Article
Multidisciplinary Sciences
Hong-Wen Tang, Kerstin Spirohn, Yanhui Hu, Tong Hao, Istvan A. Kovacs, Yue Gao, Richard Binari, Donghui Yang-Zhou, Kenneth H. Wan, Joel S. Bader, Dawit Balcha, Wenting Bian, Benjamin W. Booth, Atina G. Cote, Steffi de Rouck, Alice Desbuleux, Kah Yong Goh, Dae-Kyum Kim, Jennifer J. Knapp, Wen Xing Lee, Irma Lemmens, Cathleen Li, Mian Li, Roujia Li, Hyobin Julianne Lim, Yifang Liu, Katja Luck, Dylan Markey, Carl Pollis, Sudharshan Rangarajan, Jonathan Rodiger, Sadie Schlabach, Yun Shen, Dayag Sheykhkarimli, Bridget TeeKing, Frederick P. Roth, Jan Tavernier, Michael A. Calderwood, David E. Hill, Susan E. Celniker, Marc Vidal, Norbert Perrimon, Stephanie E. Mohr
Summary: This study uses advanced methods to identify protein-protein interactions in Drosophila, generating widely useful physical and data resources for the identification of new components in pathways, complexes, and processes. The generation of reference maps of interactome networks provides a protein-centric approach to discover new components in existing pathways, complexes, and processes, which is helpful for genetic studies. The results include the FlyBi dataset and the DroRI reference interaction network, which provide a foundation for building new hypotheses about protein networks and function.
NATURE COMMUNICATIONS
(2023)
Review
Biochemical Research Methods
Alba Gutierrez-Sacristan, Carlos De Niz, Cartik Kothari, Sek Won Kong, Kenneth D. Mandl, Paul Avillach
Summary: Precision medicine aims to provide the best diagnosis, treatment, and prognosis for each individual by tailoring therapeutic approaches to their genetic profile, lifestyle, and environmental exposures. However, to achieve this goal, researchers need access to large-scale clinical and genomic data repositories, which can be challenging to locate and obtain.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Chemistry, Multidisciplinary
Jamie M. Cameron, Conrad Holc, Alexander J. Kibler, Catherine L. Peake, Darren A. Walsh, Graham N. Newton, Lee R. Johnson
Summary: This Tutorial Review highlights the importance of redox-active molecules in unlocking the potential of lithium-air, lithium-sulfur, and redox-flow batteries. The role of these molecules varies depending on the type of battery, but their solubility, electrochemical and chemical stability, and redox potentials are crucial factors influencing their performance. Collaborations within the chemical community are essential for the development and utilization of redox-active molecules in next-generation batteries.
CHEMICAL SOCIETY REVIEWS
(2021)
Review
Biochemistry & Molecular Biology
Domenico Tierno, Gabriele Grassi, Serena Scomersi, Marina Bortul, Daniele Generali, Fabrizio Zanconati, Bruna Scaggiante
Summary: The poor survival of triple-negative breast cancer (TNBC) is attributed to its aggressive behavior, large heterogeneity, and high risk of recurrence. Next-generation sequencing (NGS) has been used to investigate the molecular characteristics of TNBC, revealing recurrent pathogenic alterations in TP53, immunocheckpoint response genes, and PIK3CA and DNA repair pathways. NGS has also identified potential personalized treatments and novel biomarkers such as AURKA, MYC, and JARID2 mutations. Additionally, NGS studies have identified ethnicity-specific alterations in African and African American TNBC, including EZH2 overexpression, BRCA1 alterations, and a BRCA2-delaAAGA mutation. The development of long-read sequencing methods and their combination with optimized short-read techniques hold promise for improving the efficiency of NGS approaches in future clinical use.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Physics, Particles & Fields
Sheean Jolicoeur, Roy Maartens, Simthembile Dlamini
Summary: Surveys of the matter distribution contain information on potential non-Gaussianity in the early Universe. By combining different surveys, the cosmic variance can be reduced and the precision of primordial non-Gaussianity can be improved. A combination of optical galaxy surveys and 21 cm intensity mapping surveys can deliver precision comparable to that from the CMB.
