Article
Oncology
H. Welsh, C. M. P. F. Batalha, W. Li, K. L. Mpye, N. C. Souza-Pinto, M. S. Naslavsky, E. J. Parra
Summary: This study evaluated the performance of different normalization methods on the Infinium EPIC array and found that the SeSAMe 2 method was the best performing method, while quantile-based methods were the worst performing. Normalizing the data with SeSAMe 2 improved the reproducibility of CpG sites, suggesting that the reliability of the data is primarily due to limited biological variation rather than technical measurement variation.
CLINICAL EPIGENETICS
(2023)
Article
Biochemistry & Molecular Biology
Steffan Noe Christiansen, Jeppe Dyrberg Andersen, Marie-Louise Kampmann, Jing Liu, Mikkel Meyer Andersen, Jacob Tfelt-Hansen, Niels Morling
Summary: The Infinium MethylationEPIC BeadChip (EPIC) is a reliable method for measuring DNA methylation. This study showed that high reproducibility results are obtained with DNA amounts in the range 125-500 ng, while DNA amounts below 63 ng gave less reproducible results.
Article
Immunology
Anna J. Henningsson, Sandra Hellberg, Maria Lerm, Shumaila Sayyab
Summary: In this study, we conducted the first genome-wide analysis of DNA methylation in peripheral blood cells from patients with and without Lyme neuroborreliosis (LNB). The findings suggest that LNB is associated with immune-related DNA methylation changes.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Biochemistry & Molecular Biology
Sarah Holmes Watkins, Karen Ho, Christian Testa, Louise Falk, Patrice Soule, Linda Nguyen, Sophie FitzGibbon, Catherine Slack, Jarvis T. Chen, George Davey Smith, Immaculata De Vivo, Andrew J. Simpkin, Kate Tilling, Pamela D. Waterman, Nancy Krieger, Matthew Suderman, Caroline Relton
Summary: This study aimed to assess the impact of DNA input on data quality when using the Illumina Infinium MethylationEPIC BeadChip for DNA methylation analysis. The study found that as DNA input decreased, data quality decreased and larger sample sizes were required to detect associations.
Article
Biology
Nicky Staes, Elaine E. Guevara, William D. Hopkins, Steven J. Schapiro, Marcel Eens, Chet C. Sherwood, Brenda J. Bradley
Summary: This study examines the association between blood DNA methylation levels and personality traits in captive chimpanzees, and finds that methylation levels are associated with variation in personality dimensions, including reduced anxiety and aggression and increased prosocial and exploratory behavior. Unlike human studies, early social rearing conditions have minimal impact on methylation.
Article
Chemistry, Multidisciplinary
Changjia Hu, Yanwen Jin, Peng Yang, Rongxing Zhou, Lingying Xia, Lijie Du, Junbo Chen, Nansheng Cheng, Xiandeng Hou
Summary: This study introduces the principle of proximity assay into tetramolecular G-quadruplexes guided by various biomolecules, and constructs a sensing strategy based on the co-localization of intermolecular G-rich strands guided by a recognition event of a specific biomolecule to its corresponding affinity ligand. This versatile and homogeneous strategy is adaptable to different types of biomolecules.
CHEMICAL COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Daryl M. Gohl, Benjamin Auch, Amanda Certano, Brice LeFrancois, Anne Bouevitch, Evgueni Doukhanine, Christina Fragel, Jean Macklaim, Emily Hollister, John Garbe, Kenneth B. Beckman
Summary: Proofreading polymerases have the ability to correct errors during DNA replication and edit PCR primers to match template sequences. The editing activity can be measured and compared using synthetic DNA standards, revealing editing extent and effects of different polymerases and cycling conditions. Additionally, primer editing can be tuned by incorporating phosphorothioate linkages and has the potential to rescue mismatches in 16S rRNA gene-targeting primers in microbiome analysis.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Plant Sciences
Shyryn Almerekova, Yuliya Genievskaya, Saule Abugalieva, Kazuhiro Sato, Yerlan Turuspekov
Summary: The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. The study revealed that Kazakh barley samples were genetically close to samples from Africa and Europe, and the KV and KA samples were the most distant groups among six breeding origins in Kazakhstan. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.
