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Domenico Simone
Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden

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Article
Published: 12 July 2021 in Nature Communications
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While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.

ACS Style

Maliheh Mehrshad; Margarita Lopez-Fernandez; John Sundh; Emma Bell; Domenico Simone; Moritz Buck; Rizlan Bernier-Latmani; Stefan Bertilsson; Mark Dopson. Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nature Communications 2021, 12, 1 -12.

AMA Style

Maliheh Mehrshad, Margarita Lopez-Fernandez, John Sundh, Emma Bell, Domenico Simone, Moritz Buck, Rizlan Bernier-Latmani, Stefan Bertilsson, Mark Dopson. Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nature Communications. 2021; 12 (1):1-12.

Chicago/Turabian Style

Maliheh Mehrshad; Margarita Lopez-Fernandez; John Sundh; Emma Bell; Domenico Simone; Moritz Buck; Rizlan Bernier-Latmani; Stefan Bertilsson; Mark Dopson. 2021. "Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater." Nature Communications 12, no. 1: 1-12.

Case report
Published: 25 May 2021 in Pathogens
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Background: S. enterica subsp. houtenae has been rarely documented, and very limited genomic information is available. This report describes a rare case of primary extraintestinal salmonellosis in a young roe deer, associated with Salmonella enterica subsp. houtenae. Methods: A traditional cultural-based analysis was carried out from the contents of a neck abscess; biochemical identification and PCR assay were performed to isolate and identify the pathogen. Through whole-genome sequencing (WGS), multilocus sequence typing (MLST), core genome MLST (cgMLST), and the Salmonella pathogenicity islands (SPIs) survey, resistome and virulome genes were investigated to gain insight into the virulence and antimicrobial resistance of S. houtenae. Results: Biochemical identification and PCR confirmed the presence of Salmonella spp. in the swelling. The WGS analysis identified Salmonella enterica subspecies houtenae serovar 43:z4,z23:- and ST 958. The virulence study predicted a multidrug resistance pattern with resistance shown against aminoglycosides, tetracycline, beta-lactamase, fluoroquinolones, fosfomycin, nitroimidazole, aminocoumarin, and peptide. Fifty-three antibiotic-resistant genes were identified. No plasmids were detected. Conclusion: This study demonstrates the importance of continuous surveillance of pathogenic salmonellae. Biomolecular analyses combined with epidemiological data can provide important information about poorly described Salmonella strains and can help to improve animal welfare.

ACS Style

Adriana Trotta; Laura Del Sambro; Michela Galgano; Stefano Ciccarelli; Erika Ottone; Domenico Simone; Antonio Parisi; Domenico Buonavoglia; Marialaura Corrente. Salmonella enterica Subsp. houtenae Associated with an Abscess in Young Roe Deer (Capreolus capreolus). Pathogens 2021, 10, 654 .

AMA Style

Adriana Trotta, Laura Del Sambro, Michela Galgano, Stefano Ciccarelli, Erika Ottone, Domenico Simone, Antonio Parisi, Domenico Buonavoglia, Marialaura Corrente. Salmonella enterica Subsp. houtenae Associated with an Abscess in Young Roe Deer (Capreolus capreolus). Pathogens. 2021; 10 (6):654.

Chicago/Turabian Style

Adriana Trotta; Laura Del Sambro; Michela Galgano; Stefano Ciccarelli; Erika Ottone; Domenico Simone; Antonio Parisi; Domenico Buonavoglia; Marialaura Corrente. 2021. "Salmonella enterica Subsp. houtenae Associated with an Abscess in Young Roe Deer (Capreolus capreolus)." Pathogens 10, no. 6: 654.

Journal article
Published: 22 April 2021 in Viruses
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In order to provide insights into the evolutionary and epidemiological viral dynamics during the current COVID-19 pandemic in South Eastern Italy, a total of 298 genomes of SARS-CoV-2 strains collected in the Apulia and Basilicata regions, between March 2020 and January 2021, were sequenced. The genomic analysis performed on the draft genomes allowed us to assign the genetic clades and lineages of belonging to each sample and provide an overview of the main circulating viral variants. Our data showed the spread in Apulia and Basilicata of SARS-CoV-2 variants which have emerged during the second wave of infections and are being currently monitored worldwide for their increased transmission rate and their possible impact on vaccines and therapies. These results emphasize the importance of genome sequencing for the epidemiological surveillance of the new SARS-CoV-2 variants’ spread.

ACS Style

Loredana Capozzi; Angelica Bianco; Laura Del Sambro; Domenico Simone; Antonio Lippolis; Maria Notarnicola; Graziano Pesole; Lorenzo Pace; Domenico Galante; Antonio Parisi. Genomic Surveillance of Circulating SARS-CoV-2 in South East Italy: A One-Year Retrospective Genetic Study. Viruses 2021, 13, 731 .

