and FB1 content distribution significantly differed in the F3 progenies according to the year and the sowing time. Significant positive correlations (P < 0.01) were detected between FER and FB1 contamination, ranging from 0.72 to 0.81. A low positive correlation was determined between FB1 contamination and silking time (DTS). A genetic map was generated for the cross, based on 41 microsatellite markers and 342 single nucleotide polymorphisms (SNPs) derived from Genotyping-by-Sequencing (GBS). QTL analyses revealed 15 QTLs for FER, 17 QTLs for FB1 contamination and nine QTLs for DTS. Eight QTLs located on linkage group (LG) 1, 2, 3, 6, 7 and 9 were in common between FER and FB1, making possible the selection of genotypes with both low disease severity and low fumonisin contamination. Moreover, five QTLs on LGs 1, 2, 4, 5 and 9 located close to previously reported QTLs for resistance to other mycotoxigenic fungi. Finally, 24 candidate genes for resistance to F. verticillioides are proposed combining previous transcriptomic data with QTL mapping. CONCLUSIONS This study identified a set of QTLs and candidate genes that could accelerate breeding for resistance of maize lines showing reduced disease severity and low mycotoxin contamination determined by F. verticillioides.
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Affiliation(s)
- Valentina Maschietto
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Cinzia Colombi
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900 Lodi, Italy
| | - Raul Pirona
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900 Lodi, Italy
- Institute of Agricultural Biology and Biotechnology, CNR, Via Bassini 15, 20133 Milano, Italy
| | - Giorgio Pea
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900 Lodi, Italy
| | - Francesco Strozzi
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900 Lodi, Italy
| | - Adriano Marocco
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Laura Rossini
- Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900 Lodi, Italy
- Department of Agricultural and Environmental Sciences Production, Landscape, Agroenergy, Università degli Studi di Milano, Via Celoria 2, 20133 Milano, Italy
| | - Alessandra Lanubile
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
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20
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Tapio I, Snelling TJ, Strozzi F, Wallace RJ. The ruminal microbiome associated with methane emissions from ruminant livestock. J Anim Sci Biotechnol 2017; 8:7. [PMID: 28123698 PMCID: PMC5244708 DOI: 10.1186/s40104-017-0141-0] [Citation(s) in RCA: 167] [Impact Index Per Article: 23.9] [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: 07/31/2016] [Accepted: 01/03/2017] [Indexed: 02/06/2023] Open
Abstract
Methane emissions from ruminant livestock contribute significantly to the large environmental footprint of agriculture. The rumen is the principal source of methane, and certain features of the microbiome are associated with low/high methane phenotypes. Despite their primary role in methanogenesis, the abundance of archaea has only a weak correlation with methane emissions from individual animals. The composition of the archaeal community appears to have a stronger effect, with animals harbouring the Methanobrevibacter gottschalkii clade tending to be associated with greater methane emissions. Ciliate protozoa produce abundant H2, the main substrate for methanogenesis in the rumen, and their removal (defaunation) results in an average 11% lower methane emissions in vivo, but the results are not consistent. Different protozoal genera seem to result in greater methane emissions, though community types (A, AB, B and O) did not differ. Within the bacteria, three different ‘ruminotypes’ have been identified, two of which predispose animals to have lower methane emissions. The two low-methane ruminotypes are generally characterized by less abundant H2-producing bacteria. A lower abundance of Proteobacteria and differences in certain Bacteroidetes and anaerobic fungi seem to be associated with high methane emissions. Rumen anaerobic fungi produce abundant H2 and formate, and their abundance generally corresponds to the level of methane emissions. Thus, microbiome analysis is consistent with known pathways for H2 production and methanogenesis, but not yet in a predictive manner. The production and utilisation of formate by the ruminal microbiota is poorly understood and may be a source of variability between animals.
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Affiliation(s)
- Ilma Tapio
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
| | - Timothy J Snelling
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD UK
| | | | - R John Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD UK
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21
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Wallace RJ, Snelling TJ, McCartney CA, Tapio I, Strozzi F. Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism. Genet Sel Evol 2017; 49:9. [PMID: 28093073 PMCID: PMC5240273 DOI: 10.1186/s12711-017-0285-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 07/09/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022] Open
Abstract
Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments. Few metagenomics studies have been directly related to GHG emissions. In these studies, the main genes that differed in abundance between high and low methane emitters included archaeal genes involved in methanogenesis, with others that were not apparently related to methane metabolism. Unlike the taxonomic analysis up to now, the gene sets from metagenomes may have predictive value. Furthermore, metagenomic analysis predicts metabolic function better than only a taxonomic description, because different taxa share genes with the same function. Metatranscriptomics, the study of mRNA transcript abundance, should help to understand the dynamic of microbial activity rather than the gene abundance; to date, only one study has related the expression levels of methanogenic genes to methane emissions, where gene abundance failed to do so. Metaproteomics describes the proteins present in the ecosystem, and is therefore arguably a better indication of microbial metabolism. Both two-dimensional polyacrylamide gel electrophoresis and shotgun peptide sequencing methods have been used for ruminal analysis. In our unpublished studies, both methods showed an abundance of archaeal methanogenic enzymes, but neither was able to discriminate high and low emitters. Metabolomics can take several forms that appear to have predictive value for methane emissions; ruminal metabolites, milk fatty acid profiles, faecal long-chain alcohols and urinary metabolites have all shown promising results. Rumen microbial amino acid metabolism lies at the root of excessive nitrogen emissions from ruminants, yet only indirect inferences for nitrogen emissions can be drawn from meta-omics studies published so far. Annotation of meta-omics data depends on databases that are generally weak in rumen microbial entries. The Hungate 1000 project and Global Rumen Census initiatives are therefore essential to improve the interpretation of sequence/metabolic information.
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Affiliation(s)
- Robert J Wallace
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD, UK.
| | - Timothy J Snelling
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD, UK
| | - Christine A McCartney
- Rowett Institute of Nutrition and Health, University of Aberdeen, Foresterhill, Aberdeen, AB16 5BD, UK
| | - Ilma Tapio
- Green Technology, Natural Resources Institute Finland, Jokioinen, Finland
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22
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Whitacre LK, Hoff JL, Schnabel RD, Albarella S, Ciotola F, Peretti V, Strozzi F, Ferrandi C, Ramunno L, Sonstegard TS, Williams JL, Taylor JF, Decker JE. Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis. Sci Rep 2017; 7:39719. [PMID: 28045068 PMCID: PMC5206621 DOI: 10.1038/srep39719] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 08/08/2016] [Accepted: 11/25/2016] [Indexed: 12/30/2022] Open
Abstract
Recent strong selection for dairy traits in water buffalo has been associated with higher levels of inbreeding, leading to an increase in the prevalence of genetic diseases such as transverse hemimelia (TH), a congenital developmental abnormality characterized by absence of a variable distal portion of the hindlimbs. Limited genomic resources available for water buffalo required an original approach to identify genetic variants associated with the disease. The genomes of 4 bilateral and 7 unilateral affected cases and 14 controls were sequenced. A concordance analysis of SNPs and INDELs requiring homozygosity unique to all unilateral and bilateral cases revealed two genes, WNT7A and SMARCA4, known to play a role in embryonic hindlimb development. Additionally, SNP alleles in NOTCH1 and RARB were homozygous exclusively in the bilateral cases, suggesting an oligogenic mode of inheritance. Homozygosity mapping by whole genome de novo assembly also supported oligogenic inheritance; implicating 13 genes involved in hindlimb development in bilateral cases and 11 in unilateral cases. A genome-wide association study (GWAS) predicted additional modifier genes. Although our data show a complex inheritance of TH, we predict that homozygous variants in WNT7A and SMARCA4 are necessary for expression of TH and selection against these variants should eradicate TH.
