Article
Biotechnology & Applied Microbiology
Daniel C. Shippy, Jyoti J. Watters, Tyler K. Ulland
Summary: The study revealed that AD activates multiple signaling pathways that regulate numerous genes in microglia, contributing to Aβ phagocytosis and neuroinflammation. These findings identified several regulatory factors and biomarkers in microglia, which could be beneficial for further comprehension of AD neuropathology.
Article
Biochemistry & Molecular Biology
Yung-Te Hou, Chia-Chun Wu, Wen-Ting Wang, Wen-Tse Yang, Ying-Hsiu Liao, Chien-Yu Chen
Summary: In this study, RNA-Seq was used to monitor the maturity and dynamic characteristics of in vitro hepatocyte cultures. The results showed that RNA-Seq can be used to infer the success of in vitro hepatocyte cultures and provide a more comprehensive list of factors related to hepatocyte differentiation. This monitoring system has high potential in medical applications and may also be a novel method for diagnosing liver-related diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Multidisciplinary
Piyawat Pitikultham, Thitirat Putnin, Dechnarong Pimalai, Nuankanya Sathirapongsasuti, Chagriya Kitiyakara, Qiao Jiang, Baoquan Ding, Deanpen Japrung
Summary: In this study, a novel self-assembly approach based on rolling circle amplification and graphene oxide was proposed for the ultrasensitive detection of miRNA21 and miRNA16 in human saliva, which are oral cancer biomarkers. The proposed method exhibited ultrasensitive detection, a wide range of detection, and high selectivity, suggesting its potential application for the diagnosis and screening of early-stage oral cancer.
Article
Clinical Neurology
Liang Tang, Qin Xiang, Ju Xiang, Jianming Li
Summary: In an Aβ(25-35)-induced AD mouse model, Tripterygium glycoside can significantly improve spatial memory and inhibit the production of p-tau. Microarray analysis revealed changes in the expression of lncRNAs, mRNAs, and miRNAs in the hippocampus of mice treated with TG, and a ceRNA network and PPI network were established.
NEUROPSYCHIATRIC DISEASE AND TREATMENT
(2021)
Article
Genetics & Heredity
Eun-Gyung Lee, Sunny Chen, Lesley Leong, Jessica Tulloch, Chang-En Yu
Summary: This study found that TOMM40 RNA levels were elevated in AD brains and associated with decreased mitochondrial DNA copy number and mitochondrial membrane potential, indicating a link between differential transcription of TOMM40 RNA in the brain and mitochondrial dysfunction.
Review
Biotechnology & Applied Microbiology
Xinjie Chen, Yuan Lu
Summary: circRNA, a unique noncoding RNA molecule abundant in cells, has diverse functions such as miRNA sponge and protein scaffold. It plays a significant role in medical applications like circRNA vaccines. Researchers are working on overcoming challenges in circRNA synthesis for future applications.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mohammed Hafeezunnisa, Passong Immanual R. Chhakchhuak, Janani Krishnakumar, Ranjan Sen
Summary: The Rho-dependent transcription termination in bacteria specifically controls the expression of toxin-antitoxin modules of cryptic prophages in E. coli, enhancing bacterial innate immunity. However, this mechanism does not regulate most chromosomal TA modules.
Article
Biochemistry & Molecular Biology
How-Wing Leung, Gabriel Wei Quan Foo, Antonius M. J. VanDongen
Summary: The immediate early gene Arc plays a crucial role in regulating synaptic function and memory consolidation. It interacts with dynamic chromatin and associates with histone markers for active enhancers and transcription in cultured rat hippocampal neurons. Upregulated histone modifications associated with late-onset Alzheimer's disease have been found. Altered expression profiles of over 1900 genes, including those involved in synaptic function, neuronal plasticity, excitability, and signaling pathways, were observed when Arc induction was prevented. About 100 Arc-dependent genes are implicated in the pathophysiology of Alzheimer's disease. The induction of endogenous Arc expression in HEK293T cells increased the transcription of neuronal genes, suggesting that Arc can control gene expression independently of activated signaling pathways. These findings establish Arc as a master regulator of activity-dependent gene expression in neurons and suggest its significance in Alzheimer's disease pathophysiology.