AMA Style

Loredana Capozzi, Angelica Bianco, Laura Del Sambro, Domenico Simone, Antonio Lippolis, Maria Notarnicola, Graziano Pesole, Lorenzo Pace, Domenico Galante, Antonio Parisi. Genomic Surveillance of Circulating SARS-CoV-2 in South East Italy: A One-Year Retrospective Genetic Study. Viruses. 2021; 13 (5):731.

Chicago/Turabian Style

Loredana Capozzi; Angelica Bianco; Laura Del Sambro; Domenico Simone; Antonio Lippolis; Maria Notarnicola; Graziano Pesole; Lorenzo Pace; Domenico Galante; Antonio Parisi. 2021. "Genomic Surveillance of Circulating SARS-CoV-2 in South East Italy: A One-Year Retrospective Genetic Study." Viruses 13, no. 5: 731.

Article
Published: 28 October 2019 in Limnology and Oceanography
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Warming climate is thawing the permafrost in arctic and subarctic regions, leading to formation of thermokarst ponds. During the formation and geomorphological succession of these ponds, carbon that has been trapped in frozen soils for thousands of years is hydrologically mobilized and returned to the active carbon cycle. We sampled 12 thermokarst ponds representing three different stages of pond succession to study the potential of microbial communities to metabolize the organic carbon in the water. We investigated the quality of the dissolved organic carbon (DOC) in the water column based on the spectrophotometric and fluorometric properties of the chromophoric dissolved organic matter combined with parallel factor analysis and the potential of the microbial community for degrading these carbon compounds based on genetic markers related to carbon degradation. Our analysis showed a clear difference in the DOC quality across the different developmental stages. In the younger ponds, organic matter quality suggested that it was originating from the degrading permafrost and in the metagenomes collected from these ponds, the normalized abundance of genes related to degradation of carbon compounds was higher. There was also a shift in the degradation potential in the water column of the ponds, with higher potential for organic matter degradation in deeper, anoxic layers. In conclusion, our results show that the DOC quality and the genetic potential of the microbial community for carbon cycling change across the pond ontogeny, suggesting a capacity of the microbial communities to adapt to changing environmental conditions.

ACS Style

Sari Peura; Maxime Wauthy; Domenico Simone; Alexander Eiler; Karólína Einarsdóttir; Milla Rautio; Stefan Bertilsson. Ontogenic succession of thermokarst thaw ponds is linked to dissolved organic matter quality and microbial degradation potential. Limnology and Oceanography 2019, 65, 1 .

AMA Style

Sari Peura, Maxime Wauthy, Domenico Simone, Alexander Eiler, Karólína Einarsdóttir, Milla Rautio, Stefan Bertilsson. Ontogenic succession of thermokarst thaw ponds is linked to dissolved organic matter quality and microbial degradation potential. Limnology and Oceanography. 2019; 65 (S1):1.

Chicago/Turabian Style

Sari Peura; Maxime Wauthy; Domenico Simone; Alexander Eiler; Karólína Einarsdóttir; Milla Rautio; Stefan Bertilsson. 2019. "Ontogenic succession of thermokarst thaw ponds is linked to dissolved organic matter quality and microbial degradation potential." Limnology and Oceanography 65, no. S1: 1.

Journal article
Published: 27 August 2019 in mBio
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Despite being separated from the photosynthesis-driven surface by both distance and time, the deep biosphere is an important driver for the earth’s carbon and energy cycles. However, due to the difficulties in gaining access and low cell numbers, robust statistical omics studies have not been carried out, and this limits the conclusions that can be drawn. This study benchmarks the use of two separate sampling systems and demonstrates that they provide statistically similar RNA transcript profiles, importantly validating several previously published studies. The generated data are analyzed to identify statistically valid differences in active microbial community members and metabolic processes. The results highlight contrasting taxa and growth strategies in the modern marine waters that are influenced by recent infiltration of Baltic Sea water versus the hydrogen- and carbon dioxide-fed, extremely oligotrophic, thoroughly mixed water.

ACS Style

Margarita Lopez-Fernandez; Elias Broman; Domenico Simone; Stefan Bertilsson; Mark Dopson. Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters. mBio 2019, 10, 1 .

AMA Style

Margarita Lopez-Fernandez, Elias Broman, Domenico Simone, Stefan Bertilsson, Mark Dopson. Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters. mBio. 2019; 10 (4):1.

Chicago/Turabian Style

Margarita Lopez-Fernandez; Elias Broman; Domenico Simone; Stefan Bertilsson; Mark Dopson. 2019. "Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters." mBio 10, no. 4: 1.

