Article
Environmental Sciences
Yuxiang Chen, Jiaolin Li, Tingting Zhao, Yan Zhang, Lei Zhang, Lixin Xu
Summary: Vermicomposting is a promising method for managing corn stover, which can achieve bioresource recovery and environmental protection. The activity of β-glucosidase, abundance of GH(1) gene, TOC, and microbial communities carrying GH(1) gene were all influenced by processing time and earthworm density.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Multidisciplinary Sciences
Mingyi Yang, Omer Ali, Magnar Bjoras, Junbai Wang
Summary: In this article, a non-coding SNVs analysis tool called bpb3 is proposed to identify functional mutation blocks (FMBs) by integrating genome sequencing and transcriptome data. A two-level Bayesian approach with a biophysical model is implemented to compute TF-DNA binding affinity changes based on clustered position weight matrices (PWMs) from over 1700 TF-motifs. By testing datasets from follicular lymphoma and melanoma, bpb3 automatically and robustly identifies FMBs, providing insights into patho-mechanisms and therapeutic targets.
Review
Cell Biology
John G. Conboy
Summary: Deep intron elements play crucial roles in regulating splicing processes, such as recursive splicing exons, decoy splice sites, and RNA:RNA bridges, with mutations potentially leading to human diseases. Understanding these noncanonical splicing pathways and regulatory signals in deep introns is important for medical applications and uncovering new disease mechanisms.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2021)
Article
Genetics & Heredity
Niall P. Keegan, Steve D. Wilton, Sue Fletcher
Summary: Understanding pre-mRNA splicing is crucial for diagnosing and treating genetic diseases. Pseudoexon mutations, which create new exons within introns, are rare and difficult to predict. Deep-intronic single nucleotide variants are a common cause of pseudoexons, suggesting that certain regions involved in splicing processes may be more susceptible to exonization. A comprehensive study of pseudoexon splice events can improve genetic diagnostics and reveal new targets for splice-modulating therapies.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Xi Chen, Jian Zhou, Ran Zhang, Aaron K. Wong, Christopher Y. Park, Chandra L. Theesfeld, Olga G. Troyanskaya
Summary: The FENRIR framework integrates diverse epigenetic and functional genomics datasets to infer tissue-specific functional relationships between enhancers and identify disease-associated enhancers accurately. In a case study on autism, FENRIR effectively prioritized enhancers with pathogenic signals and experimentally validated their differential regulatory potential. FENRIR provides an accurate and effective approach to study tissue-specific enhancers and their role in diseases.
Review
Plant Sciences
Syed Sarfaraz Hussain, Manzar Abbas, Sammar Abbas, Mingke Wei, Ahmed H. El-Sappah, Yuhan Sun, Yun Li, Arthur J. Ragauskas, Quanzi Li
Summary: Alternative splicing in plants regulates gene expression through differential transcriptional modifications, allowing adaptation to environmental stresses and different growth stages. It causes the retention of introns in messenger RNA, leading to the translation of differentially expressed proteins. Additionally, alternative splicing remodels transcription factors at the post-transcriptional level, activating or repressing transcription.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biotechnology & Applied Microbiology
Haigang Geng, Ruolan Qian, Yiqing Zhong, Xiangyu Tang, Xiaojun Zhang, Linmeng Zhang, Chen Yang, Tingting Li, Zhongyi Dong, Cun Wang, Zizhen Zhang, Chunchao Zhu
Summary: This study proposes a computational strategy called Gastric cancer Specific Synthetic Lethality inference (GSSL) to identify synthetic lethal interactions in gastric cancer (GC). GSSL analysis identifies 34 candidate synthetic lethal pairs, including the TP53-CHEK1 pair, and experimental validation confirms the therapeutic potential of inhibiting CHEK1 for GC patients with TP53 mutation. Additional experimental validation of two novel synthetic lethal pairs further supports the reliability and feasibility of GSSL. Overall, GSSL is a reliable method for comprehensive analysis of synthetic lethal interactions in GC, offering novel insights for precision medicine and individualized treatment.