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Affiliation(s)
- Lynsey K Whitacre
- Informatics Institute, University of Missouri, Columbia, Missouri, USA.,Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Robert D Schnabel
- Informatics Institute, University of Missouri, Columbia, Missouri, USA.,Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Sara Albarella
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Francesca Ciotola
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | - Vincenzo Peretti
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Naples, Italy
| | | | | | - Luigi Ramunno
- Department of Agriculture, University of Naples Federico II, Portici, Napoli, Italy
| | | | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, Australia
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
| | - Jared E Decker
- Informatics Institute, University of Missouri, Columbia, Missouri, USA.,Division of Animal Sciences, University of Missouri, Columbia, Missouri, USA
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23
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Licciardello G, Ferraro R, Russo M, Strozzi F, Catara AF, Bella P, Catara V. Transcriptome analysis of Pseudomonas mediterranea and P. corrugata plant pathogens during accumulation of medium-chain-length PHAs by glycerol bioconversion. N Biotechnol 2016; 37:39-47. [PMID: 27445200 DOI: 10.1016/j.nbt.2016.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Revised: 06/11/2016] [Accepted: 07/16/2016] [Indexed: 11/30/2022]
Abstract
Pseudomonas corrugata and P. mediterranea are soil inhabitant bacteria, generally living as endophytes on symptomless plants and bare soil, but also capable of causing plant diseases. They share a similar genome size and a high proteome similarity. P. corrugata produces many biomolecules which play an important role in bacterial cell survival and fitness. Both species produce different medium-chain-length PHAs (mcl-PHAs) from the bioconversion of glycerol to a transparent film in P. mediterranea and a sticky elastomer in P. corrugata. In this work, using RNA-seq we investigated the transcriptional profiles of both bacteria at the early stationary growth phase with glycerol as the carbon source. Quantitative analysis of P. mediterranea transcripts versus P. corrugata revealed that 1756 genes were differentially expressed. A total of 175 genes were significantly upregulated in P. mediterranea, while 217 were downregulated. The largest group of upregulated genes was related to transport systems and stress response, energy and central metabolism, and carbon metabolism. Expression levels of most genes coding for enzymes related to PHA biosynthesis and central metabolic pathways showed no differences or only slight variations in pyruvate metabolism. The most relevant result was the significantly increased expression in P. mediterranea of genes involved in alginate production, an important exopolysaccharide, which in other Pseudomonas spp. plays a key role as a virulence factor or in stress tolerance and shows many industrial applications. In conclusion, the results provide useful information on the co-production of mcl-PHAs and alginate from glycerol as carbon source by P. mediterranea in the design of new strategies of genetic regulation to improve the yield of bioproducts or bacterial fitness.
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Affiliation(s)
- Grazia Licciardello
- Parco Scientifico e Tecnologico della Sicilia s.c.p.a. Via V. Lancia 57, 95121 Catania, Italy.
| | - Rosario Ferraro
- Parco Scientifico e Tecnologico della Sicilia s.c.p.a. Via V. Lancia 57, 95121 Catania, Italy
| | - Marcella Russo
- Parco Scientifico e Tecnologico della Sicilia s.c.p.a. Via V. Lancia 57, 95121 Catania, Italy
| | - Francesco Strozzi
- Parco Tecnologico Padano, via Einstein - Loc. Cascina Codazza 26900, Lodi, Italy
| | - Antonino F Catara
- Parco Scientifico e Tecnologico della Sicilia s.c.p.a. Via V. Lancia 57, 95121 Catania, Italy
| | - Patrizia Bella
- Dipartimento di Scienze Agrarie e Forestali Università degli Studi di Palermo, Viale delle Scienze, 13, 90128, Palermo, Italy
| | - Vittoria Catara
- Dipartimento di Agricoltura, Alimentazione e Ambiente, Università degli Studi di Catania, Via S. Sofia 100, 95123 Catania Italy
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24
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Bolleman JT, Mungall CJ, Strozzi F, Baran J, Dumontier M, Bonnal RJP, Buels R, Hoehndorf R, Fujisawa T, Katayama T, Cock PJA. FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation. J Biomed Semantics 2016; 7:39. [PMID: 27296299 PMCID: PMC4907002 DOI: 10.1186/s13326-016-0067-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 03/17/2016] [Indexed: 11/18/2022] Open
Abstract
Background Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. Description We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Conclusions Our ontology allows users to uniformly describe – and potentially merge – sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.
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Affiliation(s)
- Jerven T Bolleman
- Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1 rue Michel, Servet, Geneva 4, 1211, Switzerland.
| | | | | | - Joachim Baran
- CODAMONO, 5-121 Marion Street, Toronto, M6R 1E6, Ontario, Canada
| | - Michel Dumontier
- Stanford Center for Biomedical Informatics Research, 1265 Welch Road, Room X223, Stanford, 94305-5479, CA, US
| | - Raoul J P Bonnal
- Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Robert Buels
- University of California, Berkeley, Berkeley, CA, USA
| | | | - Takatomo Fujisawa
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, 1111 Yata, Mishima, Shizuoka, 411-08540, Japan
| | - Toshiaki Katayama
- Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
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25
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Hamzić E, Kjærup RB, Mach N, Minozzi G, Strozzi F, Gualdi V, Williams JL, Chen J, Wattrang E, Buitenhuis B, Juul-Madsen HR, Dalgaard TS. RNA sequencing-based analysis of the spleen transcriptome following infectious bronchitis virus infection of chickens selected for different mannose-binding lectin serum concentrations. BMC Genomics 2016; 17:82. [PMID: 26819139 PMCID: PMC4729133 DOI: 10.1186/s12864-016-2403-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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: 08/24/2015] [Accepted: 01/18/2016] [Indexed: 12/30/2022] Open
Abstract
Background Avian infectious bronchitis is a highly contagious disease of the upper-respiratory tract caused by infectious bronchitis virus (IBV). Understanding the molecular mechanisms involved in the interaction between innate and adaptive immune responses to IBV infection is a crucial element for further improvements in strategies to control IB. To this end, two chicken lines, selected for high (L10H line) and low (L10L line) serum concentration of mannose-binding lectin (MBL) were studied. In total, 32 birds from each line were used. Sixteen birds from each line were infected with IBV and sixteen were left uninfected. Eight uninfected and infected birds from each line were euthanized at 1 and 3 weeks post infection. RNA sequencing was performed on spleen samples from all 64 birds and differential gene expression analysis was performed for four comparisons: L10L line versus L10H line for uninfected birds at weeks 1 and 3, respectively, and in the same way for infected birds. Functional analysis was performed using Gene Ontology (GO) Immune System Process terms specific for Gallus gallus. Results Comparing uninfected L10H and L10L birds, we identified 1698 and 1424 differentially expressed (DE) genes at weeks 1 and 3, respectively. For the IBV-infected birds, 1934 and 866 DE genes were identified between the two lines at weeks 1 and 3, respectively. The two most enriched GO terms emerging from the comparison of uninfected birds between the two lines were “Lymphocyte activation involved in immune response” and “Somatic recombination of immunoglobulin genes involved in immune response” at weeks 1 and 3, respectively. When comparing IBV-infected birds between the two lines, the most enriched GO terms were “Alpha-beta T cell activation” and “Positive regulation of leukocyte activation” at weeks 1 and 3, respectively. Conclusions Healthy birds from the two lines showed significant differences in expression profiles for subsets of adaptive and innate immunity-related genes, whereas comparison of the IBV-infected birds from the two lines showed differences in expression of immunity-related genes involved in T cell activation and proliferation. The observed transcriptome differences between the two lines indicate that selection for MBL had influenced innate as well as adaptive immunity. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2403-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edin Hamzić
- UMR1313 Animal Genetics and Integrative Biology Unit, AgroParisTech, Université Paris-Saclay, 16 rue Claude Bernard, 75005, Paris, France. .,UMR1313 Animal Genetics and Integrative Biology Unit, INRA, Université Paris-Saclay, Domaine de Vilvert, 78350, Jouy-en-Josas, France. .,Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark.