Article
Published: 21 December 2018 in mBio
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A newly designed sampling apparatus was used to fix RNA under in situ conditions in the deep continental biosphere and benchmarks a strategy for deep biosphere metatranscriptomic sequencing. This apparatus enabled the identification of active community members and the processes they carry out in this extremely oligotrophic environment. This work presents for the first time evidence of eukaryotic, archaeal, and bacterial activity in two deep subsurface crystalline rock groundwaters from the Äspö Hard Rock Laboratory with different depths and geochemical characteristics. The findings highlight differences between organic carbon-fed shallow communities and carbon dioxide- and hydrogen-fed old saline waters. In addition, the data reveal a large portion of uncharacterized microorganisms, as well as the important role of candidate phyla in the deep biosphere, but also the disparity in microbial diversity when using standard microbial 16S rRNA gene amplification versus the large unknown portion of the community identified with unbiased metatranscriptomes.

ACS Style

Margarita Lopez-Fernandez; Domenico Simone; Xiaofen Wu; Lucile Soler; Emelie Nilsson; Karin Holmfeldt; Henrik Lantz; Stefan Bertilsson; Mark Dopson. Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere. mBio 2018, 9, e01792-18 .

AMA Style

Margarita Lopez-Fernandez, Domenico Simone, Xiaofen Wu, Lucile Soler, Emelie Nilsson, Karin Holmfeldt, Henrik Lantz, Stefan Bertilsson, Mark Dopson. Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere. mBio. 2018; 9 (6):e01792-18.

Chicago/Turabian Style

Margarita Lopez-Fernandez; Domenico Simone; Xiaofen Wu; Lucile Soler; Emelie Nilsson; Karin Holmfeldt; Henrik Lantz; Stefan Bertilsson; Mark Dopson. 2018. "Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere." mBio 9, no. 6: e01792-18.

Original research article
Published: 05 December 2018 in Frontiers in Microbiology
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Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed ‘acid mine drainage (AMD)’] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of ‘microbial fuel cells’ that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbe–mineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-like population had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylyl-sulfate released electrons and the extracellular electron transfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganic sulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.

ACS Style

Gaofeng Ni; Domenico Simone; Daniela Palma; Elias Broman; Xiaofen Wu; Stephanie Turner; Mark Dopson. A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer. Frontiers in Microbiology 2018, 9, 2945 .

AMA Style

Gaofeng Ni, Domenico Simone, Daniela Palma, Elias Broman, Xiaofen Wu, Stephanie Turner, Mark Dopson. A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer. Frontiers in Microbiology. 2018; 9 ():2945.

Chicago/Turabian Style

Gaofeng Ni; Domenico Simone; Daniela Palma; Elias Broman; Xiaofen Wu; Stephanie Turner; Mark Dopson. 2018. "A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer." Frontiers in Microbiology 9, no. : 2945.

Original research article
Published: 28 September 2018 in Frontiers in Microbiology
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Thiocyanate is a toxic compound produced by the mining and metallurgy industries that needs to be remediated prior to its release into the environment. If the industry is situated at high altitudes or near the poles, economic factors require a low temperature treatment process. Microbial fuel cells are a developing technology that have the benefits of both removing such toxic compounds while recovering electrical energy. In this study, simultaneous thiocyanate degradation and electrical current generation was demonstrated and it was suggested that extracellular electron transfer to the anode occurred. Investigation of the microbial community by 16S rRNA metatranscriptome reads supported that the anode attached and planktonic anolyte consortia were dominated by a Thiobacillus-like population. Metatranscriptomic sequencing also suggested thiocyanate degradation primarily occurred via the ‘cyanate’ degradation pathway. The generated sulfide was metabolized via sulfite and ultimately to sulfate mediated by reverse dissimilatory sulfite reductase, APS reductase, and sulfate adenylyltransferase and the released electrons were potentially transferred to the anode via soluble electron shuttles. Finally, the ammonium from thiocyanate degradation was assimilated to glutamate as nitrogen source and carbon dioxide was fixed as carbon source. This study is one of the first to demonstrate a low temperature inorganic sulfur utilizing microbial fuel cell and the first to provide evidence for pathways of thiocyanate degradation coupled to electron transfer.

ACS Style

Gaofeng Ni; Sebastian Canizales; Elias Broman; Domenico Simone; Viraja R. Palwai; Daniel Lundin; Margarita López Fernández; Tom Sleutels; Mark Dopson. Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells. Frontiers in Microbiology 2018, 9, 2308 .

