1
|
Pozzi A, Nazzicari N, Capoferri R, Radovic S, Bongioni G. Assessment of residual plant DNA in bulk milk for Grana Padano PDO production by a metabarcoding approach. PLoS One 2023; 18:e0289108. [PMID: 37490502 PMCID: PMC10368264 DOI: 10.1371/journal.pone.0289108] [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] [Received: 07/20/2022] [Accepted: 07/11/2023] [Indexed: 07/27/2023] Open
Abstract
The aim of this study was to evaluate the ability of DNA metabarcoding, by rbcl as barcode marker, to identify and classify the small traces of plant DNA isolated from raw milk used to produce Grana Padano (GP) cheese. GP is one of the most popular Italian PDO (Protected Designation of Origin) produced in Italy in accordance with the GP PDO specification rules that define which forage can be used for feeding cows. A total of 42 GP bulk tank milk samples were collected from 14 dairies located in the Grana Padano production area. For the taxonomic classification, a local database with the rbcL sequences available in NCBI on September 2020/March 2021 for the Italian flora was generated. A total of 8,399,591 reads were produced with an average of 204,868 per sample (range 37,002-408,724) resulting in 16, 31 and 28 dominant OTUs at family, genus and species level, respectively. The taxonomic analysis of plant species in milk samples identified 7 families, 14 genera and 14 species, the statistical analysis conducted using alpha and beta diversity approaches, did not highlight differences among the investigated samples. However, the milk samples are featured by a high plant variability and the lack of differences at multiple taxonomic levels could be due to the standardisation of the feed rationing, as requested by the GP rules. The results suggest that DNA metabarcoding is a valuable resource to explore plant DNA traces in a complex matrix such as milk.
Collapse
Affiliation(s)
- Anna Pozzi
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
| | - Nelson Nazzicari
- CREA-Council for Agricultural Research and Analysis of Agricultural Economics, Research Centre for Animal Production and Aquaculture, Viale Piacenza, Lodi, Italy
| | - Rossana Capoferri
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
| | | | - Graziella Bongioni
- Istituto Sperimentale Lazzaro Spallanzani, Localita' La Quercia, Rivolta d'Adda (CR), Italy
| |
Collapse
|
2
|
Zoccola R, Beltramo C, Magris G, Peletto S, Acutis P, Bozzetta E, Radovic S, Zappulla F, Porzio AM, Gennero MS, Dondo A, Pasqualini C, Griglio B, Ferrari A, Ru G, Goria M. First detection of an Italian human-to-cat outbreak of SARS-CoV-2 Alpha variant - lineage B.1.1.7. One Health 2021; 13:100295. [PMID: 34316508 PMCID: PMC8299139 DOI: 10.1016/j.onehlt.2021.100295] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 05/05/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022] Open
Abstract
The emergence of new SARS-CoV-2 variants and their rapid spread pose a threat to both human and animal health and may conceal unknown risks. This report describes an Italian human-to-cat outbreak of SARS-CoV-2 lineage B.1.1.7 (the Alpha variant) . On March 7th, 2021, approximately ten days after COVID-19 appeared in the family, the onset of respiratory signs in a cat by COVID-19-affected owners led to an in-depth diagnostic investigation, combining clinical and serological data with rt-qPCR-based virus detection and whole genome sequencing. The Alpha variant was confirmed first in the owners and a few days later in the cat that was then monitored weekly: the course was similar with one-week lag time in the cat. In addition, based on comparative analysis of genome sequences from our study and from 200 random Italian cases of Alpha variant, the familial cluster was confirmed. The temporal sequence along with the genomic data support a human-to-animal transmission. Such an event emphasizes the importance of studying the circulation and dynamics of SARS-CoV-2 variants in humans and animals to better understand and prevent potential spillover risks or unwarranted alerts involving our pet populations.
Collapse
Affiliation(s)
- Roberto Zoccola
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin I-10154, Italy
| | - Chiara Beltramo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin I-10154, Italy
| | - Gabriele Magris
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine I-33100, Italy
- Istituto di Genomica Applicata, Udine I-33100, Italy
| | - Simone Peletto
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin I-10154, Italy
| | - Pierluigi Acutis
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin I-10154, Italy
| | - Elena Bozzetta
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin I-10154, Italy
| | | | - Francesco Zappulla
- Regione Piemonte - Local Health Unit Novara - Department of Prevention, Health Service - Veterinary Services, Arona (No), I-28041, Italy
| | | | - Maria Silvia Gennero
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin I-10154, Italy
| | - Alessandro Dondo
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin I-10154, Italy
| | - Chiara Pasqualini
- Regione Piemonte - Regional Service for Surveillance and Control of Infectious Diseases (SEREMI), I-15121 Alessandria, Italy
| | | | - Angelo Ferrari
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin I-10154, Italy
| | - Giuseppe Ru
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin I-10154, Italy
| | - Maria Goria
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle d'Aosta, Turin I-10154, Italy
| |
Collapse
|
3
|
Cini G, Carnevali I, Sahnane N, Chiaravalli AM, Dell'Elice A, Maestro R, Pin E, Bestetti I, Radovic S, Armelao F, Viel A, Tibiletti MG. Lynch syndrome and Muir-Torre phenotype associated with a recurrent variant in the 3'UTR of the MSH6 gene. Cancer Genet 2021; 254-255:1-10. [PMID: 33516942 DOI: 10.1016/j.cancergen.2021.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 08/07/2020] [Revised: 12/18/2020] [Accepted: 01/15/2021] [Indexed: 02/07/2023]
Abstract
A MSH6 3'UTR variant (c.*23_26dup) was found in 13 unrelated families consulted for Lynch/Muir-Torre Syndrome. This variant, which is very rare in the genomic databases, was absent in healthy controls and strongly segregated with the disease in the studied pedigrees. All tumors were defective for MSH2/MSH6/MSH3 proteins expression, but only MSH2 somatic pathogenic mutations were found in 5 of the 12 sequenced tumors. Moreover, we had no evidence of MSH6 transcript decrease in carriers, whereas MSH2 transcript was downregulated. Additional evaluations performed in representative carriers, including karyotype, arrayCGH and Linked-Reads whole genome sequencing, failed to evidence any MSH2 germline pathogenic variant. Posterior probability of pathogenicity for MSH6 c.*23_26dup was obtained from a multifactorial analysis incorporating segregation and phenotypic data and resulted >0.999, allowing to classify the variant as pathogenic (InSiGHT Class 5). Carriers shared a common haplotype involving MSH2/MSH6 loci, then a cryptic disease-associated variant, linked with MSH6 c.*23_26dup, cannot be completely excluded. Even if it is not clear whether the MSH6 variant is pathogenic per se or simply a marker of a disease-associated MSH2/MSH6 haplotype, all data collected on patients and pedigrees prompted us to manage the variant as pathogenic and to offer predictive testing within these families.