| | - Rikke Brødsgaard Kjærup
- Department of Animal Science, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark.
| | - Núria Mach
- UMR1313 Animal Genetics and Integrative Biology Unit, INRA, Université Paris-Saclay, Domaine de Vilvert, 78350, Jouy-en-Josas, France.
| | - Guilietta Minozzi
- Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy. .,University of Milan, DIVET, Via Celoria 10, 20133, Milan, Italy.
| | | | | | - John L Williams
- Parco Tecnologico Padano, Via Einstein, 26900, Lodi, Italy. .,School of Animal and Veterinary Sciences, University of Adelaide, SA, 5371, Roseworthy, Australia.
| | - Jun Chen
- Cobb-Vantress Inc, US-412 Road, Siloam Springs, AR, 72761, USA.
| | - Eva Wattrang
- National Veterinary Institute, Ulls väg 2B, 751 89, Uppsala, Sweden.
| | - Bart Buitenhuis
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark.
| | - Helle Risdahl Juul-Madsen
- Department of Animal Science, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark.
| | - Tina Sørensen Dalgaard
- Department of Animal Science, Aarhus University, Blichers Allé 20, P.O. Box 50, 8830, Tjele, Denmark.
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Fiandanese N, Viglino A, Strozzi F, Stella A, Williams JL, Lonergan P, Forde N, Iamartino D. 71 CIRCULATING microRNAs AS POTENTIAL BIOMARKERS OF EARLY PREGNANCY IN HIGH-PRODUCING DAIRY COWS. Reprod Fertil Dev 2016. [DOI: 10.1071/rdv28n2ab71] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Lactation induces changes in the metabolic status of postpartum dairy cows that negatively affects the likelihood of pregnancy establishment. At present, pregnancy diagnosis with confidence is only possible after the third week of gestation. Earlier diagnosis could facilitate earlier re-breeding, reduce calving intervals, and improve profits for the industry. MicroRNAs (miRNAs) released in body fluids have been identified as minimally invasive biomarkers of several diseases. In addition, distinct miRNA profiles have been directly related to specific stages of human pregnancy. The aim of this study was to profile circulating miRNAs in the blood of high-producing dairy cows in order to identify biomarkers of early pregnancy. In-calf primiparous Holstein-Friesian cows (n = 22) with a similar economic breeding index were used. At calving, cows were randomly assigned to one of two groups: (1) lactating (n = 11; milked twice per day) or (2) non-lactating (n = 11; dried off immediately). Around 65 to 75 days postpartum (dpp), oestrous cycles were synchronized and a single embryo from a superovulated Holstein-Friesian donor was transferred at Day 7 post-oestrus. Plasma samples were analysed at Day 13 (initiation of conceptus elongation) and at Day 19 (initiation of implantation). Pregnancy rate, established by the presence of conceptus at Day 19, was 5/11 (45%) for lactating and 8/11 (73%) for non-lactating cows, respectively. Circulating miRNA levels were profiled in 4 animals per group in non-lactating pregnant, and lactating pregnant and nonpregnant cows at selected timepoints using Illumina HiSEqn 2000 (Illumina Inc., San Diego, CA, USA) for smallRNA sequencing. Annotation and discovery of miRNAs were done using MirDeep2, and read counts were analysed using edgeR to identify differentially expressed miRNAs. Target genes analysis was run with miRWalk and pathways interactions were built using Cytoscape (P ≤ 0.05). Differentially abundant miRNAs between lactating and non-lactating cows were found at both time points (FDR ≤ 0.05). At Day 13, non-lactating cows had a distinct miRNA profile compared with lactating cows showing 8 differentially expressed miRNA (6 v. pregnant and 2 v. nonpregnant cows). At Day 19, no significant differences were found within pregnant cows, but 5 differentially expressed miRNAs were identified between pregnant and nonpregnant cows, regardless of metabolic status. Interestingly, one miRNA, bta-mir140, was up-regulated in non-lactating pregnant cows from Day 13 onwards compared with nonpregnant cows. Furthermore, the same miRNA was up-regulated in lactating pregnant v. nonpregnant at Day 19. Among bta-mir140 target genes, CD274, SLC44A4, CXCL12, and SIRPA were strictly associated with immune tolerance. In conclusion, the maternal plasma miRNome may represent an early indicator of pregnancy status. In particular, the up-regulation of bta-mir140 in pregnant cows suggests that this miRNA may be a good candidate as an early biomarker of fertility. Furthermore, the positive correlation between this miRNA and pathways involved in T-cell response may indicate a role of immune tolerance in preventing rejection at the initiation of implantation.
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Trovato A, Panelli S, Strozzi F, Cambulli C, Barbieri I, Martinelli N, Lombardi G, Capoferri R, Williams JL. Expression of genes involved in the T cell signalling pathway in circulating immune cells of cattle 24 months following oral challenge with Bovine Amyloidotic Spongiform Encephalopathy (BASE). BMC Vet Res 2015; 11:105. [PMID: 25956229 PMCID: PMC4424883 DOI: 10.1186/s12917-015-0412-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [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: 11/15/2014] [Accepted: 04/16/2015] [Indexed: 11/19/2022] Open
Abstract
Background Bovine Amyloidotic Spongiform Encephalopathy (BASE) is a variant of classical BSE that affects cows and can be transmitted to primates and mice. BASE is biochemically different from BSE and shares some molecular and histo-pathological features with the MV2 sub-type of human sporadic Creutzfeld Jakob Disease (sCJD). Results The present work examined the effects of BASE on gene expression in circulating immune cells. Ontology analysis of genes differentially expressed between cattle orally challenged with brain homogenate from cattle following intracranial inoculation with BASE and control cattle identified three main pathways which were affected. Within the immune function pathway, the most affected genes were related to the T cell receptor-mediated T cell activation pathways. The differential expression of these genes in BASE challenged animals at 10,12 and 24 months following challenge, vs unchallenged controls, was investigated by real time PCR. Conclusions The results of this study show that the effects of prion diseases are not limited to the CNS, but involve the immune system and particularly T cell signalling during the early stage following challenge, before the appearance of clinical signs.
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Affiliation(s)
- Andrea Trovato
- Parco Tecnologico Padano, via Einstein, Lodi, 26900, Italy.
| | - Simona Panelli
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027, Rivolta d'Adda, Italy.
| | | | - Caterina Cambulli
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027, Rivolta d'Adda, Italy.
| | - Ilaria Barbieri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, via Bianchi 9, 25124, Brescia, Italy.
| | - Nicola Martinelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, via Bianchi 9, 25124, Brescia, Italy.
| | - Guerino Lombardi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, via Bianchi 9, 25124, Brescia, Italy.
| | - Rossana Capoferri
- Istituto Sperimentale Italiano Lazzaro Spallanzani, Loc. La Quercia, 26027, Rivolta d'Adda, Italy.
| | - John L Williams
- Parco Tecnologico Padano, via Einstein, Lodi, 26900, Italy. .,Present address: School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, 5371, Australia.
