Article
Genetics & Heredity
Valentina Snetkova, Athena R. Ypsilanti, Jennifer A. Akiyama, Brandon J. Mannion, Ingrid Plajzer-Frick, Catherine S. Novak, Anne N. Harrington, Quan T. Pham, Momoe Kato, Yiwen Zhu, Janeth Godoy, Eman Meky, Riana D. Hunter, Marie Shi, Evgeny Z. Kvon, Veena Afzal, Stella Tran, John L. R. Rubenstein, Axel Visel, Len A. Pennacchio, Diane E. Dickel
Summary: Mutagenesis of 23 ultraconserved enhancers and examination of their activities in transgenic mouse reporter assays show that overall their regulatory properties are robust to mutation. Manipulation of endogenous loci in mice corroborates reporter assay data.
Article
Biochemistry & Molecular Biology
Spyros Tastsoglou, Giorgos Skoufos, Marios Miliotis, Dimitra Karagkouni, Ioannis Koutsoukos, Anna Karavangeli, Filippos S. Kardaras, Artemis G. Hatzigeorgiou
Summary: DIANA-miRPath is an online miRNA analysis platform that allows exploration of combined miRNA effects through predicted or experimentally supported miRNA interactions. Its latest version introduces a customizable target-based miRNA functional analysis engine, enriched with interaction, annotation, and parameterization options. The platform integrates various datasets and enables enrichment analysis on GO terms, pathways, and expression data for a wide range of states. Additionally, it provides a module for utilizing CRISPR knock-out screen datasets to identify miRNAs with potentially crucial roles.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Masaki Takasugi, Yuya Yoshida, Yoshiki Nonaka, Naoko Ohtani
Summary: Despite comprehensive transcriptome analyses, the actual impact of transcriptome on aging and species maximum lifespan (MLS) has remained elusive. However, our study found significant similarities between transcriptomic signatures associated with mammalian MLS and aging, suggesting that gene expression patterns associated with MLS contribute to extended lifespan within and across species. Furthermore, we identified evidence of co-evolution between MLS and promoter sequences of MLS-associated genes, highlighting the evolutionary contribution of specific transcription factor binding motifs in shaping MLS-associated gene expression signature. This study emphasizes the importance of considering the adaptive aspects of aging transcriptome and demonstrates the power of cross-species genomics in understanding adaptive aging transcriptome.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Zhi-Luo Deng, Philipp C. Munch, Rene Mreches, Alice C. McHardy
Summary: This article introduces a novel software called RiboDetector, based on a bi-directional long short-term memory neural network, which can rapidly and accurately identify ribosomal RNA (rRNA) sequences from different types of RNA. The software produces fewer misclassifications compared to current state-of-the-art methods and has the ability to detect novel rRNA sequences. Additionally, RiboDetector has a much faster processing speed than other methods.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Baoxing Song, Edward S. Buckler, Hai Wang, Yaoyao Wu, Evan Rees, Elizabeth A. Kellogg, Daniel J. Gates, Merritt Khaipho-Burch, Peter J. Bradbury, Jeffrey Ross-Ibarra, Matthew B. Hufford, M. Cinta Romay
Summary: Thousands of species are set to be sequenced in the coming years, and understanding the functionality of their genomes requires molecular and evolutionary approaches. A study focusing on the Andropogoneae tribe, which includes multiple crop species, revealed highly conserved noncoding sequences rich in functional elements. These findings shed light on the evolution and functional significance of CNSs in maize.
Article
Multidisciplinary Sciences
Chengxin Zhang, Anna Marie Pyle
Summary: US-align2 is a unified protocol for sequential and non-sequential alignment of proteins and nucleic acids. It outperforms existing methods in non-sequential alignment and has the ability to detect protein-nucleic acid mimicries, with high sensitivity and fast speed, making it suitable for large-scale structural similarity detection.
