Article
Chemistry, Multidisciplinary
Weili Cui, Lei Shi, Kecheng Cao, Ute Kaiser, Takeshi Saito, Paola Ayala, Thomas Pichler
Summary: Carbyne is a one-dimensional allotrope of carbon, which is stable when grown encapsulated in carbon nanotubes. By using isotopic labeling as a tuning mechanism, researchers were able to control its properties and achieve pioneering results with around 11.9% of C-13 labeling.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Biochemical Research Methods
Hannah De los Santos, Kristin P. Bennett, Jennifer M. Hurley
Summary: This study used the MOSAIC application, which combines model selection and joint modeling of multiple omics types, to successfully recover circadian rhythms in organisms, showing excellent performance both in the proteome and transcriptome. Additionally, this approach allows for the recognition of the diversity of circadian regulation compared to non-circadian regulation.
Article
Biochemical Research Methods
Witold E. Wolski, Paolo Nanni, Jonas Grossmann, Maria d'Errico, Ralph Schlapbach, Christian Panse
Summary: Mass spectrometry is used extensively in proteomics studies for protein quantification and differential expression analysis. The prolfqua package provides a modular and easy-to-use application programming interface in R, supporting statistical procedures for proteomics data analysis. It integrates key steps of the differential expression analysis workflow and allows for modeling of simple and complex experimental designs. The methods implemented in the package enable sensitive and specific differential expression analysis and include benchmark functionality for comparing different methods. The prolfqua R-package is available on GitHub and runs on all platforms supported by the R free software environment.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Cell Biology
Giulia Pizzolato, Lavanya Moparthi, Simon Soderholm, Claudio Cantu, Stefan Koch
Summary: The forkhead box transcription factor FOXQ1 plays a crucial role in the pathogenesis of colorectal cancers by promoting tumour metastasis and activating the Wnt/beta-catenin signalling pathway. FOXQ1 enhances Wnt-induced transcription and regulates the expression of beta-catenin target genes. It also controls the expression of various Wnt target genes independently of beta-catenin. Furthermore, FOXQ1 is involved in a transcriptional program linked to EMT and cell migration, and interacts with similar co-factors as the beta-catenin-associated transcription factor Tcf711.
JOURNAL OF CELL SCIENCE
(2022)
Article
Biochemical Research Methods
Domenico Taverna, Marco Gaspari
Summary: MS-based proteomics is increasingly used in biological discovery, but accurately quantifying thousands of analytes in a single experiment remains challenging. This study assessed the diagnostic accuracy of three popular data-dependent methods for protein relative quantification and found that label-based methods consistently provided a lower false positives rate.
JOURNAL OF MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Roman Schefzik, Julian Flesch, Angela Goncalves
Summary: Researchers have developed and implemented a flexible and fast differential distribution testing procedure based on the 2-Wasserstein distance, which can detect any type of distribution difference between conditions. This method can also interpret distributional differences, capturing the relative contribution of changes in mean, variance, and shape under different conditions, and can be applied to a wide range of disciplines beyond scRNA-seq or bioinformatics.
Article
Biochemical Research Methods
Lili Blumenberg, Emily A. Kawaler, MacIntosh Cornwell, Shaleigh Smith, Kelly Ruggles, David Fenyo
Summary: Researchers use BlackSheep, a nonparametric description and differential analysis tool, to analyze molecules aberrantly enriched in small sample cohorts, complementing other differential expression analysis methods.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Miao-Hsia Lin, Pei-Shan Wu, Tzu-Hsuan Wong, I-Ying Lin, Johnathan Lin, Juergen Cox, Sung-Huan Yu
Summary: Data analysis is crucial in quantitative proteomics studies. This study compared and benchmarked different analysis tools using a proteomics dataset, and found that RNA-seq-based DE tools achieved higher accuracy in identifying differentially expressed proteins.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Thao Nguyen, Eli J. Costa, Tim Deibert, Jose Reyes, Felix C. Keber, Miroslav Tomschik, Michael Stadlmeier, Meera Gupta, Chirag K. Kumar, Edward R. Cruz, Amanda Amodeo, Jesse C. Gatlin, Martin Wuhr
Summary: The study addresses how embryos control the timing of specific gene activation in early frog development. It is found that transcription factors for early gene activation are maternally loaded and remain at constant levels, and the order of activation is based on their sequential entry into the nucleus largely determined by their respective affinity to importins.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Barbara Rita Cardoso, Larissa Lago, Aimee Linda Dordevic, Eugene Anthony Kapp, Anna M. Raines, Roger A. Sunde, Blaine Russel Roberts
Summary: The study identified candidate proteins in the liver regulated by dietary selenium intake, ranging from deficiency to toxic levels, and found a U-shaped dose-response relationship between selenium status and health outcomes. The results suggest that changes in selenium levels can impact the metabolism of glutathione, xenobiotics, and amino acids in the body.
