Article
Plant Sciences
Carlos de Tomas, Amelie Bardil, Raul Castanera, Josep M. Casacuberta, Carlos M. Vicient
Summary: The fusion of two parental genomes in the peach x almond hybrid did not result in significant changes in DNA methylation or transcription, challenging the expectation of genomic shock. This finding suggests the possibility of using interspecific peach x almond crosses for peach improvement.
HORTICULTURE RESEARCH
(2022)
Article
Multidisciplinary Sciences
Nagham Khouri-Farah, Qiuxia Guo, Kerry Morgan, Jihye Shin, James Y. H. Li
Summary: Recent studies using single-cell RNA-sequencing have identified cellular heterogeneity in the developing mammalian cerebellum, but the regulatory logic behind this diversity remains unclear. Researchers integrated single-cell RNA and ATAC analyses to understand the developmental trajectories of cerebellar progenitors and identified potential regulatory elements controlling cell state transitions. Using gene regulatory network analysis, they uncovered the molecular control of a specific progenitor zone and demonstrated its association with a common cerebellar birth defect in humans.
Article
Psychiatry
Luis F. S. Castro-de-Araujo, Jacyra Azevedo Paiva de Araujo, Richard A. A. Kanaan, Erika Fialho Morais Xavier
Summary: This study analyzed the temporal relationship between the severity of psychotic symptoms and total gray matter volume. The results showed that the worse the symptoms, the smaller the gray matter volume, and vice versa. There is a bidirectional temporal relationship between symptoms and brain volume.
JOURNAL OF PSYCHIATRIC RESEARCH
(2023)
Article
Biology
John Paul Llido, Emanuela Fioriti, Devis Pascut, Mauro Giuffre, Cristina Bottin, Fabrizio Zanconati, Claudio Tiribelli, Silvia Gazzin
Summary: Severe neonatal hyperbilirubinemia can lead to brain damage and cause motor, cognitive, and auditory abnormalities. Bilirubin has been found to control the genetic development of the cerebellum, which is susceptible to bilirubin-induced damage. This study expands the research on the impact of bilirubin on postnatal brain development in regions that correlate with human symptoms. The findings show temporary alterations in gene expression in areas related to memory, learning, cognition, and auditory functions, but permanent changes in areas controlling movements, which coincide with clinical descriptions of bilirubin-induced neurotoxicity.
Article
Genetics & Heredity
Eva Lindholm Carlstrom, Adnan Niazi, Mitra Etemadikhah, Jonatan Halvardson, Stefan Enroth, Craig A. Stockmeier, Grazyna Rajkowska, Bo Nilsson, Lars Feuk
Summary: The study identified an up-regulation of multiple immune response genes, including genes from the complement system, in schizophrenia patients, indicating important differences in disease etiology within the patient group. Weighted gene co-expression network analysis highlighted networks associated with both synaptic transmission and immune response activation. These findings suggest the importance of immune-related pathways in schizophrenia pathology and provide evidence for elevated expression of the complement cascade in the disease.
Article
Endocrinology & Metabolism
Doaa Taqi, Hanan Moussa, Timothy Schwinghamer, Maxime Ducret, Didem Dagdeviren, Jean-Marc Retrouvey, Frank Rauch, Faleh Tamimi
Summary: The study found that dental anomalies in Osteogenesis imperfecta patients vary with different genetic variants and patient age, with genetic variants being better predictors of dental phenotype. Tooth discoloration may be related to enamel thickness, while pulp obliteration is associated with patient age and malocclusion, and taurodontism is possibly linked to delayed pulpal maturation.
Article
Cell Biology
Deisy Segura-Villalobos, Monica Lamas, Claudia Gonzalez-Espinosa
Summary: This study found that the localization of mast cells within cyclic hypoxia regions in tumors can modify their transcriptional profile and activation parameters. Cyclic hypoxia causes important phenotypic changes in mast cells.
Article
Biochemistry & Molecular Biology
Uwe Schwartz, Maria Llamazares Prada, Stephanie T. Pohl, Mandy Richter, Raluca Tamas, Michael Schuler, Corinna Keller, Vedrana Mijosek, Thomas Muley, Marc A. Schneider, Karsten Quast, Joschka Hey, Claus P. Heussel, Arne Warth, Hauke Winter, Oezdemirhan Sercin, Harry Karmouty-Quintana, Soma S. K. Jyothula, Manish K. Patel, Felix Herth, Ina Koch, Giuseppe Petrosino, Alexandru Titimeaua, Balca R. Mardin, Dieter Weichenhan, Tomasz P. Jurkowski, Charles D. Imbusch, Benedikt Brors, Vladimir Benes, Birgit Jung, David Wyatt, Heiko F. Stahl, Christoph Plass, Renata Z. Jurkowska
Summary: Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. We hypothesized that COPD is associated with altered epigenetic signaling in lung cells. We generated genome-wide DNA methylation maps of primary human lung fibroblasts (HLFs) across COPD stages and found early epigenetic changes in COPD, predominantly in regulatory regions. Dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization were observed. Furthermore, we identified candidate regulators and demonstrated the potential for novel therapeutic avenues for COPD patients.