CANCER GENE THERAPY
(2023)
Article
Plant Sciences
Louis Grillet, En-Jung Hsieh, Wolfgang Schmidt
Summary: Iron is an essential element for all forms of life, including plants, and its homeostasis is crucial for cellular processes. This study investigated the mechanisms of systemic iron transport mediated by OPT3, activation of IMA genes in the phloem, and iron uptake in the root epidermis. The results revealed potential regulators of cellular iron homeostasis and identified plastid-encoded loci that may be involved in retrograde control of root iron uptake.
Correction
Biochemical Research Methods
M. Grace Gordon, Fumitaka Inoue, Beth Martin, Max Schubach, Vikram Agarwal, Sean Whalen, Shiyun Feng, Jingjing Zhao, Tal Ashuach, Ryan Ziffra, Anat Kreimer, Ilias Georgakopoulos-Soares, Nir Yosef, Chun Jimmie Ye, Katherine S. Pollard, Jay Shendure, Martin Kircher, Nadav Ahituv
Summary: The paper has a published amendment which can be accessed through a link at the top of the paper.
Article
Cell Biology
Yiqun Zhang, Fengju Chen, Erin Pleasance, Laura Williamson, Cameron J. Grisdale, Emma Titmuss, Janessa Laskin, Steven J. M. Jones, Isidro Cortes-Ciriano, Marco A. Marra, Chad J. Creighton
Summary: The study found that somatic structural variants (SVs) have an impact on gene regulation in advanced tumors, leading to altered expression of hundreds of genes near SV breakpoints. Some of these SV-expression associations are correlated with patient survival rates, while a high overall SV burden is associated with treatment using specific drugs.
Article
Genetics & Heredity
Hiroki Kiyose, Hidewaki Nakagawa, Atsushi Ono, Hiroshi Aikata, Masaki Ueno, Shinya Hayami, Hiroki Yamaue, Kazuaki Chayama, Mihoko Shimada, Jing Hao Wong, Akihiro Fujimoto
Summary: This study utilized the Oxford Nanopore sequencer to analyze cDNA sequences from hepatocellular carcinoma and matched non-cancerous livers, revealing numerous novel transcripts and thousands of differentially expressed transcripts. Experimental results demonstrated that differentially expressed transcripts can promote cell growth, and fusion gene detection uncovered novel fusion events.
Article
Biochemistry & Molecular Biology
Tao Li, Nianzhi Ning, Angelo Iacobino, Liangyan Zhang, Hui Wang, Giovanna Franciosa
Summary: Whole genome sequences of four neurotoxigenic C. butyricum type E strains from China revealed the presence of a novel putative transposable element (TE) upstream of the bont/e gene in all strains. Similar putative TEs were also found in the megaplasmids and chromosomes of other C. butyricum strains, as well as in a single C. botulinum type E strain, suggesting potential transposition events.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
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
Biochemistry & Molecular Biology
Mahdieh Labani, Amin Beheshti, Ahmadreza Argha, Hamid Alinejad-Rokny
Summary: Prostate cancer is highly prevalent and genomic alterations play a key role in its development and progression. In this study, an integrative analysis pipeline was used to identify 646 putative regulatory variants in prostate cancer, of which 30 significantly affected the expression of protein-coding genes. These variants could potentially impact 131 coding and non-coding genes, many of which are involved in disease-related pathways with targeted treatment options already available. Additionally, non-coding RNAs were identified as potential enhancer elements for certain protein-coding genes. Overall, this study provides a comprehensive map of genomic variants in prostate cancer and their potential contribution to the disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Ryan Loker, Jordyn E. Sanner, Richard S. Mann
Summary: Hox proteins modulate segment identity by changing chromatin accessibility and binding of transcription factors like Scalloped in a spatially-regulated manner, with their transcriptional activity dependent on the availability of cofactors.
Article
Genetics & Heredity
Simona Mellone, Chiara Puricelli, Denise Vurchio, Sara Ronzani, Simone Favini, Arianna Maruzzi, Cinzia Peruzzi, Amanda Papa, Alice Spano, Fabio Sirchia, Giorgia Mandrile, Alessandra Pelle, Paolo Rasmini, Fabiana Vercellino, Andrea Zonta, Ivana Rabbone, Umberto Dianzani, Maurizio Viri, Mara Giordano
Summary: This study evaluated the clinical performance of a targeted next-generation sequencing gene panel as a second-tier test in undiagnosed patients with neurodevelopmental disorders (NDDs). The results showed that the panel significantly increased the diagnostic yield in different types of NDDs, particularly in females, Autism Spectrum Disorders (ASD), and Epilepsy patients.