Review
Biochemistry & Molecular Biology
Simon Maksour, Lezanne Ooi
Summary: Microglia play an important role in the pathogenesis of Alzheimer's disease (AD) through specific or predominant expression of risk factor genes. Studies on human tissue and animal models have shown that microglia undergo significant morphological and phenotypic changes during AD progression. However, limitations exist due to the representation of a single time point or lack of conservation between species. Recent innovations, such as the use of pluripotent stem cell-derived microglia, transdifferentiation of patient monocytes, and xenotransplantation into mouse brains, have advanced our understanding of microglia in AD. This review outlines the strengths and limitations of these approaches and provides recommendations for future research.
JOURNAL OF NEUROCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Claire Chung, Bert M. Verheijen, Xinmin Zhang, Biao Huang, Aeowynn Coakley, Eric McGann, Emily Wade, Olivia Dinep-Schneider, Jessica LaGosh, Maria-Eleni Anagnostou, Stephen Simpson, Kelly Thomas, Mimi Ernst, Allison Rattray, Michael Lynch, Mikhail Kashlev, Berenice A. Benayoun, Zhongwei Li, Jeffrey Strathern, Jean-Francois Gout, Marc Vermulst
Summary: To determine the error rate of transcription in human cells, researchers analyzed the transcriptome of H1 human embryonic stem cells using a high-fidelity circle-sequencing approach. They found approximately 100,000 errors in major RNA species, indicating that different RNA species have different error rates. Cross-referencing the errors with genetic and epigenetic features revealed that the error rate changes along the transcript length and is modified by genetic context, repetitive elements, and epigenetic markers. The study also discovered a novel role of BRCA1 in suppressing transcription errors and found that transcription errors preferentially occur in neurons, suggesting their involvement in neurological disorders.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Multidisciplinary
Douglas Magde, Arvin Akoopie, Michael D. Magde, Ulrich F. Muller
Summary: In the early history of life, RNA may have had catalytic functions that have since disappeared. To explore this possibility, researchers conducted in vitro selection experiments to identify catalytically active RNAs. By using microfluidics to create nanodroplets for large-scale in emulsio selection experiments, they were able to produce stable emulsions ideal for their purposes.
Article
Biochemistry & Molecular Biology
Thiago B. Taketa, Cynthia R. A. Mahl, Guilherme B. Calais, Marisa M. Beppu
Summary: Chitosan-based materials were shown to have enhanced copper ion adsorption capacity in the presence of histidine, with amino acid functionalization promoting an increase in adsorption capacity. The order of addition of histidine to the system influenced the adsorption behavior, and simultaneous addition of chitosan and histidine prevented a decrease in adsorption capacity.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Multidisciplinary Sciences
Ekin Bolukbasi, Nathaniel S. Woodling, Dobril K. Ivanov, Jennifer Adcott, Andrea Foley, Arjunan Rajasingam, Lauren M. Gittings, Benjamin Aleyakpo, Teresa Niccoli, Janet M. Thornton, Linda Partridge
Summary: Reduced activity of the insulin/insulin-like growth factor signaling pathway has been shown to increase healthy lifespan in various animal species. In the adult nervous system of Drosophila, specific transcription factors like neuronal FKH and glial FOXO play independent roles in extending healthy lifespan. The importance of cell type-specific mapping of transcription factor activity for preserving healthy function with age is highlighted in this study.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Microbiology
Patrick Waindok, Elisabeth Janecek-Erfurth, Dimitri L. Lindenwald, Esther Wilk, Klaus Schughart, Robert Geffers, Christina Strube
Summary: This study investigated the gene expression changes in the brains of mice infected with Toxocara and identified dysregulated pathways associated with cholesterol biosynthesis, apoptosis signaling, and immune response. The findings provide insights into the pathogenesis of neurotoxocarosis and suggest a potential link between Toxocara infection and dementia or Alzheimer's disease.
Article
Virology
Serdal Arslan, Mehmet Bakir, Burcu Bayyurt, Eylem Aydemir, Kenan Kinaci, Aynur Engin
Summary: This study investigated the lncRNA gene expression profiles in CCHF using microarray for the first time. Several lncRNAs were found to be significantly regulated in both case and fatal case groups. These lncRNAs could be considered as important therapeutic targets for further studies on CCHF.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Biochemistry & Molecular Biology
Stephen D. Ginsberg, Thomas A. Neubert, Sahil Sharma, Chander S. Digwal, Pengrong Yan, Calin Timbus, Tai Wang, Gabriela Chiosis
Summary: The article discusses the relationship between stressor-induced protein interactome network perturbations and the formation of pathologic scaffolds, proposing how epichaperomics can reliably obtain context-dependent interactomes to advance the definition, understanding, and control of complex disease interactome networks.
