Article
Biochemistry & Molecular Biology
Chaowei Zhang, Kerry Reid, Arthur F. Sands, Antoine Fraimout, Mikkel Heide Schierup, Juha Merila
Summary: Mutation rate is a critical parameter in population genetics, but accurate estimates for wild organisms are limited. This study estimated mutation rates in two marine populations of nine-spined stickleback using pedigrees, whole-genome resequencing, and a high-quality reference genome. The results showed high levels of parental mosaicism and increased estimated divergence times after recalibration with the mutation rate.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Endocrinology & Metabolism
Rayhan A. Lal, Hannah P. Moeller, Ella A. Thomson, Timothy M. Horton, Sooyeon Lee, Raquel Freeman, Priya Prahalad, Ada S. Y. Poon, Justin P. Annes
Summary: In this study, a novel INS gene mutation (p.T97P) was identified, which disrupts proinsulin folding and processing, leading to the development of MIDY. This mutation induces endoplasmic reticulum stress and impairs insulin secretion.
Article
Biochemistry & Molecular Biology
Eugenio Lopez-Cortegano, Rory J. Craig, Jobran Chebib, Toby Samuels, Andrew D. Morgan, Susanne A. Kraemer, Katharina B. Boendel, Rob W. Ness, Nick Colegrave, Peter D. Keightley
Summary: De novo mutations play a crucial role in evolution by providing genetic variation, but studying them is challenging and often limited to model species, leading to a restricted understanding of mutation rate evolution among closely related species. Through a mutation accumulation experiment and comparative analysis between Chlamydomonas incerta and Chlamydomonas reinhardtii, researchers found variability in the mutation rate and differing mutation spectra, indicating similarities in genomic factors influencing mutation rate but a greater divergence in mutation spectra between the two species.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Haoling Xie, Wen Li, Yuqiong Hu, Cheng Yang, Jiansen Lu, Yuqing Guo, Lu Wen, Fuchou Tang
Summary: This study achieved high continuity human genome assembly using single-cell genome long-read sequencing technology and explored the impact of different assemblers and sequencing strategies on genome assembly. It is of great significance for the practice of single-cell genome de novo assembly.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Genetics & Heredity
Mohiuddin Mohiuddin, R. Frank Kooy, Christopher E. Pearson
Summary: Mosaicism, the existence of genetically distinct populations of cells, is a significant cause of genetic diseases. Neurodevelopmental or neuropsychiatric disorders, such as autism, often arise from de novo mutations that are not present in either parent. The timing and mode of mutations can affect the burden and distribution of mutations.
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
G. Ozan Bozdag, Seyed Alireza Zamani-Dahaj, Thomas C. Day, Penelope C. Kahn, Anthony J. Burnetti, Dung T. Lac, Kai Tong, Peter L. Conlin, Aishwarya H. Balwani, Eva L. Dyer, Peter J. Yunker, William C. Ratcliff
Summary: This study investigates the evolution of multicellular organisms using a long-term experiment with snowflake yeast as the model system. The results show that snowflake yeast evolved to be macroscopic in anaerobic conditions, while remaining microscopic in aerobic conditions. This research provides insights into how simple groups of cells overcome biophysical limitations through gradual multicellular evolution.
Article
Biochemistry & Molecular Biology
Matthew A. Lines, Alexanne Cuillerier, Pranesh Chakraborty, Turaya Naas, M. Laura Duque Lasio, Jean Michaud, Chantal Pileggi, Mary-Ellen Harper, Yan Burelle, Tomi L. Toler, Neal Sondheimer, Heather P. Crawford, Francisca Millan, Michael T. Geraghty
Summary: Mitochondrial disorders are a rare group of degenerative multisystem disorders affecting core bioenergetic and signalling functions of cells. This study identified a novel neonatal-onset mitochondriopathy in three infants, characterized by failure to thrive, high lactate and ammonia levels. Exome sequencing revealed a recurrent de novo substitution in ATP5F1A, leading to deficits in complex V function and expression in patient-derived fibroblasts. The long-term prognosis of this disorder, which presents with life-threatening neonatal manifestations, remains unclear.