Review
Neurosciences
Zachary M. Harvanek, Marco P. Boks, Christiaan H. Vinkers, Albert T. Higgins-Chen
Summary: Individuals with psychiatric disorders have an increased risk of age-related diseases and early mortality. Recent studies have shown a connection between mental health and aging through epigenetic clocks, which are biomarkers based on DNA methylation. However, the relationship between epigenetic clocks and mental health is mostly correlational, and the mechanisms are not well understood. This review explores the molecular and cellular processes behind epigenetic clocks, as well as new technologies for further studying the causes and consequences of epigenetic aging. It also examines the current literature on how epigenetic clocks relate to specific aspects of mental health, including stress, medications, substance use, health behaviors, and symptom clusters. The review proposes an integrated framework that breaks down mental health and epigenetic aging into distinct processes, linking them together using stress and schizophrenia as examples. This framework considers the heterogeneity and complexity of both mental health conditions and aging, and provides a basis for further research on potential causal mechanisms linking aging and mental health.
BIOLOGICAL PSYCHIATRY
(2023)
Article
Multidisciplinary Sciences
Sara Svensson Akusjarvi, Anoop T. Ambikan, Shuba Krishnan, Soham Gupta, Maike Sperk, Akos Vegvari, Flora Mikaeloff, Katie Healy, Jan Vesterbacka, Piotr Nowak, Anders Sonnerborg, Ujjwal Neogi
Summary: This study identified HIF signaling and glycolysis as specific traits of the elite controller phenotype in HIV-1 infection. The activation of the HIF signaling pathway was observed in male elite controllers, along with elevated intracellular glucose levels. These findings provide new insights into the natural control of HIV-1.
Editorial Material
Biochemical Research Methods
Vivien Marx
Summary: Chemical modifications to DNA, histones and RNA play a crucial role in making functional changes. Scientists are actively studying methods to monitor and understand these modifications and their interactions.
Article
Endocrinology & Metabolism
Zheyi Xiang, Le Bai, Jennifer Q. Zhou, Ricardo R. Cevallos, Jonathan R. Sanders, Gang Liu, Karen Bernard, Yan Y. Sanders
Summary: This study investigates the role of glutaminolysis and its metabolite α-ketoglutarate in idiopathic pulmonary fibrosis (IPF) fibroblast phenotype and gene expression. The lack of glutamine in culture medium alters the pro-fibrotic phenotype of fibroblasts. Adding exogenous α-ketoglutarate only partially restores the pro-fibrotic phenotype and gene expression. Reduced glutaminolysis affects histone H3K27me3 levels and its association with fibrotic gene promoters. In a mouse model of lung fibrosis, reducing glutaminolysis significantly reduces fibrotic markers.
MOLECULAR METABOLISM
(2023)
Article
Biochemistry & Molecular Biology
Ao Chen, Sha Liao, Mengnan Cheng, Kailong Ma, Liang Wu, Yiwei Lai, Xiaojie Qiu, Jin Yang, Jiangshan Xu, Shijie Hao, Xin Wang, Huifang Lu, Xi Chen, Xing Liu, Xin Huang, Zhao Li, Yan Hong, Yujia Jiang, Jian Peng, Shuai Liu, Mengzhe Shen, Chuanyu Liu, Quanshui Li, Yue Yuan, Xiaoyu Wei, Huiwen Zheng, Weimin Feng, Zhifeng Wang, Yang Liu, Zhaohui Wang, Yunzhi Yang, Haitao Xiang, Lei Han, Baoming Qin, Pengcheng Guo, Guangyao Lai, Pura Munoz-Canoves, Patrick H. Maxwell, Jean Paul Thiery, Qing-Feng Wu, Fuxiang Zhao, Bichao Chen, Mei Li, Xi Dai, Shuai Wang, Haoyan Kuang, Junhou Hui, Liqun Wang, Ji-Feng Fei, Ou Wang, Xiaofeng Wei, Haorong Lu, Bo Wang, Shiping Liu, Ying Gu, Ming Ni, Wenwei Zhang, Feng Mu, Ye Yin, Huanming Yang, Michael Lisby, Richard J. Cornall, Jan Mulder, Mathias Uhlen, Miguel A. Esteban, Yuxiang Li, Longqi Liu, Xun Xu, Jian Wang
Summary: Spatially resolved transcriptomic technologies enable us to study complex biological processes such as mammalian embryogenesis. However, current methods have limitations in resolution, gene capture, and field of view, which hinders their systematic application to large and three-dimensional mid- and late-gestation embryos. In this study, we developed Stereo-seq, a spatially enhanced resolution omics-sequencing method, by combining DNA nanoball-patterned arrays and in situ RNA capture. We used Stereo-seq to generate the mouse organogenesis spatiotemporal transcriptomic atlas, MOSTA, which provides single cell resolution and high sensitivity for mapping the kinetics and directionality of transcriptional variation during mouse organogenesis. By utilizing this atlas, we investigated the molecular basis of spatial cell heterogeneity and cell fate specification in developing tissues like the dorsal midbrain. Our panoramic atlas will facilitate in-depth research into long-standing questions about normal and abnormal mammalian development.