Article
Multidisciplinary Sciences
Angelina Volkova, Kelly Ruggles, Anjelique Schulfer, Zhan Gao, Stephen D. Ginsberg, Martin J. Blaser
Summary: The study established experimental systems to evaluate the impact of early-life exposure to antibiotics on the intestinal microbiota and gene expression in the brain. It found substantial changes in both microbiota population structure and composition, as well as transcriptomic alterations indicating pathways perturbed in neurodevelopmental and neuropsychiatric disorders. Additionally, there were significant effects on gene expression in the frontal cortex and amygdala, with linkages identified between specific intestinal microbial populations and early-life expression of affected genes.
Article
Neurosciences
John S. Beck, Zachary Madaj, Calvin T. Cheema, Betul Kara, David A. Bennett, Julie A. Schneider, Marcia N. Gordon, Stephen D. Ginsberg, Elliott J. Mufson, Scott E. Counts
Summary: The mechanisms of Alzheimer's disease and mild cognitive impairment involve dysregulation of multiple molecular pathways. This study analyzed gene expression patterns and found that insulin signaling was associated with clinical diagnosis, potentially playing a role in disease onset. Additionally, the platelet-endothelium-leucocyte cell adhesion pathways and hypoxia-oxidative stress were linked to neuropathological diagnostic criteria, potentially impacting disease progression and clinical presentation.
Review
Biochemistry & Molecular Biology
Stephen D. Ginsberg, Suhasini Joshi, Sahil Sharma, Gianny Guzman, Tai Wang, Ottavio Arancio, Gabriela Chiosis
Summary: The adaptation to stress in central nervous system disorders involves a wide range of factors, including changes in homeostasis, protein connectivity, and disease-related pathologic scaffolds. These stressors may disrupt cellular homeostasis, leading to alterations in brain networks and potential therapeutic opportunities for neurodegenerative disorders like Alzheimer's disease.
JOURNAL OF NEUROCHEMISTRY
(2021)
Correction
Neurosciences
Melissa J. Alldred, Sai C. Penikalapati, Sang Han Lee, Adriana Heguy, Panos Roussos, Stephen D. Ginsberg
MOLECULAR NEUROBIOLOGY
(2022)
Article
Geriatrics & Gerontology
Brian E. Powers, Ramon Velazquez, Myla S. Strawderman, Stephen D. Ginsberg, Elliott J. Mufson, Barbara J. Strupp
Summary: Maternal choline supplementation is a promising therapy for Down syndrome, improving cognitive and emotional functions in offspring by enhancing septohippocampal circuitry. However, the benefits may diminish with age due to the development of Alzheimer's disease-like neuropathology. Increasing maternal choline intake during pregnancy could have population-wide benefits for both neurotypical and DS offspring.
FRONTIERS IN AGING NEUROSCIENCE
(2021)
Editorial Material
Geriatrics & Gerontology
Elliott J. Mufson, Stephen D. Ginsberg, Tao Ma, Aurelie Ledreux, Sylvia E. Perez
FRONTIERS IN AGING NEUROSCIENCE
(2021)
Article
Biology
Suhasini Joshi, Erica DaGama Gomes, Tai Wang, Adriana Corben, Tony Taldone, Srinivasa Gandu, Chao Xu, Sahil Sharma, Salma Buddaseth, Pengrong Yan, Lon Yin L. Chan, Askan Gokce, Vinagolu K. Rajasekhar, Lisa Shrestha, Palak Panchal, Justina Almodovar, Chander S. Digwal, Anna Rodina, Swathi Merugu, NagaVaraKishore Pillarsetty, Vlad Miclea, Radu I. Peter, Wanyan Wang, Stephen D. Ginsberg, Laura Tang, Marissa Mattar, Elisa de Stanchina, Kenneth H. Yu, Maeve Lowery, Olivera Grbovic-Huezo, Eileen M. O'Reilly, Yelena Janjigian, John H. Healey, William R. Jarnagin, Peter J. Allen, Chris Sander, Hediye Erdjument-Bromage, Thomas A. Neubert, Steven D. Leach, Gabriela Chiosis
Summary: By manipulating epichaperomes pharmacologically, the interactomes within tumors can be re-engineered for vulnerability and improved treatment efficacy, offering a paradigm to overcome drug resistance through pharmacologic manipulation of proteome-wide protein-protein interaction networks.