EUROPEAN PHYSICAL JOURNAL C
(2023)
Review
Chemistry, Physical
Suzan Yilmaz, Akos Nyerges, John van der Oost, George M. Church, Nico J. Claassens
Summary: Metabolic engineering has the potential to transform the chemical industry and support the transition into a circular bioeconomy by modifying cellular biocatalysts to convert sustainable substrates into desired products. However, despite decades of research, its industrial application has been limited. To fully unleash its potential, it is crucial to optimize the synthetic and native metabolic networks of cell factories at the system and genome-wide level, incorporating machine learning and efficient screening or selection approaches.
Review
Biology
Heena Satam, Kandarp Joshi, Upasana Mangrolia, Sanober Waghoo, Gulnaz Zaidi, Shravani Rawool, Ritesh P. Thakare, Shahid Banday, Alok K. Mishra, Gautam Das, Sunil K. Malonia
Summary: Next-generation sequencing (NGS) is a powerful tool that can sequence millions of DNA fragments simultaneously, providing detailed information about genomes, genetic variations, gene activity, and changes in gene behavior. Recent advancements have focused on improving sequencing speed and accuracy, reducing costs, and enhancing data analysis. These advancements have great potential for advancing genomics research and improving our understanding of diseases and personalized healthcare.
Article
Genetics & Heredity
Chiara Frascarelli, Nadia Zanetti, Alessia Nasca, Rossella Izzo, Costanza Lamperti, Eleonora Lamantea, Andrea Legati, Daniele Ghezzi
Summary: Primary mitochondrial diseases are progressive genetic disorders characterized by mitochondrial dysfunction. They can be caused by mutations in nuclear genes or genetic defects in mitochondrial genome. Traditional sequencing methods are limited in detecting structural alterations in mtDNA, but new long-read NGS technologies show promise in this regard. This study presents optimized protocols using long-read Oxford Nanopore Technology for the detection of mtDNA structural alterations, which may become the method of choice for genetic studies on mtDNA.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Tobias Fehlmann, Fabian Kern, Omar Lahaml, Christina Backes, Jeffrey Solomon, Pascal Hirsch, Carsten Volz, Rolf Mueller, Andreas Keller
Summary: miRMaster is a tool for analyzing small non-coding RNA sequencing data, with a wide range of features and updates that support analysis of multiple species and non-coding RNA classes. It includes new downstream analysis modules, sample embeddings, batch effect analysis, and support for new output formats and single cell small-RNA sequencing data analysis.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Biotechnology & Applied Microbiology
Chao Ye, Xinyu Wei, Tianqiong Shi, Xiaoman Sun, Nan Xu, Cong Gao, Wei Zou
Summary: This article reviews the development of genome-scale metabolic network models and discusses their importance in industrial biotechnology and human health applications. The challenges and future trends of GSMMs are also addressed.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Ewa Goljan, Mohammed Abouelhoda, Mohamed M. ElKalioby, Amjad Jabaan, Nada Alghithi, Brian F. Meyer, Dorota Monies
Summary: This study provides a comprehensive overview of pharmacogenetic variation in the Saudi population. It identifies functional variants in pharmacogenes, particularly in CYP genes, and highlights the high polymorphism of VKORC1 gene in this population. Unique rare variants are also found in the Saudi population.
Article
Mathematics
M. Rehan Usman, M. Arslan Usman, Soo Young Shin, Gandeva Bayu Satrya, Rizwan A. Naqvi, Maria G. Martini, Christos Politis
Summary: This paper proposes a joint strategy for hybrid-access small-cells using WHT with NOMA and IRC to achieve high performance gains and mitigate intercell interference. Jointly applying WHT and NOMA ensures better performance gains and reduces cross-tier interference caused by macrocell users.
Article
Medicine, Research & Experimental
Bryce A. Schuler, Erica T. Nelson, Mary Koziura, Joy D. Cogan, Rizwan Hamid, John A. Phillips
Summary: This review aims to increase the familiarity of non-genetics providers with genetic testing strategies, helping them to understand and interpret genetic testing results. The paper introduces commonly used genetic testing approaches, types of genetic and genomic variations, challenges in variant identification, and opportunities for improvement in the clinical application of next-generation sequencing (NGS).
