Article
Gastroenterology & Hepatology
Laura Conde de la Rosa, Carmen Garcia-Ruiz, Carmen Vallejo, Anna Baulies, Susana Nunez, Maria J. Monte, Jose J. G. Marin, Lucia Baila-Rueda, Ana Cenarro, Fernando Civeira, Josep Fuster, Juan C. Garcia-Valdecasas, Joana Ferrer, Michael Karin, Vicent Ribas, Jose C. Fernandez-Checa
Summary: The study revealed an unrecognized role of STARD1 in the pathogenesis of HCC, promoting the synthesis of primary BAs through the mitochondrial pathway, which stimulate hepatocyte pluripotency, self-renewal, and inflammation in tumour-initiated stem-like cells (TICs).
JOURNAL OF HEPATOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Zhiming Ma, Yanbiao Sun, Xinlu Zhu, Liang Yang, Xu Chen, Yansong Miao
Summary: This study demonstrates that the condensation of nanodomain constituents and the self-assembly of remorin proteins regulate the condensation and activity of formins during innate immunity in Arabidopsis thaliana. Through interaction with formins, remorin enhances actin nucleation, influencing the transduction of immune signals. Such nanodomain- and remorin-mediated regulation is expected to be a common feature in plant innate immune responses, creating spatially separated biochemical compartments and fine-tuning membrane properties for immune signal transduction in the host.
Article
Biochemistry & Molecular Biology
S. Baumgartner, D. Luetjohann, C. Husche, A. Kerksiek, A. K. Groen, R. P. Mensink, J. Plat
Summary: In this study, we evaluated the concentrations of oxyphytosterol (OPS) in plasma and various tissues of two genetically modified mouse models. The findings showed that while the levels of plant sterols (PS) were significantly elevated in the plasma of the dKO mice, the concentrations of OPS were comparable or even lower. This suggests that OPS are primarily formed in the liver and their presence in plasma is due to spill-over from the liver.
JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)
Article
Biology
Maia Kinnebrew, Giovanni Luchetti, Ria Sircar, Sara Frigui, Lucrezia Vittoria Viti, Tomoki Naito, Francis Beckert, Yasunori Saheki, Christian Siebold, Arun Radhakrishnan, Rajat Rohatgi
Summary: The study reveals that PTCH1 inhibits the activity of Smoothened by depleting accessible cholesterol from the outer leaflet of the plasma membrane, potentially involving an exchange of potassium ions. This finding establishes a general framework for investigating how proteins change cholesterol accessibility to regulate membrane-dependent processes in cells.
Article
Neurosciences
Ze-Lin Hu, Yang-Qi Yuan, Zhen Tong, Mei-Qing Liao, Shun-Ling Yuan, Ye Jian, Jia-Lun Yang, Wen-Feng Liu
Summary: Alzheimer's disease is a degenerative disease of the central nervous system. Imbalances in cholesterol homeostasis have been found in the brains of AD patients. Cholesterol deposition occurs in AD brains even without entry through the blood-brain barrier. Cholesterol metabolism in the brain is associated with various pathological conditions.
MOLECULAR NEUROBIOLOGY
(2023)
Review
Pharmacology & Pharmacy
Lorena Diaz Sanchez, Lorenzo Pontini, Maura Marinozzi, Lissette Carolina Sanchez-Aranguren, Ana Reis, Irundika H. K. Dias
Summary: Cholesterol and oxysterol sulfates play crucial roles in lipid metabolism, inflammation, cell apoptosis, and survival. However, further research is needed to analyze and understand the physiological and pathophysiological roles of oxysterol sulfates.
BRITISH JOURNAL OF PHARMACOLOGY
(2021)
Article
Cell Biology
Caitlin E. O'Brien, Susan H. Younger, Lily Yeh Jan, Yuh Nung Jan
Summary: The study by O'Brien et al. demonstrates that both the GARP and EARP complexes play a role in dendrite development and highlights the importance of sterol transport in this process.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Giuseppe Poli, Valerio Leoni, Fiorella Biasi, Federico Canzoneri, Davide Risso, Roberto Menta
Summary: There is increasing attention on the translational application of biochemical and biological findings, including cholesterol oxidation products. Non-enzymatic oxysterols are being used as molecular markers in clinical biochemistry for the diagnosis and monitoring of various human and veterinary diseases. Enzymatic oxysterols show promise as pharmaceutical agents. Recently, non-enzymatic oxysterols are being quantified to evaluate and improve the quality and shelf life of cholesterol-based food ingredients.