EUROPEAN JOURNAL OF HUMAN GENETICS
(2021)
Article
Biochemistry & Molecular Biology
Tengfei Luo, Kuokuo Li, Zhengbao Ling, Guihu Zhao, Bin Li, Zheng Wang, Xiaomeng Wang, Ying Han, Lu Xia, Yi Zhang, Qiao Zhou, Zhenghuan Fang, Yijing Wang, Qian Chen, Xun Zhou, Hongxu Pan, Yuwen Zhao, Yige Wang, Lijie Dong, Yuanfeng Huang, Zhengmao Hu, Qian Pan, Kun Xia, Jinchen Li
Summary: The study identified an association between de novo mutations in folate-related genes and the risk of developmental disorders. By analyzing genetic data, 96 candidate disease-associated genes were prioritized, playing crucial roles in development. The findings contribute to the discovery of biomarkers and therapeutic targets for developmental disorders.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Jose Carlos Montanes, Marta Huertas, Xavier Messeguer, M. Mar Alba
Summary: The formation of new genes can occur through gene duplication or de novo formation from noncoding sequences. Both mechanisms show similarities in terms of low sequence constraints in the initial evolutionary stages, high turnover rates at the species level, and comparable persistence rates in deeper branches. Additionally, de novo proteins tend to have an excess of substitutions between charged amino acids, leading to rapid loss of their initial highly basic character.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Dolma Michellod, Tanja Bien, Daniel Birgel, Marlene Violette, Manuel Kleiner, Sarah Fearn, Caroline Zeidler, Harald R. Gruber-Vodicka, Nicole Dubilier, Manuel Liebeke
Summary: Using various techniques, such as metabolite imaging and enzyme assays, we have discovered that gutless marine annelids synthesize the plant sterol sitosterol, which is commonly found in plants. This synthesis is facilitated by a noncanonical C-24 sterol methyltransferase, an enzyme that is essential for sitosterol synthesis in plants but not widely known in most animals. Our phylogenetic analyses also indicate that this enzyme is present in representatives of at least five animal phyla, suggesting that the synthesis of plant-like sterols is more common in animals than previously believed.
Editorial Material
Biochemistry & Molecular Biology
Xin-Guang Zhu, Jian-Kang Zhu
Summary: The de novo domestication process has the potential to leverage desirable traits of wild plants quickly, introducing a novel staple food crop to support global food security as demonstrated in the recent study by Yu et al. in Cell.
Article
Multidisciplinary Sciences
M. S. Oud, R. M. Smits, H. E. Smith, F. K. Mastrorosa, G. S. Holt, B. J. Houston, P. F. de Vries, B. K. S. Alobaidi, L. E. Batty, H. Ismail, J. Greenwood, H. Sheth, A. Mikulasova, G. D. N. Astuti, C. Gilissen, K. McEleny, H. Turner, J. Coxhead, S. Cockell, D. D. M. Braat, K. Fleischer, K. W. M. D'Hauwers, E. Schaafsma, L. Nagirnaja, D. F. Conrad, C. Friedrich, S. Kliesch, K. I. Aston, A. Riera-Escamilla, C. Krausz, C. Gonzaga-Jauregui, M. Santibanez-Koref, D. J. Elliott, L. E. L. M. Vissers, F. Tuettelmann, M. K. O'Bryan, L. Ramos, M. J. Xavier, G. W. van der Heijden, J. A. Veltman
Summary: This study examines the role of de novo mutations in severe male infertility. Through trio-based exome sequencing, the researchers identified a significant enrichment of loss-of-function de novo mutations in infertile men. They also identified a new candidate gene, RBM5, which is associated with male infertility. This study provides evidence for the importance of de novo mutations in male infertility and identifies potential genetic causes.
NATURE COMMUNICATIONS
(2022)
Article
Psychology, Developmental
Kuokuo Li, Zhenghuan Fang, Guihu Zhao, Bin Li, Chao Chen, Lu Xia, Lin Wang, Tengfei Luo, Xiaomeng Wang, Zheng Wang, Yi Zhang, Yi Jiang, Qian Pan, Zhengmao Hu, Hui Guo, Beisha Tang, Chunyu Liu, Zhongsheng Sun, Kun Xia, Jinchen Li
Summary: The study found that different neuropsychiatric disorders share clinical similarities and genetic basis, but the level of genetic association varies among different disorder types. Cross-disorder analysis identified 321 candidate genes, indicating that genes shared in more disorders are more likely to exhibit specific biological features.