Collapse
Affiliation(s)
- Giulia Cini
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy
| | - Ileana Carnevali
- Department of Pathology, Circolo Hospital ASST Settelaghi, via O. Rossi 9, 21100, Varese, Italy; Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, via O. Rossi 9, 21100, Varese, Italy
| | - Nora Sahnane
- Department of Pathology, Circolo Hospital ASST Settelaghi, via O. Rossi 9, 21100, Varese, Italy; Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, via O. Rossi 9, 21100, Varese, Italy
| | - Anna Maria Chiaravalli
- Department of Pathology, Circolo Hospital ASST Settelaghi, via O. Rossi 9, 21100, Varese, Italy; Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, via O. Rossi 9, 21100, Varese, Italy
| | - Anastasia Dell'Elice
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy
| | - Roberta Maestro
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy
| | - Elisa Pin
- Division of Affinity Proteomics, Department of Protein Science, SciLifeLab, The Royal Institute of Technology KTH, Tomtebodavägen 23B, 171 65 Solna, Stockholm, Sweden
| | - Ilaria Bestetti
- Research Laboratory of Medical Cytogenetics and Molecular Genetics, IRCCS Istituto Auxologico Italiano, Via Zucchi, 18 - 20095 Cusano Milanino (MI); Department of Medical Biotechnology and Translational Medicine, University of Milan, Via Vanvitelli 32, 20133 Milan, Italy
| | | | - Franco Armelao
- U.O. Gastroenterologia ed Endoscopia Digestiva, Ospedale S. Chiara, APSS, Via A. de Gasperi 79 - 38123, Trento, Italy
| | - Alessandra Viel
- Unit of Functional Oncogenomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO) IRCCS, Via F. Gallini 2, 33081 Aviano, Italy.
| | - Maria Grazia Tibiletti
- Department of Pathology, Circolo Hospital ASST Settelaghi, via O. Rossi 9, 21100, Varese, Italy; Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, via O. Rossi 9, 21100, Varese, Italy
| |
Collapse
|
4
|
Caponnetto F, Dalla E, Mangoni D, Piazza S, Radovic S, Ius T, Skrap M, Di Loreto C, Beltrami AP, Manini I, Cesselli D. The miRNA Content of Exosomes Released from the Glioma Microenvironment Can Affect Malignant Progression. Biomedicines 2020; 8:biomedicines8120564. [PMID: 33287106 PMCID: PMC7761654 DOI: 10.3390/biomedicines8120564] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/27/2020] [Accepted: 12/01/2020] [Indexed: 12/13/2022] Open
Abstract
Low-grade gliomas (LGG) are infiltrative primary brain tumors that in 70% of the cases undergo anaplastic transformation, deeply affecting prognosis. However, the timing of progression is heterogeneous. Recently, the tumor microenvironment (TME) has gained much attention either as prognostic factor or therapeutic target. Through the release of extracellular vesicles, the TME contributes to tumor progression by transferring bioactive molecules such as microRNA. The aim of the study was to take advantage of glioma-associated stem cells (GASC), an in vitro model of the glioma microenvironment endowed with a prognostic significance, and their released exosomes, to investigate the possible role of exosome miRNAs in favoring the anaplastic transformation of LGG. Therefore, by deep sequencing, we analyzed and compared the miRNA profile of GASC and exosomes obtained from LGG patients characterized by different prognosis. Results showed that exosomes presented a different signature, when compared to their cellular counterpart and that, although sharing several miRNAs, exosomes of patients with a bad prognosis, selectively expressed some miRNAs possibly responsible for the more aggressive phenotype. These findings get insights into the value of TME and exosomes as potential biomarkers for precision medicine approaches aimed at improving LGG prognostic stratification and therapeutic strategies.
Collapse
Affiliation(s)
- Federica Caponnetto
- Department of Medicine, University of Udine, 33100 Udine, Italy; (E.D.); (C.D.L.); (A.P.B.); (D.C.)
- Correspondence: (F.C.); (I.M.); Tel.: +39-0432-559-412 (F.C. & I.M.)
| | - Emiliano Dalla
- Department of Medicine, University of Udine, 33100 Udine, Italy; (E.D.); (C.D.L.); (A.P.B.); (D.C.)
| | - Damiano Mangoni
- Central RNA Laboratory, Istituto Italiano di Tecnologia (IIT), 16163 Genova, Italy;
| | - Silvano Piazza
- International Center for Genetic Engineering and Biotechnology (ICGEB), 34149 Trieste, Italy;
| | | | - Tamara Ius
- Neurosurgery Unit, Department of Neurosciences, University Hospital of Udine, 33100 Udine, Italy; (T.I.); (M.S.)
| | - Miran Skrap
- Neurosurgery Unit, Department of Neurosciences, University Hospital of Udine, 33100 Udine, Italy; (T.I.); (M.S.)
| | - Carla Di Loreto
- Department of Medicine, University of Udine, 33100 Udine, Italy; (E.D.); (C.D.L.); (A.P.B.); (D.C.)
- Institute of Pathology, University Hospital of Udine, 33100 Udine, Italy
| | - Antonio Paolo Beltrami
- Department of Medicine, University of Udine, 33100 Udine, Italy; (E.D.); (C.D.L.); (A.P.B.); (D.C.)
| | - Ivana Manini
- Institute of Pathology, University Hospital of Udine, 33100 Udine, Italy
- Correspondence: (F.C.); (I.M.); Tel.: +39-0432-559-412 (F.C. & I.M.)
| | - Daniela Cesselli
- Department of Medicine, University of Udine, 33100 Udine, Italy; (E.D.); (C.D.L.); (A.P.B.); (D.C.)
- Institute of Pathology, University Hospital of Udine, 33100 Udine, Italy
| |
Collapse
|
5
|
Todorovic J, Terzic-Supic Z, Divjak J, Kocic S, Radovic S, Ukropina S, Mijatovic-Jovanovic V, Mirkovic M. The reliability of the Study burnout inventory among Medical students. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa165.341] [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: 11/13/2022] Open
Abstract
Abstract
Background
The burnout syndrome is increasingly recognized as the factor compromising the mental health of health-care workers. The demands of higher education were reported to influence the development of burnout syndrome among students. Medical students are a significant population as both future health care workers and students with high academic demands. The burnout among medical students has been studied using different questionnaires. The aim of this study was to assess the psychometric characteristics of the Study Burnout inventory for the assessment of burnout among medical students.