COMMUNICATIONS BIOLOGY
(2021)
Article
Neurosciences
Yann Dromard, Margarita Arango-Lievano, Amelie Borie, Maheva Dedin, Pierre Fontanaud, Joan Torrent, Michael J. Garabedian, Stephen D. Ginsberg, Freddy Jeanneteau
Summary: Aberrant cortisol and activation of the glucocorticoid receptor (GR) contribute to the progression of Alzheimer's disease (AD). Disrupting BDNF-dependent GR phosphorylation exacerbates the detrimental effects of AD in mice, while downregulated BDNF signaling and upregulated cortisol pathway activation are observed in postmortem AD subjects. These findings suggest that targeting the neurotrophin-mediated GR phosphorylation pathway could be a novel approach to treat AD dementia.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2022)
Article
Immunology
Anne-Laure Hemonnot-Girard, Cedric Meersseman, Manuela Pastore, Valentin Garcia, Nathalie Linck, Catherine Rey, Amine Chebbi, Freddy Jeanneteau, Stephen D. Ginsberg, Joel Lachuer, Christelle Reynes, Francois Rassendren, Helene Hirbec
Summary: This study used cell-specific laser capture microdissection and RNA-seq analysis to isolate and analyze plaque-associated and plaque-distant microglia in an AD mouse model. The results showed distinct transcriptional differences between these two microglial subtypes, indicating their different roles in AD progression.
JOURNAL OF NEUROINFLAMMATION
(2022)
Review
Pharmacology & Pharmacy
Stephen D. Ginsberg, Sahil Sharma, Larry Norton, Gabriela Chiosis
Summary: Diseases are complex manifestations of changes in protein-protein interaction networks caused by stressors, genetics, environment, and their combinations, affecting molecular interactions and disrupting the normal function of cells, tissues, and organisms. Disrupting epichaperomes, which enable dysfunctional rewiring of these networks, is proposed as a mechanism for reverting context-specific dysfunction to a normative state. This has potential implications for precision medicine in detecting and treating complex diseases like cancer and neurodegenerative disorders.
TRENDS IN PHARMACOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Melissa J. Alldred, Harshitha Pidikiti, Adriana Heguy, Panos Roussos, Stephen D. Ginsberg
Summary: Basal forebrain cholinergic neuron (BFCN) degeneration is a characteristic of Down syndrome (DS) and Alzheimer's disease (AD). Maternal choline supplementation (MCS) has been shown to attenuate the degeneration of BFCNs in a mouse model, suggesting a potential therapeutic effect for DS and AD.
Article
Medicine, General & Internal
Melissa J. J. Alldred, Stephen D. D. Ginsberg
Summary: Single-cell and single-population RNA sequencing is a valuable tool in studying the transcriptomic profiles of neurons based on their spatial localization. Laser capture microdissection and RNA purification allow for the isolation of desired neurons for downstream analysis, such as differential gene expression and pathway exploration.
JOURNAL OF CLINICAL MEDICINE
(2023)
Article
Clinical Neurology
Christy M. Kelley, Stephen D. Ginsberg, Winnie S. Liang, Scott E. Counts, Elliott J. Mufson
Summary: RNA-seq analysis of the posterior cingulate cortex in aged individuals revealed differential gene expression and transcription factor binding sites between different Braak stages, suggesting a potential role for synaptic genes in cognitive resilience.
BRAIN COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Nicole Beaulieu Perez, Allison A. Vorderstrasse, Gary Yu, Gail D'Eramo Melkus, Fay Wright, Stephen D. Ginsberg, Cindy A. Crusto, Yan Sun, Jacquelyn Y. Taylor
Summary: In African American women, the associations between age acceleration, depressive symptoms, and cardiometabolic traits are complex and may be influenced by factors other than age acceleration. Factors other than age acceleration may explain the connection between depressive symptoms and cardiometabolic traits in this population. African American women with cardiometabolic traits may be at increased risk of accelerated aging.