JOURNAL OF CLINICAL INVESTIGATION
(2022)
Article
Oncology
Akira Sugimoto, Shingo Matsumoto, Hibiki Udagawa, Ryo Itotani, Yuko Usui, Shigeki Umemura, Kazumi Nishino, Ichiro Nakachi, Shoichi Kuyama, Haruko Daga, Satoshi Hara, Shingo Miyamoto, Terufumi Kato, Jun Sakakibara-Konishi, Eriko Tabata, Taku Nakagawa, Tomoy Kawaguchi, Tetsuya Sakai, Yuji Shibata, Hiroki Izumi, Kaname Nosaki, Yoshitaka Zenke, Kiyotaka Yoh, Koichi Goto
Summary: In this study, concordance between plasma cfDNA and tissue-based sequencing for oncogenic driver detection in NSCLC was evaluated. The results showed that plasma cfDNA sequencing had relatively high sensitivity for detecting gene mutations, but low sensitivity for gene fusions and MET exon 14 skipping, compared to tissue-based sequencing.
CLINICAL CANCER RESEARCH
(2023)
Article
Multidisciplinary Sciences
L. G. Fearnley, M. F. Bennett, M. Bahlo
Summary: This article presents a superfast method called superSTR for detecting short tandem repeat expansions without requiring alignment information. The method has been successfully applied to process whole-genome and whole-exome sequencing data, and it was used to analyze short tandem repeats in the UK Biobank. Furthermore, the method was also able to detect repeat expansions in RNA sequencing data.
SCIENTIFIC REPORTS
(2022)
Article
Oncology
Alessandra Santangelo, Marzia Rossato, Giuseppe Lombardi, Salvatore Benfatto, Denise Lavezzari, Gian Luca De Salvo, Stefano Indraccolo, Maria Cristina Dechecchi, Paola Prandini, Roberto Gambari, Chiara Scapoli, Gianfranco Di Gennaro, Mario Caccese, Marica Eoli, Roberta Ruda, Alba Ariela Brandes, Toni Ibrahim, Simona Rizzato, Ivan Lolli, Giuseppe Lippi, Massimo Delledonne, Vittorina Zagonel, Giulio Cabrini
Summary: The study identified a signature based on the expression of 5 biomarkers that could help identify a subgroup of GBM patients exhibiting a striking survival advantage when treated with regorafenib. Further validation in larger replication cohorts is needed, but potential biomarker options have been highlighted to guide clinical decision-making between regorafenib and other treatments in patients with relapsing GBM.
Article
Plant Sciences
Valerio Di Vittori, Elena Bitocchi, Monica Rodriguez, Saleh Alseekh, Elisa Bellucci, Laura Nanni, Tania Gioia, Stefania Marzario, Giuseppina Logozzo, Marzia Rossato, Concetta De Quattro, Maria L. Murgia, Juan Jose Ferreira, Ana Campa, Chunming Xu, Fabio Fiorani, Arun Sampathkumar, Anja Froehlich, Giovanna Attene, Massimo Delledonne, Bjoern Usadel, Alisdair R. Fernie, Domenico Rau, Roberto Papa
Summary: Through gene expression and histological analysis of dehiscent and indehiscent pods, a potential candidate gene controlling pod indehiscence was identified. Pod shattering is associated with the lack of a functional abscission layer in the ventral sheath, and key anatomical modifications related to pod shattering occur early in pod development. Loss of pod shattering in legumes is proposed to result from histological convergent evolution and selection at orthologous loci.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biodiversity Conservation
Hendrik Freitag, Rick de Vries, Marta Paterno, Simone Maestri, Massimo Delledonne, Cameron G. Thompson, Helena Lamed, Rebekah Lambert, Michael F. Fox, Mariela C. Gonzalez, Emmanuel D. Delocado, Marc R. Sabordo, Clister Pangantihon, Iva Njunjic
Summary: During a taxon expedition in Montenegro, a new species of Long-palped Water Beetle was discovered and compared to closely-related congeners. Additionally, five new species and DNA barcodes for previously unidentified species were provided, with discussions on genetic distances and divergence between species.