AMA Style

Gaofeng Ni, Sebastian Canizales, Elias Broman, Domenico Simone, Viraja R. Palwai, Daniel Lundin, Margarita López Fernández, Tom Sleutels, Mark Dopson. Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells. Frontiers in Microbiology. 2018; 9 ():2308.

Chicago/Turabian Style

Gaofeng Ni; Sebastian Canizales; Elias Broman; Domenico Simone; Viraja R. Palwai; Daniel Lundin; Margarita López Fernández; Tom Sleutels; Mark Dopson. 2018. "Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells." Frontiers in Microbiology 9, no. : 2308.

Comment
Published: 08 August 2017 in Human Reproduction
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ACS Style

M. Cristina Magli; Sara De Fanti; Saverio Vicario; Martin Lang; Domenico Simone; Donata Luiselli; Giovanni Romeo; Luca Gianaroli. Reply: Purifying selection on mitochondrial DNA: a strategy for the oocyte to preserve competence. Human Reproduction 2017, 32, 1949 -1950.

AMA Style

M. Cristina Magli, Sara De Fanti, Saverio Vicario, Martin Lang, Domenico Simone, Donata Luiselli, Giovanni Romeo, Luca Gianaroli. Reply: Purifying selection on mitochondrial DNA: a strategy for the oocyte to preserve competence. Human Reproduction. 2017; 32 (9):1949-1950.

Chicago/Turabian Style

M. Cristina Magli; Sara De Fanti; Saverio Vicario; Martin Lang; Domenico Simone; Donata Luiselli; Giovanni Romeo; Luca Gianaroli. 2017. "Reply: Purifying selection on mitochondrial DNA: a strategy for the oocyte to preserve competence." Human Reproduction 32, no. 9: 1949-1950.

Journal article
Published: 09 March 2017 in Human Reproduction
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STUDY QUESTIONDoes selection for mtDNA mutations occur in human oocytes?SUMMARY ANSWERWe provide statistical evidence in favor of the existence of purifying selection for mtDNA mutations in human oocytes acting between the expulsion of the first and second polar bodies (PBs).WHAT IS KNOWN ALREADYSeveral lines of evidence in Metazoa, including humans, indicate that variation within the germline of mitochondrial genomes is under purifying selection. The presence of this internal selection filter in the germline has important consequences for the evolutionary trajectory of mtDNA. However, the nature and localization of this internal filter are still unclear while several hypotheses are proposed in the literature.STUDY DESIGN, SIZE, DURATIONIn this study, 60 mitochondrial genomes were sequenced from 17 sets of oocytes, first and second PBs, and peripheral blood taken from nine women between 38 and 43 years of age.PARTICIPANTS/MATERIALS, SETTING, METHODSWhole genome amplification was performed only on the single cell samples and Sanger sequencing was performed on amplicons. The comparison of variant profiles between first and second PB sequences showed no difference in substitution rates but displayed instead a sharp difference in pathogenicity scores of protein-coding sequences using three different metrics (MutPred, Polyphen and SNPs&GO).MAIN RESULTS AND THE ROLE OF CHANCEUnlike the first, second PBs showed no significant differences in pathogenic scores with blood and oocyte sequences. This suggests that a filtering mechanism for disadvantageous variants operates during oocyte development between the expulsion of the first and second PB.LARGE SCALE DATAN/A.LIMITATIONS, REASONS FOR CAUTIONThe sample size is small and further studies are needed before this approach can be used in clinical practice. Studies on a model organism would allow the sample size to be increased.WIDER IMPLICATIONS OF THE FINDINGSThis work opens the way to the study of the correlation between mtDNA mutations, mitochondrial capacity and viability of oocytes.STUDY FUNDING/COMPETING INTEREST(S)This work was supported by a SISMER grant. Laboratory facilities and skills were freely provided by SISMER, and by the Alma Mater Studiorum, University of Bologna. The authors have no conflict of interest to disclose.

ACS Style

Sara De Fanti; Saverio Vicario; Martin Lang; Domenico Simone; Cristina Magli; Donata Luiselli; Luca Gianaroli; Giovanni Romeo. Intra-individual purifying selection on mitochondrial DNA variants during human oogenesis. Human Reproduction 2017, 32, 1100 -1107.

AMA Style

Sara De Fanti, Saverio Vicario, Martin Lang, Domenico Simone, Cristina Magli, Donata Luiselli, Luca Gianaroli, Giovanni Romeo. Intra-individual purifying selection on mitochondrial DNA variants during human oogenesis. Human Reproduction. 2017; 32 (5):1100-1107.

Chicago/Turabian Style

Sara De Fanti; Saverio Vicario; Martin Lang; Domenico Simone; Cristina Magli; Donata Luiselli; Luca Gianaroli; Giovanni Romeo. 2017. "Intra-individual purifying selection on mitochondrial DNA variants during human oogenesis." Human Reproduction 32, no. 5: 1100-1107.