Methods
The cross-sectional study was conducted during December of 2019 among the fifth year Medical students at the five Universities in Serbia (University of Belgrade, Novi Sad, Kragujevac, Nis, and Kosovska Mitrovica). The questionnaire used was the Study Burnout Inventory, nine-item scale, measuring three dimensions of burnout (exhaustion from studying- EXH; cynicism toward the meaningfulness of studying-CYN; the sense of inadequacy as a student-INAD). Answers were given on a six-point Lickert scale. The assessment of psychometric characteristics of the questionnaire was done using the reliability analysis (Cronbach alpha-α) and test-retest reliability (intra-class coefficient-ICC). Sensitivity and specificity were assessed using the Receiver operation curves (ROC) compared to the total burnout assessed by the Copenhagen burnout inventory.
Results
A total of 493 students filled-in the questionnaire. The mean score was 28.95±8.87/54. The Cronbach alpha for the total scale was α = 0.839, for the EXH scale was α = 0.724, for the CYN scale was α = 0.767, and for the INAD scale was α = 0.431. The test-retest reliability was ICC=0.750. The total area under the curve was 0.756 (95% CI: 0.711-0.800).
Conclusions
The Study Burnout Inventory has good reliability and can be used for rapid assessment of burnout among Medical students, as this scale is short and convenient for the participants.
Key messages
The Study burnout inventory has a good reliability as a total scale. This short scale is convenient for the participants and can be used for assessment of burnout.
Collapse
Affiliation(s)
- J Todorovic
- Institute of Social Medicine, Medical Faculty, Belgrade University, Belgrade, Serbia
| | - Z Terzic-Supic
- Institute of Social Medicine, Medical Faculty, Belgrade University, Belgrade, Serbia
| | - J Divjak
- Institute of Social Medicine, Medical Faculty, Belgrade University, Belgrade, Serbia
| | - S Kocic
- University of Kragujevac, Faculty of Medicine, Kragujevac, Serbia
| | - S Radovic
- University of Kragujevac, Faculty of Medicine, Kragujevac, Serbia
| | - S Ukropina
- Institute of Public Health of Vojvodina, Novi Sad, Serbia
| | | | - M Mirkovic
- University of Pristina-Kosovska Mitrovica, Faculty of Medicine, Kosovska Mitrovica, Serbia
| |
Collapse
|
6
|
Terzic-Supic Z, Todorovic J, Divjak J, Kocic S, Radovic S, Ukropina S, Mijatovic-Jovanovic V, Mirkovic M. Anxiety among the Medical students at five Universities in Serbia. Eur J Public Health 2020. [DOI: 10.1093/eurpub/ckaa166.1052] [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: 11/13/2022] Open
Abstract
Abstract
Background
Medical education is both academically and emotionally demanding. The demands of medical school can influence the development of anxiety among medical students. The aim of this study was to assess the prevalence of anxiety and factors associated with it among the fifth year medical students at the five universities in Serbia.
Methods
The cross-sectional study was conducted during December of 2019 and included a total of 493 students at the five Universities in Serbia (Belgrade, Novi Sad, Kragujevac, Nis, and Kosovska Mitrovica). The questionnaire used was developed based on the questionnaires from similar research and included the sections on social characteristics, lifestyle characteristics, study engagement, Beck depression inventory, Copenhagen burnout inventory, and Zung anxiety scale. Based on the score on Zung anxiety scale students were classified in two groups: with anxiety (scores ≥45) and without anxiety (scores 20-44).
Results
The mean Zung anxiety scale score was 35.39±8.31 (minimum=20, maximum=69). A total of 64/493 students (13%) was in the group with anxiety. The multivariate logistic regression analysis with the anxiety as an outcome variable showed that anxiety was associated with female sex (OR: 4.20, 95% CI: 1.41-12.50), higher scores on Beck depression inventory (OR: 1.18, 95% CI: 1.12-1.26), and total burnout (OR: 3.98, 95% CI: 1.66-9.54).
Conclusions
This study shows that students with anxiety have a higher likelihood of higher scores on Beck depression inventory and a higher likelihood of having burnout syndrome. The clustering of mental health problems, along with the high prevalence of anxiety among medical students is alarming.
Key messages
One in eight medical students in Serbia has scores on Zung anxiety scale indicative of at least mild anxiety. The anxiety was associated with female gender, higher score on Beck depression inventory and total burnout.
Collapse
Affiliation(s)
- Z Terzic-Supic
- Institute of Social Medicine, Medical Faculty, Belgrade University, Belgrade, Serbia
| | - J Todorovic
- Institute of Social Medicine, Medical Faculty, Belgrade University, Belgrade, Serbia
| | - J Divjak
- Institute of Social Medicine, Medical Faculty, Belgrade University, Belgrade, Serbia
| | - S Kocic
- University of Kragujevac, Faculty of Medicine, Kragujevac, Serbia
| | - S Radovic
- University of Kragujevac, Faculty of Medicine, Kragujevac, Serbia
| | - S Ukropina
- Institute of Public Health of Vojvodina, Novi Sad, Serbia
| | | | - M Mirkovic
- University of Pristina-Kosovska Mitrovica, Faculty of Medicine, Kosovska Mitrovica, Serbia
| |
Collapse
|
7
|
Ius T, Ciani Y, Ruaro ME, Isola M, Sorrentino M, Bulfoni M, Candotti V, Correcig C, Bourkoula E, Manini I, Pegolo E, Mangoni D, Marzinotto S, Radovic S, Toffoletto B, Caponnetto F, Zanello A, Mariuzzi L, Di Loreto C, Beltrami AP, Piazza S, Skrap M, Cesselli D. An NF-κB signature predicts low-grade glioma prognosis: a precision medicine approach based on patient-derived stem cells. Neuro Oncol 2019; 20:776-787. [PMID: 29228370 DOI: 10.1093/neuonc/nox234] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background While recent genome-wide association studies have suggested novel low-grade glioma (LGG) stratification models based on a molecular classification, we explored the potential clinical utility of patient-derived cells. Specifically, we assayed glioma-associated stem cells (GASC) that are patient-derived and representative of the glioma microenvironment. Methods By next-generation sequencing, we analyzed the transcriptional profile of GASC derived from patients who underwent anaplastic transformation either within 48 months (GASC-BAD) or ≥7 years (GASC-GOOD) after surgery. Gene set enrichment and pathway enrichment analyses were applied. The prognostic role of a nuclear factor-kappaB (NF-κB) signature derived from GASC-BAD was tested in 530 newly diagnosed diffuse LGG patients comprised within The Cancer Genome Atlas (TCGA) database. The prognostic value of the GASC upstream regulator p65 NF-κB was assessed, by univariate and multivariate Cox analyses, in a single center case study, including 146 grade II LGGs. Results The key elements differentiating the transcriptome of GASC isolated from LGG with different prognoses were mostly related to hallmarks of cancer (eg, inflammatory/immune process, NF-κB activation). Consistently, the NF-κB signature extrapolated from the GASC study was prognostic in the dataset of TCGA. Finally, the nuclear expression of the NF-kB-p65 protein, assessed using an inexpensive immunohistochemical method, was an independent predictor of both overall survival and malignant progression-free survival in 146 grade II LGGs. Conclusion This study demonstrates for the first time the independent prognostic role of NF-kB activation in LGG and outlines the role of patient-based stem cell models as a tool for precision medicine approaches.