JOURNAL OF NUTRITIONAL BIOCHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Isabel V. L. Wilkinson, Max Bottlinger, Yassmine El Harraoui, Stephan A. Sieber
Summary: Heme is a cofactor that plays myriad roles and is essential to almost all living organisms. It is now recognized as a tightly controlled signaling molecule that regulates protein expression. However, our understanding of heme acquisition, biosynthesis, and regulation is limited, especially in bacteria. In this study, a chemical proteomics method was developed to profile heme-binding proteins in live cells for the first time. This strategy successfully identified a significant portion of the heme-binding proteome in Gram-positive and Gram-negative bacteria and has the potential to fuel future research in heme biology.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Chemistry, Multidisciplinary
Isabel V. L. Wilkinson, Martin Pfanzelt, Stephan A. Sieber
Summary: Cofactors are essential for enzyme reactions, and their functions and binding partners still remain partly unknown. The use of cofactor mimics and chemical proteomics approaches can help uncover their activities and biological properties. The diverse activities of cofactors have inspired various applications, such as antibiotic therapeutics, inhibitors, and biosensors.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Endocrinology & Metabolism
Taylor L. Harris, Matthew J. Silva
Summary: Using Laser Capture Microdissection, osteocytes enriched intracortical bone tissues were analyzed for gene expression, revealing differential regulation of genes like Ngf, Wnt1, and MMP13 under mechanical loading. This method provided insights into the molecular changes in osteocytes in response to mechanical stimuli.
Article
Chemistry, Applied
Sarah Mazzotta, Giovanna Baron, Laura Fumagalli
Summary: This study reports a procedure to obtain isotopologues of sitosteryl ferulate, one of the major components of gamma-oryzanol, which can be used as an analytical tool to assess the potential nutraceutical exploitation of rice.
Article
Clinical Neurology
Rafael Romero-Garcia, Ayan S. Mandal, Richard A. Bethlehem, Benedicto Crespo-Facorro, Michael G. Hart, John Suckling
Summary: This study investigates the spatial patterns of brain tumour occurrence and identifies the functional connectivity and transcriptomic correlates of vulnerability to low-grade glioma and glioblastoma multiforme. By combining open-access data from various sources and analyzing MRI and mRNA transcription data, the researchers reveal the associations between grade-related frequency, expression, and brain network features. These findings shed light on the mechanisms underlying brain tumour occurrence and provide insights into potential therapeutic targets.
Article
Genetics & Heredity
Silvia Burra, Daniela Marasco, Matilde Clarissa Malfatti, Giulia Antoniali, Antonella Virgilio, Veronica Esposito, Bruce Demple, Aldo Galeone, Gianluca Tell
Article
Biochemistry & Molecular Biology
Barbara Frossi, Giulia Antoniali, Kefei Yu, Nahid Akhtar, Mark H. Kaplan, Mark R. Kelley, Gianluca Tell, Carlo E. M. Pucillo
JOURNAL OF BIOLOGICAL CHEMISTRY
(2019)
Review
Genetics & Heredity
Matilde Clarissa Malfatti, Giulia Antoniali, Marta Codrich, Silvia Burra, Giovanna Mangiapane, Emiliano Dalla, Gianluca Tell
Article
Multidisciplinary Sciences
Dilara Ayyildiz, Giulia Antoniali, Chiara D'Ambrosio, Giovanna Mangiapane, Emiliano Dalla, Andrea Scaloni, Gianluca Tell, Silvano Piazza
SCIENTIFIC REPORTS
(2020)
Article
Biochemistry & Molecular Biology
Lisa Lirussi, Giulia Antoniali, Pasqualina Liana Scognamiglio, Daniela Marasco, Emiliano Dalla, Chiara D'Ambrosio, Simona Arena, Andrea Scaloni, Gianluca Tell
Article
Microbiology
Sarah K. Hewitt, Kobchai Duangrattanalert, Tim Burgis, Leo A. H. Zeef, Samina Naseeb, Daniela Delneri
Article
Microbiology
Soukaina Timouma, Jean-Marc Schwartz, Daniela Delneri
Article
Biochemistry & Molecular Biology
Antonio Paolo Beltrami, Maria De Martino, Emiliano Dalla, Matilde Clarissa Malfatti, Federica Caponnetto, Marta Codrich, Daniele Stefanizzi, Martina Fabris, Emanuela Sozio, Federica D'Aurizio, Carlo E. M. Pucillo, Leonardo A. Sechi, Carlo Tascini, Francesco Curcio, Gian Luca Foresti, Claudio Piciarelli, Axel De Nardin, Gianluca Tell, Miriam Isola