BIODIVERSITY DATA JOURNAL
(2021)
Article
Cell Biology
Chiara Pirazzini, Tiago Azevedo, Luca Baldelli, Anna Bartoletti-Stella, Giovanna Calandra-Buonaura, Alessandra Dal Molin, Giovanna Maria Dimitri, Ivan Doykov, Pilar Gomez-Garre, Sara Hagg, Jenny Hallqvist, Claire Halsband, Wendy Heywood, Silvia Jesus, Juulia Jylhava, Katarzyna Malgorzata Kwiatkowska, Miguel A. Labrador-Espinosa, Cristina Licari, Maria Giovanna Maturo, Giacomo Mengozzi, Gaia Meoni, Maddalena Milazzo, Maria Teresa Perinan-Tocino, Francesco Ravaioli, Claudia Sala, Luisa Sambati, Sebastian Schade, Sebastian Schreglmann, Simeon Spasov, Leonardo Tenori, Dylan Williams, Luciano Xumerle, Elisa Zago, Kailash P. Bhatia, Sabina Capellari, Pietro Cortelli, Paolo Garagnani, Henry Houlden, Pietro Lio, Claudio Luchinat, Massimo Delledonne, Kevin Mills, Pablo Mir, Brit Mollenhauer, Christine Nardini, Nancy L. Pedersen, Federica Provini, Stephen Strom, Claudia Trenkwalder, Paola Turano, Maria Giulia Bacalini, Claudio Franceschi
Summary: The PROPAG-AGEING project aims to characterize the contribution of the ageing process to PD development, focusing on the continuum between ageing and PD and using a Geroscience approach. The project emphasizes the role of inflammaging and utilizes a multi-omic characterization of peripheral samples to identify molecular perturbations that can lead to PD development.
MECHANISMS OF AGEING AND DEVELOPMENT
(2021)
Article
Microbiology
Alessandro Passera, Marzia Rossato, John S. Oliver, Giovanna Battelli, Gul-I-Rayna Shahzad, Emanuela Cosentino, Jay M. Sage, Silvia L. Toffolatti, Giulia Lopatriello, Jennifer R. Davis, Michael D. Kaiser, Massimo Delledonne, Paola Casati
Summary: This study characterized Lysinibacillus fusiformis strain S4C11 isolated from the roots of an apple tree in northern Italy using various approaches such as in vitro, in vivo, in planta, and in silico methods. The strain exhibited antifungal activity, plant growth promotion abilities, and its genome analysis revealed genes related to biocontrol effects observed in experimental trials.
MICROBIOLOGICAL RESEARCH
(2021)
Article
Plant Sciences
Valentina di Rienzo, Zahra Imanifard, Isabella Mascio, Charles S. Gasser, Debra J. Skinner, Ciro Leonardo Pierri, Martina Marini, Valentina Fanelli, Wilma Sabetta, Cinzia Montemurro, Diana Bellin
Summary: This study focused on the Vitis vinifera INNER NO OUTER (INO) gene as a candidate for seedless fruit production, based on an interesting case of seedless fruit production in the Annona squamosa crop species. The VviINO gene was found to play a crucial role in the formation of ovule outer integument and seed set, with similar activity and protein targets in grapevine as in Arabidopsis. The findings have potential implications for grapevine breeding.
HORTICULTURE RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Chiara Degli Esposti, Barbara Iadarola, Simone Maestri, Cristina Beltrami, Denise Lavezzari, Martina Morini, Patrizia De Marco, Giovanni Erminio, Alberto Garaventa, Federico Zara, Massimo Delledonne, Marzia Ognibene, Annalisa Pezzolo
Summary: Studying exosomal DNA isolated from plasma of neuroblastoma patients may aid in detecting somatic mutations in tumor cells, providing a non-invasive biomarker for molecular diagnosis of neuroblastoma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Microbiology
Luca Marcolungo, Alessandro Passera, Simone Maestri, Elena Segala, Massimiliano Alfano, Francesca Gaffuri, Giovanni Marturano, Paola Casati, Piero Attilio Bianco, Massimo Delledonne
Summary: Rapid and sensitive diagnostic assays for plant pathogens are essential for crop disease management. This study established and evaluated a novel nanopore sequencing-based diagnostic assay, which can detect and characterize quarantine pathogens simultaneously, achieving detection and typing within 13 minutes.