Collapse
Affiliation(s)
- Tamara Ius
- Department of Neurosurgery, University Hospital of Udine, Udine, Italy
| | - Yari Ciani
- Laboratorio Nazionale, Consorzio Interuniversitario Biotecnologie (LNCIB), Trieste, Italy
| | - Maria Elisabetta Ruaro
- Department of Neurosurgery, University Hospital of Udine, Udine, Italy.,Department of Medicine, University of Udine, Udine, Italy
| | - Miriam Isola
- Department of Medicine, University of Udine, Udine, Italy
| | - Marisa Sorrentino
- Department of Neurosurgery, University Hospital of Udine, Udine, Italy.,Department of Pathology, University Hospital of Udine, Udine, Italy
| | | | | | - Cecilia Correcig
- Department of Pathology, University Hospital of Udine, Udine, Italy
| | | | - Ivana Manini
- Department of Medicine, University of Udine, Udine, Italy
| | - Enrico Pegolo
- Department of Pathology, University Hospital of Udine, Udine, Italy
| | | | | | | | | | | | - Andrea Zanello
- Department of Medicine, University of Udine, Udine, Italy
| | - Laura Mariuzzi
- Department of Medicine, University of Udine, Udine, Italy.,Department of Pathology, University Hospital of Udine, Udine, Italy
| | - Carla Di Loreto
- Department of Medicine, University of Udine, Udine, Italy.,Department of Pathology, University Hospital of Udine, Udine, Italy
| | | | - Silvano Piazza
- Laboratorio Nazionale, Consorzio Interuniversitario Biotecnologie (LNCIB), Trieste, Italy.,Bioinformatics Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, Trento, Italy
| | - Miran Skrap
- Department of Neurosurgery, University Hospital of Udine, Udine, Italy.,Department of Pathology, University Hospital of Udine, Udine, Italy
| | | |
Collapse
|
8
|
Abstract
Shotgun metagenomics sequencing is a powerful tool for the characterization of complex biological matrices, enabling analysis of prokaryotic and eukaryotic organisms and viruses in a single experiment, with the possibility of reconstructing
de novo the whole metagenome or a set of genes of interest. One of the main factors limiting the use of shotgun metagenomics on wide scale projects is the high cost associated with the approach. We set out to determine if it is possible to use shallow shotgun metagenomics to characterize complex biological matrices while reducing costs. We used a staggered mock community to estimate the optimal threshold for species detection. We measured the variation of several summary statistics simulating a decrease in sequencing depth by randomly subsampling a number of reads. The main statistics that were compared are diversity estimates, species abundance, and ability of reconstructing
de novo the metagenome in terms of length and completeness. Our results show that diversity indices of complex prokaryotic, eukaryotic and viral communities can be accurately estimated with 500,000 reads or less, although particularly complex samples may require 1,000,000 reads. On the contrary, any task involving the reconstruction of the metagenome performed poorly, even with the largest simulated subsample (1,000,000 reads). The length of the reconstructed assembly was smaller than the length obtained with the full dataset, and the proportion of conserved genes that were identified in the meta-genome was drastically reduced compared to the full sample. Shallow shotgun metagenomics can be a useful tool to describe the structure of complex matrices, but it is not adequate to reconstruct—even partially—the metagenome.
Collapse
Affiliation(s)
| | | | | | - Fabio Marroni
- IGA Technology Services Srl, Udine, Udine, 33100, Italy.,Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, 33100, Italy
| |
Collapse
|
9
|
Radovic S, Dubsky De Wittenau G, Mandl N, Betto E, Curcio F, Morgante M, Lonigro IR. A versatile method for gene dosage quantification: multiplex PCR and single base extension for copy number and gene-conversion identification of SMN genes. J BIOL REG HOMEOS AG 2018; 32:115-121. [PMID: 29504374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A comparison of the individual genomes within a species demonstrates that structural variation, including copy number variation (CNV), is a major contributor to phenotypic diversity and evolutionary adaptation. CNVs lead to the under/over-expression of a gene, according to the changes in the gene dosage, which account for the development of a number of genomic disorders. Thus, the development of efficient, rapid and accurate CNV screening is of fundamental importance. We report a method that enables the simultaneous determination of the copy numbers of several different targets as well as the discrimination among highly similar/almost identical targets that differ by only one single nucleotide variant, which establishes their copy numbers. The PCR co-amplification and single-base extension technologies are used to identify the copy number of a target sequence relative to a reference sequence of known genomic copy number in a given sample. This efficient and accurate quantification platform was successfully used to quantify the copy numbers of the primary spinal muscular atrophy-determining gene, SMN1, and the disease modifier gene, SMN2. The reliability, low-cost and potential for high-throughput make our method suitable for screening large populations as well as for use as a tool in clinical settings for genetic diagnosis/prognosis.
Collapse
Affiliation(s)
- S Radovic
- IGA Technology Services, Udine, Italy
| | | | - N Mandl
- Medical and Pharmaceutical Biotechnology, University of Applied Sciences, Krems, Austria
| | - E Betto
- Department of Medical Area, University of Udine, Udine, Italy
| | - F Curcio
- Department of Medical Area, University of Udine, Udine, Italy
- Department of Laboratory Medicine, SOC Institute of Clinical Pathology, ASUI of Udine,Udine, Italy
| | - M Morgante
- Institute of Applied Genomics, Udine, Italy
- Department of Agrofood, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - I R Lonigro
- Department of Medical Area, University of Udine, Udine, Italy
- Department of Laboratory Medicine, SOC Institute of Clinical Pathology, ASUI of Udine,Udine, Italy
| |
Collapse
|
10
|
Antoniali G, Serra F, Lirussi L, Tanaka M, D'Ambrosio C, Zhang S, Radovic S, Dalla E, Ciani Y, Scaloni A, Li M, Piazza S, Tell G. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Nat Commun 2017; 8:797. [PMID: 28986522 PMCID: PMC5630600 DOI: 10.1038/s41467-017-00842-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/28/2017] [Indexed: 01/31/2023] Open
Abstract
Mammalian apurinic/apyrimidinic endonuclease 1 is a DNA repair enzyme involved in genome stability and expression of genes involved in oxidative stress responses, tumor progression and chemoresistance. However, the molecular mechanisms underlying the role of apurinic/apyrimidinic endonuclease 1 in these processes are still unclear. Recent findings point to a novel role of apurinic/apyrimidinic endonuclease 1 in RNA metabolism. Through the characterization of the interactomes of apurinic/apyrimidinic endonuclease 1 with RNA and other proteins, we demonstrate here a role for apurinic/apyrimidinic endonuclease 1 in pri-miRNA processing and stability via association with the DROSHA-processing complex during genotoxic stress. We also show that endonuclease activity of apurinic/apyrimidinic endonuclease 1 is required for the processing of miR-221/222 in regulating expression of the tumor suppressor PTEN. Analysis of a cohort of different cancers supports the relevance of our findings for tumor biology. We also show that apurinic/apyrimidinic endonuclease 1 participates in RNA-interactomes and protein-interactomes involved in cancer development, thus indicating an unsuspected post-transcriptional effect on cancer genes. APE1 plays an important role in the cellular response to oxidative stress, and mutations are linked to tumor progression and chemoresistance. Here, the authors characterize the interactions of APE1 with RNA and demonstrate a role in microRNA processing.