Article
Health Care Sciences & Services
Kevin Z. Wang, Zanib Chaudhary, Jessica Qian, Christopher Adanty, Ariel Graff-Guerrero, Philip Gerretsen, Clement C. Zai, Vincenzo De Luca
Summary: This study investigated the relationship between genome-wide DNA methylation and severity of suicidal ideation in schizophrenia patients, providing valuable insights for future research. Further large-scale studies are needed to confirm and validate the findings presented here.
Article
Oncology
Emilie Willoch Olstad, Hedvig Marie Egeland Nordeng, Geir Kjetil Sandve, Robert Lyle, Kristina Gervin
Summary: This study investigates the concordance between two different platforms for measuring DNA methylation levels in cord blood, and finds differences between the platforms. These findings have important implications for future epigenome-wide association studies.
CLINICAL EPIGENETICS
(2022)
Article
Biochemical Research Methods
Masanori Goto, Yuji Baba, Wataru Yoshida
Summary: In this study, a sensing system was developed to detect CpG methylation levels based on G-quadruplex and intercalated motif-forming regions. The system can directly quantify methylation levels at a constant temperature without the need for additional processing. The results demonstrate that the system can accurately detect methylation levels by affecting the onset of amplification.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2022)
Article
Genetics & Heredity
Ze Zhang, Min Kyung Lee, Laurent Perreard, Karl T. Kelsey, Brock C. Christensen, Lucas A. Salas
Summary: This study compared the data quality of BS-treated and oxBS-treated samples and observed a consistent loss of high-quality data in oxBS-treated samples. The authors offer a bioinformatic tool to evaluate potential quality issues in the process and provide some technical advice to reduce false signals in the data. Therefore, they emphasize the importance of preserving DNA integrity when using tandem BS- and oxBS-treated DNA to measure 5-methylcytosine and 5hmC.
Article
Biochemistry & Molecular Biology
Zarmik Moqtaderi, Susan Brown, Welcome Bender
Summary: In eukaryotic genomes, G+C content and evolutionary conservation oscillate together, with conserved regions having higher G+C content. Loci with large regulatory regions exhibit more regular oscillation, while coding sequences and heterochromatic regions show little to no oscillation. Species with few repeats show oscillations in both G+C density and sequence conservation, possibly reflecting optimal spacing of cis-regulatory elements.
Article
Biochemistry & Molecular Biology
Jia Li, Haiping Wu, Yurong Yan, Taixian Yuan, Yue Shu, Xin Gao, Lu Zhang, Siqiao Li, Shijia Ding, Wei Cheng
Summary: Our study introduced a novel strategy, PECA, to enhance the catalytic capacity of G4/hemin DNAzyme, resulting in the development of a highly efficient HRP mimic called Z-G4/H. This innovative approach showed promising applications in sensitive gene rearrangement detection and imaging of HER2 protein dimerization on cell surfaces, indicating universal diagnostic potential in clinical settings and biomolecule interaction research.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Engineering, Environmental
Wei Lin Lee, Maxim Imakaev, Federica Armas, Kyle A. McElroy, Xiaoqiong Gu, Claire Duvallet, Franciscus Chandra, Hongjie Chen, Mats Leifels, Samuel Mendola, Roisin Floyd-O'Sullivan, Morgan M. Powell, Shane T. Wilson, Karl L. J. Berge, Claire Y. J. Lim, Fuqing Wu, Amy Xiao, Katya Moniz, Newsha Ghaeli, Mariana Matus, Janelle Thompson, Eric J. Alm
Summary: This study developed a detection method for tracking the B.1.1.7 variant in wastewater, which can reliably detect low levels of B.1.1.7 and provide rapid and inexpensive surveillance of SARS-CoV-2 variants.