Article
Biochemistry & Molecular Biology
Arif Canakoglu, Pietro Pinoli, Anna Bernasconi, Tommaso Alfonsi, Damianos P. Melidis, Stefano Ceri
Summary: ViruSurf is a large public database containing viral sequences and curated metadata from various sources, offering complex search functionalities. It includes harmful virus species to humans and enables faster responses to potential threats from new viruses in the future.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Si-Yi Chen, Tao Yue, Qian Lei, An-Yuan Guo
Summary: TCRdb is a comprehensive human TCR sequences database, containing over 277 million highly reliable TCR sequences from over 8265 TCR-Seq samples, with unique features including a powerful search function and interactive data visualization charts for comparing TCR repertoire in different samples. It will serve as a valuable resource for the research and application community of T cell immunology.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Hongtao Song, Qi Wang, Zhonghua Zhang, Kui Lin, Erli Pang
Summary: This study presents a computational approach to predict putative cis-regulatory elements in the Cucurbitaceae genomes. The researchers identified a large number of cis-regulatory elements using whole-genome alignment and validated their predictions using various datasets. The results provide valuable resources for functionally annotating conserved non-coding sequences and studying their regulatory roles in Cucurbitaceae genomes.
HORTICULTURE RESEARCH
(2023)
Article
Genetics & Heredity
Feng Xu, Yifan Wang, Yunchao Ling, Chenfen Zhou, Haizhou Wang, Andrew E. Teschendorff, Yi Zhao, Haitao Zhao, Yungang He, Guoqing Zhang, Zhen Yang
Summary: MicroRNAs play important roles in gene expression regulation, and their dysregulation is widely reported in pathological cellular states. The dbDEMC database was constructed to store and query differentially expressed miRNAs (DEMs) in human cancers. The updated version, dbDEMC 3.0, contains more data entries and includes data from mice and rats. It provides a valuable resource for studying the molecular functions and regulatory mechanisms of DEMs in human cancers.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Jeremy M. Beaulieu, Brian C. O'Meara, Michael A. Gilchrist
Summary: UCEs are highly conserved elements containing phylogenetic information. The SeION model provides a better understanding of selection on UCEs and their variability, aiding in elucidating the biological mechanisms responsible for their preservation.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Jesus A. Ballesteros, Emily V. W. Setton, Carlos E. Santibanez-Lopez, Claudia P. Arango, Georg Brenneis, Saskia Brix, Kevin F. Corbett, Esperanza Cano-Sanchez, Merai Dandouch, Geoffrey F. Dilly, Marc P. Eleaume, Guilherme Gainett, Cyril Gallut, Sean McAtee, Lauren McIntyre, Amy L. Moran, Randy Moran, Pablo J. Lopez-Gonzalez, Gerhard Scholtz, Clay Williamson, H. Arthur Woods, Jakob T. Zehms, Ward C. Wheeler, Prashant P. Sharma
Summary: This study utilized multiple molecular data categories to resolve the phylogenetic relationships of sea spiders, revealing their basal topology and including families that were not fully sampled before. In addition, molecular divergence time estimation confirmed the Ordovician origin of crown group sea spiders, showing that in the evolutionary process sea spiders exhibit greater resilience to mass extinction episodes compared to mollusk and echinoderm lineages.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
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)
Article
Oncology
Sara Terreri, Sara Mancinelli, Matteo Ferro, Maria Concetta Vitale, Sisto Perdona, Luigi Castaldo, Vincenzo Gigantino, Vincenzo Mercadante, Rossella De Cecio, Gabriella Aquino, Marco Montella, Claudia Angelini, Eugenio Del Prete, Marianna Aprile, Angelo Ciaramella, Giovanna L. Liguori, Valerio Costa, George A. Calin, Evelina La Civita, Daniela Terracciano, Ferdinando Febbraio, Amelia Cimmino
Summary: Ultra-conserved-transcript-8+ (uc.8+) levels correlate with the grading and staging of bladder cancer, showing localization in both cytoplasm and nucleus of bladder cells at early stages and prevalent cytoplasmic localization in advanced stages. The study suggests that uc.8+ localization can serve as a potential prognostic biomarker for bladder cancer.
Review
Gastroenterology & Hepatology
Shen-Shuo Gao, Zhi-Kai Zhang, Xu-Bin Wang, Yan Ma, Guo-Qing Yin, Xiao-Bo Guo
Summary: This article reviews the research on T-UCRs in GC and discusses their regulatory role in the occurrence and development of GC, providing new strategies for diagnosis and treatment of GC.