Collapse
Affiliation(s)
- Giulia Antoniali
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy
| | - Fabrizio Serra
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.,Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, I.R.C.C.S., via Franco Gallini 2, Aviano (PN), 33081, Italy
| | - Lisa Lirussi
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.,Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Sykehusveien 27, Nordbyhagen, 1474, Norway
| | - Mikiei Tanaka
- Laboratory of Biochemistry, National Heart Lung and Blood Institute, National Institutes of Health, 50 South Drive, MSC-8012, Bethesda, MD, 20892-8012, USA
| | - Chiara D'Ambrosio
- Proteomics and Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment (ISPAAM) National Research Council (CNR) of Italy, via Argine 1085, Naples, 80147, Italy
| | - Shiheng Zhang
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, 400042, China
| | | | - Emiliano Dalla
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy
| | - Yari Ciani
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy
| | - Andrea Scaloni
- Proteomics and Mass Spectrometry Laboratory, Institute for the Animal Production System in the Mediterranean Environment (ISPAAM) National Research Council (CNR) of Italy, via Argine 1085, Naples, 80147, Italy
| | - Mengxia Li
- Cancer Center of Daping Hospital, Third Military Medical University, Chongqing, 400042, China.
| | - Silvano Piazza
- Laboratorio Nazionale CIB, Area Science Park Padriciano, Trieste, 34149, Italy. .,Bioinformatics Core Facility, Centre for Integrative Biology, CIBIO, University of Trento, via Sommarive 18, Povo, Trento, TN, 38123, Italy.
| | - Gianluca Tell
- Department of Medicine, Laboratory of Molecular Biology and DNA repair, University of Udine, p.le M. Kolbe 4, Udine, 33100, Italy.
| |
Collapse
|
11
|
Dazzo E, Fanciulli M, Serioli E, Minervini G, Pulitano P, Binelli S, Di Bonaventura C, Luisi C, Pasini E, Striano S, Striano P, Coppola G, Chiavegato A, Radovic S, Spadotto A, Uzzau S, La Neve A, Giallonardo AT, Mecarelli O, Tosatto SCE, Ottman R, Michelucci R, Nobile C. Heterozygous reelin mutations cause autosomal-dominant lateral temporal epilepsy. Am J Hum Genet 2015; 96:992-1000. [PMID: 26046367 PMCID: PMC4457960 DOI: 10.1016/j.ajhg.2015.04.020] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [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] [Received: 02/11/2015] [Accepted: 04/29/2015] [Indexed: 01/28/2023] Open
Abstract
Autosomal-dominant lateral temporal epilepsy (ADLTE) is a genetic epilepsy syndrome clinically characterized by focal seizures with prominent auditory symptoms. ADLTE is genetically heterogeneous, and mutations in LGI1 account for fewer than 50% of affected families. Here, we report the identification of causal mutations in reelin (RELN) in seven ADLTE-affected families without LGI1 mutations. We initially investigated 13 ADLTE-affected families by performing SNP-array linkage analysis and whole-exome sequencing and identified three heterozygous missense mutations co-segregating with the syndrome. Subsequent analysis of 15 small ADLTE-affected families revealed four additional missense mutations. 3D modeling predicted that all mutations have structural effects on protein-domain folding. Overall, RELN mutations occurred in 7/40 (17.5%) ADLTE-affected families. RELN encodes a secreted protein, Reelin, which has important functions in both the developing and adult brain and is also found in the blood serum. We show that ADLTE-related mutations significantly decrease serum levels of Reelin, suggesting an inhibitory effect of mutations on protein secretion. We also show that Reelin and LGI1 co-localize in a subset of rat brain neurons, supporting an involvement of both proteins in a common molecular pathway underlying ADLTE. Homozygous RELN mutations are known to cause lissencephaly with cerebellar hypoplasia. Our findings extend the spectrum of neurological disorders associated with RELN mutations and establish a link between RELN and LGI1, which play key regulatory roles in both the developing and adult brain.