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Nicolazzi EL, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C, Pirani A, Soans C, Brew F, Jorjani H, Evans G, Simpson B, Tosser-Klopp G, Brauning R, Williams JL, Stella A. SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species. BMC Genomics 2015; 16:283. [PMID: 25881165 PMCID: PMC4399246 DOI: 10.1186/s12864-015-1497-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/27/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In recent years, the use of genomic information in livestock species for genetic improvement, association studies and many other fields has become routine. In order to accommodate different market requirements in terms of genotyping cost, manufacturers of single nucleotide polymorphism (SNP) arrays, private companies and international consortia have developed a large number of arrays with different content and different SNP density. The number of currently available SNP arrays differs among species: ranging from one for goats to more than ten for cattle, and the number of arrays available is increasing rapidly. However, there is limited or no effort to standardize and integrate array- specific (e.g. SNP IDs, allele coding) and species-specific (i.e. past and current assemblies) SNP information. RESULTS Here we present SNPchiMp v.3, a solution to these issues for the six major livestock species (cow, pig, horse, sheep, goat and chicken). Original data was collected directly from SNP array producers and specific international genome consortia, and stored in a MySQL database. The database was then linked to an open-access web tool and to public databases. SNPchiMp v.3 ensures fast access to the database (retrieving within/across SNP array data) and the possibility of annotating SNP array data in a user-friendly fashion. CONCLUSIONS This platform allows easy integration and standardization, and it is aimed at both industry and research. It also enables users to easily link the information available from the array producer with data in public databases, without the need of additional bioinformatics tools or pipelines. In recognition of the open-access use of Ensembl resources, SNPchiMp v.3 was officially credited as an Ensembl E!mpowered tool. Availability at http://bioinformatics.tecnoparco.org/SNPchimp.
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Affiliation(s)
- Ezequiel L Nicolazzi
- Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy.
| | - Andrea Caprera
- Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy.
| | - Nelson Nazzicari
- Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy.
| | - Paolo Cozzi
- Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy.
| | - Francesco Strozzi
- Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy.
| | - Cindy Lawley
- Illumina Inc, 5200 Illumina Way, San Diego, CA, 92121, USA.
| | - Ali Pirani
- Affymetrix Inc, 3420 Central Expressway, Santa Clara, CA, 95051, USA.
| | | | - Fiona Brew
- Affymetrix UK Ltd, Mercury Park, Wycombe Lane, High Wycombe, HP10 0HH, UK.
| | | | - Gary Evans
- GeneSeek, a Neogen Company, Auchincruive, Ayr KA6 5HU, Scotland, UK.
| | - Barry Simpson
- GeneSeek, a Neogen Company, Lincoln, NE, 68504, USA.
| | - Gwenola Tosser-Klopp
- Génétique, Physiologie et Systèmes d'Élevage, Institut National de la Recherche Agronomique & Ecole Nationale Vétérinaire de Toulouse & Ecole Nationale Supérieure Agronomique de Toulouse, Castanet-Tolosan, 31326, France.
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, PB 50034, Mosgiel, New Zealand.
| | - John L Williams
- Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy.
| | - Alessandra Stella
- Bioinformatics and Biostatistical Genomics group, Fondazione Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900, Lodi, Italy.
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Via Einstein, Cascina Codazza, Lodi 26900, Italy.
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Möller S, Afgan E, Banck M, Bonnal RJP, Booth T, Chilton J, Cock PJA, Gumbel M, Harris N, Holland R, Kalaš M, Kaján L, Kibukawa E, Powel DR, Prins P, Quinn J, Sallou O, Strozzi F, Seemann T, Sloggett C, Soiland-Reyes S, Spooner W, Steinbiss S, Tille A, Travis AJ, Guimera R, Katayama T, Chapman BA. Community-driven development for computational biology at Sprints, Hackathons and Codefests. BMC Bioinformatics 2014; 15 Suppl 14:S7. [PMID: 25472764 PMCID: PMC4255748 DOI: 10.1186/1471-2105-15-s14-s7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. Results This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe differences in how these are organised, how their audience is addressed, and their outreach to their respective communities. Conclusions Hackathons, Codefests and Sprints share a stimulating atmosphere that encourages participants to jointly brainstorm and tackle problems of shared interest in a self-driven proactive environment, as well as providing an opportunity for new participants to get involved in collaborative projects.
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Vendramin E, Pea G, Dondini L, Pacheco I, Dettori MT, Gazza L, Scalabrin S, Strozzi F, Tartarini S, Bassi D, Verde I, Rossini L. A unique mutation in a MYB gene cosegregates with the nectarine phenotype in peach. PLoS One 2014; 9:e90574. [PMID: 24595269 PMCID: PMC3940905 DOI: 10.1371/journal.pone.0090574] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 02/01/2014] [Indexed: 12/30/2022] Open
Abstract
Nectarines play a key role in peach industry; the fuzzless skin has implications for consumer acceptance. The peach/nectarine (G/g) trait was described as monogenic and previously mapped on chromosome 5. Here, the position of the G locus was delimited within a 1.1 cM interval (635 kb) based on linkage analysis of an F2 progeny from the cross ‘Contender’ (C, peach) x ‘Ambra’ (A, nectarine). Careful inspection of the genes annotated in the corresponding genomic sequence (Peach v1.0), coupled with variant discovery, led to the identification of MYB gene PpeMYB25 as a candidate for trichome formation on fruit skin. Analysis of genomic re-sequencing data from five peach/nectarine accessions pointed to the insertion of a LTR retroelement in exon 3 of the PpeMYB25 gene as the cause of the recessive glabrous phenotype. A functional marker (indelG) developed on the LTR insertion cosegregated with the trait in the CxA F2 progeny and was validated on a broad panel of genotypes, including all known putative donors of the nectarine trait. This marker was shown to efficiently discriminate between peach and nectarine plants, indicating that a unique mutational event gave rise to the nectarine trait and providing a useful diagnostic tool for early seedling selection in peach breeding programs.
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Affiliation(s)
- Elisa Vendramin
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura – Centro di Ricerca per la Frutticoltura (CRA-FRU), Rome, Italy
| | - Giorgio Pea
- Parco Tecnologico Padano, Via Einstein, Loc. C.na Codazza, Lodi, Italy
| | | | - Igor Pacheco
- Università degli Studi di Milano, DiSAA, Milan, Italy
| | - Maria Teresa Dettori
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura – Centro di Ricerca per la Frutticoltura (CRA-FRU), Rome, Italy
| | - Laura Gazza
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura – Centro di Ricerca per la Frutticoltura (CRA-FRU), Rome, Italy
| | | | - Francesco Strozzi
- Parco Tecnologico Padano, Via Einstein, Loc. C.na Codazza, Lodi, Italy
| | | | - Daniele Bassi
- Università degli Studi di Milano, DiSAA, Milan, Italy
| | - Ignazio Verde
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura – Centro di Ricerca per la Frutticoltura (CRA-FRU), Rome, Italy
- * E-mail: (IV); (LR)
| | - Laura Rossini
- Parco Tecnologico Padano, Via Einstein, Loc. C.na Codazza, Lodi, Italy
- Università degli Studi di Milano, DiSAA, Milan, Italy
- * E-mail: (IV); (LR)
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Nicolazzi EL, Picciolini M, Strozzi F, Schnabel RD, Lawley C, Pirani A, Brew F, Stella A. SNPchiMp: a database to disentangle the SNPchip jungle in bovine livestock. BMC Genomics 2014; 15:123. [PMID: 24517501 PMCID: PMC3923093 DOI: 10.1186/1471-2164-15-123] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [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: 09/03/2013] [Accepted: 02/06/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Currently, six commercial whole-genome SNP chips are available for cattle genotyping, produced by two different genotyping platforms. Technical issues need to be addressed to combine data that originates from the different platforms, or different versions of the same array generated by the manufacturer. For example: i) genome coordinates for SNPs may refer to different genome assemblies; ii) reference genome sequences are updated over time changing the positions, or even removing sequences which contain SNPs; iii) not all commercial SNP ID's are searchable within public databases; iv) SNPs can be coded using different formats and referencing different strands (e.g. A/B or A/C/T/G alleles, referencing forward/reverse, top/bottom or plus/minus strand); v) Due to new information being discovered, higher density chips do not necessarily include all the SNPs present in the lower density chips; and, vi) SNP IDs may not be consistent across chips and platforms. Most researchers and breed associations manage SNP data in real-time and thus require tools to standardise data in a user-friendly manner. DESCRIPTION Here we present SNPchiMp, a MySQL database linked to an open access web-based interface. Features of this interface include, but are not limited to, the following functions: 1) referencing the SNP mapping information to the latest genome assembly, 2) extraction of information contained in dbSNP for SNPs present in all commercially available bovine chips, and 3) identification of SNPs in common between two or more bovine chips (e.g. for SNP imputation from lower to higher density). In addition, SNPchiMp can retrieve this information on subsets of SNPs, accessing such data either via physical position on a supported assembly, or by a list of SNP IDs, rs or ss identifiers. CONCLUSIONS This tool combines many different sources of information, that otherwise are time consuming to obtain and difficult to integrate. The SNPchiMp not only provides the information in a user-friendly format, but also enables researchers to perform a large number of operations with a few clicks of the mouse. This significantly reduces the time needed to execute the large number of operations required to manage SNP data.