Journal article
Published: 28 November 2016 in Nucleic Acids Research
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The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/.

ACS Style

Rosanna Clima; Roberto Preste; Claudia Calabrese; Maria Angela Diroma; Mariangela Santorsola; Gaetano Scioscia; Domenico Simone; Lishuang Shen; Giuseppe Gasparre; Marcella Attimonelli. HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor. Nucleic Acids Research 2016, 45, D698 -D706.

AMA Style

Rosanna Clima, Roberto Preste, Claudia Calabrese, Maria Angela Diroma, Mariangela Santorsola, Gaetano Scioscia, Domenico Simone, Lishuang Shen, Giuseppe Gasparre, Marcella Attimonelli. HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor. Nucleic Acids Research. 2016; 45 (D1):D698-D706.

Chicago/Turabian Style

Rosanna Clima; Roberto Preste; Claudia Calabrese; Maria Angela Diroma; Mariangela Santorsola; Gaetano Scioscia; Domenico Simone; Lishuang Shen; Giuseppe Gasparre; Marcella Attimonelli. 2016. "HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor." Nucleic Acids Research 45, no. D1: D698-D706.

Journal article
Published: 03 December 2014 in BMC Bioinformatics
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Expressed sequences (e.g. ESTs) are a strong source of evidence to improve gene structures and predict reliable alternative splicing events. When a genome assembly is available, ESTs are suitable to generate gene-oriented clusters through the well-established EasyCluster software. Nowadays, EST-like sequences can be massively produced using Next Generation Sequencing (NGS) technologies. In order to handle genome-scale transcriptome data, we present here EasyCluster2, a reimplementation of EasyCluster able to speed up the creation of gene-oriented clusters and facilitate downstream analyses as the assembly of full-length transcripts and the detection of splicing isoforms.

ACS Style

Vitoantonio Bevilacqua; Nicola Pietroleonardo; Ely Ignazio Giannino; Fabio Stroppa; Domenico Simone; Graziano Pesole; Ernesto Picardi. EasyCluster2: an improved tool for clustering and assembling long transcriptome reads. BMC Bioinformatics 2014, 15, S7 -S7.

AMA Style

Vitoantonio Bevilacqua, Nicola Pietroleonardo, Ely Ignazio Giannino, Fabio Stroppa, Domenico Simone, Graziano Pesole, Ernesto Picardi. EasyCluster2: an improved tool for clustering and assembling long transcriptome reads. BMC Bioinformatics. 2014; 15 (S15):S7-S7.

Chicago/Turabian Style

Vitoantonio Bevilacqua; Nicola Pietroleonardo; Ely Ignazio Giannino; Fabio Stroppa; Domenico Simone; Graziano Pesole; Ernesto Picardi. 2014. "EasyCluster2: an improved tool for clustering and assembling long transcriptome reads." BMC Bioinformatics 15, no. S15: S7-S7.

Journal article
Published: 14 July 2014 in Bioinformatics
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Motivation: The increasing availability of mitochondria-targeted and off-target sequencing data in whole-exome and whole-genome sequencing studies (WXS and WGS) has risen the demand of effective pipelines to accurately measure heteroplasmy and to easily recognize the most functionally important mitochondrial variants among a huge number of candidates. To this purpose, we developed MToolBox, a highly automated pipeline to reconstruct and analyze human mitochondrial DNA from high-throughput sequencing data.

ACS Style

Claudia Calabrese; Domenico Simone; Maria Angela Diroma; Mariangela Santorsola; Cristiano Guttà; Giuseppe Gasparre; Ernesto Picardi; Graziano Pesole; Marcella Attimonelli. MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinformatics 2014, 30, 3115 -3117.

AMA Style

Claudia Calabrese, Domenico Simone, Maria Angela Diroma, Mariangela Santorsola, Cristiano Guttà, Giuseppe Gasparre, Ernesto Picardi, Graziano Pesole, Marcella Attimonelli. MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinformatics. 2014; 30 (21):3115-3117.

Chicago/Turabian Style

Claudia Calabrese; Domenico Simone; Maria Angela Diroma; Mariangela Santorsola; Cristiano Guttà; Giuseppe Gasparre; Ernesto Picardi; Graziano Pesole; Marcella Attimonelli. 2014. "MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing." Bioinformatics 30, no. 21: 3115-3117.

