Article
Engineering, Biomedical
Lakshmi Kavitha Sthanam, Tanusri Roy, Sejal Patwardhan, Avi Shukla, Shipra Sharma, Pradip Shinde, Hanuman Tulasiram Kale, P. Chandra Shekar, Kiran Kondabagil, Shamik Sen
Summary: Stem cell differentiation is influenced by the interaction between cells and their extracellular matrix, with matrix metalloproteinases (MMPs) playing a role in this process. Differentiation of mouse embryonic stem cells (mESCs) on varying matrices led to changes in MMP expression and activity, affecting integrin expression, mechanotransduction pathways, and germ layer-specific markers. Inhibition of MMP activity altered the germ layer commitment of differentiating mESCs, demonstrating the importance of MMPs in regulating stem cell differentiation.
Article
Cell Biology
Meghali Aich, Asgar Hussain Ansari, Li Ding, Vytautas Iesmantavicius, Deepanjan Paul, Chunaram Choudhary, Souvik Maiti, Frank Buchholz, Debojyoti Chakraborty
Summary: This study reveals that the lncRNA-associated protein TOBF1 regulates the alternative splicing of transcripts necessary for maintaining stem cell identity in mouse ESCs. One of the affected genes is serine/arginine splicing factor 1 (SRSF1), whose splicing leads to global changes in splicing and expression of downstream genes involved in the maintenance of ESC pluripotency. The study shows that TOBF1 chromatin occupancy, pluripotency-associated OCT-SOX binding motifs, and transcripts undergoing differential expression and splicing converge in specific nuclear territories, collectively contributing to the maintenance of mouse ESC identity.
Article
Cell Biology
Ahmad Salti, Solmaz Etemad, Marta Suarez Cubero, Eva Albertini, Beata Kovacs-Szalka, Max Holzknecht, Elia Cappuccio, Maria Cavinato, Frank Edenhofer, Pidder Jansen Durr
Summary: By studying the role of mitochondria in cellular reprogramming processes, it was found that FAHD1 plays an important role in regulating mitochondrial function, potentially acting as a negative regulator of cell reprogramming.
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
Biology
Chenxiao Liu, Karolina Skorupinska-Tudek, Sven-Goran Eriksson, Ingela Parmry
Summary: This study aims to characterize the proliferation and cytotoxic potential of Vγ9Vδ2 T cells for the optimization of immunotherapy. It was found that supplementation with freshly thawed human serum enhanced Vγ9Vδ2 T cell proliferation, and a flow cytometry-based single cell assessment method provided clearer results for measuring cytotoxicity. Additionally, HMBPP was found to enhance the cytotoxicity of Vγ9Vδ2 T cells against colon cancer cells.
Article
Cell Biology
Masahiro Otsu, Zubair Ahmed, Daniel Fulton
Summary: A simple method was developed to generate immature oligodendrocyte lineage cells from mouse ESC-derived neural stem cells, which showed potential for differentiation into mature OPC under specific conditions. Interestingly, these cells retained multipotentiality and could differentiate into neurons or astrocytes. However, their efficiency in myelinating axons was lower compared to primary OPC.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Hiroyuki Omori, Masahiro Otsu, Haruo Nogami, Masayoshi Shibata
Summary: Cells have a regulatory mechanism called heat shock (HS) response, which is sensitive to both exogenous and endogenous factors, leading to both positive and negative effects on cells. The response of neural stem cells to heat shock is unclear, but studies have shown that extending the pre-culture period significantly affects the heat shock response and cell survival.
Article
Cell Biology
Jose Manuel Inacio, Joao von Gilsa Lopes, Ana Mafalda Silva, Fernando Cristo, Sara Marques, Matthias E. Futschik, Jose Antonio Belo
Summary: Deciphering the clues of a regenerative mechanism for the mammalian adult heart, particularly focusing on the role of DAND5, could potentially lead to the development of more effective treatment options for heart failure. Further research on the transcriptional profiling sequencing and quantitative RT-PCR assays of DAND5 may provide insights into the generation and expansion of pluripotent stem cell-derived cardiomyocytes systems for clinical applications.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Neurosciences
Olga Gordeeva, Vitaliy Safandeev
Summary: In this study, the regulatory effects of serotonin precursor 5-HTP on cell proliferation and cell death in mouse embryonic stem cells and embryonic fibroblasts were investigated. The results showed that 5-HTP treatment inhibited cell proliferation, induced cell cycle arrest, and increased apoptotic and necrotic cell death. Furthermore, 5-HTP treatment upregulated the gene expression of enzymes involved in 5-HT synthesis and metabolism, leading to toxic effects through enhancing protein modifications mediated by 5-HT.