ENVIRONMENTAL SCIENCE & TECHNOLOGY LETTERS
(2021)
Article
Psychology, Clinical
Victoria Rodriguez, Luis Alameda, Diego Quattrone, Giada Tripoli, Charlotte Gayer-Anderson, Edoardo Spinazzola, Giulia Trotta, Hannah E. Jongsma, Simona Stilo, Caterina La Cascia, Laura Ferraro, Daniele La Barbera, Antonio Lasalvia, Sarah Tosato, Ilaria Tarricone, Elena Bonora, Stephane Jamain, Jean-Paul Selten, Eva Velthorst, Lieuwe de Haan, Pierre-Michel Llorca, Manuel Arrojo, Julio Bobes, Miguel Bernardo, Celso Arango, James Kirkbride, Peter B. Jones, Bart P. Rutten, Alexander Richards, Pak C. Sham, Michael O'Donovan, Jim Van Os, Craig Morgan, Marta Di Forti, Robin M. Murray, Evangelos Vassos
Summary: This study suggests that combining polygenic risk scores (PRS) for severe psychiatric disorders with prediction models for psychosis phenotypes can improve discrimination ability and enhance our understanding of these phenotypes. PRS may have potential usefulness in specific populations such as those at high risk or in the early stages of psychosis.
PSYCHOLOGICAL MEDICINE
(2023)
Article
Medicine, General & Internal
Nathan Risch, Jonathan Dubois, Katia M'bailara, Irena Cussac, Bruno Etain, Raoul Belzeaux, Caroline Dubertret, Emmanuel Haffen, Raymund Schwan, Ludovic Samalin, Paul Roux, Mircea Polosan, Marion Leboyer, Philippe Courtet, Emilie Olie
Summary: In patients with bipolar disorder, pain prevalence is close to 30%. This study found that pain was associated with depressive symptomatology, emotional reactivity, and personality traits. Furthermore, pain predicted depression and lower global life functioning in the long-term.
JOURNAL OF CLINICAL MEDICINE
(2022)
Review
Clinical Neurology
Melvin G. McInnis, Ole A. Andreassen, Ana C. Andreazza, Uri Alon, Michael Berk, Teri Brister, Katherine E. Burdick, Donghong Cui, Mark Frye, Marion Leboyer, Philip B. Mitchell, Kathleen Merikangas, Andrew A. Nierenberg, John Nurnberger, Daniel Pham, Eduard Vieta, Lakshmi N. Yatham, Allan H. Young
Summary: Bipolar disorder is a complex condition with onset in late adolescence, complicated by comorbid medical and psychiatric disorders. The etiology and reliable biological markers remain unknown, suggesting the need for large-scale global longitudinal studies to determine causes and improve treatment.
Article
Psychiatry
Luana Spano, Bruno Etain, Jean-Louis Laplanche, Marion Leboyer, Sebastien Gard, Frank Bellivier, Cynthia Marie-Claire
Summary: This study finds consistency in cellular aging biomarkers between individuals with bipolar disorder and their siblings, suggesting shared environmental or genetic factors.
WORLD JOURNAL OF BIOLOGICAL PSYCHIATRY
(2023)
Editorial Material
Biochemical Research Methods
Miranda D. Stobbe, Abel Gonzalez-Perez, Nuria Lopez-Bigas, Glynne Gut
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Emanuela Oldoni, Gary Saunders, Florence Bietrix, Maria Laura Garcia Bermejo, Anna Niehues, Peter A. C. 't Hoen, Jessica Nordlund, Marian Hajduch, Andreas Scherer, Katja Kivinen, Esa Pitkanen, Tomi Pekka Makela, Ivo Gut, Serena Scollen, Lukasz Kozera, Manel Esteller, Leming Shi, Anton Ussi, Antonio L. Andreu, Alain J. van Gool
Summary: Personalised medicine (PM) offers a great opportunity to enhance individualized healthcare. Advances in -omics technologies have enabled the study of complex human diseases, supporting the development of PM. This article summarizes the outcomes of a workshop that aimed to outline common promises and challenges in multi-omics research, assess the potential of new technologies like artificial intelligence, and foster collaboration between key initiatives.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Archaeology
K. N. White, D. Chiasserini, R. Loynes, A. R. David, B. E. van Dongen, K. Drosou, R. Forshaw, S. Fraser, P. Causey-Freeman, J. Metcalfe, E. Murphy, M. Regan, P. J. Reimer, D. G. Tosh, A. Whetton, A. J. Freemont
Summary: Scientific examination of mummies provides insights into human ancestry, diet, disease, cultures, and societies. However, invasive methods have raised concerns. A minimally invasive approach using imaging techniques and biopsy sampling allows for the collection of valuable data without significant disturbance to the mummy. This study on Takabuti demonstrates the potential of such methods.