Article
Genetics & Heredity
Elaine E. Guevara, William D. Hopkins, Patrick R. Hof, John J. Ely, Brenda J. Bradley, Chet C. Sherwood
Summary: By conducting genome-wide epigenetic profiling of the lateral cerebellum and comparing it with the prefrontal cortex of humans, chimpanzees, and rhesus macaque monkeys, researchers found that humans showed greater differential CpG methylation in the cerebellum, with methylation differences at genes related to neurodevelopment, neuroinflammation, synaptic plasticity, and lipid metabolism. These differences underscore the potential importance of the cerebellum in human brain evolution and cognition, shedding light on neural specializations unique to humans and their relevance to neurodegenerative conditions associated with aging.
Article
Biochemistry & Molecular Biology
Ankit Hanmandlu, Lisha Zhu, Tinne C. J. Mertens, Scott Collum, Weizhen Bi, Feng Xiong, Ruoyu Wang, Rajarajan T. Amirthalingam, Dewei Ren, Leng Han, Soma S. S. K. Jyothula, Wenbo Li, W. Jim Zheng, Harry Karmouty-Quintana
Summary: Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease associated with fibroblast expansion and excessive extracellular matrix deposition. This study identified genetic differences between IPF fibroblasts and healthy fibroblasts, and discovered important genes and pathways related to IPF. Modulation of chromatin accessibility may play a significant role in the pathogenesis of lung fibrosis.
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
(2022)
Article
Cardiac & Cardiovascular Systems
Rongtao Jiang, Vince D. Calhoun, Stephanie Noble, Jing Sui, Qinghao Liang, Shile Qi, Dustin Scheinost
Summary: This study utilizes machine learning and functional connectivity to investigate the neurobiological correlates of blood pressure at an individual level. The results identify specific brain regions that are associated with blood pressure and provide evidence for meaningful neural representations of blood pressure in connectivity profiles.
CARDIOVASCULAR RESEARCH
(2023)
Article
Psychology, Developmental
Na Luo, Xiangsheng Luo, Suli Zheng, Dongren Yao, Min Zhao, Yue Cui, Yu Zhu, Vince D. Calhoun, Li Sun, Jing Sui
Summary: This study investigates the temporal and frequency abnormalities in ADHD and its subtypes using high-density EEG. The results show differences in the salience network and frequency power between ADHD patients and healthy controls. Subtype differences primarily exist in the visual network, with ADHD-C patients showing a more activated visual network. Furthermore, the support vector machine model achieves high accuracy in classifying ADHD and its subtypes.
EUROPEAN CHILD & ADOLESCENT PSYCHIATRY
(2023)
Article
Neurosciences
Md Abdur Rahaman, Jiayu Chen, Zening Fu, Noah Lewis, Armin Iraji, Theo G. M. van Erp, Vince D. Calhoun
Summary: Characterizing neuropsychiatric disorders is challenging, but combining structural and functional neuroimaging with genomic data in a multimodal classification framework can improve the classification of disorders and explore underlying neural and biological mechanisms. By developing neural networks for feature learning and implementing an adaptive control unit for fusion, we achieved high accuracy in schizophrenia prediction and identified critical neural features and genes/biological pathways associated with the disorder.
HUMAN BRAIN MAPPING
(2023)
Article
Neurosciences
Kaicheng Li, Qingze Zeng, Xiao Luo, Shile Qi, Xiaopei Xu, Zening Fu, Luwei Hong, Xiaocao Liu, Zheyu Li, Yanv Fu, Yanxing Chen, Zhirong Liu, Vince D. Calhoun, Peiyu Huang, Minming Zhang
Summary: The study found that concomitant neuropsychiatric symptoms are associated with accelerated Alzheimer's disease progression. Using multimodal brain imaging, a pattern associated with these symptoms was identified and found to be correlated with the development of Alzheimer's disease. The pattern was also found to be associated with multiple cognitive domains and could predict cognitive decline.