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Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJ, Buttigieg PL, Campbell MP, Chen YA, Chiba H, Cock PJ, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics 2014; 5:5. [PMID: 24495517 PMCID: PMC3978116 DOI: 10.1186/2041-1480-5-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [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: 05/16/2013] [Accepted: 11/26/2013] [Indexed: 01/24/2023] Open
Abstract
The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years. Here we provide a review of the activities and outcomes from the BioHackathons held in 2011 in Kyoto and 2012 in Toyama. In order to efficiently implement semantic technologies in the life sciences, participants formed various sub-groups and worked on the following topics: Resource Description Framework (RDF) models for specific domains, text mining of the literature, ontology development, essential metadata for biological databases, platforms to enable efficient Semantic Web technology development and interoperability, and the development of applications for Semantic Web data. In this review, we briefly introduce the themes covered by these sub-groups. The observations made, conclusions drawn, and software development projects that emerged from these activities are discussed.
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Affiliation(s)
- Toshiaki Katayama
- Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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Ramírez M, Guillén G, Fuentes SI, Iñiguez LP, Aparicio-Fabre R, Zamorano-Sánchez D, Encarnación-Guevara S, Panzeri D, Castiglioni B, Cremonesi P, Strozzi F, Stella A, Girard L, Sparvoli F, Hernández G. Transcript profiling of common bean nodules subjected to oxidative stress. Physiol Plant 2013; 149:389-407. [PMID: 23432573 DOI: 10.1111/ppl.12040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 01/25/2013] [Accepted: 01/28/2013] [Indexed: 06/01/2023]
Abstract
Several environmental stresses generate high amounts of reactive oxygen species (ROS) in plant cells, resulting in oxidative stress. Symbiotic nitrogen fixation (SNF) in the legume-rhizobia symbiosis is sensitive to damage from oxidative stress. Active nodules of the common bean (Phaseolus vulgaris) exposed to the herbicide paraquat (1,1'-dimethyl-4,4'-bipyridinium dichloride hydrate), which stimulates ROS accumulation, exhibited reduced nitrogenase activity and ureide content. We analyzed the global gene response of nodules subjected to oxidative stress using the Bean Custom Array 90K, which includes probes from 30,000 expressed sequence tags (ESTs). A total of 4280 ESTs were differentially expressed in stressed bean nodules; of these, 2218 were repressed. Based on Gene Ontology analysis, these genes were grouped into 42 different biological process categories. Analysis with the PathExpress bioinformatic tool, adapted for bean, identified five significantly repressed metabolic pathways related to carbon/nitrogen metabolism, which is crucial for nodule function. Quantitative reverse transcription (qRT)-PCR analysis of transcription factor (TF) gene expression showed that 67 TF genes were differentially expressed in nodules exposed to oxidative stress. Putative cis-elements recognized by highly responsive TF were detected in promoter regions of oxidative stress regulated genes. The expression of oxidative stress responsive genes and of genes important for SNF in bacteroids analyzed in stressed nodules revealed that these conditions elicited a transcriptional response.
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Affiliation(s)
- Mario Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Cuernavaca, Mor. 62209, Mexico
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Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 2013; 8:1494-1512. [PMID: 23845962 DOI: 10.1038/nprot.2013.084.de] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.
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Affiliation(s)
- Brian J Haas
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA
| | - Alexie Papanicolaou
- CSIRO Ecosystem Sciences, Black Mountain Labs, Canberra, ACT 2601, Australia
| | - Moran Yassour
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA
- The Selim and Rachel Benin School of Computer Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Manfred Grabherr
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Philip D Blood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Joshua Bowden
- CSIRO Information Management & Technology, 306 Carmody Rd, St Lucia QLD 4067, Australia
| | - Matthew Brian Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, USA
| | - David Eccles
- Genomics Research Centre, Griffith University, Gold Coast Campus, Qld 4222, Australia
| | - Bo Li
- Department of Computer Sciences, University of Wisconsin, Madison, WI, 53706, USA
| | - Matthias Lieber
- Technische Universität Dresden, Dresden, Saxony 01062, Germany
| | - Matthew D MacManes
- University of California, Berkeley and California Institute for Quantitative Biosciences Berkeley, CA 94720, USA
| | - Michael Ott
- CSIRO Ecosystem Sciences, Black Mountain Labs, Canberra, ACT 2601, Australia
| | - Joshua Orvis
- Institute for Genome Sciences, Baltimore, MD, 21201, USA
| | - Nathalie Pochet
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA
- Department of Plant Systems Biology, VIB, Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | | | - Nathan Weeks
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture--Agricultural Research Service, Ames, IA 50011, USA
| | - Rick Westerman
- Genomics facility, Purdue University, West Lafayette, IN, 47907, USA
| | - Thomas William
- GWT-TUD GmbH, Blasewitzer Strasse 43, Dresden, Saxony 01307, Germany
| | - Colin N Dewey
- Department of Computer Sciences, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53706, USA
| | - Robert Henschel
- Indiana University, 2709 East 10th Street, Bloomington, IN 47408,USA
| | - Richard D LeDuc
- Indiana University, 2709 East 10th Street, Bloomington, IN 47408,USA
| | - Nir Friedman
- The Selim and Rachel Benin School of Computer Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Aviv Regev
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140
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Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 2013; 8:1494-512. [PMID: 23845962 PMCID: PMC3875132 DOI: 10.1038/nprot.2013.084] [Citation(s) in RCA: 5070] [Impact Index Per Article: 460.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.