FRONTIERS IN GENETICS
(2022)
Article
Genetics & Heredity
Simona Mellone, Enrica Bertelli, Barbara Roviglione, Denise Vurchio, Sara Ronzani, Andrea Secco, Enrico Felici, Mariachiara Martina Strozzi, Federico Schena, Mara Giordano
Summary: Congenital adrenal hyperplasia (CAH) is a group of genetic disorders caused by enzyme deficiencies in cortisol biosynthesis. This study reports a case of Moroccan twins with CAH, who exhibited a disorder of sexual differentiation and hyponatremia. Molecular diagnosis revealed a likely pathogenic gene variant in both twins.
Article
Endocrinology & Metabolism
F. Prodam, M. Caputo, M. Romanisio, S. Brasili, M. Zavattaro, M. T. Sama, A. Ferrero, S. Costelli, F. R. Lenzi, A. Petri, E. Basso, S. Bellone, G. Aimaretti
Summary: This study evaluated the clinical and epidemiological characteristics of outpatients transitioning from Pediatric Endocrine Department to Adult Endocrine Department in a tertiary center, as well as the features of the transition process and predictors of drop-out. The findings showed that the patients were heterogeneous, with different ages, follow-up durations, and types of endocrine diseases. The number of visits was associated with the number and type of endocrine diseases, and adherence to follow-up was predicted by thyroid disorders and multiple comorbidities. A study exploring a specific transition plan for chronic endocrine diseases.
JOURNAL OF ENDOCRINOLOGICAL INVESTIGATION
(2023)
Article
Pediatrics
Valentina Mancioppi, Valentina Antoniotti, Arianna Solito, Elisabetta Mingoia, Alice Monzani, Giulia Genoni, Ivana Rabbone, Flavia Prodam, Simonetta Bellone
Summary: This study investigated subclinical hypothyroidism in newborns and observed the changes in thyroid hormone levels over time until four years of age. The results showed that more than half of the newborns did not require treatment and had either normal or slightly increased thyroid function. The study also suggested the importance of long-term follow-up to monitor thyroid hormone levels.
Article
Biochemistry & Molecular Biology
Daria Apostolo, Davide D'Onghia, Stelvio Tonello, Rosalba Minisini, Alessio Baricich, Carla Gramaglia, Filippo Patrucco, Patrizia Zeppegno, Antonio Acquaviva, Piero Emilio Balbo, Luigi Mario Castello, Giuseppe Cappellano, Annalisa Chiocchetti, Chiara Gerevini, Mara Giordano, Fatiha Laaguid, Marcello Manfredi, Davide Raineri, Cristina Rigamonti, Roberta Rolla, Valentina Romano, Marco Confalonieri, Paola Savoia, Elisa Zavattaro, Mario Pirisi, Barbara Ruaro, Pier Paolo Sainaghi, Mattia Bellan
Summary: Post-acute conditions are common after COVID-19, and the underlying mechanisms are not yet fully understood. This study suggests that Gas6 and its soluble receptors, sAxl and sMer, may be implicated in these conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Chiara Puricelli, Elena Boggio, Casimiro Luca Gigliotti, Ian Stoppa, Salvatore Sutti, Mara Giordano, Umberto Dianzani, Roberta Rolla
Summary: Platelets play a crucial role in hemostasis and coagulation, but their functions extend beyond that. They are involved in various physiological processes and can be targeted for therapeutic purposes in different pathologies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Endocrinology & Metabolism
Cristina Partenope, Quincy Pedranzini, Antonella Petri, Ivana Rabbone, Flavia Prodam, Simonetta Bellone
Summary: The report presents a case of a 16-year-old boy who developed polyuria, polydipsia, and weight loss after receiving the COVID-19 vaccine. Diagnosis revealed neuroinfundibulohypophysitis, a rare disorder characterized by inflammation of the pituitary gland and stalk. Further studies are needed to explore the possible causal link between the COVID-19 vaccine and AVP deficiency.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Federica Costa, Eleonora Beltrami, Simona Mellone, Sara Sacchetti, Elena Boggio, Casimiro Luca Gigliotti, Ian Stoppa, Umberto Dianzani, Roberta Rolla, Mara Giordano
Summary: Monogenic autoimmune disorders are important for understanding the mechanisms of immune tolerance. Various genetic and environmental factors contribute to the imbalance of immune activation/tolerance, making disease control difficult. Genetic analysis has improved diagnosis, but limited research on rare diseases restricts management to treating clinical manifestations. Recent studies have explored the correlation between microbiota composition and the development of autoimmune disorders, offering new perspectives on treating monogenic autoimmune diseases.