JOURNAL OF ARCHAEOLOGICAL SCIENCE-REPORTS
(2023)
Article
Clinical Neurology
Chiara C. Bortolasci, Srisaiyini Kidnapillai, Briana Spolding, Trang T. T. Truong, Timothy Connor, Courtney Swinton, Bruna Panizzutti, Zoe S. J. Liu, Andrew Sanigorski, Olivia M. Dean, Tamsyn Crowley, Mark Richardson, Kiymet Bozaoglu, Katerina Vlahos, Stephanie Cowdery, Brad Watmuff, Stephan F. Steyn, De Wet Wolmarans, Barend J. Engelbrecht, Christina Perry, Katherine Drummond, Terence Pang, Stephane Jamain, Laura Gray, Sean L. McGee, Brian H. Harvey, Jee Hyun Kim, Marion Leboyer, Michael Berk, Ken Walder
Summary: The aim of this study was to identify a drug for repurposing in the treatment of bipolar depression. A gene expression signature was generated using human neuronal-like cells to represent the effects of drugs used to treat bipolar disorder. Trimetazidine was identified as a potential candidate for repurposing based on its similar transcriptional effects and its ability to increase ATP production.
Article
Psychiatry
Lucia Sideli, Monica Aas, Diego Quattrone, Daniele La Barbera, Caterina La Cascia, Laura Ferraro, Luis Alameda, Eva Velthorst, Giulia Trotta, Giada Tripoli, Adriano Schimmenti, Andrea Fontana, Charlotte Gayer-Anderson, Simona Stilo, Fabio Seminerio, Crocettarachele Sartorio, Giovanna Marrazzo, Antonio Lasalvia, Sarah Tosato, Ilaria Tarricone, Domenico Berardi, Giuseppe D'Andrea, Celso Arango, Manuel Arrojo, Miguel Bernardo, Julio Bobes, Julio Sanjuan, Jose Luis Santos, Paulo Rossi Menezes, Cristina Marta Del-Ben, Hannah E. Jongsma, Peter B. Jones, James B. Kirkbride, Pierre-Michel Llorca, Andrea Tortell, Baptiste Pignon, Lieuwe de Haan, Jean-Paul Selten, Jim Van Os, Bart P. Rutten, Richard Bentall, Marta Di Fort, Robin M. Murray, Craig Morgan, Helen L. Fisher
Summary: This study aimed to investigate whether the relationship between childhood maltreatment and cognition in patients with psychosis and community controls was influenced by genetic factors related to psychosis. The study included first-episode psychosis patients (N=755) and unaffected controls (N=1219) from the EU-GEI study, who were assessed for childhood maltreatment, intelligence quotient (IQ), family history of psychosis (FH), and polygenic risk score for schizophrenia (SZ-PRS). The results showed that controlling for FH and SZ-PRS did not weaken the association between childhood maltreatment and IQ in either cases or controls, suggesting that genetic liability factors do not explain the lower levels of cognition in adults who experienced childhood maltreatment.
SOCIAL PSYCHIATRY AND PSYCHIATRIC EPIDEMIOLOGY
(2023)
Article
Genetics & Heredity
Yannis Elandaloussi, Dorothea L. Floris, Pierrick Coupe, Edouard Duchesnay, Angeline Mihailov, Antoine Grigis, Indrit Begue, Julie Victor, Vincent Frouin, Marion Leboyer, Josselin Houenou, Charles Laidi
Summary: This study analyzed structural MRI data from a large pediatric and transdiagnostic sample and found a significant association between cerebellar volume and social difficulties. The results reveal a complex relationship between cerebellar structure, social performance, and IQ.