Article
Multidisciplinary Sciences
Sarah Bertels, Mona Jaggy, Benjamin Richter, Stephan Keppler, Kerstin Weber, Elisa Genthner, Andrea C. Fischer, Michael Thiel, Martin Wegener, Alexandra M. Greiner, Tatjana J. Autenrieth, Martin Bastmeyer
Summary: Mechanotransduction via YAP is crucial for decision-making in mESCs. The geometry of the extracellular environment influences CDR and YAP localization in single mESCs, with changes in cell shape linked to a high CDR.
SCIENTIFIC REPORTS
(2021)
Article
Cell Biology
Yuting Fu, Fangyuan Liu, Shuo Cao, Jia Zhang, Huizhi Wang, Baojiang Wu, Yongli Song, Shuguang Duo, Xihe Li, Siqin Bao
Summary: This study reveals that Bdh2 deficiency has no impact on pluripotency and self-renewal of ESCs, but promotes endoderm differentiation and is essential for maintaining DNA methylation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
T. Deckers, J-M Aerts, V Bloemen
Summary: In this study, a novel cell detachment feature was developed using lens-free imaging technology, allowing quantitative monitoring of the detachment response and determination of the optimal time for enzyme inhibition.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Ayaka Yanagida, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, Ruby Peters, Henry De Belly, Davide A. D. Cassani, Sarra Achouri, Raphael Blumenfeld, Kristian Franze, Edouard Hannezo, Ewa K. Paluch, Jennifer Nichols, Kevin J. Chalut
Summary: This study investigates the mechanical basis of spatial segregation between the primitive endoderm and the epiblast. It proposes that differential surface fluctuations and cellular fluidity play a crucial role in ensuring physical lineage sorting.
Article
Toxicology
Hitoshi Terui, Yutaka Kimura, Chizu Fujimura, Setsuya Aiba
Summary: This study demonstrated that various haptens can increase the expression of IL-1 alpha and IL-1 beta in human monocyte cell line THP-1, and introduced a stable IL-1 beta reporter cell line THP-G1b for in vitro skin sensitization testing, showing that most haptens can stimulate IL-1 beta reporter activity.
ARCHIVES OF TOXICOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Taro Chaya, Yamato Maeda, Ryo Sugimura, Daisuke Okuzaki, Satoshi Watanabe, Leah R. Varner, Daisuke Motooka, Daichi Gyoten, Haruka Yamamoto, Hidemasa Kato, Takahisa Furukawa
Summary: This study found that miR-124a plays an important role in neuronal maturation rather than neurogenesis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Thomas Sheffield, Jason Brown, Sarah Davidson, Katie Paul Friedman, Richard Judson
Summary: Many chemical screening applications require the extraction of appropriate parameters such as activity and concentration from concentration-response data. tcpl is a widely used system for managing high-throughput screening data, while Tcplfit2 is a stand-alone version that allows for curve fitting and hit calling.
Review
Environmental Sciences
Laura M. Carlson, Michelle Angrish, Avanti V. Shirke, Elizabeth G. Radke, Brittany Schulz, Andrew Kraft, Richard Judson, Grace Patlewicz, Robyn Blain, Cynthia Lin, Nicole Vetter, Courtney Lemeris, Pamela Hartman, Heidi Hubbard, Xabier Arzuaga, Allen Davis, Laura V. Dishaw, Ingrid L. Druwe, Hillary Hollinger, Ryan Jones, J. Phillip Kaiser, Lucina Lizarraga, Pamela D. Noyes, Michele Taylor, Andrew J. Shapiro, Antony J. Williams, Kristina A. Thayer
Summary: The study utilized SEM methods to summarize epidemiological and animal bioassay evidence for approximately 150 PFAS, revealing data scarcity and lack of evidence for many PFAS. By disseminating this information and identifying key research needs, the study aims to support a more comprehensive understanding of potential health effects from PFAS exposures.