Article
Endocrinology & Metabolism
M. Caputo, T. Daffara, A. Ferrero, M. Romanisio, E. Monti, C. Mele, M. Zavattaro, S. Tricca, A. Siani, A. Clemente, C. Palumbo, S. De Cilla, A. Carriero, A. Volpe, P. Marzullo, G. Aimaretti, F. Prodam
Summary: The aim of this study was to identify risk factors for morphological changes in adrenal incidentalomas (AIs) during follow-up. High body weight, dehydroepiandrosterone sulfate (DHEAS), and direct renin concentration (DRC) were found to be associated with tumor enlargement, while aldosterone levels were lower in these cases. Additionally, glaucoma and dysglycemia had a higher prevalence in patients with tumor enlargement and were identified as independent predictors.
JOURNAL OF ENDOCRINOLOGICAL INVESTIGATION
(2023)
Article
Endocrinology & Metabolism
Martina Romanisio, Rosa Pitino, Alice Ferrero, Francesca Pizzolitto, Samuele Costelli, Valentina Antoniotti, Paolo Marzullo, Gianluca Aimaretti, Flavia Prodam, Marina Caputo
Summary: This study evaluated metabolic comorbidities in surgically treated acromegalic patients and found that the discrepancy between GH and IGF-1 levels does not appear to be a risk factor for their presence or persistence. Further extended studies are needed to confirm these results in the long term.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Review
Endocrinology & Metabolism
Valentina Mancioppi, Tommaso Daffara, Martina Romanisio, Giovanni Ceccarini, Caterina Pelosini, Ferruccio Santini, Simonetta Bellone, Simona Mellone, Alessio Baricich, Ivana Rabbone, Gianluca Aimaretti, Baris Akinci, Mara Giordano, Flavia Prodam
Summary: This article describes a rare lipodystrophy syndrome called congenital generalized lipodystrophy type 4 (CGL4), which is caused by mutations in the PTRF gene. Two early childhood patients presented with features such as reduced subcutaneous fat, muscular hypertrophy, distinctive facial features, myopathy, and atlantoaxial instability. Blood tests showed elevated CK and triglyceride levels, and undetectable leptin and adiponectin concentrations.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Oncology
Edda Cava, Daniele Spadaccini, Gianluca Aimaretti, Paolo Marzullo, Beatrice Cavigiolo, Deborah Farinelli, Alessandra Gennari, Chiara Saggia, Maria Grazia Carbonelli, Sergio Riso, Flavia Prodam
Summary: This retrospective observational cohort study aimed to assess the impact of a Mediterranean diet on weight and anthropometric changes in women completing active breast cancer treatment. The study found that implementing a Mediterranean diet can lead to weight and anthropometric improvements in breast cancer survivors. However, further research is necessary to explore the long-term effects of weight loss on these individuals and consider specific predictors of dropout.
Article
Endocrinology & Metabolism
Valentina Antoniotti, Martina Amore, Marina Caputo, Chiara Fania, Valentina Mancioppi, Gloria Casoli, Sabrina Tini, Alessandro Antonioli, Gianluca Aimaretti, Ivana Rabbone, Simonetta Bellone, Flavia Prodam
Summary: This study aimed to explore the relationship between childhood obesity and insulin resistance, glucose alterations, hypertension, and the renin-angiotensin-aldosterone system (RAAS). The results showed that 87.6% of pediatric obesity patients had hypertension, and those with glucose alterations were more likely to have hypertension. Blood pressure levels were positively correlated with glucose alterations, and insulin sensitivity was lower in hypertensive individuals. The study highlights the importance of close clinical surveillance in specific risk categories.
JOURNAL OF THE ENDOCRINE SOCIETY
(2023)