Article
Biochemistry & Molecular Biology
Baptiste Pignon, Valentina Decio, Philippe Pirard, Olivier Bouaziz, Emmanuelle Corruble, Pierre A. Geoffroy, Viviane Kovess-Masfety, Marion Leboyer, Cedric Lemogne, Jonathan Messika, Vittorio Perduca, Franck Schurhoff, Nolwenn Regnault, Sarah Tebeka
Summary: COVID-19 may not increase the risk of hospitalization for psychotic disorders, as patients initially hospitalized for COVID-19 had a lower rate of subsequent hospitalization for psychotic disorders compared to those initially hospitalized for other reasons. This finding contradicts the hypothesis that there is an increased risk of psychotic disorders after a severe COVID-19 infection. Importantly, a history of psychotic disorder was found to be a major determinant of hospitalization for psychotic disorders.
MOLECULAR PSYCHIATRY
(2023)
Correction
Genetics & Heredity
Yannis Elandaloussi, Dorothea L. L. Floris, Pierrick Coupe, Edouard Duchesnay, Angeline Mihailov, Antoine Grigis, Indrit Begue, Julie Victor, Vincent Frouin, Marion Leboyer, Josselin Houenou, Charles Laidi
Article
Neurosciences
Alexis Vancappel, Yecodji Dansou, Ophelia Godin, Emmanuel Haffen, Antoine Yrondi, Florian Stephan, Raphaelle Marie Richieri, Fanny Moliere, Jerome Holtzmann, Mathilde Horn, Etienne Allauze, Jean Baptiste Genty, Alex Bouvard, Jean-Michel Dorey, Vincent Hennion, Vincent Camus, Guillaume Fond, Barbara Peran, Michel Walter, Loic Anguill, Charlotte Scotto D'apolina, Estelle Vila, Benjamin Fredembach, Jean Petrucci, Romain Rey, Anne Sophie Nguon, Bruno Etain, Mathilde Carminati, Philippe Courtet, Guillaume Vaiva, Pierre Michel Llorca, Marion Leboyer, Bruno Aouizerate, Djamila Bennabi, Wissam El Hage
Summary: This study examines the relationship between cognitive impairments and treatment response in patients with treatment-resistant depression. The findings suggest that cognitive scores improve after therapeutic response, with greater improvement observed in patients with better treatment response. Therefore, cognitive remediation should be provided after therapeutic response to enhance patients' daily functioning.
Article
Genetics & Heredity
Ana Lokmer, Charanraj Goud Alladi, Rejane Troudet, Delphine Bacq-Daian, Anne Boland-Auge, Violaine Latapie, Jean-Francois Deleuze, Ravi Philip RajKumar, Deepak Gopal Shewade, Frank Belivier, Cynthia Marie-Claire, Stephane Jamain
Summary: The use of antipsychotic medication to treat schizophrenia is not always effective for all patients. Researchers have analyzed the blood DNA of patients and identified specific marks that could serve as biomarkers of antipsychotic response. Although specific predictive marks were not identified, valuable targets for future research have been identified.
Article
Psychiatry
B. Pignon, H. Peyre, A. Ayrolles, J. B. Kirkbride, S. Jamain, A. Ferchiou, J. R. Richard, G. Baudin, S. Tosato, H. Jongsma, L. de Haan, I Tarricone, M. Bernardo, E. Velthorst, M. Braca, C. Arango, M. Arrojo, J. Bobes, C. M. Del-Ben, M. Di Forti, C. Gayer-Anderson, P. B. Jones, C. La Cascia, A. Lasalvia, P. R. Menezes, D. Quattrone, J. Sanjuan, J. P. Selten, A. Tortelli, P. M. Llorca, J. van Os, B. P. F. Rutten, R. M. Murray, C. Morgan, M. Leboyer, A. Szoke, F. Schurhoff
Summary: This study on subjects without psychotic disorders suggests that the positive dimension of subclinical psychosis may be particularly influenced by both genetic and environmental factors independently, and interactions between genetic and individual environmental factors were not identified in this sample.
EPIDEMIOLOGY AND PSYCHIATRIC SCIENCES
(2022)