HUMAN BRAIN MAPPING
(2023)
Article
Computer Science, Interdisciplinary Applications
Irina Belyaeva, Ben Gabrielson, Yu-Ping Wang, Tony W. Wilson, Vince D. Calhoun, Julia M. Stephen, Tulay Adali
Summary: Identification of informative signatures from electrophysiological signals is important for understanding brain developmental patterns. This study proposes a tensor-based approach for extracting developmental signatures of multi-subject MEG data. The results demonstrate that this approach can produce descriptive features of the multidimensional MEG data and be used to study group differences in brain patterns and cognitive function of healthy children.
Article
Computer Science, Interdisciplinary Applications
Harshvardhan Gazula, Kelly Rootes-Murdy, Bharath Holla, Sunitha Basodi, Zuo Zhang, Eric Verner, Ross Kelly, Pratima Murthy, Amit Chakrabarti, Debasish Basu, Subodh Bhagyalakshmi Nanjayya, Rajkumar Lenin Singh, Roshan Lourembam Singh, Kartik Kalyanram, Kamakshi Kartik, Kumaran Kalyanaraman, Krishnaveni Ghattu, Rebecca Kuriyan, Sunita Simon Kurpad, Gareth J. Barker, Rose Dawn Bharath, Sylvane Desrivieres, Meera Purushottam, Dimitri Papadopoulos Orfanos, Eesha Sharma, Matthew Hickman, Mireille Toledano, Nilakshi Vaidya, Tobias Banaschewski, Arun L. W. Bokde, Herta Flor, Antoine Grigis, Hugh Garavan, Penny Gowland, Andreas Heinz, Rudiger Bruhl, Jean-Luc Martinot, Marie-Laure Paillere Martinot, Eric Artiges, Frauke Nees, Tomas Paus, Luise Poustka, Juliane H. Frohner, Lauren Robinson, Michael N. Smolka, Henrik Walter, Jeanne Winterer, Robert Whelan, Jessica A. Turner, Anand D. Sarwate, Sergey M. Plis, Vivek Benegal, Gunter Schumann, Vince D. Calhoun
Summary: With the growth of decentralized/federated analysis approaches in neuroimaging, the opportunities to study brain disorders using data from multiple sites has grown multi-fold. One such initiative is the Neuromark, a fully automated spatially constrained independent component analysis (ICA) that is used to link brain network abnormalities among different datasets, studies, and disorders while leveraging subject-specific networks.
Article
Computer Science, Information Systems
Xiang Li, Sheri L. Towe, Ryan P. Bell, Rongtao Jiang, Shana A. Hall, Vince D. Calhoun, Christina S. Meade, Jing Sui
Summary: Neurocognitive impairment is common in people living with HIV, and identifying reliable biomarkers is crucial for understanding neural foundations and clinical care. This study used connectome-based predictive modeling to predict cognitive functioning in PLWH, achieving high prediction accuracy by combining multiple modalities and incorporating clinical measures.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2023)
Article
Computer Science, Information Systems
Ying Xing, Peter Kochunov, Theo G. M. van Erp, Tianzhou Ma, Vince D. Calhoun, Yuhui Du
Summary: Feature selection is important in identifying biomarkers of mental disorders. In this study, a new method based on neighborhood rough set (NRS) was proposed to select biomarkers of schizophrenia using fMRI data. The method combined NRS with information entropy and multi-granularity fusion to obtain the most discriminative features. The method achieved higher classification accuracies compared to other methods, revealing meaningful substrates of schizophrenia. This study highlights the potential of exploring neuroimaging-based biomarkers using the NRS-based feature selection method.
IEEE JOURNAL OF BIOMEDICAL AND HEALTH INFORMATICS
(2023)
Article
Neurosciences
Noah Lewis, Robyn Miller, Harshvardhan Gazula, Vince Calhoun
Summary: Deep learning is effective for classifying biological sex based on fMRI, but research on the most relevant brain features for this classification is lacking. Model interpretability is important for understanding deep learning models, but little work has been done on the relationship between temporal dimension of fMRI signals and sex classification. In this study, a methodology is provided to address underspecification and instability in feature explanation models, and sex differences in functional brain networks are explored using intrinsic connectivity networks.