WORLD JOURNAL OF GASTROENTEROLOGY
(2022)
Review
Biochemistry & Molecular Biology
Ilaria Plantamura, Alessandra Cataldo, Giulia Cosentino, Marilena V. Iorio
Summary: Despite controversial roles in different cancer types, miR-205 is mainly described as an oncosuppressive miRNA in breast cancer. Its expression decreases from less aggressive to more aggressive subtypes and influences metastasis capability, therapy response, and patient survival. MiR-205 plays a role in breast cancer initiation and progression, stemness maintenance, tumor microenvironment, and may serve as a biomarker with relevance in normal breast physiology. Additionally, some lncRNAs are implicated in breast cancer progression by acting as sponges of miR-205.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Multidisciplinary Sciences
Francesca Lovat, Pierluigi Gasparini, Giovanni Nigita, Karilyn Larkin, John C. Byrd, Mark D. Minden, Michael Andreeff, Bing Z. Carter, Carlo M. Croce
Summary: The study found that the loss of both miR-15/16 clusters may act as a potential oncogenic driver in the transition from chronic phase to blast crisis in CML patients.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Felice Pepe, Laura Z. Rassenti, Yuri Pekarsky, Jadwiga Labanowska, Tatsuya Nakamura, Giovanni Nigita, Thomas J. Kipps, Veronica Balatti, Carlo M. Croce
Summary: Chronic lymphocytic leukemia (CLL) is a common adult leukemia characterized by chromosomal aberrations. This study found that some CLL patients have undetected microdeletions, which are closely associated with chromosomal alterations in cancer. These findings may have clinical relevance for successful stratification of patients.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Oncology
Rosario Distefano, Giovanni Nigita, Patricia Le, Giulia Romano, Mario Acunzo, Patrick Nana-Sinkam
Summary: Post-transcriptional modifications in miRNA molecules have provided new insights into cancer biology and potential cancer biomarkers. In this study, we analyzed the profiles of canonical and non-canonical miRNAs in lung cancer patients of different races. We identified distinct post-transcriptional modifications in lung cancer tissues, indicating the relevance of miRNA isoforms as potential biomarkers. Concurrent profiling of canonical and non-canonical miRNAs may help identify additional biological pathways and biomarkers in lung cancer.
Article
Computer Science, Artificial Intelligence
Chiara Vischioni, Fabio Bove, Federica Mandreoli, Riccardo Martoglia, Valentino Pisi, Cristian Taccioli
Summary: The study of Copy Number Variations (CNVs) is a hot topic in biomedical cancer research. VarNuCopy is a novel platform that allows visual, interactive exploration and analysis of CNV data across multiple species, providing a comprehensive and efficient solution for researchers to identify complex trends and patterns in a large amount of data.
Article
Biochemistry & Molecular Biology
Elisabetta D'Aversa, Giulia Breveglieri, Effrossyni Boutou, Angeliki Balassopoulou, Ersi Voskaridou, Patrizia Pellegatti, Giovanni Guerra, Chiara Scapoli, Roberto Gambari, Monica Borgatti
Summary: In this study, we developed two non-invasive prenatal testing (NIPT) assays for detecting the two most common beta thalassemia mutations in the Mediterranean area. The assays were based on sensitive droplet digital PCR (ddPCR) technology, and were optimized to accurately determine the fetal genotype from maternal plasma samples at different gestational ages. The diagnostic outcomes were confirmed by DNA sequencing. This study provides a simple and sensitive diagnostic tool for NIPT of beta thalassemia mutations, and may have applicability for other single point mutations causing monogenic diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Genetics & Heredity
Chiara Vischioni, Fabio Bove, Matteo De Chiara, Federica Mandreoli, Riccardo Martoglia, Valentino Pisi, Gianni Liti, Cristian Taccioli
Summary: This study identified novel gene targets linked to tumor predisposition and found that miRNA copy number patterns are associated with cancer progression and susceptibility.