Journal article
Published: 01 January 2014 in BMC Genomics
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Whole Exome Sequencing (WES) is one of the most used and cost-effective next generation technologies that allows sequencing of all nuclear exons. Off-target regions may be captured if they present high sequence similarity with baits. Bioinformatics tools have been optimized to retrieve a large amount of WES off-target mitochondrial DNA (mtDNA), by exploiting the aspecificity of probes, partially overlapping to Nuclear mitochondrial Sequences (NumtS). The 1000 Genomes project represents one of the widest resources to extract mtDNA sequences from WES data, considering the large effort the scientific community is undertaking to reconstruct human population history using mtDNA as marker, and the involvement of mtDNA in pathology.

ACS Style

Maria Angela Diroma; Claudia Calabrese; Domenico Simone; Mariangela Santorsola; Francesco Maria Calabrese; Giuseppe Gasparre; Marcella Attimonelli. Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data. BMC Genomics 2014, 15, S2 .

AMA Style

Maria Angela Diroma, Claudia Calabrese, Domenico Simone, Mariangela Santorsola, Francesco Maria Calabrese, Giuseppe Gasparre, Marcella Attimonelli. Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data. BMC Genomics. 2014; 15 (Suppl 3):S2.

Chicago/Turabian Style

Maria Angela Diroma; Claudia Calabrese; Domenico Simone; Mariangela Santorsola; Francesco Maria Calabrese; Giuseppe Gasparre; Marcella Attimonelli. 2014. "Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data." BMC Genomics 15, no. Suppl 3: S2.

Research article
Published: 13 November 2013 in PLOS ONE
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The twin-arginine translocation (Tat) protein export system enables the transport of fully folded proteins across a membrane. This system is composed of two integral membrane proteins belonging to TatA and TatC protein families and in some systems a third component, TatB, a homolog of TatA. TatC participates in substrate protein recognition through its interaction with a twin arginine leader peptide sequence. The aim of this study was to explore TatC diversity, evolution and sequence conservation in bacteria to identify how TatC is evolving and diversifying in various bacterial phyla. Surveying bacterial genomes revealed that 77% of all species possess one or more tatC loci and half of these classes possessed only tatC and tatA genes. Phylogenetic analysis of diverse TatC homologues showed that they were primarily inherited but identified a small subset of taxonomically unrelated bacteria that exhibited evidence supporting lateral gene transfer within an ecological niche. Examination of bacilli tatCd/tatCy isoform operons identified a number of known and potentially new Tat substrate genes based on their frequent association to tatC loci. Evolutionary analysis of these Bacilli isoforms determined that TatCy was the progenitor of TatCd. A bacterial TatC consensus sequence was determined and highlighted conserved and variable regions within a three dimensional model of the Escherichia coli TatC protein. Comparative analysis between the TatC consensus sequence and Bacilli TatCd/y isoform consensus sequences revealed unique sites that may contribute to isoform substrate specificity or make TatA specific contacts. Synonymous to non-synonymous nucleotide substitution analyses of bacterial tatC homologues determined that tatC sequence variation differs dramatically between various classes and suggests TatC specialization in these species. TatC proteins appear to be diversifying within particular bacterial classes and its specialization may be driven by the substrates it transports and the environment of its host.

ACS Style

Domenico Simone; Denice C. Bay; Thorin Leach; Raymond J. Turner. Diversity and Evolution of Bacterial Twin Arginine Translocase Protein, TatC, Reveals a Protein Secretion System That Is Evolving to Fit Its Environmental Niche. PLOS ONE 2013, 8, e78742 .

AMA Style

Domenico Simone, Denice C. Bay, Thorin Leach, Raymond J. Turner. Diversity and Evolution of Bacterial Twin Arginine Translocase Protein, TatC, Reveals a Protein Secretion System That Is Evolving to Fit Its Environmental Niche. PLOS ONE. 2013; 8 (11):e78742.

Chicago/Turabian Style

Domenico Simone; Denice C. Bay; Thorin Leach; Raymond J. Turner. 2013. "Diversity and Evolution of Bacterial Twin Arginine Translocase Protein, TatC, Reveals a Protein Secretion System That Is Evolving to Fit Its Environmental Niche." PLOS ONE 8, no. 11: e78742.

Article
Published: 15 August 2012 in Journal of Bacteriology
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Pseudomonas pseudoalcaligenes KF707 is a soil polychlorinated biphenyl (PCB) degrader, able to grow both planktonically and as a biofilm in the presence of various toxic metals and metalloids. Here we report the genome sequence (5,957,359 bp) of P. pseudoalcaligenes KF707, which provides insights into metabolic degradation pathways, flagellar motility, and chemotaxis.

ACS Style

Tania Triscari-Barberi; Domenico Simone; Francesco Maria Calabrese; Marcella Attimonelli; Kristen R. Hahn; Kingsley K. Amoako; Raymond J. Turner; Stefano Fedi; Davide Zannoni. Genome Sequence of the Polychlorinated-Biphenyl Degrader Pseudomonas pseudoalcaligenes KF707. Journal of Bacteriology 2012, 194, 4426 -4427.