Summary: This study identified nine potential serum biomarkers for predicting the severity of COVID-19 by analyzing serum proteins and clinical data. Three of these biomarkers were associated with central nervous system pathologies and protective factors, and were downregulated in the most severe cases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Alkisti Manousaki, James Bagnall, David Spiller, Laura Natalia Balarezo-Cisneros, Michael White, Daniela Delneri
Summary: This study successfully quantified low abundant membrane-binding proteins using fluorescence correlation spectroscopy and found that the localization and copy number of Fis1p and Mdv1p proteins in mitochondria are influenced by the environment. In addition, a compensatory mechanism was observed in Fis1p protein upon deletion of one allele.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Marta Codrich, Monica Degrassi, Matilde Clarissa Malfatti, Giulia Antoniali, Andrea Gorassini, Dilara Ayyildiz, Rossella De Marco, Giancarlo Verardo, Gianluca Tell
Summary: This study found that APE1 protein is involved in the elimination of damaged RNA after treatment with cisplatin and 5-fluorouracil, and its interaction with MTR4 is stimulated by these treatments. Depletion of APE1 and MTR4 leads to the formation of R-loop structures, which activate the DNA damage response pathway.
Article
Biochemistry & Molecular Biology
Matilde Clarissa Malfatti, Marta Codrich, Emiliano Dalla, Chiara D'Ambrosio, Francesca Storici, Andrea Scaloni, Gianluca Tell
Summary: The aim of this study is to investigate the existence of modified ribonucleotide monophosphates in genomic DNA under oxidative stress conditions. The research discovered that AUF1 can specifically recognize and promote APE1 endoribonuclease activity on 8-oxo-guanosine embedded in DNA. These findings provide new insights into the genome stability in mammalian cells under oxidative stress-related damages.
ANTIOXIDANTS & REDOX SIGNALING
(2023)
Review
Biochemistry & Molecular Biology
Giuseppe Dall'Agnese, Alessandra Dall'Agnese, Salman F. Banani, Marta Codrich, Matilde Clarissa Malfatti, Giulia Antoniali, Gianluca Tell
Summary: The article summarizes the key features of biomolecular condensates and their potential involvement in repairing DNA double-strand breaks. It also discusses evidence suggesting their role in repairing other types of DNA damage and raises questions that could be addressed considering the properties of condensates, including chemo-resistance mechanisms.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Review
Cell Biology
Matilde Clarissa Malfatti, Alessia Bellina, Giulia Antoniali, Gianluca Tell
Summary: APE1 is an essential endodeoxyribonuclease involved in maintaining genome stability through the base excision repair pathway. It has been identified as a key factor promoting tumor progression and chemoresistance by controlling gene expression through a redox-based mechanism. APE1 is overexpressed and secreted in various cancers, making it a prognostic factor and potential non-invasive biomarker. Inhibition of APE1's functions has shown therapeutic potential, with some inhibitors currently undergoing clinical trials. Additionally, recent evidence suggests novel roles of APE1 in RNA metabolism that are not fully understood, including its involvement in chemoresistant phenotypes, onco-miRNA maturation, and oxidized RNA decay. The discovery of APE1's role in miRNA processing presents new perspectives for personalized cancer therapy.
Article
Gastroenterology & Hepatology
Giovanna Mangiapane, Devis Pascut, Emiliano Dalla, Giulia Antoniali, Monica Degrassi, Lory Saveria Croce, Veronica De Sanctis, Silvano Piazza, Giulia Canarutto, Claudio Tiribelli, Gianluca Tell
Summary: This study investigates the prognostic value of APE1 in HCC and identifies miRNAs regulated by APE1 that are associated with cell proliferation, transformation, and angiogenesis. The overexpression of APE1 in HCC tissues and the correlation between specific miRNAs and lower overall survival in HCC patients are discovered.
JOURNAL OF CLINICAL AND TRANSLATIONAL HEPATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Giovanna Mangiapane, Isabella Parolini, Kristel Conte, Matilde Clarissa Malfatti, Jessica Corsi, Massimo Sanchez, Agostina Pietrantoni, Vito G. D'Agostino, Gianluca Tell
Summary: The study elucidated the mechanisms by which APE1 is secreted through exosomes and revealed its delivery in response to genotoxic stresses, shedding new light on its noncanonical biological functions in cancer biology.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