Article
Biochemistry & Molecular Biology
Nicoletta Bianchi, Luisa Doneda, Luca Elli, Cristian Taccioli, Valentina Vaira, Alice Scricciolo, Vincenza Lombardo, Anna Terrazzan, Patrizia Colapietro, Leonardo Terranova, Carlo Bergamini, Maurizio Vecchi, Lucia Scaramella, Nicoletta Nandi, Leda Roncoroni
Summary: This study identified a set of microRNAs in serum that can differentiate between different types of refractory diseases and aid in monitoring disease progression. The study also revealed the functions of these microRNAs, including cell signaling, epigenetic regulation, and inflammatory profiles.
Article
Biology
Carlo M. Bergamini, Nicoletta Bianchi, Valerio Giaccone, Paolo Catellani, Leonardo Alberghini, Alessandra Stella, Stefano Biffani, Sachithra Kalhari Yaddehige, Tania Bobbo, Cristian Taccioli
Summary: This study demonstrates for the first time that machine learning algorithms can identify and discriminate probiotic bacteria from pathogenic organisms in the human gut. The information content within tRNA sequences was found to be the key genomic feature in characterizing probiotics.
Biographical-Item
Oncology
Gary S. Stein, Carlo M. Croce
Article
Oncology
Alessandro La Ferlita, Nipin Sp, Marina Goryunova, Giovanni Nigita, Raphael E. Pollock, Carlo M. Croce, Joal D. Beane
Summary: Soft-tissue sarcomas (STS), a rare and diverse group of tumors, have various subtypes characterized by differences in tumor biology and clinical outcomes. Small non-coding RNAs (sncRNAs), including miRNAs and tRNA-derived ncRNAs, play important roles in STS tumorigenesis and differentiation. However, the translation of these findings into clinical applications, such as biomarkers or therapeutic targets, remains challenging. This review summarizes the current understanding of sncRNAs in STS, with a focus on liposarcoma, and discusses their potential as novel biomarkers and therapeutic targets.
MOLECULAR CANCER RESEARCH
(2023)
Article
Agriculture, Dairy & Animal Science
Yazavinder Singh, Marco Cullere, Davide Bertelli, Severino Segato, Giovanni Franzo, Antonio Frangipane di Regalbono, Paolo Catellani, Cristian Taccioli, Silvia Cappellozza, Antonella Dalle Zotte
Summary: Insects, such as silkworm chrysalis, can be a sustainable and alternative feed ingredient due to their rich nutritional profile. This research aimed to understand the potential of silkworm chrysalis as a feedstuff for laying quails, finding that it can be included up to 12% in the feed formulation for optimal performance and egg quality.
Article
Biochemistry & Molecular Biology
Henry R. Kilgore, Peter G. Mikhael, Kalon J. Overholt, Ann Boija, Nancy M. Hannett, Catherine Van Dongen, Tong Ihn Lee, Young-Tae Chang, Regina Barzilay, Richard A. Young
Summary: This research reveals that different types of intracellular condensates have distinct chemical environments that affect molecular distribution. Machine learning approaches can predict the selective partitioning of molecules in condensates, providing insights for the development of small molecule therapeutics with optimal subcellular distribution and therapeutic benefits.
NATURE CHEMICAL BIOLOGY
(2023)
Review
Biology
Roberto Gambari, Cristina Zuccato, Lucia Carmela Cosenza, Matteo Zurlo, Jessica Gasparello, Alessia Finotti, Maria Rita Gamberini, Marco Prosdocimi
Summary: This review article presents the fascinating story of sirolimus (rapamycin), a drug known to induce fetal hemoglobin and of great interest for the treatment of beta-thalassemia. It discusses the discovery of rapamycin, its antimicrobial properties, its inhibition of tumor cell growth, and its potential immunosuppressive effects. The article also highlights recent findings regarding rapamycin's ability to induce fetal hemoglobin, paving the way for clinical trials on beta-thalassemia patients.
Meeting Abstract
Oncology
Lucia Casadei, Patricia Sarchet, Luciano Cascione, Giovanni Nigita, Fernanda Costas Casal de Faria, Carlo Maria Croce, Valerie Grignol, Raphael E. Pollock