AMA Style

Tania Triscari-Barberi, Domenico Simone, Francesco Maria Calabrese, Marcella Attimonelli, Kristen R. Hahn, Kingsley K. Amoako, Raymond J. Turner, Stefano Fedi, Davide Zannoni. Genome Sequence of the Polychlorinated-Biphenyl Degrader Pseudomonas pseudoalcaligenes KF707. Journal of Bacteriology. 2012; 194 (16):4426-4427.

Chicago/Turabian Style

Tania Triscari-Barberi; Domenico Simone; Francesco Maria Calabrese; Marcella Attimonelli; Kristen R. Hahn; Kingsley K. Amoako; Raymond J. Turner; Stefano Fedi; Davide Zannoni. 2012. "Genome Sequence of the Polychlorinated-Biphenyl Degrader Pseudomonas pseudoalcaligenes KF707." Journal of Bacteriology 194, no. 16: 4426-4427.

Comparative study
Published: 29 February 2012 in Biotechnology Advances
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Mitochondrial DNA (mtDNA) mutations have been involved in disease, aging and cancer and furthermore exploited for evolutionary and forensic investigation. When investigating mtDNA mutations the peculiar aspects of mitochondrial genetics, such as heteroplasmy and threshold effect, require suitable approaches which must be sensitive enough to detect low-level heteroplasmy and, precise enough to quantify the exact mutational load. In order to establish the optimal approach for the evaluation of heteroplasmy, six methods were experimentally compared for their capacity to reveal and quantify mtDNA variants. Drawbacks and advantages of cloning, Fluorescent PCR (F-PCR), denaturing High Performance Liquid Chromatography (dHPLC), quantitative Real-Time PCR (qRTPCR), High Resolution Melting (HRM) and 454 pyrosequencing were determined. In particular, detection and quantification of a mutation in a difficult sequence context were investigated, through analysis of an insertion in a homopolymeric stretch (m.3571insC).

ACS Style

Ivana Kurelac; Martin Lang; Roberta Zuntini; Claudia Calabrese; Domenico Simone; Saverio Vicario; Monica Santamaria; Marcella Attimonelli; Giovanni Romeo; Giuseppe Gasparre. Searching for a needle in the haystack: Comparing six methods to evaluate heteroplasmy in difficult sequence context. Biotechnology Advances 2012, 30, 363 -371.

AMA Style

Ivana Kurelac, Martin Lang, Roberta Zuntini, Claudia Calabrese, Domenico Simone, Saverio Vicario, Monica Santamaria, Marcella Attimonelli, Giovanni Romeo, Giuseppe Gasparre. Searching for a needle in the haystack: Comparing six methods to evaluate heteroplasmy in difficult sequence context. Biotechnology Advances. 2012; 30 (1):363-371.

Chicago/Turabian Style

Ivana Kurelac; Martin Lang; Roberta Zuntini; Claudia Calabrese; Domenico Simone; Saverio Vicario; Monica Santamaria; Marcella Attimonelli; Giovanni Romeo; Giuseppe Gasparre. 2012. "Searching for a needle in the haystack: Comparing six methods to evaluate heteroplasmy in difficult sequence context." Biotechnology Advances 30, no. 1: 363-371.

Journal article
Published: 01 January 2012 in BMC Bioinformatics
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NumtS (Nuclear MiTochondrial Sequences) are mitochondrial DNA sequences that, after stress events involving the mitochondrion, colonized the nuclear genome. Accurate mapping of NumtS avoids contamination during mtDNA PCR amplification, thus supplying reliable bases for detecting false heteroplasmies. In addition, since they commonly populate mammalian genomes (especially primates) and are polymorphic, in terms of presence/absence and content of SNPs, they may be used as evolutionary markers in intra- and inter-species population analyses.

ACS Style

Francesco Maria Calabrese; Domenico Simone; Marcella Attimonelli. Primates and mouse NumtS in the UCSC Genome Browser. BMC Bioinformatics 2012, 13, S15 -S15.

AMA Style

Francesco Maria Calabrese, Domenico Simone, Marcella Attimonelli. Primates and mouse NumtS in the UCSC Genome Browser. BMC Bioinformatics. 2012; 13 (uppl 4):S15-S15.

Chicago/Turabian Style

Francesco Maria Calabrese; Domenico Simone; Marcella Attimonelli. 2012. "Primates and mouse NumtS in the UCSC Genome Browser." BMC Bioinformatics 13, no. uppl 4: S15-S15.