Article
Neurosciences
Marlena Duda, Armin Iraji, Judith M. Ford, Kelvin O. Lim, Daniel H. Mathalon, Bryon A. Mueller, Steven G. Potkin, Adrian Preda, Theo G. M. Van Erp, Vince D. Calhoun
Summary: By using spatially constrained independent component analysis (scICA), this study found that rsfMRI scans of just 2-5 minutes can provide good clinical utility without significant loss of individual functional network connectivity (FNC) information from longer scan lengths.
HUMAN BRAIN MAPPING
(2023)
Article
Engineering, Biomedical
Anton Orlichenko, Gang Qu, Gemeng Zhang, Binish Patel, Tony W. W. Wilson, Julia M. M. Stephen, Vince D. D. Calhoun, Yu-Ping Wang
Summary: In this study, we developed an interpretable multivariate classification/regression algorithm called LatSim, which is suitable for small sample size and high feature dimension datasets. Results showed that LatSim achieved higher predictive accuracy compared to other methods, and identified functional brain networks associated with brain age, sex, and intelligence prediction. This research provides new insights for algorithm design and neuroscience research.
IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING
(2023)
Correction
Biochemistry & Molecular Biology
Sean R. McWhinney, Katharina Brosch, Vince D. Calhoun, Benedicto Crespo-Facorro, Nicolas A. Crossley, Udo Dannlowski, Erin Dickie, Lorielle M. F. Dietze, Gary Donohoe, Stefan Du Plessis, Stefan Ehrlich, Robin Emsley, Petra Furstova, David C. Glahn, Alfonso Gonzalez-Valderrama, Dominik Grotegerd, Laurena Holleran, Tilo T. J. Kircher, Pavel Knytl, Marian Kolenic, Rebekka Lencer, Igor Nenadic, Nils Opel, Julia-Katharina Pfarr, Amanda L. Rodrigue, Kelly Rootes-Murdy, Alex J. Ross, Kang Sim, Antonin Skoch, Filip Spaniel, Frederike Stein, Patrik Svancer, Diana Tordesillas-Gutierrez, Juan Undurraga, Javier Vaquez-Bourgon, Aristotle Voineskos, Esther Walton, Thomas W. Weickert, Cynthia Shannon Weickert, Paul M. Thompson, Theo G. M. van Erp, Jessica A. Turner, Tomas Hajek
MOLECULAR PSYCHIATRY
(2023)
Article
Psychiatry
Zening Fu, Christopher C. Abbott, Jeremy Miller, Zhi-De Deng, Shawn M. McClintock, Mohammad S. E. Sendi, Jing Sui, Vince D. Calhoun
Summary: Electroconvulsive therapy (ECT) is effective for depression treatment, and its mechanism involves changing brain's functional organization through electrical current stimulation. This study investigated the relationship between whole-brain electric field (E-field), cerebro-cerebellar functional network connectivity (FNC), and clinical outcomes of ECT. The results showed that E-field influenced cognitive performance through cerebellum to middle occipital gyrus (MOG)/posterior cingulate cortex (PCC) FNC mediation, and had an effect on antidepressant outcomes through cerebellum to parietal lobule FNC mediation. Furthermore, larger E-field was associated with increased FNC between cerebellum and MOG and decreased FNC between cerebellum and PCC, which were linked with decreased cognitive performance.
TRANSLATIONAL PSYCHIATRY
(2023)
Article
Psychiatry
Kuaikuai Duan, Jiayu Chen, Vince D. D. Calhoun, Wenhao Jiang, Kelly Rootes-Murdy, Gido Schoenmacker, Rogers F. F. Silva, Barbara Franke, Jan K. K. Buitelaar, Martine Hoogman, Jaap Oosterlaan, Pieter J. J. Hoekstra, Dirk Heslenfeld, Catharina A. A. Hartman, Emma Sprooten, Alejandro Arias-Vasquez, Jessica A. A. Turner, Jingyu Liu
Summary: In this study, a genomic pattern underlying the gray matter variation in the frontal cortex related to working memory deficit in ADHD was revealed through a multivariate analysis. The identified genes are involved in modulating neuronal substrates underlying high-level cognition in ADHD, providing insights into the pathology of ADHD persistence.
TRANSLATIONAL PSYCHIATRY
(2023)
Article
Engineering, Biomedical
Lan Yang, Chen Qiao, Huiyu Zhou, Vince D. Calhoun, Julia M. Stephen, Tony W. Wilson, Yuping Wang
Summary: This study proposes an explainable multimodal deep dictionary learning method to uncover the commonality and specificity of different modalities in brain developmental differences. The results show that the proposed model can achieve better reconstruction and identify age-related differences in reoccurring patterns.
IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING
(2023)