EPIGENETICS INSIGHTS
(2022)
Article
Biochemical Research Methods
Aline Silva da Cruz, Maria Margarida Drehmer, Wagner Baetas-da-Cruz, Joao Carlos Machado
Summary: This study quantified microcirculation cerebral blood flow in a rat model of ischemic stroke using ultrasound biomicroscopy and ultrasound contrast agents. The results showed high sensitivity and specificity of this method, making it a valuable tool for preclinical studies.
JOURNAL OF NEUROSCIENCE METHODS
(2024)
Article
Biochemical Research Methods
Christina Dalla, Ivana Jaric, Pavlina Pavlidi, Georgia E. Hodes, Nikolaos Kokras, Anton Bespalov, Martien J. Kas, Thomas Steckler, Mohamed Kabbaj, Hanno Wuerbel, Jordan Marrocco, Jessica Tollkuhn, Rebecca Shansky, Debra Bangasser, Jill B. Becker, Margaret McCarthy, Chantelle Ferland-Beckham
Summary: Many funding agencies have emphasized the importance of considering sex as a biological variable in experimental design to improve the reproducibility and translational relevance of preclinical research. Omitting the female sex from experimental designs in neuroscience and pharmacology can result in biased or limited understanding of disease mechanisms. This article provides methodological considerations for incorporating sex as a biological variable in in vitro and in vivo experiments, including the influence of age and hormone levels, and proposes strategies to enhance methodological rigor and translational relevance in preclinical research.
JOURNAL OF NEUROSCIENCE METHODS
(2024)
Article
Biochemical Research Methods
Wenyu Gu, Dongxu Li, Jia-Hong Gao
Summary: We developed a precise and rapid method for positioning and labelling triaxial OPMs on a wearable magnetoencephalography (MEG) system, improving the efficiency of OPM positioning and labelling.
JOURNAL OF NEUROSCIENCE METHODS
(2024)
Article
Biochemical Research Methods
Kai Lin, Linhang Zhang, Jing Cai, Jiaqi Sun, Wenjie Cui, Guangda Liu
Summary: The article introduces an EEG feature map processing model for emotion recognition, which achieves significantly improved accuracy by fusing EEG information at different spatial scales and introducing a channel attention mechanism.
JOURNAL OF NEUROSCIENCE METHODS
(2024)
Article
Biochemical Research Methods
John E. Parker, Asier Aristieta, Aryn H. Gittis, Jonathan E. Rubin
Summary: This work presents a toolbox that implements a methodology for automated classification of neural responses based on spike train recordings. The toolbox provides a user-friendly and efficient approach to detect various types of neuronal responses that may not be identified by traditional methods.
JOURNAL OF NEUROSCIENCE METHODS
(2024)
Article
Biochemical Research Methods
Yun Liang, Ke Bo, Sreenivasan Meyyappan, Mingzhou Ding
Summary: This study compared the performance of SVM and CNN on the same datasets and found that CNN achieved consistently higher classification accuracies. The classification accuracies of SVM and CNN were generally not correlated, and the heatmaps derived from them did not overlap significantly.
JOURNAL OF NEUROSCIENCE METHODS
(2024)
Article
Biochemical Research Methods
Antonino Visalli, Maria Montefinese, Giada Viviani, Livio Finos, Antonino Vallesi, Ettore Ambrosini
Summary: This study introduces an analytical strategy that allows the use of mixed-effects models (LMM) in mass univariate analyses of EEG data. The proposed method overcomes the computational costs and shows excellent performance properties, making it increasingly important in the field of neuroscience.
JOURNAL OF NEUROSCIENCE METHODS
(2024)
Article
Biochemical Research Methods
Xavier Cano-Ferrer, Alexandra Tran -Van -Minh, Ede Rancz
Summary: This study developed a novel rotation platform for studying neural processes and spatial navigation. The platform is modular, affordable, and easy to build, and can be driven by the experimenter or animal movement. The research demonstrated the utility of the platform, which combines the benefits of head fixation and intact vestibular activity.
JOURNAL OF NEUROSCIENCE METHODS
(2024)