Collapse
MESH Headings
- Animals
- Base Sequence
- Cell Adhesion Molecules, Neuronal/blood
- Cell Adhesion Molecules, Neuronal/chemistry
- Cell Adhesion Molecules, Neuronal/genetics
- Cell Adhesion Molecules, Neuronal/metabolism
- Chromosome Mapping
- Epilepsy, Frontal Lobe/genetics
- Epilepsy, Frontal Lobe/pathology
- Exome
- Extracellular Matrix Proteins/blood
- Extracellular Matrix Proteins/chemistry
- Extracellular Matrix Proteins/genetics
- Extracellular Matrix Proteins/metabolism
- Fluorescent Antibody Technique
- Gene Components
- Humans
- Immunoblotting
- Intercellular Signaling Peptides and Proteins
- Models, Molecular
- Molecular Sequence Data
- Mutation, Missense/genetics
- Nerve Tissue Proteins/blood
- Nerve Tissue Proteins/chemistry
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Pedigree
- Polymorphism, Single Nucleotide/genetics
- Protein Conformation
- Protein Folding
- Proteins/metabolism
- Rats
- Reelin Protein
- Sequence Analysis, DNA
- Serine Endopeptidases/blood
- Serine Endopeptidases/chemistry
- Serine Endopeptidases/genetics
- Serine Endopeptidases/metabolism
- Sleep Wake Disorders/genetics
- Sleep Wake Disorders/pathology
Collapse
Affiliation(s)
- Emanuela Dazzo
- Section of Padua, Institute of Neuroscience, Consiglio Nazionale delle Ricerche, 35121 Padova, Italy
| | | | - Elena Serioli
- Section of Padua, Institute of Neuroscience, Consiglio Nazionale delle Ricerche, 35121 Padova, Italy
| | - Giovanni Minervini
- Department of Biomedical Sciences, University of Padua, 35121 Padova, Italy
| | - Patrizia Pulitano
- Department of Neurology and Psychiatry, Sapienza University of Rome, 00185 Roma, Italy
| | - Simona Binelli
- Carlo Besta Foundation Neurological Institute, 20133 Milano, Italy
| | - Carlo Di Bonaventura
- Department of Neurology and Psychiatry, Sapienza University of Rome, 00185 Roma, Italy
| | | | - Elena Pasini
- IRCCS-Institute of Neurological Sciences, Bellaria Hospital, 40139 Bologna, Italy
| | - Salvatore Striano
- Department of Neurosciences and Reproductive and Odontostomatological Sciences, School of Medicine, University of Naples Federico II, 80131 Napoli, Italy
| | - Pasquale Striano
- Department of Neuroscience, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa and Giannina Gaslini Institute, 16148 Genova, Italy
| | - Giangennaro Coppola
- Child and Adolescent Psychiatry, Faculty of Medicine and Surgery, University of Salerno, 84100 Salerno, Italy
| | - Angela Chiavegato
- Section of Padua, Institute of Neuroscience, Consiglio Nazionale delle Ricerche, 35121 Padova, Italy
| | | | | | - Sergio Uzzau
- Porto Conte Ricerche, 07041 Alghero, Sassari, Italy
| | | | | | - Oriano Mecarelli
- Department of Neurology and Psychiatry, Sapienza University of Rome, 00185 Roma, Italy
| | - Silvio C E Tosatto
- Section of Padua, Institute of Neuroscience, Consiglio Nazionale delle Ricerche, 35121 Padova, Italy; Department of Biomedical Sciences, University of Padua, 35121 Padova, Italy
| | - Ruth Ottman
- Departments of Epidemiology and Neurology and the Gertrude H. Sergievsky Center, Columbia University, New York, NY 10032, USA; Division of Epidemiology, New York State Psychiatric Institute, New York, NY 10032, USA
| | - Roberto Michelucci
- IRCCS-Institute of Neurological Sciences, Bellaria Hospital, 40139 Bologna, Italy
| | - Carlo Nobile
- Section of Padua, Institute of Neuroscience, Consiglio Nazionale delle Ricerche, 35121 Padova, Italy; Department of Biomedical Sciences, University of Padua, 35121 Padova, Italy.
| |
Collapse
|
12
|
Fanciulli M, Di Bonaventura C, Egeo G, Fattouch J, Dazzo E, Radovic S, Spadotto A, Giallonardo AT, Nobile C. Suggestive linkage of familial mesial temporal lobe epilepsy to chromosome 3q26. Epilepsy Res 2013; 108:232-40. [PMID: 24315020 DOI: 10.1016/j.eplepsyres.2013.11.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 09/26/2013] [Accepted: 11/03/2013] [Indexed: 12/01/2022]
Abstract
PURPOSE To describe the clinical findings in a family with a benign form of mesial temporal lobe epilepsy and to identify the causative genetic factors. METHODS All participants were personally interviewed and underwent neurologic examination. The affected subjects underwent EEG and most of them neuroradiological examinations (MRI). All family members were genotyped with the HumanCytoSNP-12 v1.0 beadchip and linkage analysis was performed with Merlin and Simwalk2 programs. Exome sequencing was performed on HiSeq2000, after exome capture with SureSelect 50 Mb kit v2.0. RESULTS The family had 6 members with temporal lobe epilepsy. Age at seizure onset ranged from 8 to 13 years. Five patients had epigastric auras often associated to oro-alimentary automatic activity, 3 patients presented loss of contact, and 2 experienced secondary generalizations. Febrile seizures occurred in 2 family members, 1 of whom also had temporal lobe epilepsy. EEG showed focal slow waves and epileptic abnormalities on temporal regions in 1 patient and was normal in the other affected individuals. MRI was normal in all temporal lobe epilepsy patients. We performed single nucleotide polymorphism-array linkage analysis of the family and found suggestive evidence of linkage (LOD score=2.106) to a region on chromosome 3q26. Haplotype reconstruction supported the linkage data and showed that the majority of unaffected family members carried the haplotype at risk. Whole exome sequencing failed to identify pathogenic mutations in genes of the candidate region. CONCLUSIONS Our data suggest the existence of a novel locus for benign familial mesial temporal lobe epilepsy on chromosome 3q26. Our failure to identify pathogenic mutations in genes of this region may be due to limitations of the exome sequencing technology.
Collapse
Affiliation(s)
| | | | - Gabriella Egeo
- Department of Neurological Sciences, University of Rome "Sapienza", Roma, Italy; IRCCS San Raffaele Pisana, Roma, Italy
| | - Jinane Fattouch
- Department of Neurological Sciences, University of Rome "Sapienza", Roma, Italy
| | - Emanuela Dazzo
- CNR - Institute of Neurosciences, Section of Padua, Padova, Italy
| | | | | | | | - Carlo Nobile
- CNR - Institute of Neurosciences, Section of Padua, Padova, Italy.
| |
Collapse
|
13
|
Druka A, Franckowiak J, Lundqvist U, Bonar N, Alexander J, Houston K, Radovic S, Shahinnia F, Vendramin V, Morgante M, Stein N, Waugh R. Genetic dissection of barley morphology and development. Plant Physiol 2011; 155:617-27. [PMID: 21088227 PMCID: PMC3032454 DOI: 10.1104/pp.110.166249] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Accepted: 11/14/2010] [Indexed: 05/18/2023]
Abstract
Since the early 20th century, barley (Hordeum vulgare) has been a model for investigating the effects of physical and chemical mutagens and for exploring the potential of mutation breeding in crop improvement. As a consequence, extensive and well-characterized collections of morphological and developmental mutants have been assembled that represent a valuable resource for exploring a wide range of complex and fundamental biological processes. We constructed a collection of 881 backcrossed lines containing mutant alleles that induce a majority of the morphological and developmental variation described in this species. After genotyping these lines with up to 3,072 single nucleotide polymorphisms, comparison to their recurrent parent defined the genetic location of 426 mutant alleles to chromosomal segments, each representing on average <3% of the barley genetic map. We show how the gene content in these segments can be predicted through conservation of synteny with model cereal genomes, providing a route to rapid gene identification.