Article
Biodiversity Conservation
Menno Schilthuizen, Cameron Graham Thompson, Rick de Vries, Anthonie D. P. van Peursen, Marta Paterno, Simone Maestri, Luca Marcolongo, Chiara Degli Esposti, Massimo Delledonne, Iva Njunjic
Summary: The taxonomy of the European giant keelback slugs of the genus Limax is not well understood, and there may be many unidentified species based on preliminary morphological and molecular data.
BIODIVERSITY DATA JOURNAL
(2022)
Article
Agronomy
Jessica A. Vervalle, Laura Costantini, Silvia Lorenzi, Massimo Pindo, Riccardo Mora, Giada Bolognesi, Martina Marini, Justin G. Lashbrooke, Ken R. Tobutt, Melane A. Vivier, Rouvay Roodt-Wilding, Maria Stella Grando, Diana Bellin
Summary: This article presents a high-density integrated map for grapevine, utilizing the Vitis18K SNP chip for genetic linkage mapping, which serves as a useful tool for further elucidating the grapevine genome and complex traits.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Agronomy
Alessandro Passera, Valentina Grosso, Niccolo Miotti, Marzia Rossato, Francesca Gaffuri, Paola Casati, Massimo Delledonne, Piero Attilio Bianco
Summary: In this study, two qPCR-based diagnostic methods were successfully adapted for use with a nanoplate-based digital PCR assay, demonstrating similar sensitivity and accuracy in detecting and quantifying plant pathogens as qPCR.
PHYTOPATHOLOGIA MEDITERRANEA
(2022)
Review
Plant Sciences
Chiara Broccanello, Diana Bellin, Giovanni DalCorso, Antonella Furini, Francesca Taranto
Summary: Addressing climate change challenges in durum wheat production is crucial for ensuring food and nutrition security in the Mediterranean region. Exploiting the genetic variability in landrace populations has emerged as a strategy to enhance durum wheat adaptation to environmental stresses. This review highlights the importance of durum wheat landraces as a genetic resource for improving the sustainability of Mediterranean agroecosystems, focusing on adaptive traits and the development of molecular markers for selection.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Luca Marcolungo, Leonardo Vincenzi, Matteo Ballottari, Michela Cecchin, Emanuela Cosentino, Thomas Mignani, Antonina Limongi, Irene Ferraris, Matteo Orlandi, Marzia Rossato, Massimo Delledonne
Summary: High-throughput chromosome conformation capture (Hi-C) is commonly used in de novo assembly for its ability to produce highly contiguous genomes. However, its statistical approach can introduce connection errors. We used optical mapping to evaluate the quality of Hi-C reconstructed scaffolds and found numerous inconsistencies. Manual inspection confirmed that some of these conflicts were caused by Hi-C joining errors. We conclude that integrating optical mapping data after Hi-C-based scaffolding improves the assembly quality by identifying and investigating misjoins.
Review
Plant Sciences
Elisa Fasani, Gianluigi Giannelli, Serena Varotto, Giovanna Visioli, Diana Bellin, Antonella Furini, Giovanni Dalcorso
Summary: This review summarizes the epigenetic response of plants to soil contamination by heavy metals and metalloids, as well as the transgenerational transfer of this epigenetic status, with consideration of the impact of the microbial community inhabiting the rhizosphere.
Article
Health Care Sciences & Services
Keenan A. Ramsey, Carel G. M. Meskers, Marijke C. Trappenburg, Maria Giulia Bacalini, Massimo Delledonne, Paolo Garagnani, Carolyn Greig, Victor Kallen, Nico van Meeteren, Natal van Riel, Nadine Correia Santos, Sarianna Sipila, Janice L. Thompson, Anna C. Whittaker, Andrea B. Maier
Summary: The PANINI Toolkit aims to provide a standardized assessment tool for evaluating multiple domains of health in older adults, with a focus on nutrition and physical activity. It was developed through consensus of experts within the PANINI consortium and has been implemented successfully in various countries and populations.