ENVIRONMENTAL HEALTH PERSPECTIVES
(2022)
Article
Engineering, Environmental
Lisa Truong, Yvonne Rericha, Preethi Thunga, Skylar Marvel, Dylan Wallis, Michael T. Simonich, Jennifer A. Field, Dunping Cao, David M. Reif, Robyn L. Tanguay
Summary: This study conducted an extensive in vivo developmental toxicity screen on 139 PFAS, and found that 49 of them exhibited bioactivity in at least one assay. Perfluorooctanesulfonamide (FOSA) was the only structure that showed bioactivity in all assays. The study also revealed a correlation between low volatility of PFAS and developmental toxicity, while no association was found between bioactivity and other physicochemical parameters.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Public, Environmental & Occupational Health
Amy Wolkin, Sarah Collier, John House, David Reif, Alison Motsinger-Reif, Lindsey Duca, Danielle Sharpe
Summary: This article describes the three vulnerability indices used by the CDC for the COVID-19 response, including the CDC Social Vulnerability Index (CDC-SVI), the US COVID-19 Community Vulnerability Index (CCVI), and the Pandemic Vulnerability Index (PVI). These indices provide important information for public health officials to understand the vulnerability of communities to disease and help plan resources and interventions.
PUBLIC HEALTH REPORTS
(2022)
Article
Toxicology
Prarthana Shankar, Gloria R. Garcia, Jane K. LaDu, Christopher M. Sullivan, Cheryl L. Dunham, Britton C. Goodale, Katrina M. Waters, Stanislau Stanisheuski, Claudia S. Maier, Preethi Thunga, David M. Reif, Robyn L. Tanguay
Summary: The study reveals the role of wfikkn1 in AHR signaling, suggesting its involvement in skeletal muscle development and neurological pathways. Mutant zebrafish show behavior deficiencies, but the absence of Wfikkn1 does not significantly alter TCDD-induced behavior effects.
TOXICOLOGICAL SCIENCES
(2022)
Article
Toxicology
AtLee T. D. Watson, Aldo Carmona Baez, Dereje Jima, David Reif, Jun Ding, Reade Roberts, Seth W. Kullman
Summary: This study aims to investigate the regulatory mechanisms of osteoblast differentiation through global transcriptomic analysis of human bone-derived mesenchymal stem cells (hBMSCs) exposed to TCDD. The results show that TCDD exposure attenuates osteoblast differentiation of hBMSCs and leads to altered gene expression.
TOXICOLOGICAL SCIENCES
(2023)
Article
Toxicology
Drake W. Phelps, Anika I. Palekar, Haleigh E. Conley, Giuliano Ferrero, Jacob H. Driggers, Keith E. Linder, Seth W. Kullman, David M. Reif, M. Katie Sheats, Jamie C. DeWitt, Jeffrey A. Yoder
Summary: This report investigates the impact of nine environmentally-relevant PFASs on the respiratory burst, and finds that PFHxA and GenX can suppress the respiratory burst. The study demonstrates for the first time that these PFASs can suppress neutrophil function, and supports the use of zebrafish larvae and a human cell line as screening tools for identifying chemicals that may suppress human immune function.
JOURNAL OF IMMUNOTOXICOLOGY
(2023)
Article
Statistics & Probability
Bora Jin, David B. Dunson, Julia E. Rager, David M. Reif, Stephanie M. Engel, Amy H. Herring
Summary: We propose a Bayesian hierarchical framework to infer bioactivity of chemicals by assay endpoint combination, addressing the sparsity of toxicology data. Our approach borrows information across different chemicals and assay endpoints, allows out-of-sample prediction of activity, quantifies uncertainty of predicted activity, and adjusts for multiplicity in hypothesis testing. Furthermore, this study makes a novel attempt in toxicology to simultaneously model heteroscedastic errors and a nonparametric mean function, leading to a broader definition of activity suggested by toxicologists. Real application identifies chemicals most likely active for neurodevelopmental disorders and obesity.