Collapse
Affiliation(s)
- Arnis Druka
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Passon N, Dubsky de Wittenau G, Jurman I, Radovic S, Bregant E, Molinis C, Damante G, Lonigro IR. Quick MLPA test for quantification of SMN1 and SMN2 copy numbers. Mol Cell Probes 2010; 24:310-4. [PMID: 20659551 DOI: 10.1016/j.mcp.2010.07.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 07/08/2010] [Accepted: 07/09/2010] [Indexed: 12/23/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive disease caused in about 95% of SMA patients by homozygous deletion of the survival motor neuron 1 (SMN1) gene or its conversion to the highly homologous SMN2 gene. In the majority of cases, disease severity correlates inversely with increased SMN2 copy number. Because of the comparatively high incidence of healthy carriers and severity of the disease, detection of sequence alterations and quantification of SMN1 and SMN2 copy numbers are essential for exact diagnosis and genetic counselling. Several assays have been developed for this purpose. Multiplex ligation-dependent probe amplification (MLPA) is a versatile technique for relative quantification of different nucleic acid sequences in a single reaction. Here, we establish a quick MLPA-based assay for the detection of SMN1 and SMN2 copy numbers with high specificity and low complexity.
Collapse
Affiliation(s)
- Nadia Passon
- Dipartimento di Scienze e Tecnologie Biomediche, Università di Udine, P.le M. Kolbe 1, 33100 Udine, Italy
| | | | | | | | | | | | | | | |
Collapse
|
15
|
von Korff M, Radovic S, Choumane W, Stamati K, Udupa SM, Grando S, Ceccarelli S, Mackay I, Powell W, Baum M, Morgante M. Asymmetric allele-specific expression in relation to developmental variation and drought stress in barley hybrids. Plant J 2009; 59:14-26. [PMID: 19309461 DOI: 10.1111/j.1365-313x.2009.03848.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In the present study, we analysed allele-specific expression (ASE) in the selfing species barley to assess the frequency of cis-acting regulatory variation and the effects of genetic background, developmental differences and drought stress on allelic expression levels. We measured ASE ratios in 30 genes putatively involved in stress responses in five hybrids and their reciprocals, namely Hordeum spontaneum 41-1/Alexis (HAl), Hordeum spontaneum 41-1/Arta (HAr), Sloop/WI3408 (SW), Tadmor/Sloop (TS) and Tadmor/WI3408 (TW). In order to detect cis-acting variation related to drought and developmental changes, the barley hybrids were grown under control and water-limited conditions, and leaf tissue was harvested at two developmental stages. The analysis demonstrated that more than half of the genes measured (63%) showed allelic differences in expression of up to 19-fold due to cis-regulatory variation in at least one cross by treatment/stage combination. Drought stress induced changes in allelic expression ratios, indicating differences between drought responsive cis-elements. In addition, ASE differences between developmental stages suggested the presence of cis-acting elements interacting with developmental cues. We were also able to demonstrate that the levels and frequency of allelic imbalance and hence differences in cis-regulatory elements are correlated with the genetic divergence between the parental lines, but may also arise as an adaptation to diverse habitats. Our findings suggest that cis-regulatory variation is a common phenomenon in barley, and may provide a molecular basis of transgression. Differential expression of near-isogenic members of the same gene family could potentially result in hybrid lines out performing their parents in terms of expression level, timing and response to developmental and environmental cues. Identification and targeted manipulation of cis-regulatory elements will assist in breeding improved crops with a better adaptation to changing environments.
Collapse
Affiliation(s)
- Maria von Korff
- International Center for Agricultural Research in the Dry Areas, PO Box 5466, Aleppo, Syria
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Castronovo M, Radovic S, Grunwald C, Casalis L, Morgante M, Scoles G. Control of steric hindrance on restriction enzyme reactions with surface-bound DNA nanostructures. Nano Lett 2008; 8:4140-4145. [PMID: 19367999 DOI: 10.1021/nl802370g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To understand better enzyme/DNA interactions and to design innovative detectors based on DNA nanoarrays, we need to study the effect of nanometric confinement on the biochemical activity of the DNA molecules. We focus on the study of the restriction enzyme reactions (DpnII) within DNA nanostructures on flat gold films by atomic force microscopy (AFM). Typically we work with a few patches of DNA self assembled monolayers (SAMs) that are hundred nm in size and are lithographically fabricated within alkylthiol SAMs by AFM nanografting. We start by nanografting a few patches of a single-stranded DNA (ssDNA) molecule of 44 base pairs (bps) with a 4 bps recognition sequence (specific for DpnII) in the middle. Afterwards, reaction-ready DNA nanopatches are obtained by hybridization with a complementary 44bps ssDNA sequence. The enzymatic reactions were carried out over nanopatches with different density. By carrying out AFM height measurements, we are able to show that the capability of the DpnII enzyme to reach and react at the recognition site is easily varied by controlling the DNA packing in the nanostructures. We have found strong evidence that inside our ordered DNA nanostructures the enzyme (that works as a dimer) can operate down to the limit in which the space between adjacent DNA molecules is equal to the size of the DNA/enzyme complex. Similar experiments were carried out with a DNA sequence without the recognition site, clearly finding that in that case the enzymatic reaction did not lead to digestion of the molecules. These findings suggest that it is possible to tune the efficiency of an enzymatic reaction on a surface by controlling the steric hindrance inside the DNA nanopatches without vary any further physical or chemical variable. These findings are opening the door to novel applications in both the fields of biosensing and fundamental biophysics.
Collapse
Affiliation(s)
- Matteo Castronovo
- Sincrotrone Trieste S.C.p.A., S.S. 14 Km 163.5, 34012 Basovizza, Trieste, Italy
| | | | | | | | | | | |
Collapse
|
17
|
Salvi S, Sponza G, Morgante M, Tomes D, Niu X, Fengler KA, Meeley R, Ananiev EV, Svitashev S, Bruggemann E, Li B, Hainey CF, Radovic S, Zaina G, Rafalski JA, Tingey SV, Miao GH, Phillips RL, Tuberosa R. Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci U S A 2007; 104:11376-81. [PMID: 17595297 PMCID: PMC2040906 DOI: 10.1073/pnas.0704145104] [Citation(s) in RCA: 354] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Flowering time is a fundamental trait of maize adaptation to different agricultural environments. Although a large body of information is available on the map position of quantitative trait loci for flowering time, little is known about the molecular basis of quantitative trait loci. Through positional cloning and association mapping, we resolved the major flowering-time quantitative trait locus, Vegetative to generative transition 1 (Vgt1), to an approximately 2-kb noncoding region positioned 70 kb upstream of an Ap2-like transcription factor that we have shown to be involved in flowering-time control. Vgt1 functions as a cis-acting regulatory element as indicated by the correlation of the Vgt1 alleles with the transcript expression levels of the downstream gene. Additionally, within Vgt1, we identified evolutionarily conserved noncoding sequences across the maize-sorghum-rice lineages. Our results support the notion that changes in distant cis-acting regulatory regions are a key component of plant genetic adaptation throughout breeding and evolution.