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Affiliation(s)
- Brian J. Haas
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA
| | - Alexie Papanicolaou
- CSIRO Ecosystem Sciences, Black Mountain Labs, Canberra, ACT 2601, Australia
| | - Moran Yassour
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA
- The Selim and Rachel Benin School of Computer Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Manfred Grabherr
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Philip D. Blood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Joshua Bowden
- CSIRO Information Management & Technology, 306 Carmody Rd, St Lucia QLD 4067, Australia
| | - Matthew Brian Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, USA
| | - David Eccles
- Genomics Research Centre, Griffith University, Gold Coast Campus, Qld 4222, Australia
| | - Bo Li
- Department of Computer Sciences, University of Wisconsin, Madison, WI, 53706, USA
| | - Matthias Lieber
- Technische Universität Dresden, Dresden, Saxony 01062, Germany
| | - Matthew D. MacManes
- University of California, Berkeley and California Institute for Quantitative Biosciences Berkeley, CA 94720, USA
| | - Michael Ott
- CSIRO Ecosystem Sciences, Black Mountain Labs, Canberra, ACT 2601, Australia
| | - Joshua Orvis
- Institute for Genome Sciences, Baltimore, MD, 21201, USA
| | - Nathalie Pochet
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA
- Department of Plant Systems Biology, VIB, Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | | | - Nathan Weeks
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture--Agricultural Research Service, Ames, IA 50011, USA
| | - Rick Westerman
- Genomics facility, Purdue University, West Lafayette, IN, 47907, USA
| | - Thomas William
- GWT-TUD GmbH, Blasewitzer Strasse 43, Dresden, Saxony 01307, Germany
| | - Colin N. Dewey
- Department of Computer Sciences, University of Wisconsin, Madison, WI, 53706, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53706, USA
| | - Robert Henschel
- Indiana University, 2709 East 10th Street, Bloomington, IN 47408,USA
| | - Richard D. LeDuc
- Indiana University, 2709 East 10th Street, Bloomington, IN 47408,USA
| | - Nir Friedman
- The Selim and Rachel Benin School of Computer Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Aviv Regev
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140
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Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD, Ott M, Orvis J, Pochet N, Strozzi F, Weeks N, Westerman R, William T, Dewey CN, Henschel R, LeDuc RD, Friedman N, Regev A. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc 2013. [PMID: 23845962 DOI: 10.1038/nprot.2013.084.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
De novo assembly of RNA-seq data enables researchers to study transcriptomes without the need for a genome sequence; this approach can be usefully applied, for instance, in research on 'non-model organisms' of ecological and evolutionary importance, cancer samples or the microbiome. In this protocol we describe the use of the Trinity platform for de novo transcriptome assembly from RNA-seq data in non-model organisms. We also present Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes. In the procedure, we provide a workflow for genome-independent transcriptome analysis leveraging the Trinity platform. The software, documentation and demonstrations are freely available from http://trinityrnaseq.sourceforge.net. The run time of this protocol is highly dependent on the size and complexity of data to be analyzed. The example data set analyzed in the procedure detailed herein can be processed in less than 5 h.
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Affiliation(s)
- Brian J Haas
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA
| | - Alexie Papanicolaou
- CSIRO Ecosystem Sciences, Black Mountain Labs, Canberra, ACT 2601, Australia
| | - Moran Yassour
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.,The Selim and Rachel Benin School of Computer Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Manfred Grabherr
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Philip D Blood
- Pittsburgh Supercomputing Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Joshua Bowden
- CSIRO Information Management & Technology, 306 Carmody Rd, St Lucia QLD 4067, Australia
| | - Matthew Brian Couger
- Department of Microbiology and Molecular Genetics, Oklahoma State University, USA
| | - David Eccles
- Genomics Research Centre, Griffith University, Gold Coast Campus, Qld 4222, Australia
| | - Bo Li
- Department of Computer Sciences, University of Wisconsin, Madison, WI, 53706, USA
| | - Matthias Lieber
- Technische Universität Dresden, Dresden, Saxony 01062, Germany
| | - Matthew D MacManes
- University of California, Berkeley and California Institute for Quantitative Biosciences Berkeley, CA 94720, USA
| | - Michael Ott
- CSIRO Ecosystem Sciences, Black Mountain Labs, Canberra, ACT 2601, Australia
| | - Joshua Orvis
- Institute for Genome Sciences, Baltimore, MD, 21201, USA
| | - Nathalie Pochet
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.,Department of Plant Systems Biology, VIB, Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium
| | | | - Nathan Weeks
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture--Agricultural Research Service, Ames, IA 50011, USA
| | - Rick Westerman
- Genomics facility, Purdue University, West Lafayette, IN, 47907, USA
| | - Thomas William
- GWT-TUD GmbH, Blasewitzer Strasse 43, Dresden, Saxony 01307, Germany
| | - Colin N Dewey
- Department of Computer Sciences, University of Wisconsin, Madison, WI, 53706, USA.,Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI 53706, USA
| | - Robert Henschel
- Indiana University, 2709 East 10th Street, Bloomington, IN 47408,USA
| | - Richard D LeDuc
- Indiana University, 2709 East 10th Street, Bloomington, IN 47408,USA
| | - Nir Friedman
- The Selim and Rachel Benin School of Computer Science, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Aviv Regev
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA, 02142, USA.,Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02140
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Aparicio-Fabre R, Guillén G, Loredo M, Arellano J, Valdés-López O, Ramírez M, Íñiguez LP, Panzeri D, Castiglioni B, Cremonesi P, Strozzi F, Stella A, Girard L, Sparvoli F, Hernández G. Common bean (Phaseolus vulgaris L.) PvTIFY orchestrates global changes in transcript profile response to jasmonate and phosphorus deficiency. BMC Plant Biol 2013; 13:26. [PMID: 23402340 PMCID: PMC3621168 DOI: 10.1186/1471-2229-13-26] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Accepted: 01/29/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND TIFY is a large plant-specific transcription factor gene family. A subgroup of TIFY genes named JAZ (Jasmonate-ZIM domain) has been identified as repressors of jasmonate (JA)-regulated transcription in Arabidopsis and other plants. JA signaling is involved in many aspects of plant growth/development and in defense responses to biotic and abiotic stresses. Here, we identified the TIFY genes (designated PvTIFY) from the legume common bean (Phaseolus vulgaris) and functionally characterized PvTIFY10C as a transcriptional regulator. RESULTS Nineteen genes from the PvTIFY gene family were identified through whole-genome sequence analysis. Most of these were induced upon methyl-JA elicitation. We selected PvTIFY10C as a representative JA-responsive PvTIFY gene for further functional analysis. Transcriptome analysis via microarray hybridization using the newly designed Bean Custom Array 90 K was performed on transgenic roots of composite plants with modulated (RNAi-silencing or over-expression) PvTIFY10C gene expression. Data were interpreted using Gene Ontology and MapMan adapted to common bean. Microarray differential gene expression data were validated by real-time qRT-PCR expression analysis. Comparative global gene expression analysis revealed opposite regulatory changes in processes such as RNA and protein regulation, stress responses and metabolism in PvTIFY10C silenced vs. over-expressing roots. These data point to transcript reprogramming (mainly repression) orchestrated by PvTIFY10C. In addition, we found that several PvTIFY genes, as well as genes from the JA biosynthetic pathway, responded to P-deficiency. Relevant P-responsive genes that participate in carbon metabolic pathways, cell wall synthesis, lipid metabolism, transport, DNA, RNA and protein regulation, and signaling were oppositely-regulated in control vs. PvTIFY10C-silenced roots of composite plants under P-stress. These data indicate that PvTIFY10C regulates, directly or indirectly, the expression of some P-responsive genes; this process could be mediated by JA-signaling. CONCLUSION Our work contributes to the functional characterization of PvTIFY transcriptional regulators in common bean, an agronomically important legume. Members from the large PvTIFY gene family are important global transcriptional regulators that could participate as repressors in the JA signaling pathway. In addition, we propose that the JA-signaling pathway involving PvTIFY genes might play a role in regulating the plant response/adaptation to P-starvation.