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS
(2023)
Article
Cell Biology
George W. Small, Farida S. Akhtari, Adrian J. Green, Tammy M. Havener, Michael Sikes, Julia Quintanhila, Ricardo D. Gonzalez, David M. Reif, Alison A. Motsinger-Reif, Howard L. McLeod, Tim Wiltshire
Summary: Monoclonal antibody (mAb) therapy directed against CD20 is an important tool in the treatment of B cell disorders. GWAS analysis identified several novel gene candidates that may influence sensitivity to treatment. The efficacy of anti-CD20 mAb therapy may be influenced by B cell developmental status as well as polymorphism in the MKL1 gene. Pretreatment with prednisolone could partly reverse the resistant phenotype, suggesting a potential clinical benefit.
Article
Chemistry, Medicinal
Ricardo D. Gonzalez, George W. Small, Adrian J. Green, Farida S. Akhtari, Tammy M. Havener, Julia C. F. Quintanilha, Amber B. Cipriani, David M. Reif, Howard L. McLeod, Alison A. Motsinger-Reif, Tim Wiltshire
Summary: Temozolomide (TMZ) chemotherapy is a significant treatment for glioma brain tumors. Our study identified a potential association between SNP rs4470517 in the RYK gene and TMZ drug response, and found that RYK gene expression status significantly impacts survival and progression-free survival in glioma patients, especially in IDH mutant gliomas.
Article
Chemistry, Medicinal
Ricardo D. Gonzalez, George W. Small, Adrian J. Green, Farida S. Akhtari, Alison A. Motsinger-Reif, Julia C. F. Quintanilha, Tammy M. Havener, David M. Reif, Howard L. McLeod, Tim Wiltshire
Summary: A genetic variant in the lncRNA gene MKX-AS1 and its paired sense gene MKX could impact the response of cell lines to oxaliplatin treatment. Patients with high MKX-AS1 expression had worse overall survival, while those with high MKX expression had better overall survival. This suggests that MKX-AS1 and MKX expression status could be useful as prognostic markers in colorectal cancer treatment.
Review
Biochemical Research Methods
Jessie R. Chappel, Kaylie I. Kirkwood-Donelson, David M. Reif, Erin S. Baker
Summary: The goal of lipidomic studies is to provide a comprehensive characterization of cellular lipids and their changes in a specific sample. Recent research in lipidomics has revealed the diverse roles of lipids in cellular processes and their dynamic response to perturbations. However, the analysis of lipidomics data is challenging due to the size of the datasets and the correlated nature of lipid data. This review presents statistical approaches and bioinformatic tools commonly used to analyze lipidomic datasets, providing a framework for interpreting and contextualizing the results.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2023)
Article
Chemistry, Analytical
Jessie R. Chappel, Mary E. King, Jonathon Fleming, Livia S. Eberlin, David M. Reif, Erin S. Baker
Summary: Mass spectrometry imaging (MSI) is popular for tissue-based diagnostics, but current statistical approaches often fail to visualize subtle molecular changes. To address this, researchers developed aggregated molecular phenotype (AMP) scores using ensemble machine learning. AMP scores can evaluate multiple features simultaneously and accurately distinguish phenotypes. When combined with spatial coordinates, AMP scores allow for visualization of tissue sections, highlighting their diagnostic utility.
ANALYTICAL CHEMISTRY
(2023)
Article
Engineering, Environmental
Dylan J. Wallis, Nadine Kotlarz, Detlef R. U. Knappe, David N. Collier, C. Suzanne Lea, David Reif, James McCord, Mark Strynar, Jamie C. DeWitt, Jane A. Hoppin
Summary: The GenX Exposure Study estimated the half-lives for novel fluoroethers and developed a model to predict PFAS half-lives based on structural properties. While certain properties can predict the half-lives of PFAS, further understanding is needed.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Article
Neurosciences
William P. Marinello, Sagi Enicole A. Gillera, Lynn Huang, John Rollman, David M. Reif, Heather B. Patisaul
Summary: This study utilized a factor analysis approach to extract underlying factors that potentially explain patterns within the behavior data of FM 550 exposure. The results showed that exposure to FM 550 significantly decreased activity and sociability.