Collapse
Affiliation(s)
- Silvio Salvi
- *Department of Agroenvironmental Science and Technology, University of Bologna, Viale Fanin, 44, 40127 Bologna, Italy
- To whom correspondence may be addressed. E-mail: or
| | - Giorgio Sponza
- *Department of Agroenvironmental Science and Technology, University of Bologna, Viale Fanin, 44, 40127 Bologna, Italy
| | - Michele Morgante
- Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze, 208, 33100 Udine, Italy
| | - Dwight Tomes
- Pioneer Hi-Bred International, 7250 NW 62nd Avenue, Johnston, IA 50131
| | - Xiaomu Niu
- Pioneer Hi-Bred International, 7250 NW 62nd Avenue, Johnston, IA 50131
| | - Kevin A. Fengler
- Experimental Station, Crop Genetics Research and Development, DuPont, Wilmington, DE 19880; and
| | - Robert Meeley
- Pioneer Hi-Bred International, 7250 NW 62nd Avenue, Johnston, IA 50131
| | | | - Sergei Svitashev
- Pioneer Hi-Bred International, 7250 NW 62nd Avenue, Johnston, IA 50131
| | - Edward Bruggemann
- Pioneer Hi-Bred International, 7250 NW 62nd Avenue, Johnston, IA 50131
| | - Bailin Li
- Experimental Station, Crop Genetics Research and Development, DuPont, Wilmington, DE 19880; and
| | - Christine F. Hainey
- Experimental Station, Crop Genetics Research and Development, DuPont, Wilmington, DE 19880; and
| | - Slobodanka Radovic
- Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze, 208, 33100 Udine, Italy
| | - Giusi Zaina
- Department of Agricultural and Environmental Sciences, University of Udine, Via delle Scienze, 208, 33100 Udine, Italy
| | - J.-Antoni Rafalski
- Experimental Station, Crop Genetics Research and Development, DuPont, Wilmington, DE 19880; and
| | - Scott V. Tingey
- Experimental Station, Crop Genetics Research and Development, DuPont, Wilmington, DE 19880; and
| | - Guo-Hua Miao
- Pioneer Hi-Bred International, 7250 NW 62nd Avenue, Johnston, IA 50131
| | - Ronald L. Phillips
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, St. Paul, MN 55108
- To whom correspondence may be addressed. E-mail: or
| | - Roberto Tuberosa
- *Department of Agroenvironmental Science and Technology, University of Bologna, Viale Fanin, 44, 40127 Bologna, Italy
| |
Collapse
|
18
|
Morgante M, De Paoli E, Radovic S. Transposable elements and the plant pan-genomes. Curr Opin Plant Biol 2007; 10:149-55. [PMID: 17300983 DOI: 10.1016/j.pbi.2007.02.001] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Accepted: 02/01/2007] [Indexed: 05/09/2023]
Abstract
The comparative sequencing of several grass genomes has revealed that transposable elements are largely responsible for extensive variation in both intergenic and local genic content, not only between closely related species but also among individuals within a species. These observations indicate that a single genome sequence might not reflect the entire genomic complement of a species, and prompted us to introduce the concept of the plant pan-genome, which includes core genomic features that are common to all individuals and a dispensable genome composed of partially shared and/or non-shared DNA sequence elements. Uncovering the intriguing nature of the dispensable genome, namely its composition, origin and function, represents a step forward towards an understanding of the processes that generate genetic diversity and phenotypic variation. The developing view of transcriptional regulation as a complex and modular system, in which long-range interactions and the involvement of transposable elements are frequently observed, lends support to the possibility of an important functional role for the dispensable genome and could make it less dispensable than previously thought.
Collapse
Affiliation(s)
- Michele Morgante
- Dipartimento di Scienze Agrarie ed Ambientali, Universita' di Udine, Via delle Scienze 208, I-33100 Udine, Italy.
| | | | | |
Collapse
|
19
|
Radovic S, Rapisarda VA, Tosato V, Bruschi CV. Functional and comparative characterization of Saccharomyces cerevisiae RVB1 and RVB2 genes with bacterial Ruv homologues. FEMS Yeast Res 2007; 7:527-39. [PMID: 17302941 DOI: 10.1111/j.1567-1364.2006.00205.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Expression of yeast RuvB-like gene analogues of bacterial RuvB is self-regulated, as episomal overexpression of RVB1 and RVB2 decreases the expression of their chromosomal copies by 85%. Heterozygosity for either gene correlates with lower double-strand break repair of inverted-repeat DNA and decreased survival after UV irradiation, suggesting their haploinsufficiency, while overexpression of the bacterial RuvAB complex improves UV survival in yeast. Rvb2p preferentially binds artificial DNA Holiday junctions like the bacterial RuvAB complex, whereas Rvb1p binds to duplex or cruciform DNA. As both proteins also interact with chromatin, their role in recombination and repair through chromatin remodelling, and their evolutionary relationship to the bacterial homologue, is discussed.
Collapse
Affiliation(s)
- Slobodanka Radovic
- Yeast Molecular Genetics Group, ICGEB, Area Science Park - W, Trieste, Italy
| | | | | | | |
Collapse
|
20
|
Waghmare SK, Caputo V, Radovic S, Bruschi CV. Specific targeted integration of kanamycin resistance-associated nonselectable DNA in the genome of the yeast Saccharomyces cerevisiae. Biotechniques 2003; 34:1024-8, 1033. [PMID: 12765029 DOI: 10.2144/03345rr02] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Sophisticated genome manipulation requires the possibility to modify any intergenic or intragenic DNA sequence at will, without leaving large amounts of undesired vector DNA at the site of alteration. To this end, a series of vectors was developed from a previous gene knockout plasmid system to integrate nonselectable foreign DNA at any desired genomic location in yeast, with a minimum amount of residual plasmid DNA. These vectors have two mutated Flp recognition targets (FRT) sequences flanking the KanMX4 gene and multiple sites for subcloning the DNA fragment to be integrated. The selectable marker can be recycled by Flp site-specific excision between the identical FRTs, thereby allowing the integration of further DNA fragments. With this system, the NLS-tetR-GFP and DsRed genes were successfully integrated at the thr1 locus, and the RVB1 gene was tagged at the C-terminus with the V5-epitope-6-histidine tag. This plasmid system provides for a new molecular tool to integrate any DNA fragment at any genome location in [cir+] yeast strains. Moreover, the system can be extrapolated to other eukaryotic cells in which the FLP/FRT system functions efficiently.
Collapse
Affiliation(s)
- Sanjeev K Waghmare
- International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | | |
Collapse
|