JOURNAL OF AUTISM AND DEVELOPMENTAL DISORDERS
(2022)
Article
Psychology, Developmental
Julie C. Chow, Fereydoun Hormozdiari
Summary: Early detection of neurodevelopmental disorders (NDDs) is crucial for improving patient outcomes. By analyzing the differential burden of genetic mutations, a subset of NDD cases can be accurately predicted and prioritized for further clinical study.
JOURNAL OF AUTISM AND DEVELOPMENTAL DISORDERS
(2023)
Article
Biochemical Research Methods
Aojie Lian, James Guevara, Kun Xia, Jonathan Sebat
Summary: SynthDNM is a random-forest based classifier that can adapt to new sequencing or variant-calling pipelines by constructing simulated training examples from real data using a flexible approach. The optimized SynthDNM classifiers accurately predict de novo SNPs and indels across multiple variant calling methods.
Letter
Hematology
M. Rinelli, E. Bellacchio, F. Berardinelli, G. Pascolini, P. Grammatico, A. Sgura, A. P. Iori, L. Quattrocchi, A. Novelli, S. Majore, E. Agolini
ANNALS OF HEMATOLOGY
(2019)
Article
Neurosciences
Ginevra Zanni, P. De Magistris, M. Nardella, E. Bellacchio, S. Barresi, A. Sferra, A. Ciolfi, M. Motta, H. Lue, D. Moreno-Andres, M. Tartaglia, E. Bertini, Wolfram Antonin
Correction
Neurosciences
Ginevra Zanni, P. De Magistris, M. Nardella, E. Bellacchio, S. Barresi, A. Sferra, A. Ciolfi, M. Motta, H. Lue, D. Moreno-Andres, M. Tartaglia, E. Bertini, Wolfram Antonin
Article
Genetics & Heredity
Daniela Verrigni, Michela Di Nottia, Anna Ardissone, Enrico Baruffini, Alessia Nasca, Andrea Legati, Emanuele Bellacchio, Gigliola Fagiolari, Diego Martinelli, Lucia Fusco, Domenica Battaglia, Giulia Trani, Gianmarco Versienti, Silvia Marchet, Alessandra Torraco, Teresa Rizza, Margherita Verardo, Adele D'Amico, Daria Diodato, Isabella Moroni, Costanza Lamperti, Stefania Petrini, Maurizio Moggio, Paola Goffrini, Daniele Ghezzi, Rosalba Carrozzo, Enrico Bertini
Article
Anesthesiology
Francesca Bertino, Kyra Firestone, Emanuele Bellacchio, Kelly E. Jackson, Alexander Asamoah, Joseph Hersh, Veronica Fiorito, Francesca Destefanis, Rusty Gonser, Megan E. Tucker, Fiorella Altruda, Emanuela Tolosano, Deborah Chiabrando
Article
Clinical Neurology
Sabina Barresi, Maria Lisa Dentici, Francesca Manzoni, Emanuele Bellacchio, Emanuele Agolini, Simone Pizzi, Andrea Ciolfi, Mark Tarnopolsky, Lauren Brady, Giacomo Garone, Antonio Novelli, Davide Mei, Renzo Guerrini, Alessandro Capuano, Chiara Pantaleoni, Marco Tartaglia
PEDIATRIC NEUROLOGY
(2020)
Article
Genetics & Heredity
Fabrizia Stregapede, Lorena Travaglini, Adriana P. Rebelo, Vivian Pedigone Cintra, Emanuele Bellacchio, Luca Bosco, Paolo Alfieri, Stefano Pro, Stephan Zuchner, Enrico Bertini, Francesco Nicita
Article
Otorhinolaryngology
Sara Giannantonio, Emanuele Agolini, Alessandro Scorpecci, Roberta Anzivino, Emanuele Bellacchio, Dario Cocciadiferro, Antonio Novelli, Maria Cristina Digilio, Pasquale Marsella
INTERNATIONAL JOURNAL OF PEDIATRIC OTORHINOLARYNGOLOGY
(2020)
Letter
Oncology
Isabella Giovannoni, Sabina Barresi, Sabrina Rossi, Alessandra Stracuzzi, Maria Grazia Argentieri, Rita Alaggio
GENES CHROMOSOMES & CANCER
(2021)
Article
Oncology
Sabina Barresi, Isabella Giovannoni, Sabrina Rossi, Alessandra Stracuzzi, Denise Quacquarini, Barbara Cafferata, Domenico Piscitelli, Francesco De Leonardis, Andrea Marzullo, Rita Alaggio
Summary: Epithelioid malignant peripheral nerve sheath tumors (MPNST) are a rare subgroup characterized by diffuse S100 and CD34 expression, often combined with INI-1 loss. This study describes a case of an epithelioid malignancy of the orbit in a 10-year-old girl, with NGS analysis revealing a novel BRD4-LEUTX fusion gene. The fusion gene leads to the re-activation of LEUTX, which has not been reported previously, raising questions about the classification of this tumor entity.