Article
Biochemistry & Molecular Biology
Jordan E. Otto, Oana Ursu, Alexander P. Wu, Evan B. Winter, Michael S. Cuoco, Sai Ma, Kristin Qian, Brittany C. Michel, Jason D. Buenrostro, Bonnie Berger, Aviv Regev, Cigall Kadoch
Summary: The mammalian SWI/SNF (mSWI/SNF or BAF) family of chromatin remodeling complexes are important for regulating DNA accessibility and gene expression. In this study, Perturb-seq-based CRISPR-Cas9 knockout screens were performed to investigate the roles of individual subunits of mSWI/SNF. The findings reveal the specific contributions of subunits to gene regulatory networks and highlight the potential of Perturb-seq in dissecting the impacts of multi-component master regulatory complexes.
Article
Biochemistry & Molecular Biology
Anita Wnetrzak, Anna Chachaj-Brekiesz, Karolina Kus, Ewelina Lipiec, Patrycja Dynarowicz-Latka
Summary: This paper investigates the influence of oxysterols on the fusion process between viral and host cell membranes. The results show that oxysterols hinder the fusion by modifying the biophysical properties of the host cell membranes and can reverse the changes caused by viral infection.
JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Medicinal
John L. Gilmore, Hai-Yun Xiao, T. G. Murali Dhar, Michael Yang, Zili Xiao, Xiaoxia Yang, Tracy L. Taylor, Kim W. McIntyre, Bethanne M. Warrack, Hong Shi, Paul C. Levesque, Anthony M. Marino, Georgia Cornelius, Arvind Mathur, Ding Ren Shen, Jian Pang, Mary Ellen Cvijic, Lois D. Lehman-McKeeman, Huadong Sun, Jenny Xie, Luisa Salter-Cid, Percy H. Carter, Alaric J. Dyckman
Summary: The discovery of compounds 12 and 24, highly potent and biased agonists of S1P(1), with shorter in vivo half-lives and robust efficacy in models of arthritis, represent a promising advancement in the development of therapeutics for autoimmune disorders.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Emanuela Teveroni, Fiorella Di Nicuolo, Edoardo Vergani, Carmine Bruno, Giuseppe Maulucci, Giada Bianchetti, Anna Laura Astorri, Giuseppe Grande, Jacopo Gervasoni, Lavinia Santucci, Marco De Spirito, Andrea Urbani, Alfredo Pontecorvi, Francesca Mancini, Domenico Milardi
Summary: The study demonstrates the activation of sperm cells through the olfactory receptor 51E2 (OR51E2) upon stimulation with volatile short-chain fatty acids (SCFAs). SCFAs promote sperm migration and a more linear sperm-cell orientation. The study also reveals the ability of cervical mucus to directly activate sperm cells. These findings provide insights into the role of chemosensory receptors in reproductive activity and offer potential strategies for the treatment of infertility.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Sathvika Venugopal, Melanie Galano, Rachel Chan, Esha Sanyal, Leeyah Issop, Sunghoon Lee, Lorne Taylor, Pushwinder Kaur, Edward Daly, Vassilios Papadopoulos
Summary: The study demonstrated that cAMP stimulation during steroidogenesis leads to significant lipidome remodeling, with changes in lipid composition in different organelles. The findings suggest that lipid trafficking between organelles plays a crucial role in hormone-induced steroid production, indicating extensive organelle remodeling.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Yutong Fan, Jinyue Zhou, Junjie Chen, Chunhui Shen, Shanjun Gao
Summary: Recently, the development of high-performance and durable anion exchange membranes for fuel cells has been prioritized. In this study, polyaryl piperidine anion exchange membranes with hydrophilic side chains were synthesized via a superacid-catalyzed Friedel-Crafts reaction. The membranes exhibited a distinct microphase separation structure between the hydrophilic side chain and hydrophobic main chain. The introduction of the hydrophilic side chain improved the ionic conductivity and alkaline resistance of the membranes, as indicated by their higher conductivity and lower weight loss after alkaline treatment compared to membranes without the hydrophilic side chain.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2023)
Article
Biochemistry & Molecular Biology
Lijun Liu, Yimin Zhao, Jian Ming, Jia Chen, Guohua Zhao, Zhen-Yu Chen, Yujie Wang, Lin Lei
Summary: This study found that polyphenol extract and essential oil from Amomum tsao-ko had similar effects in reducing plasma total cholesterol levels, possibly by increasing the fecal elimination of total acidic sterols. Both substances were also able to alleviate hypercholesterolemia in hamsters by interacting with gut microbiota and bile acid metabolism.