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Affiliation(s)
- Rosaura Aparicio-Fabre
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Mor. 62209, Cuernacaca, México
| | - Gabriel Guillén
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 1001, Mor. 62209, Cuernacaca, México
| | - Montserrat Loredo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Mor. 62209, Cuernacaca, México
| | - Jesús Arellano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Mor. 62209, Cuernacaca, México
| | - Oswaldo Valdés-López
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Mor. 62209, Cuernacaca, México
| | - Mario Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Mor. 62209, Cuernacaca, México
| | - Luis P Íñiguez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Mor. 62209, Cuernacaca, México
| | - Dario Panzeri
- Istituto di Biologia e Biotecnologia Agraria, CNR, Via Bassini 15, 20133, Milano, Italy
| | - Bianca Castiglioni
- Istituto di Biologia e Biotecnologia Agraria, CNR, Via Bassini 15, 20133, Milano, Italy
| | - Paola Cremonesi
- Istituto di Biologia e Biotecnologia Agraria, CNR, Via Bassini 15, 20133, Milano, Italy
| | - Francesco Strozzi
- Istituto di Biologia e Biotecnologia Agraria, CNR, Via Bassini 15, 20133, Milano, Italy
| | - Alessandra Stella
- Istituto di Biologia e Biotecnologia Agraria, CNR, Via Bassini 15, 20133, Milano, Italy
| | - Lourdes Girard
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Mor. 62209, Cuernacaca, México
| | - Francesca Sparvoli
- Istituto di Biologia e Biotecnologia Agraria, CNR, Via Bassini 15, 20133, Milano, Italy
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad 1001, Mor. 62209, Cuernacaca, México
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Cremonesi P, Capoferri R, Pisoni G, Del Corvo M, Strozzi F, Rupp R, Caillat H, Modesto P, Moroni P, Williams JL, Castiglioni B, Stella A. Response of the goat mammary gland to infection with Staphylococcus aureus revealed by gene expression profiling in milk somatic and white blood cells. BMC Genomics 2012; 13:540. [PMID: 23046560 PMCID: PMC3532242 DOI: 10.1186/1471-2164-13-540] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [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: 03/05/2012] [Accepted: 09/28/2012] [Indexed: 11/10/2022] Open
Abstract
Background S. aureus is one of the main pathogens responsible for the intra-mammary infection in dairy ruminants. Although much work has been carried out to understand the complex physiological and cellular events that occur in the mammary gland in response to S. aureus, the protective mechanisms are still poorly understood. The objectives of the present study were to investigate gene expression during the early response of the goat mammary gland to an experimental challenge with S. aureus, in order to better understand the local and systemic response and to compare them in two divergent lines of goat selected for high and low milk somatic cell scores. Results No differences in gene expression were found between high and low SCS (Somatic Cells Score) selection lines. Analysing the two groups together, an expression of 300 genes were found to change from T0 before infection, and T4 at 24 hours and T5 at 30 hours following challenge. In blood derived white blood cells 8 genes showed increased expression between T0 and T5 and 1 gene has reduced expression. The genes showing the greatest increase in expression following challenge (5.65 to 3.16 fold change) play an important role in (i) immune and inflammatory response (NFKB1, TNFAIP6, BASP1, IRF1, PLEK, BATF3); (ii) the regulation of innate resistance to pathogens (PTX3); and (iii) the regulation of cell metabolism (CYTH4, SLC2A6, ARG2). The genes with reduced expression (−1.5 to −2.5 fold) included genes involved in (i) lipid metabolism (ABCG2, FASN), (ii) chemokine, cytokine and intracellular signalling (SPPI), and (iii) cell cytoskeleton and extracellular matrix (KRT19). Conclusions Analysis of genes with differential expression following infection showed an inverse relationship between immune response and lipid metabolism in the early response of the mammary gland to the S. aureus challenge. PTX3 showed a large change in expression in both milk and blood, and is therefore a candidate for further studies on immune response associated with mastitis.
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Affiliation(s)
- Paola Cremonesi
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Lodi, Italy
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Minozzi G, Williams JL, Stella A, Strozzi F, Luini M, Settles ML, Taylor JF, Whitlock RH, Zanella R, Neibergs HL. Meta-analysis of two genome-wide association studies of bovine paratuberculosis. PLoS One 2012; 7:e32578. [PMID: 22396781 PMCID: PMC3292576 DOI: 10.1371/journal.pone.0032578] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [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: 09/21/2011] [Accepted: 01/27/2012] [Indexed: 11/18/2022] Open
Abstract
Background Bovine paratuberculosis (ParaTB) also known as Johne's disease, is a contagious fatal disease resulting from infection by Mycobacterium avium subspecies paratuberculosis (MAP). Previous studies have identified loci associated with ParaTB using different measurements to define cases and controls. The objective of this study was to combine the data from two recent studies to identify genetic loci associated with MAP tissue infection and humoral immune response, defined by MAP ELISA-positive cattle, by comparing cases and control animals for one or both measures of infection. Methodology/Principal Findings The two populations used for the association analyses were a cohort of MAP tissue infected animals and control Holstein cows from the USA and the second cohort composed of ELISA-positive and ELISA-negative Holstein cows from Italy. Altogether 1190 cattle were genotyped with the Illumina BovineSNP50 BeadChip. SNP markers were removed if the minor allele frequency <0.01 or genotyping failure was >5%. Animals were removed with >5% genotyping failure. Whole genome association analyses were conducted with the GRAMMAR-CG method using two different definitions of control populations. Conclusion/Significance The analyses identified several loci (P<5 e-05) associated with ParaTB, defined by positive ELISA and presence of bacteria in tissue compared to ELISA and tissue negative animals, on chromosomes 1, 12 and 15 and one unassigned SNP. These results confirmed associations on chromosome 12 and the unassigned SNP with ParaTB which had been found in the Italian population alone. Furthermore, several additional genomic regions were found associated with ParaTB when ELISA and tissue positive animals were compared with tissue negative samples. These loci were on chromosomes 1, 6, 7, 13, 16, 21,23 and 25 (P<5 e-05). The results clearly indicate the importance of the phenotype definition when seeking to identify markers associated with different disease responses.
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Bonnal RJP, Aerts J, Githinji G, Goto N, MacLean D, Miller CA, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom TJ, Woodcroft BJ, Katayama T, Prins P. Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics 2012; 28:1035-7. [PMID: 22332238 PMCID: PMC3315718 DOI: 10.1093/bioinformatics/bts080] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [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] [Indexed: 11/14/2022] Open
Abstract
SUMMARY Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. AVAILABILITY Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html CONTACT bonnal@ingm.org.
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Affiliation(s)
- Raoul J P Bonnal
- Integrative Biology Program, Istituto Nazionale Genetica Molecolare, Milan 20122, Italy.
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Minozzi G, Nicolazzi EL, Strozzi F, Stella A, Negrini R, Ajmone-Marsan P, Williams JL. Genome wide scan for somatic cell counts in holstein bulls. BMC Proc 2011; 5 Suppl 4:S17. [PMID: 21645296 PMCID: PMC3108211 DOI: 10.1186/1753-6561-5-s4-s17] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Background Mastitis is the most costly disease for dairy production, and control of the disease is often difficult, due to its multi-factorial nature. Susceptibility to mastitis is under partial genetic control and the industry uses indirect selection for decreased concentrations of somatic cells in milk to reduce mastitis. Methods A genome-wide scan was performed to identify genomic regions associated with deregressed estimated breeding values (EBVs) for somatic cell counts (SCC) in Holstein bulls. In total 1183 proven bulls of the Italian of Holstein population, were genotyped with the BovineSNP50 BeadChip (Illumina, San Diego, CA) and a whole genome association analysis was performed using the R package GenABEL. Results Two chromosomal regions showed association with SCC, a region on chromosome 14 with high significance (P < 5x10-6) and a region on chromosome 6 with moderate significance (P < 5x10-5). Conclusions Two regions with effects on SCC have been identified with good statistical support. A further study of these candidate regions will be performed to verify the results and identify the causal mutations.
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Affiliation(s)
- Giulietta Minozzi
- Parco Tecnologico Padano, Via Einstein, Polo Universitario, Lodi 26900, Italy.
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Abstract
UNLABELLED The Ensembl database makes genomic features available via its Genome Browser. It is also possible to access the underlying data through a Perl API for advanced querying. We have developed a full-featured Ruby API to the Ensembl databases, providing the same functionality as the Perl interface with additional features. A single Ruby API is used to access different releases of the Ensembl databases and is also able to query multi-species databases. AVAILABILITY AND IMPLEMENTATION Most functionality of the API is provided using the ActiveRecord pattern. The library depends on introspection to make it release independent. The API is available through the Rubygem system and can be installed with the command gem install ruby-ensembl-api.