GENES CHROMOSOMES & CANCER
(2021)
Review
Pathology
Sabrina Rossi, Sabina Barresi, Alessandra Stracuzzi, Oscar Lopez-Nunez, Stefano Chiaravalli, Andrea Ferrari, Andrea Ciolfi, Giuseppe Maria Milano, Isabella Giovannoni, Marco Tartaglia, Evelina Miele, Rita Alaggio
Summary: This study reports two DICER1-related malignancies with teratoma-like features, expanding their morphologic spectrum and highlighting the multipotentiality of their presumed cell of origin. Furthermore, it describes the first extracranial ETMR with confirmed DICER1 biallelic inactivation and suggests the potential role of other molecular alterations such as KRAS and CTNNB1 mutations in defining the phenotype of embryonal and primitive DICER1-associated neoplasms.
PATHOLOGY RESEARCH AND PRACTICE
(2021)
Article
Cell Biology
Anna Taranta, Mohamed A. Elmonem, Francesco Bellomo, Ester De Leo, Sara Boenzi, Manoe J. Janssen, Amer Jamalpoor, Sara Cairoli, Anna Pastore, Cristiano De Stefanis, Manuela Colucci, Laura R. Rega, Isabella Giovannoni, Paola Francalanci, Lambertus P. van den Heuvel, Carlo Dionisi-Vici, Bianca M. Goffredo, Rosalinde Masereeuw, Elena Levtchenko, Francesco Emma
Summary: Nephropathic cystinosis is a rare disease caused by mutations of the CTNS gene, leading to cystine accumulation in tissues. Treatment with DSF shows partial reversal of the disease, but high dosage inhibits growth, while low dosage fails to reduce cystine accumulation and causes adverse effects.
Review
Pediatrics
Antonella Mosca, Luca Della Volpe, Maria Rita Sartorelli, Donatella Comparcola, Silvio Veraldi, Anna Alisi, Giuseppe Maggiore
Summary: Non-alcoholic fatty liver disease (NAFLD) is a hepatic sign of metabolic syndrome and the most frequent cause of chronic liver disease. The interaction between genetic predisposition and environmental factors plays a vital role in the development of NAFLD and metabolic disorders. Early diagnosis and intervention are crucial for preventing disease progression.
CURRENT PEDIATRIC REVIEWS
(2023)
Article
Medicine, Research & Experimental
Chiara Lago, Aniello Federico, Gloria Leva, Norman L. Mack, Benjamin Schwalm, Claudio Ballabio, Matteo Gianesello, Luana Abballe, Isabella Giovannoni, Sofia Reddel, Sabrina Rossi, Nicolas Leone, Andrea Carai, Angela Mastronuzzi, Alessandra Bisio, Alessia Soldano, Concetta Quintarelli, Franco Locatelli, Marcel Kool, Evelina Miele, Luca Tiberi
Summary: This study presents a protocol for efficient generation, expansion, and biobanking of pediatric brain cancer organoids. These organoids recapitulate histological features, DNA methylation profiles, and intratumor heterogeneity of the tumors. The study also shows that the organoids respond similarly to the same therapeutic regimens as the patients. These findings highlight the potential of organoids for research and personalized medicine.
EMBO MOLECULAR MEDICINE
(2023)
Article
Endocrinology & Metabolism
Alessandra di Masi, Loris Leboffe, Armida Sodo, Gaia Tabacco, Roberto Cesareo, Marco Sbroscia, Isabella Giovannoni, Chiara Taffon, Pierfilippo Crucitti, Filippo Longo, Silvia Manfrini, Maria Antonietta Ricci, Paolo Ascenzi, Anna Crescenzi, Andrea Palermo