Article
Chemistry, Multidisciplinary
Lisa E. Felberg, David H. Brookes, Eng-Hui Yap, Elizabeth Jurrus, Nathan A. Baker, Teresa Head-Gordon
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2017)
Article
Computer Science, Interdisciplinary Applications
Xiu Yang, Huan Lei, Nathan A. Baker, Guang Lin
JOURNAL OF COMPUTATIONAL PHYSICS
(2016)
Article
Chemistry, Physical
Emilie Purvine, Kyle Monson, Elizabeth Jurrus, Keith Star, Nathan A. Baker
JOURNAL OF PHYSICAL CHEMISTRY B
(2016)
Article
Physics, Multidisciplinary
Aleksander V. Drozdetski, Igor S. Tolokh, Lois Pollack, Nathan Baker, Alexey V. Onufriev
PHYSICAL REVIEW LETTERS
(2016)
Article
Multidisciplinary Sciences
Huan Lei, Nathan A. Bakera, Xiantao Li
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2016)
Article
Chemistry, Physical
Luke J. Gosink, Christopher C. Overall, Sarah M. Reehl, Paul D. Whitney, David L. Mobley, Nathan A. Baker
JOURNAL OF PHYSICAL CHEMISTRY B
(2017)
Article
Biochemistry & Molecular Biology
Elizabeth Jurrus, Dave Engel, Keith Star, Kyle Monson, Juan Brandi, Lisa E. Felberg, David H. Brookes, Leighton Wilson, Jiahui Chen, Karina Liles, Minju Chun, Peter Li, David W. Gohara, Todd Dolinsky, Robert Konecny, David R. Koes, Jens Erik Nielsen, Teresa Head-Gordon, Weihua Geng, Robert Krasny, Guo-Wei Wei, Michael J. Holst, J. Andrew McCammon, Nathan A. Baker
Article
Chemistry, Physical
Xiu Yang, Huan Lei, Peiyuan Gao, Dennis G. Thomas, David L. Mobley, Nathan A. Baker
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2018)
Article
Engineering, Multidisciplinary
Huan Lei, Jing Li, Peiyuan Gao, Panagiotis Stinis, Nathan A. Baker
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2019)
Article
Biochemistry & Molecular Biology
Joseph A. Laureanti, Juan Brandi, Elvis Offor, David Engel, Robert Rallo, Bojana Ginovska, Xavier Martinez, Marc Baaden, Nathan A. Baker
Article
Computer Science, Interdisciplinary Applications
Francesca Grogan, Huan Lei, Xiantao Li, Nathan A. Baker
JOURNAL OF COMPUTATIONAL PHYSICS
(2020)
Article
Chemistry, Physical
Nicholas P. Bauman, Hongbin Liu, Eric J. Bylaska, Sriram Krishnamoorthy, Guang Hao Low, Christopher E. Granade, Nathan Wiebe, Nathan A. Baker, Bo Peng, Martin Roetteler, Matthias Troyer, Karol Kowalski
Summary: This paper investigates the use of the quantum phase estimation (QPE) algorithm in calculating high-energy excited states characterized by promotion of electrons occupying core-level shells. Results obtained with QPE are compared with various high-accuracy many-body techniques, discussing the feasibility of identifying challenging shake-up states and targeting excitations from specific centers in molecules. Additionally, the application of the lowest-order Trotter formula to reduce complexity of ansatz without affecting error is discussed.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Proceedings Paper
Computer Science, Hardware & Architecture
Samuel Stein, Nathan Wiebe, Yufei Ding, Peng Bo, Karol Kowalski, Nathan Baker, James Ang, Ang Li
Summary: This paper introduces a virtualized approach for building a quantum backend for variational quantum algorithms (VQA), which involves constructing a quantum ensemble that dynamically distributes quantum tasks and adjusts the ensemble configuration based on machine status. This approach reduces noise and improves training speed for VQA. The paper also presents a novel VQA training framework called EQC, which enables asynchronous parallel training, evaluates circuit output quality, and adjusts the computational contribution of the quantum ensemble based on system performance.
PROCEEDINGS OF THE 2022 THE 49TH ANNUAL INTERNATIONAL SYMPOSIUM ON COMPUTER ARCHITECTURE (ISCA '22)
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Garrett B. Goh, Charles Siegel, Abhinav Vishnu, Nathan Hodas, Nathan Baker
2018 IEEE WINTER CONFERENCE ON APPLICATIONS OF COMPUTER VISION (WACV 2018)
(2018)
Article
Biophysics
Andrea M. Katz, Igor S. Tolokh, Suzette A. Pabit, Nathan Baker, Alexey V. Onufriev, Lois Pollack
BIOPHYSICAL JOURNAL
(2017)