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Panelli S, Strozzi F, Capoferri R, Barbieri I, Martinelli N, Capucci L, Lombardi G, Williams JL. Analysis of gene expression in white blood cells of cattle orally challenged with bovine amyloidotic spongiform encephalopathy. J Toxicol Environ Health A 2011; 74:96-102. [PMID: 21218338 DOI: 10.1080/15287394.2011.529059] [Citation(s) in RCA: 9] [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] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Bovine amyloidotic spongiform encephalopathy (BASE) is one of the recently discovered atypical forms of BSE, which is transmissible to primates, and may be the bovine equivalent of sporadic Creutzfeldt-Jacob disease (CJD) in humans. Although it is transmissible, it is unknown whether BASE is acquired through infection or arises spontaneously. In the present study, the gene expression of white blood cells (WBCs) from 5 cattle at 1 yr after oral BASE challenge was compared with negative controls using a custom microarray containing 43,768 unique gene probes. In total, 56 genes were found to be differentially expressed between BASE and control animals with a log fold change of 2 or greater. Of these, 39 were upregulated in BASE animals, while 17 were downregulated. The majority of these genes are related to immune function. In particular, BASE animals appeared to have significantly modified expression of genes linked to T- and B-cell development and activation, and to inflammatory responses. The potential impacts of these gene expression changes are described.
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Affiliation(s)
- Simona Panelli
- IDRA-LAB, Parco Tecnologico Padano, via Einstein, Lodi, Italy
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Minozzi G, Buggiotti L, Stella A, Strozzi F, Luini M, Williams JL. Genetic loci involved in antibody response to Mycobacterium avium ssp. paratuberculosis in cattle. PLoS One 2010; 5:e11117. [PMID: 20559561 PMCID: PMC2886106 DOI: 10.1371/journal.pone.0011117] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [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: 03/19/2010] [Accepted: 05/17/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Mycobacterium avium subsp. paratuberculosis (MAP) causes chronic enteritis in a wide range of animal species. In cattle, MAP causes a chronic disease called Johne's disease, or paratuberculosis, that is not treatable and the efficacy of vaccine control is controversial. The clinical phase of the disease is characterised by diarrhoea, weight loss, drop in milk production and eventually death. Susceptibility to MAP infection is heritable with heritability estimates ranging from 0.06 to 0.10. There have been several studies over the last few years that have identified genetic loci putatively associated with MAP susceptibility, however, with the availability of genome-wide high density SNP maker panels it is now possible to carry out association studies that have higher precision. METHODOLOGY/PRINCIPAL FINDINGS The objective of the current study was to localize genes having an impact on Johne's disease susceptibility using the latest bovine genome information and a high density SNP panel (Illumina BovineSNP50 BeadChip) to perform a case/control, genome-wide association analysis. Samples from MAP case and negative controls were selected from field samples collected in 2007 and 2008 in the province of Lombardy, Italy. Cases were defined as animals serologically positive for MAP by ELISA. In total 966 samples were genotyped: 483 MAP ELISA positive and 483 ELISA negative. Samples were selected randomly among those collected from 119 farms which had at least one positive animal. CONCLUSION/SIGNIFICANCE THE ANALYSIS OF THE GENOTYPE DATA IDENTIFIED SEVERAL CHROMOSOMAL REGIONS ASSOCIATED WITH DISEASE STATUS: a region on chromosome 12 with high significance (P<5x10(-6)), while regions on chromosome 9, 11, and 12 had moderate significance (P<5x10(-5)). These results provide evidence for genetic loci involved in the humoral response to MAP. Knowledge of genetic variations related to susceptibility will facilitate the incorporation of this information into breeding programmes for the improvement of health status.
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Mazza R, Strozzi F, Caprera A, Ajmone-Marsan P, Williams JL. The other side of comparative genomics: genes with no orthologs between the cow and other mammalian species. BMC Genomics 2009; 10:604. [PMID: 20003425 PMCID: PMC2808326 DOI: 10.1186/1471-2164-10-604] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 12/14/2009] [Indexed: 11/10/2022] Open
Abstract
Background With the rapid growth in the availability of genome sequence data, the automated identification of orthologous genes between species (orthologs) is of fundamental importance to facilitate functional annotation and studies on comparative and evolutionary genomics. Genes with no apparent orthologs between the bovine and human genome may be responsible for major differences between the species, however, such genes are often neglected in functional genomics studies. Results A BLAST-based method was exploited to explore the current annotation and orthology predictions in Ensembl. Genes with no orthologs between the two genomes were classified into groups based on alignments, ontology, manual curation and publicly available information. Starting from a high quality and specific set of orthology predictions, as provided by Ensembl, hidden relationship between genes and genomes of different mammalian species were unveiled using a highly sensitive approach, based on sequence similarity and genomic comparison. Conclusions The analysis identified 3,801 bovine genes with no orthologs in human and 1010 human genes with no orthologs in cow, among which 411 and 43 genes, respectively, had no match at all in the other species. Most of the apparently non-orthologous genes may potentially have orthologs which were missed in the annotation process, despite having a high percentage of identity, because of differences in gene length and structure. The comparative analysis reported here identified gene variants, new genes and species-specific features and gave an overview of the other side of orthology which may help to improve the annotation of the bovine genome and the knowledge of structural differences between species.
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Affiliation(s)
- Raffaele Mazza
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, 29100 Piacenza, Italy.
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Affiliation(s)
- F Strozzi
- IDRA Lab, Parco Tecnologico Padano, Via Einstein, Loc. Cascina Codazza, 26900 Lodi, Italy
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Bosch J, Strozzi F, Snee T, Hare J, Zaldívar J. A comparative analysis between temperature and pressure measurements for early detection of runaway initiation. J Loss Prev Process Ind 2004. [DOI: 10.1016/j.jlp.2004.07.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Affiliation(s)
- J. Bosch
- European Commission, Joint Research Centre, Institute for Environment and Sustainability, TP272, 21020 Ispra (VA), Italy, Health and Safety Laboratory, Harpur Hill, Buxton, Derbyshire SK17 9JN, U.K., and Quantitative Methods Group, Engineering Department, Carlo Cattaneo University, Castellanza (VA), Italy
| | - D. C. Kerr
- European Commission, Joint Research Centre, Institute for Environment and Sustainability, TP272, 21020 Ispra (VA), Italy, Health and Safety Laboratory, Harpur Hill, Buxton, Derbyshire SK17 9JN, U.K., and Quantitative Methods Group, Engineering Department, Carlo Cattaneo University, Castellanza (VA), Italy
| | - T. J. Snee
- European Commission, Joint Research Centre, Institute for Environment and Sustainability, TP272, 21020 Ispra (VA), Italy, Health and Safety Laboratory, Harpur Hill, Buxton, Derbyshire SK17 9JN, U.K., and Quantitative Methods Group, Engineering Department, Carlo Cattaneo University, Castellanza (VA), Italy
| | - F. Strozzi
- European Commission, Joint Research Centre, Institute for Environment and Sustainability, TP272, 21020 Ispra (VA), Italy, Health and Safety Laboratory, Harpur Hill, Buxton, Derbyshire SK17 9JN, U.K., and Quantitative Methods Group, Engineering Department, Carlo Cattaneo University, Castellanza (VA), Italy
| | - J. M. Zaldívar
- European Commission, Joint Research Centre, Institute for Environment and Sustainability, TP272, 21020 Ispra (VA), Italy, Health and Safety Laboratory, Harpur Hill, Buxton, Derbyshire SK17 9JN, U.K., and Quantitative Methods Group, Engineering Department, Carlo Cattaneo University, Castellanza (VA), Italy
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Bosch J, Strozzi F, Zbilut J, Zaldı́var J. On-line runaway detection in isoperibolic batch and semibatch reactors using the divergence criterion. Comput Chem Eng 2004. [DOI: 10.1016/j.compchemeng.2003.08.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [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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