Journal article
Published: 08 December 2011 in Quality of Life Research
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The human genome is constantly subjected to evolutionary forces which shape its architecture. Insertions of mitochondrial DNA sequences into nuclear genome (NumtS) have been described in several eukaryotic species, including Homo sapiens and other primates. The ongoing process of the generation of NumtS has made them valuable markers in primate phylogenetic studies, as well as potentially informative loci for reconstructing the genetic history of modern humans. Here, we report the identification of 53 human-specific NumtS by inspection of the UCSC genome browser, showing that they may be direct insertions of mitochondrial DNA into the human nuclear DNA after the human-chimpanzee split. In silico analyses allowed us to identify 14 NumtS which are polymorphic in terms of their presence/absence within the human genome in individuals of different ancestry. The allele frequencies of these polymorphic NumtS were calculated for 1000 Genomes Project sequence data from 13 populations worldwide, and principal components analysis and hierarchical clustering methods allowed the detection of strong signals of geographical structure related to the genetic diversity of these loci. All identified polymorphic human-specific NumtS together with a tandemly duplicated NumtS have also been validated by PCR amplification on a panel of 60 samples belonging to five native populations worldwide, confirming the expected NumtS variability. On the basis of these findings, we have succeeded in depicting the landscape of variation of a series of NumtS in several ethnic groups, making an advance in their identification as useful markers in the study on human population genetics.

ACS Style

Martin Lang; Marco Sazzini; Francesco Maria Calabrese; Domenico Simone; Alessio Boattini; Giovanni Romeo; Donata Luiselli; Marcella Attimonelli; Giuseppe Gasparre. Polymorphic NumtS trace human population relationships. Quality of Life Research 2011, 131, 757 -771.

AMA Style

Martin Lang, Marco Sazzini, Francesco Maria Calabrese, Domenico Simone, Alessio Boattini, Giovanni Romeo, Donata Luiselli, Marcella Attimonelli, Giuseppe Gasparre. Polymorphic NumtS trace human population relationships. Quality of Life Research. 2011; 131 (5):757-771.

Chicago/Turabian Style

Martin Lang; Marco Sazzini; Francesco Maria Calabrese; Domenico Simone; Alessio Boattini; Giovanni Romeo; Donata Luiselli; Marcella Attimonelli; Giuseppe Gasparre. 2011. "Polymorphic NumtS trace human population relationships." Quality of Life Research 131, no. 5: 757-771.

Journal article
Published: 01 December 2011 in Nucleic Acids Research
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HmtDB (http://www.hmtdb.uniba.it:8080/hmdb) is a open resource created to support population genetics and mitochondrial disease studies. The database hosts human mitochondrial genome sequences annotated with population and variability data, the latter being estimated through the application of the SiteVar software based on site-specific nucleotide and amino acid variability calculations. The annotations are manually curated thus adding value to the quality of the information provided to the end-user. Classifier tools implemented in HmtDB allow the prediction of the haplogroup for any human mitochondrial genome currently stored in HmtDB or externally submitted de novo by an end-user. Haplogroup definition is based on the Phylotree system. End-users accessing HmtDB are hence allowed to (i) browse the database through the use of a multi-criterion ‘query’ system; (ii) analyze their own human mitochondrial sequences via the ‘classify’ tool (for complete genomes) or by downloading the ‘fragment-classifier’ tool (for partial sequences); (iii) download multi-alignments with reference genomes as well as variability data.

ACS Style

Francesco Rubino; Roberta Piredda; Francesco Maria Calabrese; Domenico Simone; Martin Lang; Claudia Calabrese; Vittoria Petruzzella; Mila Tommaseo-Ponzetta; Giuseppe Gasparre; Marcella Attimonelli. HmtDB, a genomic resource for mitochondrion-based human variability studies. Nucleic Acids Research 2011, 40, D1150 -D1159.

AMA Style

Francesco Rubino, Roberta Piredda, Francesco Maria Calabrese, Domenico Simone, Martin Lang, Claudia Calabrese, Vittoria Petruzzella, Mila Tommaseo-Ponzetta, Giuseppe Gasparre, Marcella Attimonelli. HmtDB, a genomic resource for mitochondrion-based human variability studies. Nucleic Acids Research. 2011; 40 (D1):D1150-D1159.

Chicago/Turabian Style

Francesco Rubino; Roberta Piredda; Francesco Maria Calabrese; Domenico Simone; Martin Lang; Claudia Calabrese; Vittoria Petruzzella; Mila Tommaseo-Ponzetta; Giuseppe Gasparre; Marcella Attimonelli. 2011. "HmtDB, a genomic resource for mitochondrion-based human variability studies." Nucleic Acids Research 40, no. D1: D1150-D1159.